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ChemBioFinder 12.0

1. Program execution commands call up external processes and pass data to them All require an argument which may need multiple compo nents CALL executes a specified CAL script If the call is made from within another script when the called script finishes executing it returns control to the caller CALL must be followed by a scriptname as described above DOS executes a DOS command line Follow the DOS keyword with any string you might type ata DOS command prompt If you do not type any arguments after the DOS command you get an interactive command prompt win dow You can use this feature to manipulate files execute programs or batch files get directory listings format disks etc During execution of the command a command prompt window appears on the screen when finished the window goes away and control returns to the calling script EXEC starts a Windows program and option ally passes it command line arguments Follow the EXEC keyword with any string you might use in the Program Manager s File Run com mand This command starts a program but does not return from it To return to ChemBio Finder you need to use Task Manager or click in the ChemBioFinder frame window EXEC_BUTTON transfers execution to the script connected to a particular button where boxname is the button s box name in the Box Properties dialog box usually the same as the text on the button DDE sends a Dynamic Data Exchange mes s
2. 3 RS i ee i i 3 i S i i 2 i i 0 280 560 840 1120 1400 i Mol Weight i Notes Median x 237 38 Mean Y 0 94 Standard Deviation Y 3 84 R Squared 0 18 Figure 17 18 Plot with statistical analysis The following table describes how to perform various functions in BioViz if you want to then result See which data point navigate to the record using the The data point is highlighted corresponds to a particular ChemBioFinder Record Toolbar record View the structure or data mouse over the data point The Structure window displays the values of a data point structure for the data point the Details window displays the values of selected fields The current record in the form does not change Select a database record __ click on a data point The form displays the matching data from the plot record 308 Tutorials Chapter 17 if you want to then result Display plotted variable s for a query select or create the query The plot displays the current query Create a query from the plot On the BioViz context menu 1 If a check mark appears next to Zoom on Drag click to deselect it 2 Drag over the points of inter est to select them 3 Click Selection to List on the context menu The selected points become a new query Prevent a plot from changing when you select queries or change vari ables check the Lock option in
3. ChemBioFinder amp BioViz 371 User Guide If you want to Then click Require that the stereo Match stereochem chemistry of the target istry and click How structure match that of to set how the the query structure stereochemistry is matched Tuning The Tuning tab of the Preferences dialog box has settings for special query conditions On this tab there are check boxes for e full word text matching e case insensitive matching for Oracle e matching stereochemistry The only box that is checked by default is the Match Stereochemistry box See the figure below Preferences Display Color Search Type Details Tuning General Text Searching Tl Text query matches full word only I Case insensitive match Oracle Stereochemistry IV Match stereochemistry Cancel 372 Queries Chapter 21 Setting stereochemical search preferences The Stereochemical Search Preferences dialog box is activated from the Tuning tab of the Pref erences dialog box To set Stereochemical preferences 1 Click File gt Preferences The Preferences dialog box appears 2 Click the How button on the Tuning tab of the Preferences dialog box The Stereochemical Search Preferences dialog box appears Stereochemical Search Preferences Tetrahedral stereo center hits A Same C Either ta Ba DJ BJ I Thick bonds represent c Ary relative stereochemistry Double bond hits a e
4. paste relational and structural data from the clipboard Paste Perform all of the above functions Cut copy paste 5 Click the plus sign next to Browse to display the options take the appropriate action Table 30 Browsing security options If you want users to Then click browse databases Browse database records view data informs in a table View form as table view data in contin uous view View in continuous forms view ChemBioFinder amp BioViz 329 User Guide Table 30 Browsing security options If you want users to Then click edit and view struc tures in Chem amp Bio Draw Edit view struc tures in Chem amp Bio Draw view structures in Chem amp Bio 3D View structures in Chem amp Bio 3D perform all of the above options Browse 6 Click the plus sign next to Search to dis play the options take the appropriate action Table 31 Searching security options If you want users to Then click submit queries Query database records use current hit list for Search over current searching list search the entire data base Search over full database save and manipulate hit lists Enable hit list tools search exact structure only Full structure search substructures only Substructure search similar struc tures only Similarity 330 Forms Chap
5. 2 Go to the Field tab of the dialog If the selected field is indexed the index name is shown in the properties box In the example below the index is named 1X50 Form Properties CF HITLISTS A Database Table Field Form Oracle CF_SETTINGS CSDOHITLIST structure 1 CSDOHITLISTID DB_QUERY a es DB_QUERY_ITEM Table JD_TEST Native Type 00 MOL_ID Inde STRUCTURE lt F Formula_STRUCT WF MolWeight_STRU 2 00 MOLREGNO fhe MOLNAME fhe CORP_ID fhe DATE fhe ACTIVITY Create Index Set As Structure FR TFST2 Mi Create Field Create Index Index name ESI Cancel 1 Field name ChemBioFinder amp BioViz 419 User Guide 2 Index name NOTE If there is no index or the field is not indexable the Index line does not appear in the list 3 If there is no index click Create Index NOTE If this button does not appear it means the selected field is not a candidate for indexing 4 In the Create Index dialog provide a name for the new index and click OK The index is created You will get an error message from Oracle if e You provide an index name which is already in use OR e The column already has an index ChemBioFinder Oracle does not provide a direct way to delete or overwrite an index but the CAL SQL command can be used for this purpose To create a primary key index The process is the same as for a structu
6. By date modified Locates structures updated recently or some other point in time It applies to structures only not to the other database fields It is not implemented for Oracle at this time Also while it applies to the last time a structure was added or edited it misses deletions The way it works is to read the modification date written within the structure Deleted records have no such date e Check structures Locates records by checking the properties specified in the Check structures in database dialog box Depending on the specified properties and whether the database is read only it may be possible to automatically re register the structure with a corrected version By default this scan begins at the currently dis played record and proceeds to the end of the 378 Queries Chapter 21 record set or until the scan is aborted You can change this by unchecking the box at the bottom of the dialog box Check structures in database Things to check V Ambiguous stereochemistry MV Yalence charge J Net charge present MV Unrecognized atoms Mass imbalance reactions only Doubly drawn atoms 3D not scaled in Angstroms MV Misc nonsensical isotopes False stereomarks CDX lt gt Mst correspondence Atom atom maps Locate deleted structures V Representational Drift Defaults Interactive C Tofile C Documents and Settings sseng BI V Scan will begin at current record Figure 21 26 Chec
7. In the Data Table View Browse the table to view the records In the Continuous Forms View view mul tiple records in their own forms To toggle between the different views go to View gt Switch Views or Ctrl W To browse the hit list use the Record menu commands or their keyboard shortcut equiva lents NOTE As you keep on viewing the records counters in the Status bar indicate the current record the current list size and the total size of the database To view the database in a table that shows the records in a list do one of the following e Go to View gt Data Table gt In Current Window e Click the Switch to Table tool e Type Ctrl t NOTE The Switch to Table tool is a toggle Selecting it again will return you to the Form view The Table view appears and displays all the records of the current list in this case the 12 records that were hit by the search in a table You can sort the records for a specific field in Table View To sort records in Table view by the Mol Weight field Double click on the MolWeight table header The molecular weight field is sorted in increasing order To change the column widths of your table Position the pointer over a table header divider and drag to the width you want To use continuous forms to browse your records Go to View gt Continuous Forms The Continuous Forms view appears By default the Continuous Forms view shows the same form as the Form
8. NOTE Undo and Redo work over multiple changes Either command can be used repeat edly to reverse multi step operations Ordering objects The Bring to Front and Send to Back commands place data boxes in a specific sequence They have two effects e Select which overlapping data box is on top e Set the order in which the cursor moves when you press the Tab key ChemBioFinder amp BioViz 325 User Guide To put a box on top or bottom 1 Click the box to select it 2 Do one of the following e Click Edit gt Bring to Front to put it on top or e Click Edit gt Send to Back to put it on the bottom The order in which data boxes are created is the order in which the cursor moves as you press the Tab key You can set which data box the cursor moves to first or last To set the cursor to move to a data box first 1 Select the data box 2 Click Edit gt Send to Back 3 Press the Tab key The cursor moves to the box you set To set the cursor to move to a data box last 1 Select the data box 2 Click Edit gt Bring to Front The box you set is the last box the cursor moves to when you press Tab repeatedly Aligning and distributing objects You can line up objects relative to each other by aligning them and space objects at an equal distance apart by distributing them NOTE In framed dialog boxes the inner data box is aligned not the frame 326 Forms Chapter 18 To line up objects on a f
9. Same C Any Figure 21 24 Stereochemistry search preferences 3 Set the Tetrahedral stereo center hits If you want a tetrahe Then dral stereocenter in the query to match the target exactly in Tetrahedral stereo center hits click Same match same or opposite in Tetrahedral stereo configuration at the center hits click center of the target Either in Tetrahedral stereo center hits click Any match any target match a relative rela click Thick bonds tionship between centers represent relative stereochemistry NOTE When Thick bonds represent relative stereochemistry box is cleared default thick bonds are interchangeable with hash wedge bonds When the box is checked and Tetrahedral stereo center hits is set to Same a query marked with thick bonds will only hit a target that has the same relative relationship between centers 4 Set the Double bond hits If you want the con Then in figuration of a dou ble bond in the query to match the target struc Double bond hits ture exactly click Same match any configura Double bond hits tion in the target click Any 5 Click OK Entering query mode To clear the form and enter Query Mode Click Search gt Enter Query You are in Query mode In Query mode e The form background color changes e QRY appears in the status bar e Form boxes which do not permit data entry
10. filters changes in the current list list coloring BioViz Plot Properties dialog box options except Name are blocked The Display and Analysis tab options are all blocked even though they are not grayed out Selection and mouse overs are not affected Log scale Select this option to display a log scale Base Base of the log scale You must enter a number thus for a base e log scale you would enter 2 718281828 Point limit Sets the maximum number of points in the plot Used to limit the plotting time with very large datasets Name BioViz automatically names plots with sequential numbers BioViz1 etc Edit this field if you want to give your plot a different name 426 BioViz Chapter 26 Table 25 BioViz preferences General tab Dialog Option Point shape Description Selects the point shape circle square diamond triangle cross or star Menu option Description Point size Selects the point size Values from 2 20 may be dialed in Comment Text box for a comment or legend Background Selects the background color of the plot Label Show grid Text box for custom label for both X and Y axes Option to display a grid X and Y axes may be selected separately Zoom on Drag A toggle which selects the mode of operation when you drag a rectangle on the plot If Zoom On Drag is checked the rectangle defines th
11. Normal C Exact E C Similar I Search over current list Tautomeric Non tautomeric Defaults KY crea Figure 21 23 Search type preferences 2 Take the appropriate action If you want to Then click If you want to Then click find structures containing a common structural component Substructure find a particular structure Full Structure search with variability in Normal the query search for a precise match Exact 370 Queries Chapter 21 find structures having features similar to the Similar and set the degree of query similarity NOTE The higher the value the fewer hits found find structures that are Tautomeric tautomeric forms of the query match bonds as drawn Non tauto without tautomeric forms meric 3 Click OK TIP You don t always have to access the Pref erences dialog to change search preferences Switches on the Search menu allow you to tog gle Substructure Full Structure and Nor mal Similarity Seiting search details preferences You can set preferences for the details of each search To set search details preferences 1 Click File gt Preferences The Preferences dialog box appears 2 Click the Details tab The Details tab appears 3 Take the appropriate action If you want to Then click If you want to Then click Allow uncharged n
12. 6 Enter a name for the plot optional 7 Click OK The high and low values of each bar are displayed under the plot 306 Tutorials Chapter 17 Two variable plots In two variable plots you choose both the X and the Y coordinates To create a two variable plot 1 Click BioViz Plots gt New on the View menu 2 Click the Two Variable option in the Dimension box Select fields for both the X and Y axes Click the Scatter plot option in the Style box Enter a name for the plot optional Click OK Oy oe p You may select the axes in either order Once you have selected a field for an axis it is dis played in the context menu Properties Data Source Field Bioviz Plot gt On Axis Mol_ID Sort R On Y Axis 1 D Plot v Mol_ID Reset X Y Structure Filter Window Formula MolWeight MOL_Name Calculate Property gt Figure 17 17 Two variable selection with the context menu If you want to change the axis assigned to a field select Reset X Y and start over Working with plots Three optional windows facilitate working with BioViz plots Structure Filter and Details e Structure displays structures of data points as you mouse over them used when the form is not visible or is displaying a dif ferent record e Details displays data for selected fields either from the database or from child tables as you mouse over data points used when the form is not visible or is displaying a
13. A tautomeric search is one in which the loca tion of single and double bonds may vary from query to target A hit occurs if in addition to the atom types matching the target possesses a tautomeric form whose bond orders match the query s Which tautomers are recognized is under some degree of control Tautomers of the form x y e XY Z Figure 21 7 Tautomeric structure are always recognized when at least one of X and Z is not carbon The lone pair may include a migrating proton It is also possible to include tautomers in which X and Z may both be carbon The choice must be made at the time the database is created or upgraded because it affects how structures are stored Mesomers resonance structures are also picked up in tautomeric searches Tautomerism involving formation or cleavage of sigma bonds is not currently supported The principal categories are ring chain tautomerism as in the open vs cyclic forms of sugars and valence tautomerism Tautomeric searching is slower than non tauto meric but is the mode of choice when you think the target might have a slightly different layout of double bonds NOTE If the database has not been indexed the tautomer searches may be slow Stereochemistry You can specify whether or not you want a structure search to consider stereochemistry Given a structure with one or more stereocen ters you can store four different possibilities e A given absolute c
14. CHIRAL 1 current mol is marked chiral 0 not chiral CLIPBOARD text from Windows Clipboard CURF_DIR current working directory CURR_TABLE current table name DATE current date DTBA_NAME_L database full path Angle bracketed lt item gt is required bracketed item optional lt rect gt four integers left top right bottom lt box gt a point within box x y or a box name Box name a user assigned box name b field name casei y Figure D 1 The CAL scripting window Menu commands CAL commands MENU syntax Menu commands consist of a two word com mand from the main menu and in some cases an optional argument Following are examples of commands file new edit paste search find record next ChemBioFinder amp BioViz 499 User Guide You do not need to spell out menu commands You can enter just enough letters to uniquely identify the menu option For example to exe cute the Record Next command type rec n Some menu commands open a dialog box and wait for user feedback To avoid this a limited number of menu commands can take explicit arguments FILE OPEN filename FILE SAVE filename RECORD GO TO RECORD recno The command menu menuitem param executes any menu command as if selected from the menu The menu commands have the following argu ments Part Description menu Stringstring_definition containing the name of the menu
15. ChemBioFinder 12 0 About this document This document is the ChemBioFinder section of the manual Chem amp Bio Office Chem amp Bio3D Finder amp Bio Viz and is made available as an excerpt for fast downloading To read the manual in its entirety or to download other sections see the desktop support site at www cambridgesoft com Contents What s NEW ssssssesssssssesssssssesosssssessssssse 281 Chapter 15 ChemBioFinder amp BioViz 0000 283 About ChemBioFinder 12 0 283 About BiOVIZ cccecccessesseeeeceeeeeeees 283 About this guide 283 Additional information 000 284 Chapter 16 The User Interface sssscccssssssssscreess 285 The ChemBioFinder User Interface 285 More UI features nssoonneneneesesess00o 289 Opening ChemBioFinder 12 0 290 Using ChemBioFinder with databases 290 Chapter 17 TutorialS sesesossesesesccsesosoesesesocoesosoesesese 293 Tutorial 1 Creating forms 293 Tutorial 2 Opening a database 295 Tutorial 3 Creating a database 296 Tutorial 4 Searching a database 298 Tutorial 5 Reaction queries 301 Tutorial 6 Creating a BioViz chart 304 Tutorial 7 Working with subforms 309 Chapter 18 Forms eseesseseseeeseseeseesescesceseecesoeseecoscesceeee 311 Creating forms automatically 311 Saving a form 313 Creating forms
16. F T P BUTTON coords scriptname S A F To create a new box on the form 1 Specify the box type with the appropriate keyword 2 Type four integers giving the rectangular coordinates of the box after the keyword 3 If desired type a text string giving further information appropriate to the box type as shown below Box Type String Data box name of database field to be displayed in the box Frame static label for upper left Text static text 502 CAL Commands Appendix D Box Type String Picture pathname of a Windows metafile Button pathname of a script file or name as it appears on Scripts menu Subform lt nothing gt Arrowbox lt nothing gt Framedbox name of database field to be displayed in the box and static label for upper left If the text string is omitted you can supply it later using SETFIELD or SETTEXT For a button you must use SETTEXT if you want its visible label to be different from the name of its script Box coordinates are specified in this order left top right bottom Units are in pixels the origin is at the upper left with coordinates increasing from left to right and top to bottom so that coordinates will range from left 0 to right 640 or 1024 or whatever fits your screen and from top 0 to bottom 480 or 768 or similar When a new box is created it adopts the cur rent font To specify a particular font for a box use the FONT
17. Fast move caching scheme on page 542 The state of this check box is saved with the formfile Currently when you check or uncheck this box you must save and reopen the form before proceeding e SQL Trace to file Check this box to gener ate a text file of the SQL being sent from ChemBioFinder 12 0 to Oracle To specify an output file enter a pathname or use the browse button The file is never overwrit ten new data are always appended Tracing begins when this box is checked and ends when it is unchecked If you exit ChemBio Finder 12 0 with tracing in effect it will be in effect the next time you start up and you will be given a quick warning about it on the status bar CAUTION The trace file can become very large if you turn on this feature and forget about it Updating and adding data If you have privileges to add update and delete in the table connected to your form then ChemBioFinder amp BioViz 417 User Guide you should be able to do these operations on records in the database just as in ChemBio Finder 12 0 However there are some cautions e Do not modify data in an existing Web Server RegDB or E Notebook database ChemBioFinder Oracle does not automati cally prevent you from doing this but you are sure to foul up those systems unless you go through their normal registration proce dures or know exactly what you re doing Most database alterations are possible as in ChemBioFinder
18. The Preferences dialog box allows you to cus tomize the display of molecules pictures and forms and set options for searching and exporting General instructions for using the Preferences dialog box 1 Click the tab containing the preferences to set 2 Select the preferences and click OK Display preferences To set the Display preferences Click the File gt Preferences menu command The Preferences dialog box appears with the Display tab on top Structure display To display carbon atoms on methyl groups or on interior aliphatic or aromatic chains check the relevant check boxes in the Carbon labels section To display hydrogen atoms on heteroatoms or on terminal carbons Select the Fill valence option in the Hydrogen Labels section Hydrogen labels C As drawn Fill valence C No implicit C NoH atoms Select No H atoms in the Hydrogen Labels section ChemBioFinder amp BioViz 451 User Guide Hydrogen labels C As drawn C Fill valence C No implicit NoH atoms NOTE Selecting No implicit means these types are displayed without implicit hydrogens Using keyboard shortcuts When using a form you can use keyboard shortcuts to show or hide atom to atom maps reaction centers atom numbers and bond numbers To use keyboard shortcuts Select the Enable keyboard shortcuts check box on the Display tab of the Preferences dialog box When keyboard shortcuts are enabled the fol
19. an element in a non standard valence This parameter can be set manually in the General tab of the Prefer ences dialog The default is 0 do not warn PRINT_OPTIO NS PRINT_BORDER Whether or not to displaya Oor1 border around forms when printing The default is 1 print a border ChemBioFinder amp BioViz 523 User Guide Section Preference Description Values PRINT_OPTIO PRINT_FOOTER NS The contents of the footer to string be printed at the bottom of all pages containing forms Any text is valid as well as the following special codes D current date F name of the CFX file P page number T current time The default is ChemBio Finder D T Record P PRINT_OPTIO PRINT_HEADER NS The contents of the header to string be printed at the top of all pages containing forms Any text is valid as well as the same special codes recog nized for the footer The default is F file name SEARCHING EXACT 524 CAL Commands Appendix D Whether or not to allow a 0 or substructure match when searching This parameter can be set manually in the Search tab of the Preferences dialog The default is 0 substruc ture Section Preference Description Values SEARCHING FIND_CHARGED_CARBO N Whether or not to allow Oor 1 uncharged carbon atoms to match charged ones when searching This parameter can be set manually
20. cost wt 0 00 0 06 7 00 score 0 10 dist 0 70 Formula 7 mMolname 5 CgHsEr MolVYeight f 57 008 Figure 28 2 Profile box form Each field in the profile box form is assigned a cost and weight Right click on the profile box CLOGP and choose Cluster By Profile the clustering engine uses all the three values of each record in the hitlist together with their weight and cost and displays a normalized dis tance in the records Bromobenzene Modifying Clustering To modify the cluster dialog click the black drop down arrow that appears below the 3D structure in the CS Clustering dialog This drop down control panel has two tabs Dendogram and Clusters NOTE The Dendogram and Clusters tabs may appear by default as well in the CS Clustering window ChemBioFinder amp BioViz 447 User Guide Dendogram Properties CS Clustering Form s Arial 6 pt Dendopemutess SS Figure 28 3 Dendogram options e Inthe Style Frame you can change the ori entation of the diagram using the Invert X Invert Y Horizontal check boxes In Tee pee style lines moves from nodes to sub nodes i e it displays the dendogram in a non standard way Click the Line color Highlight or Back ground button Colors dialog box will open By default the dendogram lines are in navy blue color highlighted items are in 448 Clustering in BioViz Chapter 28 red color and background is in light grey color
21. lowing keys toggle these properties e A show hide atom numbers B show hide bond numbers e M show hide atom to atom maps e R show hide reaction centers e S show hide stereochemistry Scaling structures To scale each structure so that it is as large as possible within its structure box Click the Fit to box radio button in the Structure Scaling section of the Display tab 452 Customizing ChemBioFinder 12 0 Chapter 29 To display all structures with a constant bond length 1 Click the Uniform bond length radio button in the Structure Scaling section of the Dis play tab 2 Select the bond length percentage With Uniform bond length selected structures may be reduced in size if they are too large to fit within the structure box but they will never be enlarged Framing pictures To select whether the pictures in a form are surrounded by a border Select the Framed radio button in the Pictures section of the Display tab Grid spacing To set the grid spacing in pixels on a form Type in a number or press the up and down arrows to change the current value by one unit in the Grid Spacing section of the Display tab Choosing a small grid spacing allows you to place objects more precisely by snapping to a tighter matrix Color preferences To set the color preferences Click the Color tab of the Preferences dialog box The color tab allows you to specify the color of various interface element
22. text String to attach to the target Depending on the box type the text is attached to different places Box type Text location data box Within the text box wrapped to fit frame On the top border aligned to the left text box Within the text box wrapped to fit button Centered within the button CAL commands ACTIVATE syntax Marks a subform on the active form to become the new active form It is equivalent to clicking on the subform with the pointer tool ACTIVATE subform The ACTIVATE command has the following argument Part Description Box identifier indicating the subform to activate subform NOTE This command will change the active form Remarks The ACTIVATE command acts only on sub forms The similar command SELECT is used for data boxes frames text boxes buttons and picture boxes CAL commands FORMEDIT syntax Determines whether the active form is in form edit mode or data edit mode FORMEDIT value The FORMEDIT command has the following settings Setting Description ON Form is set to form edit mode OFF Form is set to data edit mode Remarks When the form is in form edit mode the SELECT command affects data boxes them selves When the form is in data edit mode the SELECT command affects the data within the data boxes ChemBioFinder amp BioViz 509 User Guide CAL commands SELECT syntax Marks a box on
23. unsaturation 492 using current structure 375 query operators 556 369 equals 359 greater than gt 359 Index less than 359 minus 359 query properties conflicting 483 overview 483 Questel F1D files 389 Questel F1Q files 389 R r groups see alternative groups R special atom type 489 radicals in queries 485 ranges in queries 358 RDFiles 330 390 394 reactants in queries 368 reactants searching for 366 reaction centers 366 493 bond type 497 bond types 493 495 display preferences 454 overview 366 reaction queries 366 atom atom mapping 367 creating 375 hitting reaction centers 366 371 intermediates 368 products 368 reactants 368 reaction queries tutorial 301 reaction searches 366 reactions multiple step 366 READ indicator 289 READ indicator description 287 read structure command 392 reading a structure 392 read only access 336 read only fields 289 real fields 344 recent file list size setting 454 record number dialog box 338 record tool 338 record toolbar browsing with 338 description 287 illustration 333 records adding 289 347 current 285 289 deleting 353 duplicating 348 moving between 338 redo command 325 353 redoing changes 353 redundant reagents in RD files 390 refining queries 374 refining your search overview 478 refining your search search options 479 refining your search search tools 478 registration preferences 453 relational data and subforms 399
24. 6 You get 8 hits from the 285 records in the database Click View gt Data Table gt In Current Window The Table view appears Browse to verify that the molecular weights are correct Congratulations You have completed the tuto rial on searching a database using ChemBio Finder 12 0 You may now close the CS_Demo database Tutorial 5 Reaction queries In addition to helping you organize informa tion about individual substances ChemBio Finder 12 0 also allows you to store and search chemical reactions Searching for reactants Searching for reactants is useful if you have a known starting material and you are interested in learning more about what substances it can produce For example to search for Grignard reactions or reactants 1 Click Search gt Enter Query The form clears ChemBioFinder amp BioViz 301 User Guide 2 Double click in the Structure box The ChemDraw control appears 3 Draw the following gt Mg Nyx Figure 17 9 Entering a reactant in a query This structure represents a carbon atom bonded to a magnesium atom which is bonded to any type of halogen The arrow at the right indicates that you are looking for this substructure as a reactant 4 Select the Search gt Substructure menu option if it is not already selected 5 Deselect the Search gt Similarity menu option if it is selected 6 Click Search gt Find ChemBioFinder 12 0 begins searching The progress of the s
25. ChemBioFinder does its best to follow your instructions even if those instructions are con tradictory For example you can create a query such as the following 1 Chn 1 This bond must not be in ring That bond is already in a ring so ChemBio Finder returns no hits for this query General properties ChemBioFinder allows the following general properties to be assigned to a query e Atom e Bond e Substituents e Charges and radicals e Isotopes e Stereochemistry e Normalization Atoms Atom types specified in the query must match atoms at corresponding positions in the target Hydrogen is an exception see Substituents on page 484 Bonds All bonds explicitly drawn in the query must match in the target For certain caveats see Stereochemistry on page 486 and Normal ization on page 488 ChemBioFinder recog nizes the following standard bond types Bond Type Description Single target must have single bond here ChemBioFinder amp BioViz 483 User Guide Bond Type Description Dashed same as Single Hashed same as Single Thick same as Single Wedged specifies stereochemistry Hashed down from the point end to the wide end Wedged specifies stereochemistry up from the point end to the wide end Wavy specifies stereochemistry either at both ends Hollow same as Wedged Wedged Dative same as Single Double target must
26. Click the Apply button 7 When you have finished assigning permis sions click the OK button 8 Open the database in ChemBioFinder 12 0 Creating a database You can create a new empty database and associate it with a form To create a database 1 Open an existing form or create a new one 2 Right click in the form and click Properties The Box Properties dialog box appears 3 Click the Box Properties Database tab then click the Create Database button The Save As dialog box appears ChemBioFinder amp BioViz 335 User Guide 4 In the File Name box type a name for your database and then click the Save button A data source tree appears containing the database and its tables and fields 5 Click the OK button The Box Properties dialog box closes Opening databases When you open a database in ChemBioFinder 12 0 you can access the data in any of three ways e Normal access you can read and write data e Read Only access you can read but not write data The database is write protected e Secured access you must open the data base with a user name and password You are subject to the security restrictions applied to the database NOTE Versions of ChemBioFinder earlier than 7 0 cannot read cfw files belonging to ChemBioFinder 7 or greater Versions of Chem BioFinder earlier than 11 0 cannot read cfx files Read only access Any of the following conditions determine whethe
27. In this tutorial you open the CS_Demo data base and display the MolTable in the main form Then you display the Synonyms table of the CS_Demo database in a subform By defin ing the MOL_ID field as the linking field you display the two sets of data relationally Creating a subform To create a subform 1 Open your ChemBioFinder 12 0 form tutl cfx Opening this form connects you to the CS_Demo mdb database 2 Make some space on the right side of the form by rearranging the data boxes and making them smaller 3 Click the Subform tool 4 In the form drag to create a large subform TIP If you cannot make room on the right side of your form you can put the subform at the bottom of the form When you release the mouse button the Subform Properties dialog box appears 5 Click the Form tab then select Synonyms from the hierarchical tree display 6 Click the Generate form check box then click the Style button 310 Tutorials Chapter 17 7 Select the Plain form deselect all of the fields to be included except Synonym and click the OK button You are returned to the Subform Properties dialog box 8 Click the Subform tab 9 SYN_ID already appears as the default in the Link to SYNONYMS field section Using the drop down menu choose MOL_ID for the Link from MOLTABLE field 10 Click the OK button You have just selected the data source for your subform and linked it to the main form The MOL_ID field lin
28. In version 9 a point which has an X value but not a Y value is represented as a so called empty point on the plot with a distinctive marker If there is a Y value but no X value the point is simply omitted though noted Version 10 omits both empty X and empty Y points All omitted points are noted and may be reviewed by clicking the Notes button at the bottom of the chart Selection and mouse overs To facilitate viewing selected points when que ries are displayed the selected point is dis played as a double hollow red circle Points being moused over pointed at are displayed as red solid with a black circle Mousing over a selected point displays a double hollow red cir cle surrounded by a black circle Points belonging to queries are displayed as solid col ored points without circles Details window The Details Window displays field values other than Structure when viewing a BioViz plot To display the Details window select it from the View menu The window floats by default but can be docked with other windows To add new fields to the Details Window 1 Right click in the Details Window 2 Select the field to be displayed A check mark appears next to the selected field Fields display in the order you select them 3 Toremove a field from the Details Window right click and deselect it Creating a plot To begin working with BioViz select a set of data to work with You can plot an
29. Saving a hit list Create a query and perform the search See Entering and submitting a query on page 373 and Entering a structural query on page 374 for more information 1 When you have received the hit list click Search gt Save List The Save As dialog appears 2 Type a filename for the hit list and click the Save button The file consists of a list of values of the pri mary key of each record in the hit list If there is no primary key the molecule ID is used To edit a saved hit list open the text file with a text editor such as Notepad and edit the values you want changed Restoring a hit list Once you have saved a hit list you can per form another search and then integrate the results from the second search with the results from the first Thus you can perform Boolean operations on different searches There are two ways to integrate the results of two searches Browsing to the saved list 1 Perform a search and save the hit list 2 Perform another search 3 Click Search gt Restore List The Open dialog appears 4 Browse to the previously saved list you want to integrate with the current hit list and click the Open button The Restore Merge List dialog box appears Restore Merge List B Replace useL2 E L1 current list 2 25 hit Rk C Intersect L1 and L2 L2 E C Subtract L1 L2 C Documents and Eee Settings zchoo My C Union L1 L2 Documents Models E
30. The actual data are stored in files with MSX and MST exten sions for structure data and in files with an MDB extension for non structural data If you want to move a database to another computer you must move for a default ChemBioFinder 12 0 database at least four separate files This number might be greater if you have several forms that access the same database NOTE The MSX MST and MDB files all have the same file name but the name of the CFX files might be different depending on how you saved them After you move the database to its new loca tion open your forms to make sure the data 346 Databases Chapter 19 source links have been retained If ChemBio Finder 12 0 cannot locate the data source and displays an empty form you will need to use the File gt Database menu command to reconnect to the data source If the form is connected to a remote data source on a network you have fewer files to move The data source can remain on the remote machine and you only move the CFX file that contains your form for accessing the data You may need to reconnect it to the data source if it is not done automatically This situ ation is common in large organizations where several people access the same central data source Creating a portal database To carry out certain operations such as sorting structural data ChemBioFinder 12 0 needs to create temporary tables in a database This can not be done in a read only s
31. a Using a Selection tool right click on the double bond and set Reaction Center bond properties to Change b Using the Text tool select one of the carbon atoms Type NOT O H all uppercase with brackets as indicated and press the Enter key to replace it ChemBioFinder amp BioViz 303 User Guide c Still using the Text tool select the label right click and choose Repeat Last Label d Double click on the other carbon atom to reproduce the label The structure now looks like this Ae mm NOT O H NOT O H Figure 17 13 Modified reactant query You have specified a search for ketones by adding the restriction that the atoms adjacent to the carbon must not be oxygen atoms or hydrogen atoms You also specified that the double bond had to change not be broken 5 Press the Enter key You get 13 hits Each reaction shows the reduction of a ketone to an alcohol In the Queries Tree this search is shown as a child of the first query Queries Full List 0 to OH 23 Ketones 13 Database Queries Favorites Figure 17 14 A child search in the queries tree TIP If you plan to do several searches over a hitlist use the Set Domain to Current List com mand rather than Search Over Current List Setting a domain eliminates the need to keep restoring the original hitlist 304 Tutorials Chapter 17 Tutorial 6 Creating a BioViz chart BioViz charts are created from the View
32. adding structures 345 cells 290 creating 341 ChemBioFinder amp BioViz 549 User Guide data items 290 flat file 341 logon 337 model 290 moving 346 multiple tables 342 non chemical 342 345 opening 333 336 read only 289 resetting 354 selecting 333 size 289 vs forms 292 date fields 344 date queries see searching for dates dates display preferences 359 dBASE 342 DDE to communicate with other applica tions 467 debugging scripts 461 delete record command 353 deleting boxes 325 contents of fields 353 data 353 fields 345 objects 325 records 353 tables 341 delimited text files 395 demo database 298 details window 306 details window description 286 details window see BioViz dimension definition 426 disabling security 331 display preferences 451 distributing objects 326 550 Index domains 382 double either bond type 484 drag and drop 392 duplicate reagents in RD or SD import 390 duplicating records 348 E editing data 349 data boxes 294 fields 349 forms 324 labels 315 redo 325 structures 349 structures with ChemDraw 350 tabs 318 undo 325 element editor 457 element ranges in queries 359 elements color 458 physical data 457 selecting 457 embedded controls 458 embedded controls customizing 458 empty points see BioViz enter label dialog box 317 enter query command 373 enter script command dialog box 459 entering data 354 queries 289 369 373 reaction queries 375 structural queries 374
33. be prompted with an error message 4 Click OK The cost profile is displayed and may be edited 5 Click OK to complete the change To change a cost profile 1 On the Profile tab click one of the profiles to select it then click the Cost Profile tab Cost Profile high plateau 1050 ideal value wr 0 56 Figure 24 3 Cost profile showing the drag points and ideal value line 2 To change an inflection point drag it toa new location As you drag the X and Y coordinates of the point are displayed on the grid TIP You cannot drag past a neighboring point 3 To add a new inflection point right click on the line segment where you want the new point and click the Add point here context menu command 4 To delete a point right click on the point and click the Remove point context menu command 5 To change the ideal value drag the pink dashed line on the grid to a new location 6 To choose a different template right click anywhere in the editor window click the Choose context menu command and select a new template 7 Click OK to save changes and exit the edi tor or Cancel to exit without saving Display preferences You can change display characteristics of a profile with the Profile Display Preferences dialog box Changes you make apply only to a selected profile box unless you choose to reset the defaults To change the profile display preferences 1 Right click a profile
34. cl Figure 21 37 Overlapping substructures in the hit list ChemBioFinder amp BioViz 387 User Guide 388 Queries Chapter 21 Importing and Exporting Data You can move data into and out of a database if the data is in a supported file format You can import single files import or export data bases or add data to an existing database Supported file formats ChemBioFinder 12 0 allows you work with individual chemical structures and reactions in various file formats The supported formats are e Chem amp Bio Draw cdx e Chem amp Bio Draw XML cdxml e Connection Table ct e Delimited text csv txt e MDL Molfile and V3000 mol e MDL RXMfile and Rxn V3000 rxn e MDL RDFile rdf e MDL SDFile sdf e MDL Sketch skc e MDL Graphic tgf e SMD 4 2 smd Supported formats for output files only e Bitmap bmp e XML cfxml e Encapsulated Postscript eps e GIF gif e Microsoft Word doc TIFF tif e Windows metafile wmf For information on the cdx ct and cdxml file formats see the Chem amp Bio Draw Users Guide For information on MDL file formats see http www mdli com A document describ ing the file formats is available in PDF format Importing data ChemBioFinder 12 0 allows you to import Chem amp Bio Draw structures Structure Data files SDFiles and Reaction Data files RDFiles directly into a database In addition you can import text files that are comm
35. database Databases containing multiple tables are called relational For more on relational databases see Relational Data and Subforms on page 399 A form displays data from a single table but may contain subforms that display data from other tables If the tables have a field in com mon then any record retrieved in the form calls up the related records in the subform ChemBioFinder amp BioViz 291 User Guide Understanding forms and databases Databases are where data is stored A form dis plays the information stored in the database No data is stored in a form The form acts like a window letting you select which fields and tables you want to view While no data is stored in forms some things are saved with a ChemBioFinder 12 0 form BioViz plots database queries depending on a preference setting file paths of linked graph 292 The User Interface Chapter 16 ics and certain settings are saved with each form You can create more than one form to access the same database For example you may want to create one sample form for working with structural data and a more complicated one to include literature or lab data By switching between forms you can look at just those fields you want to see Tutorials The general steps for using ChemBioFinder 12 0 are 1 Create a form 2 Create or open a database and link it to the form 3 Add or manage data 4 Perform a search The tutorials introduce
36. in the form when you import it into ChemBio Finder After you import your form you can continue to build on it in ChemBioFinder using additional fields The fields you use can also include child tables and their fields Child tables that you add appear as subforms fields from child tables are displayed as autolink boxes To add a subform 1 In the Explorer Window select the BioSAR tab 2 Select a child table from the Child Tables directory 436 BioSAR Chapter 27 3 Double click the child table The child table appears in the form as a subform NOTE Not all fields in the child table are necessarily displayed in the subform The subform fields are limited to the same fields you selected in BioSAR and defined in the default form group To add an autolink box automatically 1 Select a child table from the Child Tables directory 2 In the child table double click an individ ual field The child table field appears in the form as an autolink box To create an autolink box manually Assume you have a structure table Molt able with a column of non unique integers Chemist_ID In a separate table Chemists there is a text column to be displayed Name and a column of unique integer record identifiers ID Each Chemist_ID in MolTable matches one ID in Chemists To set up an auto link box on the main form which shows for each structure the name of the associated chemist 1 Create a data box 2 Right c
37. is required Otherwise the com plete file path c some long path BROWSE CFS is neces sary If the CALL command is executed from within another script as opposed to from the Com mand Line the calling script will continue to execute with its next command after the called script finishes executing A CALLed script inherits all user variables from its calling script The calling script also ChemBioFinder amp BioViz 511 User Guide inherits the user variables back from the called script when it has completed executing CAL commands DOS syntax Executes a standard DOS command line DOS doscommand The DOS command has the following argu ment Part Description doscommand Any string that might be typed at a DOS command prompt Remarks This command may be used to manipulate files execute programs or batch files get directory listings format disks etc During execution a DOS command prompt window appears on the screen when finished the window goes away and control returns to the calling script CAL commands EXEC syntax Starts a Windows program and optionally passes it command line arguments EXEC filename commandargs The EXEC command has the following argu ments Part Description String containing arguments to be passed to that applica tion commandargs 512 CAL Commands Appendix D Part Description String containing the file name of any Window
38. mation on service names topic names and commands it supports The DDE command is always sent as an EXE CUTE instruction Communicating with Excel example This example uses the WRITETEXT com mand to write the current list to a file then sends two DDE commands to open that file in Microsoft Excel and resize the columns to a nice size Finally it uses the DOS command to delete the temporary file The first line starts with an asterisk and so is not executed It serves only to make the example more readable for the user TOEXCEL CFS script to send data to Excel WRITETEXT C DATA TMP DDE Excel System OPEN C DATA TMP DDE Excel System COLUMN WIDTH 1 C1 C4 3 1 DOS erase C DATA TMP General commands MSG message STATMSG message TIMEDMSG n lt msg gt W FONT fontname size style r g b SEEPTAB decisecs QUIETCLOSE HIDETABLE SET CLEAN cleanup tidy redraw denovo HELP GET v section number itemnumber SOUND filename wav SYSMETRIC v index MSG displays a message box with the speci fied text and waits for the user to click STATMSG displays information on the status line TIMEDMSG displays a message box similar to the MSG command but the message disap pears automatically after a specified number of seconds For example TIMEDMSG 10 This message will disappear automatically after 1
39. relational database definition 291 relational databases 342 399 relative tetrahedral stereochemistry 373 487 renaming tabs 318 replace current list command 383 rescale 307 rescale see also autoscale resetting the database 354 resizing boxes 325 objects 325 restore list command 383 restoring a hit list 383 restoring changes 325 reversing and restoring changes 325 R group tables 339 R group tables persistence 340 R group tables sorting 340 ring bonds 493 rules 495 S sample databases 293 save command 348 save command effect on changes 313 save dialog box 313 save list command 383 save structure command 394 saving and restoring lists 382 data sources 475 476 directory paths to search 476 files 475 forms 313 hit lists 383 pictures 317 search results 476 structures 394 subforms 313 vs committing 313 scaling structures 452 script only commands CAL 536 scripts communicating with other applications 467 debugging 461 executing 461 in subforms 403 writing 460 scroll bars adding 321 SDFiles exporting 394 396 ChemBioFinder amp BioViz 557 User Guide SDFiles importing 330 390 search examples 384 toolbar 369 type 360 search details preferences 370 search options 479 search over list command 303 search results 475 search toolbar description 287 searching by chemical formula 474 by chemical structure 473 by molecular weight 474 by multiple properties 474 by reaction type 303 by selected
40. search types e Normal e Exact e Similarity Normal and similarity searches may be in either of two modes full structure or substruc ture Normal and exact searches may also search for tautomerism Normal searches A Normal search finds structures that either contain Substructure or match Full Struc ture the query When drawing a structure query you can attach different features to a query such as atom lists and variable bond types to perform a narrower or broader search You can also modify the results of a Normal search by selecting options in the Details tab of the Preferences dialog box The query structure is highlighted in red in the hitlist structures to visualize the match Exact searches The Exact search type also known as an Iden tity search is intended for use in compound registration when you must know if a perfectly identical copy of your query compound is already present in the database The target must be chemically identical to the query including stereochemistry charges and iso topy It is a convenient shorthand for full struc ture same stereochemistry and appropriate settings of all the other options Thus generic atom and bond types such as R A and Dou ble or Aromatic in the query will match corre sponding atom and bond types in the target only if they are also of the same generic type In other words an atom labeled R in the query must find a matching atom labeled R in t
41. str recno Name molname Formula formula cfrset MoveNext recno recno 1 namefield 0 ChemBioFinder amp BioViz 465 User Guide fmlafield 0 cfrset 0 cfdoc 0 cfapp 0 Notes Lines 1 2 Comments beginning with are ignored ChemBioFinder generates lines like these whenever you create a new script Line 3 It s a good idea to add your own comment telling what a script is designed to do Line 4 Import statements are used to declare and execute code from external Python modules This one says we want to use a specific routine GetActiveObject from a module in the Win32 extension library win32com client Lines 5 7 Obtain the currently running ChemBioFinder application object the one from which the script was launched along with its active document and record set Assign them variable names Lines 8 9 Identify the fields to be included in the report and get corresponding field objects from the document Lines 10 11 Prepare to loop records Call ing MoveFirst ensures that you loop the entire list If you omit this or comment it out the loop begins at the current record Line 12 Begin the loop go until the record set reaches EOF after the last record A colon at the end of a line indicates it is the first of a compound statement 466 Customizing ChemBioFinder 12 0 Chapter 29 e Lines 13 14 Retrieve data using the Value method of the recordset e Line 15
42. 1 With the Select tool right click on the text and select Properties The Box Properties dialog box appears with the Box tab displayed 2 Select a field from the data table The Data text box becomes grayed out and the Data Source selection switches to Field 3 Click OK The contents of the field are displayed in plain text Adding pictures The Picture tool allows you to create a Picture Box to display a bitmap BMP GIF etc or Windows metafile WMF EMF picture It can display a static file or a live one stored in a picture column of a database To create a static picture 1 Click the Picture tool 2 On the form drag to create an area for the picture to occupy The Open dialog appears 3 In the Open dialog box select the file you want to display then click the Open button The picture appears in your form NOTE The file is not actually embedded in the form Only its filename is saved with the form If you move or rename the file the form will not display the corresponding picture However if you make changes to the picture and keep its filename the same the picture in the form will be updated To create a Picture box linked to a field You must have a picture field in the database See Creating fields on page 343 for more information 1 Click the Picture tool 2 On the form drag to create an area for the picture to occupy The Open dialog appears 3 Click the Cancel A blan
43. 12 0 you can add modify and delete tables and fields assuming you have the appropriate privileges Differences include e When you create a structure field you can give it any name you like e Structure columns in tables managed by the CS Oracle Cartridge can be in any of sev eral formats but ChemBioFinder Oracle does not allow you to choose one it defaults to a character CLOB column storing text encoded CDX e ChemBioFinder Oracle does not allow you to create an Oracle database in the same way ChemBioFinder 12 0 creates an Access MDB file The equivalent in Chem BioFinder Oracle is to create a table Loading You can build ChemBioFinder Oracle data bases by loading from SDFiles or using Import Structures RDFiles should work also but have not been tested However because you cannot actually create a new database the pro cedure is somewhat different from ChemBio Finder 12 0 You must already have a database open and then you can import to an existing table or have a new one created To import data and structures into a new table 418 ChemBioFinder Oracle Chapter 25 1 On an empty form right click and choose Data Source 2 Click Oracle Database and proceed as described under Opening an Oracle data base on page 414 It doesn t matter what table you select since you will be creating a new one 3 Click OK to return to the blank form You are now ready to import NOTE When you click
44. 19 11 Moving a column To resize the column widths in the Data Table 1 Place the cursor on the dividers in the top header The cursor changes to the icon shown below Figure 19 12 Changing the width of a column 2 Drag to adjust the column width NOTE To hide the column right click and choose Hide Column from the context menu To resize the row heights in the Data Table 1 Place the cursor on the dividers in the left header The cursor changes to the icon shown below Figure 19 13 Changing the height of a row 2 Click drag to adjust the row height NOTE To resize all rows right click in a column header and choose Resize Rows to Fit from the context menu R group tables In Data Table display you can display a sub structure search as table of R group substitu ents 1 Run a substructure search NOTE You cannot prepare a table from a full structure or similarity search Figure 19 14 Substructure query to set up R Group table 2 Switch to Data Table view 3 Right click in the Structure column and click R Group Table The following changes occur e the topmost structure is replaced with the template similar to the query you used ChemBioFinder amp BioViz 339 User Guide but with Rs attached at all positions which found substituents Figure 19 15 R Group query and template e new columns are generated for all the Rs e the other rows are populated with the
45. 317 data box menu 321 data boxes 294 315 databases 335 341 fields 343 forms 313 forms automatically 311 forms with the database tree 313 forms manually 313 forms tutorial 293 frames 315 multiple tables 354 403 picture boxes 316 portal databases 346 scripts 460 subforms 310 399 400 tables 341 tabs 318 text 316 creating a database tutorial 296 creating a plot 304 425 creating and editing forms 311 creating and saving forms 295 current list counter 289 description 285 size 289 current mol as query command 375 current record command 285 289 curve fitting see BioViz customizing ChemFinder 451 favorites tree 455 fonts 322 numbers 322 text 322 toolbars 456 customizing fonts 322 D data adding 347 committing 349 352 deleting 353 displaying 314 editing 349 entering 354 exporting 394 items 290 sorting 353 data box tool 315 data boxes editing 294 read only 289 data boxes creating 315 data boxes hiding or showing 321 data source command 333 342 ODBC 342 selecting 333 342 data source find chemical structures win dow 471 data table displaying 338 moving columns 338 resizing columns 339 resizing rows 339 sorting 353 subforms 402 data tables 338 data importing 389 database creating 335 database model description 290 database size display description 287 database tree using 313 database connecting to a form 295 database definition 291 databases
46. 342 buttons creating 317 C CAL box creation commands 502 box manipulation commands 507 environment variables 535 execute with button 317 file commands 527 general commands 513 help 460 499 menu commands 499 overview 459 program execution commands 510 script only commands 536 variable commands 529 CAL syntax ACTIVATE 509 APPEND 534 APPENDVAL 535 BUTTON 506 CALL 511 CLEAN 527 DBOX 503 DDE 512 DELBOX 508 DOS 512 ENDLOOP 539 EXEC 512 EXIT 539 FONT 514 FORMEDIT 509 FRAME 504 GETDATA 533 GOTO 537 HELP 527 IF 538 INPUT 533 LOOP 539 MENU 499 MSG 514 OPENDB 529 PASSWORD 533 PAUSE 539 PICT 505 PUTDATA 534 QUIETCLOSE 515 READVAL 532 SEEPTAB 515 SELECT 510 SET 516 SETFIELD 508 SETTEXT 508 SETVAL 532 SUBFM 506 TEXT 504 UNSELECT 510 WRITEVAL 532 CF _SORT table 416 CFS file format 468 CFX file format 313 chain bonds 493 changing box style 319 database scheme 354 layout of an existing subform 401 changing colors 433 changing the display 433 charges and radicals 485 charges in queries 485 check valences 453 checkboxes 317 Chem3D viewing models 351 ChemDraw editing structures 350 ChemDraw ActiveX control 481 ChemDraw format viewing in 319 ChemFinder opening options 453 toolbars 287 UI 285 ChemFinder Office customizing 480 look In tab 471 overview 471 preferences 481 ChemBioFinder amp BioViz 547 User Guide search options tab 479 s
47. 477 ChemBioFinder 6 Click OK If you choose Send To MS Word or MS Excel the document type opens a new file or the file whose name you entered The structures you send to the application appear in that applica tion as follows e If you select Send all molecules in current hitlist ChemFinder Office will create a table in your document and the molecules in the current hitlist along with their molecular formulas weights and source file paths will be entered into the table e If you select Send current molecule Chem Finder Office will export only the structure NOTE If you need to interrupt a long Send To Word operation bring ChemFinder Office to the front and click Stop To send a file to ChemFinder or ChemDraw you must save the file you want to send 1 Click the Send To menu 2 Select CS ChemFinder or CS ChemDraw Files 3 Select the appropriate radio button in the Molecules section and click OK A Save As dialog box appears NOTE If you have a ChemFinder CFW file open you have the option of selecting it in the Document section of the Send To dialog box 4 Type in a name in the File Name text box NOTE If you are sending multiple structures to ChemDraw choose a base name for the files for example if there are three molecules in the current hitlist and you specify the base name 478 ChemFinder Office Chapter 30 molecule the files will be saved as molec
48. ADD af 1 of Figure 20 1 Status bar in record addition mode Adding new data To add alphanumeric data Click in a box with an alphanumeric field and type the data To add a structure 1 Right click in a box with a structure field ChemBioFinder amp BioViz 347 User Guide 2 Do one of the following Table 20 If you want to Then draw a structure Chem amp Bio Draw mode Double click in the structure box The Chem amp Bio Draw Control appears Draw the new structure in the Structure box Click outside to box to complete the structure draw a struc ture ChemBio Finder 12 0 mode Double click in the structure box or Right click and select Edit in Chem amp Bio Draw Chem amp Bio Draw opens Draw the new structure in the Chem amp Bio Draw window Click File gt Exit and Return to or type Ctrl W to return to ChemBioFinder 12 0 and insert the structure import a struc ture ChemBio Finder 12 0 or Chem amp Bio Draw mode Right click in the struc ture box and click Read Structure The Open dialog box appears Browse to a structure file then click OK The file is inserted into ChemBioFinder 12 0 NOTE See the Chem amp Bio Draw User s Guide for information about using Chem amp Bio Draw 348 Working with Data Chapter 20 Committing the new data When you finish entering all of the dat
49. Activate with any of the following extensions e doc MS Word e xls MS Excel e cdx ChemDraw e CFX ChemFinder e The application in which the structure was saved opens In MS Word the application opens directly to the first hit in the docu ment e When you view the structure in the original application the Hit List record is not copied to the other application You can use the Hit List menu to add or remove Hit List records To add or remove Hit List records with the Hit List menu 1 In a Hit List with records right click a record The record is selected and the Hit List menu appears 2 Select Add The Open Chemical Structures window appears 3 Double click the file you want to add to the Hit List or type the name of the file in the File Name text box 4 Click Open The file appears as a record at the end of the Hit List To take a record off the hit list right click and select Remove Saving files or data sources A data source or file can be any of the follow ing e A document like an MS Word document or an MS Excel spreadsheet e A database like a ChemFinder database e Any combination of documents or data bases You can save search results as a file to search through again Chem amp Bio Office 2010 User Guide 475 ChemBioFinder Saving search results as sdf files The SDF file format saves the Hit List records as complete structures in MDL SDFile format You can
50. Bring to Front Automatic labels You can let ChemBioFinder 12 0 automati cally label your framed box with the name of the field from the data tree To automatically label a Framed Box Right click inside the data box and select the field from the drop down list The data appears in the data box and the frame label changes to match the field name You cannot automatically label a frame that was created separately from a data box Non data boxes Boxes are not only used to display data The Form toolbar contains two tools Plain text and Picture to create static displays though they may also used to display data and three others with special functions Adding plain text The Plain Text tool allows you to display text without a box or a frame You can use it to place a static label on the form but like a data box you can also use it to display live data if desired To use the Plain Text tool 316 Forms Chapter 18 1 Click the Plain Text tool 2 On the form drag to create an area to spec ify where the text will appear The Enter the Text dialog box appears 3 Type the text you want to display 4 Click OK MoLID Formula Structure MolWeight This is a demo database Figure 18 7 Creating text on a form To change the font or color of the text select it with the Form toolbar Selection tool Use the text formatting toolbar to customize the text To use plain text to display data
51. CAL editor is a simple resizable text entry window It accepts carriage returns and tabs To copy paste use Ctrl C Ctrl V To undo or redo last change only use Ctrl Z The Verify button runs the script through the CAL command parser The parser checks only that lines begin with recognized keywords so just because a script is parsed without error does not mean it will run correctly The Properties button displays a dialog box used to specify whether the script is to be stored in an external file or internally and to provide a file path or script name You can assign a script any name you like but the name must be unique among scripts on the current form The OK button saves the script The Run button saves the script and runs it To execute a script not assigned to a button Choose the script from the Scripts menu NOTE To execute a script that does not appear on the menu use the Command line and enter Call lt script filename gt Debugging a script You can step through a script line by line when debugging it To view a script line by line 1 Click the Scripts gt Command Line menu command The Enter CAL Command dialog box appears 2 Type step on and click Execute This turns on the step mode where each step is displayed 3 Runa CAL script by doing one of the fol lowing Table 30 If your script Then appears in the Scripts menu choose the appro priate script Tab
52. Databases Chapter 19 Right click in the form and click Properties 2 Click the Table tab then click the Attach Table The Attach Table dialog box appears 3 Click the Open MS Access Database The Open dialog box appears NOTE The list of file types available in the Attach Table Open dialog varies from one computer to another The files for which you have drivers installed shown For example if Paradox is not installed you may not have Paradox drivers on your system or in the drop down list If the database type you wish to access is not on the list it may not be a file based system and you need to connect using ODBC For detailed instructions see Attaching files from a non file based database on page 342 4 Choose the database to access then click OK 5 In the tree diagram click the table you want to attach then click OK The newly attached table appears in the tree diagram in the Form Properties dialog box 6 Click the Form Properties OK Attaching files from a non file based database If the database you want to attach is not file based such as Oracle you can attach it using Microsoft s Open Database Connectivity ODBC To attach a non file based database table 1 Right click in the form and click Properties 2 Click the Table tab then click the Attach Table The Attach Table dialog box appears 3 Click the Open Oracle ODBC Data Source The Select Data Source di
53. Front To resize a box Select a single box and resize it by dragging a side or corner To reposition a box Select a box point within the selection and drag the box If you select multiple boxes dragging the cen ter of a selected boxes moves all of them To edit with the Clipboard 1 Select a box 2 Try each of the following menu commands Edit gt Cut or press delete Edit gt Paste Edit gt Undo Edit gt Redo Saving a new form To save a new form 1 Draw the form using the Framed box tool and labeled it as Structure 2 Go to File gt Save As 3 In the Save As dialog box save the form as tut1 cfx in the directory of your choice 4 Go to File gt Close Tutorial 2 Opening a database After you create a form you can use it to con nect to a database In this tutorial you use the form you saved In the previous tutorial after you connect to the database data will appear on the form Connecting a database to a form To connect a database to your form 1 Go to File gt Open The Open dialog box appears 2 Select tut1 cfx and click the Open button The form you created in the previous tutorial appears with its fields are blank 3 Right click on the Structure framed box and select Data Source The Box Properties dialog box appears with the Database tab displayed 4 Select the Layout mode button on the main toolbar if it is not selected already 5 Click Open Database
54. OK to dismiss the properties dialog you will get a warning if the selected table does not have a primary key defined You can ignore this if you are about to create or load a new table Otherwise you should consider using an Oracle tool to define a primary key for the table Choose Import SDFile or Import Structures and select the source file s The Data Import dialog appears Data Import ogging Form Style Advanced Output database oraserver MEMAN Records in file 37 Data Fields Input Field Type Width Output Column M Structure Structure Structure 000 moD Long MoLID abe Formula Text Formula OTD Molw eight Double MolWeight MGOMOLREGNO Long MOLREGNO Mabe MOLNAME Text MOLNAME Mabe CORP_ID Text CORP_ID ma DATF Text DATF 1 Import tab 2 Output database text box 4 In the Output database box you see the name of the database followed by the table name in brackets To specify the table to load edit the table name by typing between the brackets If you want to create a new table enter the name you wish to give it If you want to append to an existing table enter its name 5 Set other options as desired and click Import to begin the process TIP for text fields being imported make them wider than the value determined by the input scan To do this double click the name under Input Field and enter a larger Width value Oth erwise you might have problems if you appe
55. Oracle In addition you must subsequently choose the Custom install and select Oracle Windows Interfaces If you do not have the requisite components installed an attempt to open an Oracle database will generate the error Provider cannot be found It may not be properly installed 2 Have the Oracle administrator install CS Oracle Cartridge 9 or 10 You can use ChemBioFinder Oracle to access any Oracle database but one without the CS Oracle Car tridge cannot be used to store or search chemical structures 3 Have the administrator set up a user account for you ChemBioFinder Oracle requires that you log in to a tablespace in which you have write privileges For access to corporate files the administrator needs to grant you read only privileges to tables and views of interest outside your tablespace 4 On your machine use Oracle Net Configura tion Assistant to establish a connection to each Oracle database you intend to use In principle ChemBioFinder Oracle can access any Oracle database and make sense of it In practice some preparations are recom mended e You can access data in Oracle databases which do not have the CS Oracle Cartridge installed for example biological data bases but you cannot search or sort by structure or structure related properties ChemBioFinder Oracle has been developed with CS Oracle Cartridge version 9 or 10 and is not likely to work with earlier ver sions To
56. Part Description User variable that is the basis of the comparison variable operator Comparison function value String that is to be compared to the variable command Any valid CAL command Settings The settings for operator are Setting Description lt Command will be executed if value is less than variable gt Command will be executed if value is greater than variable Command will be executed if value is equal to variable l Command will be executed if value is not equal to variable Setting Description lt gt Command will be executed if value is not equal to variable Remarks Only one CAL command may be executed by each IF statement However that one com mand may be a GOTO that skips over many other commands CAL commands LOOP ENDLOOP syntax Executes a block of statements repeatedly LOOP count statements ENDLOOP The LOOP ENDLOOP commands have the following arguments Part Description count Number of times the state ments are to be repeated Commands that are repeated a number of times statements Remarks If count is omitted the statements will be repeated a number of times equal to the num ber of records in the current list This command is useful only in a script file and has no effect when entered on the Com mand Line LOOP example This example uses the LOOP command and the Menu Command Re
57. Right click in the Formula box and click Formula 3 Right click in the ID box and click the MOL_ID Go to File gt Save As 4 In the Save As dialog box save the form as tut2 cfx in the directory of your choice 296 Tutorials Chapter 17 5 Click File gt Close Congratulations You have created your own customized form for viewing the CS_Demo database Tutorial 3 Creating a database In this tutorial you will create a new database using the automatic form generation 1 Open a new form 2 Right click in the form and click the Data Source The Form Properties dialog box appears with the Database tab displayed 3 Click the Create Database button The Save As dialog box appears 4 Type mydb and click the Save button The name of the database appears in the Properties box ChemBioFinder 12 0 creates one data table MolTable containing four fields Structure Formula MolWeight and MOL_ID 5 Click the Field tab You are now going to add two new fields to the data table 6 Click the Create Field button The Create Field dialog box appears 7 Type MolName in the text box change the width to 254 and click OK NOTE You can enter not more than 254 char acters in a text field If you want a text field to contain more than 254 characters choose Memo Rich Text from the Type drop down list 8 Click the Create Field button again Type Boiling Point in the text box change the type to Double and click
58. S55 query C6H6 AND Molnami Q2 26 555 query C6H6 AND Molnar 384 Queries Chapter 21 3 Simply drag one query item in the tree on top of another Restore Merge dialog comes up allowing you to choose the logic to be applied to the merge replace intersect subtract union and subtract from Restore Merge List ce L1 current list E Rieplece use L2 2 25 hit G2 25 hits C Intersect L1 and L2 2 ES T C Subtract L1 L2 C Documents and Settings zchoo My Z C Union L1 L2 Documents Models C Subtract fom L2 L1 Cancel A successful merge results in a new list NOTE Ifyou merge two lists and get an empty result an alert appears and the list reverts to the previous list Search examples The following are examples of searching options By specifying atom and bond proper ties you see how to use the query functions in Chem amp Bio Draw to search the database more effectively All substructure search query prop erties recognized by ChemBioFinder 12 0 are listed and described in Structural Query Fea tures on page 483 Multiple hit lists A detailed example of how you can use hitlist management to perform specific sophisticated searches follows Suppose you want to search for all compounds in the CS_Demo database that contain a ben zene substructure and have molecular weights between 50 and 200 After you perform this combined search you want to find which
59. Select a different field to plot on that axis NOTE You can only change fields when the chart is not locked In Data Table display you can display a sub structure search as table of R group substitu ents BioSAR This section explains how to export a data form from BioSAR and view it as an equiva lent form in ChemBioFinder Once in ChemBi oFinder you can manage the form using a variety of features Starting the BioSAR browser To use BioSAR you must have Internet Explorer 5 5 with SP2 or greater installed To start BioSAR 1 In Internet Explorer log into the ChemOf fice Enterprise portal 2 In the Enterprise screen under BioSAR Enterprise open a query form using either of these links e Open Form e Manage your forms Performing searches in BioSAR Before exporting a BioSAR data form to ChemBioFinder you need to search on the data in the BioSAR database 1 In BioSAR open a query form of your choosing 2 In the form enter your search criteria and click the Search button Exporting the data form to ChemBioFinder After the search is complete you are ready to export the data form to ChemBioFinder To export the form 1 Click the Display In BioViz button If the button is not visible you may need to edit the BioSAR form properties See your administrator 2 When prompted to either save the form file or open it select Open ChemBioFinder will launch 3 At the Oracle login
60. Selecting a field name from the context menu Opening a secured MS Access database To open a secured Microsoft Access database in ChemBioFinder 12 0 you need to set the appropriate permissions in MS Access NOTE If your database was created in MS Access 97 as for example were some of the ChemBioFinder 12 0 sample databases and you are using a newer version of Access you must convert the database before you can edit it These instructions assume a database cre ated in Access 2002 Other versions may differ slightly as to options and procedures To set the permissions 1 Open the desired database in MS Access 2 Click Tools gt Security gt User and Group Permissions User and Group Permissions xj Permissions Change Owner User Group Name Object Name lt New Reports gt generic_report generic report template generic on open template generic_subreport_on_open_ter Object Type Report 7 List Users Groups Permissions IZ Open Run J Read Data JV Read Design gt Update Data JV Modify Design J Insert Data Z Administer I Delete Data Current User Admin Cancel Apply Figure 19 6 User and Group Permissions dialog box 3 Select the Users or Groups radio button to assign permissions to individuals or groups 4 Select an Object Type from the drop down menu 5 Select the permissions you want to assign for that object type to each user or group 6
61. Structure field type You can work in Chem amp Bio Draw directly or work in the Structure data box using the Chem amp Bio Draw Control You choose the default in the Struc ture data box Box Properties 350 Working with Data Chapter 20 To set the preference 1 Right click in the Structure box 2 Click Properties 3 Use the drop down menu in the Box Style section to choose your default e Chem amp Bio Draw style to use the Chem amp Bio Draw Control e ChemBioFinder 12 0 style to edit in Chem amp Bio Draw TIP When Chem amp Bio Draw style is the default you Still have the option of editing directly in Chem amp Bio Draw Just right click in the Structure box and choose Edit in Chem amp Bio Draw To edit a structure Double click in the structure data box Chem amp Bio Draw opens or the Chem amp Bio Draw Control appears depending on your default If you already have a structure in a data box that structure appears in the edit window You can modify and manipulate the structure just like any other Chem amp Bio Draw structure If there is no structure in the Structure data box the edit window is blank You can draw a structure to store in the ChemBioFinder 12 0 database When you have finished do one of the follow ing e If you are editing in Chem amp Bio Draw click File gt Exit and Return to Structure or type Ctrl W e If you are editing with the Chem amp Bio Draw Control click outside
62. The files have a CPX extension and the name of each file is the name given to the template The Cost Profile Chooser displays all files in this directory having the CPX extension The inter nal format is XML readable in Notepad To remove a template from the chooser delete the corresponding file or move it to another location or change its extension To add or modify a template 1 Double click in the profile data box to open the Profile Editor then click the Cost Profile tab 2 Edit the profile until it looks the way you want 3 Right click in the edit window then click the Save context menu command 4 When prompted enter a line of descriptive comments to be displayed underneath the chooser window and click OK 5 Type the name you want to appear in the chooser and click the Save button ChemBioFinder amp BioViz 411 User Guide 412 Compound Profiles Chapter 24 PRO ChemBioFinder Oracle Users familiar with ChemBioFinder 12 0 will find that for the most part ChemBio Finder Oracle operates the same way You should be able to open a database browse search register load and so forth without wor rying about what sort of database is on the back end In practice however there are sev eral visible differences and a lot of invisible ones When you open an Oracle database in ChemB ioFinder Oracle you enter a new body of code which connects directly to Oracle and carries out all searches and
63. a CAL script to be executed when you click an item in a subform in table view The subform can then be used as a list selection box The script can use CAL com mands to retrieve the clicked item and perform an action on it For more information about CAL see CAL Commands on page 499 To specify a CAL script 1 Right click on the subform header and click the Properties context menu command The Subform Properties dialog box appears 2 In the Table script box type the name of a CAL script or click the Edit button and select a script 3 Click OK In Table view the entries are blue and underlined indicating that they are hot linked to a script 4 Click any of the hot links to run the script ChemBioFinder amp BioViz 403 User Guide 404 Relational Data and Subforms Chapter 23 Compound Profiles Compound Profiles a way of visually compar ing and ranking structures based on values of selected properties A compound profile is a graph or more typi cally a series of graphs each of which plots the value of a numerical field in the database on a vertical bar color coded to show regions of cost or undesirability These regions are defined by a cost profile associated with the field In the profile costs are normalized to score between 0 and 1 where the ideal is assigned the value of zero and the slope of the deviation to maximum 1 is user defined NOTE The function is a normalizing
64. and warnings are not displayed in dialog boxes To perform a Check structures search 1 Select the categories of interest 2 Click the Sean When a structure is flagged its record is displayed the offending atom or bond if any is flashed and an alert offers the user several choices The options are if you want to then click ignore the error and Don t know or continue checking the Ignore same structure ChemBioFinder amp BioViz 379 User Guide if you want to then click is unspecified or has stereo rewrite the MST record thus correcting the problem Continue the scan from _ Skip to Next Struc the next structure ture stop the scan Stop Scanning This leaves you on the last record that exhibited a problem flash the problematic Flash atom or bond This button only appears when the error revolves around an atom or bond Clicking the button creates a circle that moves toward the atom bond drawing the eye to it View details about a Help warning message Fix the error automati Auto Fix cally Managing queries The Queries Tree Control in the Explorer win dow maintains a list of search queries from the 380 Queries Chapter 21 current and previous sessions Queries are associated with forms and the query list is saved when you save the form When you open or activate an existing form the tree updates to show only
65. be saved with the form file and will still be in effect when you open the form again Saving and restoring lists You can save queries individually as cfq files or automatically when saving the form The old commands for saving and restoring lists as cfq files still appear on the Search menu and on the context menu displayed when you right click on a specific query If you close a form without having saved your queries or other changes you are prompted to save or discard changes On the General tab of the Preferences dialog box there is an option to save all queries the default or only those that have been renamed If you select this option there are two ways to save a query with the form e Rename the query either with the Rename command in the context right click menu or from the query properties dialog box also accessed from the context menu e Mark the query with the Keep command on the context menu Query saved in this way retain their standard name Preferences Display Color Search Type Dotais Tuning General Regstratien A Recent fle kst sze 6 3 MW Check valences F Ask to comm changes Use Query Add Window Al Startup Explorertab Favores D Show startup dalog f F Reopen test form Frame shie Whey IF Check for external scripts Query Saving C Save al quenes Discard unnamed queses No save I Open lait query on opening losn Figure 21 29 General preferences
66. become editable for entry of queries e Form boxes are displayed according to their visibility properties For more information see Hiding data boxes on page 321 Entering and submitting a query To enter the query 1 Position the cursor over the field you want to search and click to select it 2 Enter the query in the data boxes ChemBioFinder amp BioViz 373 User Guide 3 Click the Search on the Query Mode box ChemBioFinder 12 0 searches The number of hits is shown in the Status Bar at the lower right corner of the window NOTE If a search gets no hits or an error occurs an alert appears and you are returned to Query mode to enter a different query or modify the current one The hit list is a subset of the complete data base You can browse it as you would any database using the Record commands in the Record menu or toolbar For example to view the hits in tabular form Click View gt Data Table Stopping a search To stop a structure search in progress press the Esc key The query stops and you return to browse mode NOTE Only queries that involve structural data structure molecular formula and molec ular weight searches can be stopped in this manner SQL searches and searches that involved non structural data cannot be aborted Refining a search You can refine a hit list of one or more records by entering a query that searches only the hit list not the entire databas
67. box and click the Com pound Profile gt Preferences context menu command The Profile Display Preferences dialog box appears 2 To change the base color of the cost band default red select a primary color in the Cost Shading Color section 3 To reverse the polarity of the cost band deselect the Ideal white check box When checked light shades are good dark are bad when unchecked the reverse is true 4 To change the color of the value marks and the lines between them click the Values button and select a color from the color picker ChemBioFinder amp BioViz 409 User Guide 5 To change the color of range labels click the Labels color button and select a color from the color picker 6 To turn off the range labels to the right of the cost band deselect the Labels check box 7 To use the current settings as the defaults for all subsequent profile creations click the Use As Defaults button 8 When you have finished editing the set tings click OK to save the changes or Can cel to discard Search sort You get the most advantageous use of profiles in comparing compounds by using the search sort function Select one compound as your base for example an ideal compound with an overall score of zero then sort the database by increasing deviation from that score To use Search Sort to compare profiles You must be in Form View to begin this procedure 1 Browse to t
68. by a reaction This prop erty allows you to specify just how a given bond is affected Property Description Unspecified target must have a bond here but the bond can participate in the reaction in any fashion or not at all ChemBioFinder amp BioViz 493 User Guide Property Description Center target must have a bond here that directly partici pates in the reaction in some way Make Break target must have a bond here that is either made if in a product or broken if in a reactant Change target must have a bond here whose bond order changes over the course of the reaction but is not made or broken Make amp Change target must have a bond here that is either made if in a product or broken if in a reactant or whose bond order changes over the course of the reaction 494 Structural Query Features Appendix A Property Description Not Center target must have a bond here and that bond must not participate in the reaction Not Modified target must have a bond here and regardless of whether it is part of the reaction center or not its order must not change over the course of the reaction This property is only meaningful when search ing a reaction database Formula Input Rules When you type a formula in ChemBioFinder you are not required to enter symbols in any particular case This can give rise to ambigui ties This appendix
69. ccccccsssscesees 445 PMD OS a Saicdnceetceacicatstatsatacocnrateabacedtne 445 Working with Clustering 445 Modifying Clustering eee 447 CS Clustering Dialog features 449 Chapter 29 Customizing ChemBioFinder 12 0 451 Setting preferences eeeeeeeeeeteeeees 451 Favorites tree saiscscnsssscascssenceondbeavensevannes 455 6 Kore oy eee 456 Periodic table ccs cscahatesncccuatestrausieneens 457 Embedding ActiveX controls 458 BNC PG oeseri speres 459 Methods of communication 467 Chapter 30 ChemFinder Office ssscscsssessesees 471 OVETVIE Waona a 471 The user interface UD 00 00000e000en 471 Selecting files to search 0 00 eee 471 Searching by chemical structure 473 Searching by multiple properties 474 Browsing search results 0 00 0 475 Saving files or data sources 475 Searching DSD files 476 Sending a file to another application 477 Refining your search seses 478 Changing ChemFinder Office settings480 Appendix A Structural Query Features 00 483 General properties 483 Changing the scope of a search 489 Atom properties cccdcadusececaresechedeceusedecs 489 Bond Properties si secesscsscseassesesenecssevncees 493 Appendix B Formula Input Rules cccssseees 495 RUIE Seea E 495 Exam pleSirnasreii nenioo 495 Appendix C Similarity Rules sooesoosss
70. change a frame s label is in the Box Properties dialog For more information See Setting box properties on page 318 You can use a frame to show live data from the database If a frame is connected to a data base field it is updated automatically as you browse or search For example you might place a frame around a structure field where the label on the frame represents the name of the current structure The label changes every time the structure does You must use Box Properties to set up a live data connection for a frame Creating boxes with frames The Framed Box tool allows you to create a data box and a frame simultaneously You name the frame in the Enter the Label dialog box To create a framed data box 1 Click the Framed Box tool 2 On the form drag to create a box 3 In the Enter the Label dialog box type the label you want to attach to the frame and click OK The framed data box is labeled To edit the label of a framed data box ChemBioFinder amp BioViz 315 User Guide 1 Select the frame by carefully right clicking near the edge of the framed box and select Label 2 In the Enter Box Label dialog box type the new label The label does not have to match the name of the field displayed in the box 3 Click OK When you create a data box and frame with the Framed Box tool these two items are con nected To manipulate them separately Select the Framed box then click Edit gt
71. command prior to creating the box When specifying a script name give one of the following e The complete pathname of the script file e A simple name without extension if the script is stored in the standard scripts subdi rectory with the standard file extension If the script name appears on the Scripts menu you can use the name from the menu The table below shows examples of Box Cre ation Commands Part Description COMMAND ACTION Frame 1010 create frame with label at ular Formula DBOX 20 20 create data box for formula in 290 50 above frame formula TEXT 100 100 create static text string 300 150 A Label PICT 500 300 put specified picture at lower 600 400 right C LOGO WM F BUTTON 500 create button at upper right to 10 550 40 run script DEMO CFS DEMO CAL commands DBOX syntax DBOX creates a new data box on the active form DBOX left top right bottom fieldname The DBOX command has the following argu ments left Integer value representing the distance in pixels between the left edge of the box and the left edge of the active form top Integer value representing the distance in pixels between the top edge of the box and the top edge of the active form right Integer value representing the distance in pixels between the right edge of the box and the left edge of the active form bottom Integer value representing the dis
72. connected to the database FORMEDIT controls the behavior of the SELECT command With FORMEDIT ON SELECT affects boxes With FORMEDIT OFF SELECT affects the contents of those boxes SELECT and UNSELECT choose boxes to be modified by editing operations DELBOX is a shortcut for FORMEDIT ON followed by SELECT followed by Edit Clear SETFIELD connects a database field to an existing box ChemBioFinder amp BioViz 507 User Guide for a button it attaches a script name see above regarding script names SETTEXT attaches a text string to a box or replaces the one currently attached see box creation com mands above for a list of what the text strings mean for various box types ACTIVATE and DEACTIVATE are the same as SELECT and UNSELECT but work on subforms Following an ACTIVATE com mand all subsequent commands apply to the active subform and any boxes it contains The DEACTIVATE command is required to once again refer to the main form and its contents SCALE scales all items in the current form by the percentage factor you specify Use this to fit your forms to different size screens See SCALE_TO_FIT below SCALE_TO_FIT scales all elements in the form such that the string you specify will fit in the form at the currently selected font size See FONT below The table below shows examples of Box Manipulation Commands Command Action SELECT 11 select formula frame created 11 above SELEC selec
73. control If it isn t visible do the following 1 Click the View gt Explorer Window menu command 2 Click the Queries tab to display the Queries tree Query list operations Each time you perform a search or list opera tion a new query is generated in the tree ChemBioFinder assigns a name to the query and displays it in the tree along with the size of the list number of hits and a brief description The generated name is Q lt n gt where n is a sequential number and indicates that the query has not been renamed or marked for sav ing See Saving query lists on page 441 To perform list operations begin by perform ing a simple search For example you can search the database for all compounds that have a molecular weight less than 250g mol 1 Click the Enter Query icon on the Search toolbar or menu The form goes into query mode 2 Enter lt 250 in the MolWeight field of the query form and click the Search button A query labeled Q1 appears as a child of the Full List Explorer Queries Full List Q1 24715 Molweight lt 250 Database Queries Favorites BioSAR Figure 27 16 The Queries control after a typical search Changing the query name If you want you can change the name of a query to one that is more descriptive Renam ing a query also ensures that the query is saved with the form Depending on your Preferences settings queries not renamed may be automati cally discarded
74. display the Cartridge version look in the Database tab of the Properties dialog The version is listed or None if unavailable ChemBioFinder amp BioViz 541 User Guide e Any table containing structures should have a unique primary key If you connect to a table without a unique primary key you get a warning message You can set up a pri mary key in ChemBioFinder see Index ing on page 419 e ChemBioFinder Oracle users must have sufficient privileges to create tables in their own tablespaces Fast move caching scheme Normally when you open a database or do a search ChemBioFinder issues a select state ment The server then processes the statement prepares a set of records and provides a cur sor for navigating through them to retrieve the data Unfortunately when the cursor is asked to move to a position N records from the cur rent one it requires all N to be downloaded to the client In the worst case you open a large table and use Move Last to see the last record and the entire table is sent down from the server To get around this problem an alternative mechanism is available in ChemBio Finder Oracle In this scheme instead of requesting complete forms full of data over a list or query ChemBioFinder Oracle retrieves only the ID or primary key field and stores caches the results in an array in memory It then need not rely on the normal recordset cur sor When a request is made
75. distance in pixels between the bottom edge of the subform databox and the top edge of the active form Remarks It is not currently possible to set the data source or link fields of a subform using CAL SUBFM example This example uses the SUBFM command to create a large subform in the middle of the form SUBFM 50 50 600 300 Box manipulation commands FORMEDIT ON OFF SELECT box UNSELECT box DELBOX box SETFIELD box fieldname SETTEXT box text A D CTIVATE subform EACTIVATE SCALE SCALE_TO_FIT To work with a box or subform on the form you specify a keyword followed by a box iden tifier A box is identified in one of two ways e By point Give the coordinates of a point anywhere within the box When coordi nates fall in more than one box the most recently created box is used e By text The text you enter to identify a box may be e The field name if the box contains data from a database e The text label if the box contains static text such as frames or text labels e The box name assigned in Box Properties For subform boxes the table name In all cases you need not spell out the entire name just enough to be unique Often more than one box matches the text you enter for example a box displaying field molweight within a frame labelled MolWeight In this case preference is given to the box
76. entire data base or the results of database queries You can filter the plot to limit the data range within a given dataset To create a new plot 1 Click the View gt BioViz Plots gt New menu command The BioViz Plot Properties dialog box appears 2 Select a Dimension one or two variables and a Style line scatter or histogram 3 Select the variable s from the drop down list s 4 Optional select other options change the name 5 Click OK to view the plot The plot appears in a separate window In a 2D plot you may plot any numeric field on the X axis and any other on the Y Fora 1D plot you choose only the value to be plotted on the Y axis where the X axis represents record number For a histogram choose a single value to be plotted on the X axis with the fre quency plotted on Y Another way to select a field to be a variable or create a 1 D plot is to right click in a prop erty field and select BioViz Plot from the con text menu When you right click in a numeric data box you may choose that value to be plotted on either axis or as a 1D plot against record num ber In the latter case the plot appears immedi ately when you release the mouse button For a 2D plot you must first select a data box for the other axis Use the Reset X Y command to clear both X and Y settings and start again Histograms Histogram plots are only available when you select a one variable plot When you select a Hi
77. files 475 case insensitive 372 combined 368 directory paths 476 DSD files 476 enter query 479 for dates for formulas 299 for intermediates 368 for names 300 for numbers 300 358 for products 302 368 for reactants 301 368 for substructures 300 formula element ranges 359 formula query rules 359 full word 372 fullerenes 386 ISIS style 372 loose delocalization 372 more than one substructure 387 parentheses in formulas 359 558 Index procedures 369 refining 478 restore previous query 479 save results 476 search options 479 search tools 478 start 479 subforms 402 tuning 372 searching a database tutorial 298 searching combined 301 searching for dates 359 searching for formulas 358 secured Access 337 securing forms 327 security disabling 331 MS Access workgroup information 327 overriding 331 setting options 327 selecting boxes 324 data to display 334 databases 333 objects on a form 324 selection tool 324 send to back command 325 sending to another application 477 setting alerts 453 box properties 318 color 323 data box styles 318 fixed and live data 320 numeric format 322 preferences 451 recent file list size 454 search details preferences 370 search type preferences 369 security options 327 stereochemistry search preferences 372 showing annotations 452 data boxes 321 opening dialog 453 reaction centers 454 similarity rules 497 similarity searching 361 similarity searching se
78. frame and the top edge of the active form right Integer value representing the distance in pixels between the right edge of the frame and the left edge of the active form 504 CAL Commands Appendix D Part Description bottom Integer value representing the distance in pixels between the bottom edge of the frame and the top edge of the active form text String displayed as a label on the top left corner of the frame Remarks When a new frame is created it adopts the cur rent font settings These settings can be con trolled with the FONT command After a frame is created its label can be changed with the SETTEXT command CAL commands TEXT syntax Creates a new static text box on the active form TEXT left top right bottom text The TEXT command has the following argu ments Part Description left Integer value representing the distance in pixels between the left edge of the text box and the left edge of the active form top Integer value representing the distance in pixels between the top edge of the text box and the top edge of the active form Part Description right Integer value representing the distance in pixels between the right edge of the text box and the left edge of the active form bottom Integer value representing the distance in pixels between the bottom edge of the text box and the top edge of the active form text
79. have double bond stereo dictated by geometry Double Either target must have double bond any stereochemistry ok Double Bold same as Double Triple target must have triple bond here Substituents In ChemBioFinder a substituent is defined as a non hydrogen atom connected by a bond of any order For example a carbonyl oxygen is a substituent of the carbonyl carbon 484 Structural Query Features Appendix A All unfilled valences in the query may be filled by hydrogen atoms or by non hydrogen sub stituents The normal valence of an atom is determined from data in the Periodic Table window For example carbon has a valence of 4 while sulfur has valences of 2 4 and 6 Any explicit charges radicals or query properties modify the normal valence For example a carbocation has a valence of 3 Hydrogen atoms in the query may match non hydrogen substituents in the target if the hydro gen in the query is implicit on an unlabeled carbon atom or heteroatom This is the default setting Hydrogen atoms in the query must match hydrogens in the target when the query hydro gen is at the end of an explicit bond The matched hydrogen in the target may be implicit in an unlabeled carbon atom The following query with explicit hydrogens H o H N Finds any of ko HN p 8 NH2 0 Br H H Rr Does not find any of OH NH2 OH H NH Charges and radicals Charges or radicals specified on atoms in the que
80. import SDF files from Chem Finder Office into applications like Chem Finder To save search results in the sdf format after a search 1 From the File menu choose Export SDFile The Save As dialog box appears 2 In the File Name text box type a name for the file 3 Click Save The file is saved with an sdf extension For more information about exporting files to other applications see Sending a file to another application on page 477 Saving data sources as dsd files After you complete a search you can save all the records from the Hit List as a Data Source Definition dsd file so that you can search through them again You can use dsd files to search for structures substructures or structures similar to your pre vious search through the dsd file To save the results of a search as a dsd file 1 After completing a search go to File gt Save Source As The Save As dialog box appears 2 In the File Name text box type a name for the group of files 3 Click Save The files are saved with a dsd extension 476 ChemFinder Office Chapter 30 Saving lists of directory paths as dsd files NOTE Only advanced users familiar with text editors should use this procedure You can save lists of directory paths that you search as dsd files You can create these lists with a text editor such as Notepad Saving a list of directory paths as a dsd file saves the direc tories in which you sea
81. in the Search tab of the Preferences dialog The default is 1 allow the match SEARCHING FIND_CHARGED_HET Whether or not to allow Oor 1 uncharged heteroatoms to matched charged ones when searching This parameter can be set manually in the Search tab of the Preferences dialog The default is 1 allow the match SEARCHING MATCH_STEREO_DB Whether or not to match Oor 1 cis trans stereochemistry around double bonds This parameter can be set manu ally in the General tab of the Preferences dialog The default is 1 match stereo SEARCHING MATCH_STEREO_TET Whether or not to match Oor 1 tetrahedral stereochemistry This parameter can be set manually in the Search tab of the Preferences dialog The default is 1 match stereo ChemBioFinder amp BioViz User Guide 525 Section Preference Description Values SEARCHING MAX_HITS Maximum number of hits to 1 be returned by a search The default is 2500 hits SEARCHING SIMILARITY Whether or not to allow a Oor 1 similarity match when searching This parameter can be set manually in the Search tab of the Preferences dialog The default is 0 require exact match SEARCHING SRCH_TANIMOTO_PCT Cutoff percentage below 0 100 which two compounds are not considered similar This parameter can be set manu ally in the Search tab of the Preferences dialog The default
82. is 90 SEARCHING SRCH_USE_RXN_CTRS Whether or not to require that O or 1 query substructures have at least one atom or bond in the reaction center of the target This parameter can be set manually in the Search tab of the Preferences dialog The default is 1 require in center 526 CAL Commands Appendix D Section Preference Description Values SEARCHING STOP_AFTER_MAX_HITS Whether or not to stop 0 or 1 searching after the maximum number of hits have been found If this preference is turned off ChemBioFinder will report the total number of hits but will still display only the maximum number The default is 1 stop CAL commands CLEAN syntax Attempts to standardize the bond lengths and angles of the current molecule CLEAN param The CLEAN command takes the following optional arguments Part Description default Progressively stronger drawing modes starting with Tidy until something changes cleanup tidy Minimum redrawing if any redraw License to redesign rings denovo Complete redesign from scratch Remarks This command is equivalent to opening the structure in ChemDraw selecting the Clean Up Structure command and returning to ChemBi oFinder CAL commands HELP syntax Displays a list of all valid CAL commands The valid parameter types are listed for each command as is a brief description HELP Remarks This command is
83. manually 313 Setting box properties eee 318 Editin e TOTS sscseceeescaeeceariteenoud ieee 324 Chapter 19 Data ASCS sssscissiasincscassssssnsevseseasesonsasessbis 333 Selecting a database vacezsecsceserssveceaseede 333 Opening databases 336 Browsing databases eeseeeeeeeeeee 338 Creating a database 341 Creating a portal database 346 Chapter 20 Working with Data cccscccssssceseee 347 Peri d t scscs3ssciessdeeeerbeaeeteacccpience 347 Editing data aie cad ese antadetoasdduarcesndea teeters 349 Sorting data occas sa vescenasontedaceesdtasdeniecdas 353 Resetting the database ee 354 Changing the database scheme 354 Chapter 21 QUETr ES eessssecessscceesscceessscecescsccsesseceessese 357 Text SE ALC WG S sussie 357 Numeric searches s src 358 Molecular formula searches 358 Date searches 359 Find Sb ccseg eseew ea eceaieeedevtrauecuacesdeahacavee 360 Structure searches 360 Reaction searches s es 366 Combined searches 368 ChemBioFinder amp BioViz User Guide i SOL Wear CHOS si susiscsartenteaacenedeanesosarers 369 Query procedures ceiecdacksiwossseresusstustens 369 Refining a search eeren 374 Special structure searches 0 376 Managing queries 380 Search examples n se 384 Chapter 22 Importing and Exporting Data 389 Importing data eeeeeeeeeeeeeeeeree 389 Exporting data eerren 394 Chapter 23 Relational Data and Su
84. may see the writer s edits If two people are viewing the same record within a database and one person changes the data in that record the second person will not see the changes immediately The changes will be visible when the second user switches to another record and then back to it Secured access ChemBioFinder 12 0 supports the following types of security e Form access ChemBioFinder 12 0 enforces form access security by requiring a user name and password which are stored in the form CFX file e Molecule file access ChemBioFinder 12 0 enforces molecule file access security by requiring a user name and password which are stored in the database s MST file e Microsoft Jet Relational Database Engine the database engine that underlies Microsoft Access enforces security The user names and passwords are stored in an MS Access Workgroup Administrator data base For more information on Form access see Securing forms on page 327 For more infor mation on MS Access security see Opening a secured MS Access database on page 335 When you open a form or database that has security options applied to it you are prompted to enter a username and password to log on When you open a secured MS Access database from within ChemBioFinder 12 0 a username password and workgroup information file is required Contact your Access Database Administrator for this information To open a secured form 1 I
85. ment Description Details window Displays details of selected or moused over point when a plot window is displayed May be displayed as tabbed with other windows Data box A viewing area in a form linked to a field in the database associated with that form and displaying data from that field See also Control box Picture box Profile box Subform Text box Screen Ele Description ment Main form Displays data contained in one record of the database To keep the display from getting clut tered tabbed pages may be added for less important data Main toolbar Contains icons representing general purpose menu commands such as copying saving and printing Explorer window Displays information on three tabbed overlapped windows e The Database field hier archy The Queries list that will be saved with the form e A Favorites list of file paths Contains all the commands Menu bar specific to the application for managing forms tables databases and their contents New Record Displays ADD when you indicator adding a new record that had not been committed to the database Output window Displays Python output May be displayed as tabbed with other windows Filter window Displays the filters that modify the BioViz plot May be displayed as tabbed with other windows Form toolbar Contains the form creation tools Frame An
86. not be struck in a 3D search is available in both Pro and Ultra 12 0 but not in Standard version Miscellaneous Presently this checks one thing that isotopic masses seem reason able False stereomarks flags stereochemical indicators such as a wedged bond on an atom that is incapable of stereochemistry because of its geometry In a normal search such indicators are ignored The option allows you to find all such stereo chemical indications and correct any errors CDX lt gt Mst correspondence Checks whether the chemical interpretation of the original CDX drawing remains same in the latest version of the software It also checks whether the stored internal struc tures need to be regenerated from the CDX e Atom atom maps Checks whether the quality of auto generated maps is satisfac tory However user defined maps are not checked and are considered legitimate e Locate deleted structures Identifies struc tures that have been deleted from structure boxes e Representational Drift Checks several invisible aspects of stored chemical struc tures and ensures that the stored chemical structures are up to date with the latest software version NOTE When the Interactive option is selected the application displays dialog boxes with warnings and errors if any However if you select the To file option you need to provide the path for storing the log file containing warnings and errors In this case errors
87. not wish to export and select those main form fields you do wish to export 4 Click the Export button NOTE Re importing a file of this type will not regenerate the original database It will bring back the data but not in the subtables and sub forms you started with To do this export to cfxml When exporting to SDFile you may append to or overwrite existing SD files This option is only available for SD files and delimited text exports Exporting to STATISTICA To export data to STATISTICA 1 Create or open a database 2 Click File gt Export gt To STATISTICA The Data Export dialog box appears Data Export Export Text Options Output File File Data Fields Field Type Width Output Field Type o Wid G0 MoD Long MolID Long Export Cancel NOTE The preceding dialog box will appear only if STATISTICA is installed 3 Specify a name for the output xml file to which data is to be exported 4 Click the Text Options tab The following dialog box appears Data Export x Export Text Options Text File Export Tab delimited Comma delimited C Other Structure Text Export Format Include header I Export subform data I Export empty records Base64 encoded CDX C CDXML c c T Prefix output fieldnames I Select fields on current tab Export Cancel Set the text file export options based on the type o
88. of these compounds do not contain a carbon nitrogen bond By integrating hitlists you can perform this search To create the hitlist for the first part of this search 1 Open the CS_Demo database 2 Create the first query by drawing benzene in the Structure data box and entering 50 200 in the Molecular Weight Data Box 3 Search the query You get 75 hits 4 Click Search gt Save List 5 Save the hitlist as benz txt To create another hitlist for the second part of the search 1 Draw the query shown below in the Struc ture Data Box N eee 2 Search the query You get 103 hits 3 Click Search gt Save List 4 Save the hit list as c n txt Integrate the two hitlists 1 Click Search gt Restore List 2 In the Open dialog box open the benz txt file 3 In the Restore List dialog box click the Replace radio button then click OK You return to your first list of 75 hits 4 Click Search gt Restore List 5 In the Open dialog box open the c n txt file 6 In the Restore List dialog click the Subtract radio button then click OK The hit list is reduced to the 60 records with compounds containing a benzene substructure not containing a C N substructure and having molecular weights between 50 and 200 If you had chosen the Replace option in the last step then only the C N records would be dis played Choosing Intersect would display those records in either list Finally choosing Union would
89. of the ChemFinder Office display fea tures with the Preferences window Customizing the window Use the View menu to change the appearance of the ChemFinder Office window To use the View menu 1 In the Data Source Find Chemical Struc tures window click the View menu The View menu appears 2 Take the appropriate action then from the View menu If you want to show the Standard make sure the box toolbar next to the Toolbar option is checked ah e show the Status bar make sure the box next to the Status bar is checked Ready rec 2 list 29 If you want to then from the View menu hide the Status bar click Status bar The status bar disap pears show the Hit List which shows all of the places that ChemFinder Office has found the struc ture you want to find click Show List This option only appears when the list is hidden hide the Hit List click Hide List This option only appears when the list is showing customize features including Commands Tool bars Menu and Keyboard options click Customize The Customize window appears This is a standard Windows feature For more informa tion see the MS Word online Help Changing preferences To change the ChemFinder Office preferences 1 From the File menu choose Preferences The Preferences window appears 2 Take the appropriate action
90. or by starting the appli cation in Windows 2 In ChemBioFinder 12 0 obtain the hit list you want to transmit to Excel If you want to work with the entire database click the Search gt Retrieve All menu command 3 Execute a short CAL script below which exports the hit list as comma delimited text to a temporary file then instructs Excel with DDE to load that file into a spread sheet 4 Activate Excel to work with the data in the spreadsheet This procedure takes data one way from ChemBioFinder 12 0 to Excel Returning mod ified data from Excel to ChemBioFinder 12 0 can be done using other techniques described in this chapter Here is a script to start up Excel RUNEXCEL CFS script to start Excel EXEC c msoffice excel excel exe If the Excel program is on your search path you can eliminate the complete pathname and just give the executable name exec excel exe if not you may need to modify this script to indicate where EXCEL EXE is located on your system Here is a script to transfer the current hit list from ChemBioFinder 12 0 to Excel TOEXCEL CFS script to send data to Excel ChemBioFinder amp BioViz 467 User Guide WRITETEXT C DATA TMP DDE Excel System OPEN C DATA TMP DDE Excel System COLUMN WIDTH 1 C1 C4 3 1 The first line writes out the current ChemBio Finder 12 0 hit list as
91. provide your user name and password NOTE Ifyou don t want to view the form now simply save the file You can open the file in ChemBioFinder at any time ChemBioFinder file types Whenever you export a data form BioSAR creates a file with the extension bsbxml ChemBioFinder reads this file and opens the form linking it directly into the database The bsbxml file is read only Although Chem BioFinder doesn t allow you to modify the bsbxml file itself you can still edit the form and save your changes When saved the form file is assigned the ChemBioFinder extension ChemBioFinder amp BioViz 435 User Guide cfx Unlike bsbxml files cfx files are not read only You can open any cfx file in ChemBio Finder edit it and save it again Meanwhile the bsbxml file is still available whenever you need to open the original form Seiting save password If an Oracle connected form contains an invalid or blank or no password the program prompts you for a name and password on opening the form The same is true if the Save password box has not been checked in the form properties dialog This is now the default when a form comes from BioSAR You are prompted for username and password every time until you check the Save password box and save the form Subforms and autolinks When you create a form in BioSAR you select from the database which fields you want to include in the form Those same fields appear
92. rotation tool but it also can be used to select atoms or bonds If you right click in the field the context menu displayed is the Chem amp Bio 3D control context menu giving you access to Chem amp Bio 3D commands See the Chem amp Bio 3D User s Guide for more information about using Chem amp Bio 3D NOTE Unlike interaction with Chem amp Bio Draw changes you make to a model within Chem amp Bio 3D are not transmitted back to ChemBioFinder 12 0 and thus are not saved You can put a picture of the Chem amp Bio 3D model into a database by saving the Chem amp Bio 3D model as a bitmap or metafile and inserting it into a Picture field The picture does not retain a connection table and cannot be edited 352 Working with Data Chapter 20 Styled text Make changes to text fonts sizes styles col ors and alignment with the tools on the Text menu or the Text Format toolbar To display the Text Format toolbar if it is not visible Click View gt Toolbars gt Text Format The Text Format Tool appears Text Format Toolbar x Arial 10 BIUx AY SES B E 12 2 7 10 45 8 11 1 font 2 point size 3 bold 4 italics 5 underline 6 subscript 7 superscript 8 color 9 left alignment 10 center alignment 11 right alignment 12 bullets Use the toolbar to format text in Plain Text or Memo Rich Text data fields Undoing changes Before committing your te
93. structures 347 environment variables CAL 535 equals symbol in query 359 exact searching 361 exact searching see also normal searching exact searching see also similarity search ing Excel communicating with using CAL 459 communicating with using DDE 467 security setting when importing 329 explorer window description 286 exporting ASCII files 395 current hit list 383 data files 394 delimited text files 395 security settings 330 subform fields 396 Word files 396 exporting to another application 477 extraneous fragments permitting in full structure searches 371 F fields creating 343 date 344 deleting 345 deleting contents 353 editing 349 formula 341 integer 344 memo 344 Mol_ID 341 molecular weight 341 picture 344 read only 289 real 344 sorting 353 structure 341 344 text 343 fields assigning to data boxes 296 file commands CAL 527 file formats MDL 488 file formats supported 389 file based databases attaching tables 342 files DSD 476 log 391 SDF 476 selecting with look in tab 472 selecting with open file menu 472 filter window 306 filter window description 286 filtering 430 filters 307 find command 373 find current molecule command 375 find list command 360 find text command 344 first record command 338 fit to box 452 fixed labels 315 320 flat file databases 341 fonts customizing 322 form tool 314 toolbar 314 form toolbar description 286 form definition 291 forms addin
94. subform data box and click the Properties context menu command The Box Properties dialog box appears 2 In the Box Properties dialog box select the Form tab 3 Select the Generate form check box then click the Style button The Form Generation dialog box appears In the left panel all of the Fields are selected by default 4 Deselect those fields in the Choose fields to be included section that you want to exclude from the form 5 In the Form style section select the form options you want For a detailed description of the options see Creating forms auto matically on page 311 6 Click OK 7 Click the Properties dialog box A warning dialog box appears allowing you to create a new form or replace the existing form Click No to create a new form Yes to replace the existing form The subform is automatically changed Working with subforms You must select a subform to work with it The subform title bar is highlighted when the sub form is selected After a subform is selected ChemBioFinder amp BioViz 401 User Guide the toolbars affect the subform You can use the Record tools to browse the subform and add records To select a subform Click anywhere in the subform To return to the main form Click the main form To select a subform box With the selection tool click in the title bar Searching a subform You search a subform the same way you search the main form You can search a s
95. the Framed Box tool For more information See Creating boxes with frames on page 315 To resize objects on a form 1 Click the Selection tool on the Form tool bar 2 Position the pointer over an edge or corner of the object until the pointer is a double headed arrow 3 Drag in the direction you want to resize If an object is nearly the right size you can make small adjustments to get it exactly the size you want To resize objects one pixel at a time 1 Select the object you want to resize 2 Place the mouse pointer over an edge or corner of the object until it is a double headed arrow 3 Press an arrow key in the direction you want to resize the object The edge of the object moves one pixel in the direction of the arrow key Deleting objects Use the Selection tool to remove data boxes and other objects from a form To remove objects from a form 1 Click the Selection tool on the Form tool bar 2 Select the object you want to delete TIP Use Shift click to select multiple objects 3 Do one of the following e Click Edit gt Clear e Use the Backspace key The object is removed from the form Reversing and restoring changes Use the Main Toolbar icons or the Edit menu to reverse or restore recent changes to a form To reverse or restore changes Click Edit gt Undo to reverse a change or click the Undo icon Click Edit gt Redo to reverse a change or click the Redo icon
96. the context menu again the variable will appear with a check mark next to it To remove a filter Right click in the Filter window to display the context menu then click the variable to deselect it The following bio assay example shows two plots of the octanol water partition coefficient CLogP plotted against an activity measure called Fold_Above_Control The second is fil tered on molar refractivity Note that the upper chart has been locked to prevent the filter from affecting it ELLA Figure 26 11 Locking a chart To apply the filter e Press the thumb at one end of the slider and drag along the slider ChemBioFinder amp BioViz 431 User Guide e Inthe bottom diagram the plot is limited to Molar_Refractivity from 10 to 33 e pi pot eet ee ne ee po Su txoa in lt 2 I sure CO 6 5d 44 a l a4 I gt 2 24 al dhil I paler ame cet mper a ee i ae LAES ai aa a Figure 26 12 Histogram Filtering Filter slider adjustment Once the top and or bottom of the range has been set you can move the entire range For example the Boiling Point filter has been set to display a range of about 250 from 501 3 K to 753 K a a 278 11 501 34 75298 1004 62 Figure 26 13 Filter Slider Adjustments By dragging the blue part of the slider you can view any 250 range of the chart that you want The range being displayed has been moved to 651 5 K 903 2 K The size of the ra
97. the types of columns in the table Here s how it decides whether a particular column contains structures e The column must be of type CLOB or BLOB e If the column has been indexed by the CS Oracle Cartridge then it is a structure col umn e If there is no index then ChemBio Finder Oracle looks for a table of configu ration info called CF_SETTINGS If the column is listed in that table as being of type STRUCTURE then it is a structure col umn The CF_SETTINGS table is also used to deter mine whether a particular column of type BLOB contains ChemBioFinder pictures Windows metafiles To designate an unindexed column as a struc ture column 1 In the Field tab of the Properties dialog select a column of type BLOB or CLOB 2 Click Set As Structure If the CF_SETTINGS table has not yet been created an alert indicates that it is about to be created 3 Click OK to proceed and create the table or Cancel to abort without creating If the table already exists and there is already an entry for the selected column you are given an alert and a chance to cancel 4 Click OK to proceed A new entry is created in the table marking the selected column as a structure column To designate a BLOB column as a picture col umn 1 If the CF_SETTINGS table does not exist cre ate it using steps 1 3 of the above procedure 2 Edit the table one of two ways e with an Oracle client tool such as SQL Plus OR e by opening i
98. the active formactive_form_definition for further manip ulation It is equivalent to clicking in the box with the pointer tool SELECT box The SELECT command has the following argument Part Description box Box identifier indicating the box to select Remarks The SELECT command acts only on data boxes frames text boxes buttons and picture boxes The similar command ACTIVATE is used for subforms The behavior of the SELECT command is modified by the FORMEDIT command When the form is in form edit mode the SELECT command affects data boxes themselves When the form is in data edit mode the SELECT command affects the data within the data boxes CAL commands UNSELECT syntax Reverses the action of the SELECT command making sure that no boxes are marked for fur ther manipulations It is equivalent to clicking in the form background with the pointer tool UNSELECT The UNSELECT command takes no argu ments Reverses the action of the ACTIVATE com mand making sure that the main form is the active form It is equivalent to clicking in the main form background with the pointer tool 510 CAL Commands Appendix D UNSELECT The UNSELECT command takes no argu ments NOTE This command will change the active form Program execution commands CALL scriptname DOS doscommand EXEC wincommand EXEC_BUTTON boxname DDE ddecommand LAUNCH filename OUTPUT_STR string
99. the plot and zoom in To select part of the plot a Drag a rectangle across a portion of the plot The portion of the plot is displayed in red b To select more than one section use Shift drag or Ctrl drag To zoom in on part of the plot a Right click in the plot and click the Zoom on Drag context menu command ChemBioFinder amp BioViz 433 User Guide This is a toggle switch choose it again to deselect b Drag a rectangle across a portion of the plot This time when you release the mouse button the plot display zooms in to show only the points selected When the plot is zoomed scrollbars appear Use these to reposition your view of the zoomed plot Click the circled point icon on a scrollbar to restore that axis to the previous zoom Right click and click the Unzoom context menu command to restore to the full view e Changing the Style you can change the style of an existing plot For example you can turn a scatter plot into a histogram a Right click in the plot and click the 434 Properties context menu command BioViz Chapter 26 b In the properties dialog box select the style and click OK The plot displays in the new style e Changing Fields you can change the field plotted on the X or Y axis with the context menu a Point in the area of the numbers just below or to the left of an axis b Right click The context menu displays a list of plottable fields c
100. the predefined special atom types an atom list is a list of atoms one of which must match the target atom For example Cl Ag N atom must be Cl or Ag or N Atom lists may contain only elements Special atom types nicknames Ph and structural fragments NH2 OCH CH3 may not be included in an atom list ChemBioFinder rec ognizes a maximum of five atoms in an atom list Atom not lists The opposite of an atom list is a list of atoms none of which must match the target atom For example NOT O S Se atom must not be O or S or Se but may be any of the 100 other elements Atom not lists have the same restrictions as atom lists Substituents exactly This property specifies a precise value for the number of substituents on an atom including those explicitly drawn This property is only meaningful in a substructure search With a substructure search the query ee oS 1 This atom is marked with the atom property Substituents Exactly 3 490 Structural Query Features Appendix A Finds any of CI z T 0 ce Does not find any of x PSE Substituents up to This property specifies a maximum value for the number of substituents on an atom includ ing those explicitly drawn This property is only meaningful in a substructure search With a substructure search the query with sub stituent up to property u2 1 1 This atom is marked with the atom property Substitue
101. to an MS Access database MS Access provides a security sys tem that allows the creation and management of usernames and passwords and the assign ment of permissions to those usernames MS username password account information is stored in the Workgroup Information file mdw mda For more information about securing an MS Access database See Open ing a secured MS Access database on page 335 Setting security options To set what ChemBioFinder 12 0 form options are available to users 1 Right click in the form you want to secure and click the Properties The Box Properties Dialog box appears with the Form tab displayed 2 Click Security NOTE The Security button does not appear if the security on your form has been set to not allow access to the Security options The Form Security dialog box appears Form Security Logon Information Enable Disable Usemame Database security d Forms Automation Cul copy paste Browse Searching Update records Import data Export data Print RIERRERRRRIRKR Enable piee No security defined Figure 18 11 The Form Security dialog box TIP The lower left corner of the dialog box indicates whether security is defined 3 Type the Username to use for logon in the Username box The Enable button becomes available 4 Type the Password to use for logon i
102. to data boxes 296 atom lists 385 atom lists 490 atom not lists 490 atom properties 489 atom types A any 489 and bond types 385 link node 386 ChemBioFinder amp BioViz 545 User Guide M metal 489 overview 385 Q heteroatom 489 X halogen 489 atoms 483 atom to atom mapping 367 attaching files from a file based database 342 tables from other applications 342 attaching files from a non file based data base 342 attachment points defining 365 tool 365 automatic labels 316 autoscale 307 autoscale see also rescale backing up databases 346 bin definition 426 BioViz changing fields 434 curve fitting 428 description 285 details window 424 empty points 424 filter sliders 432 histogram plots 425 selecting points 424 setting display range 432 Statistical analysis 428 bitscreen 497 bond length uniform 452 types overview 385 bond properties 493 in queries 493 ring chain 493 546 Index bond types double either 484 in queries 483 special 493 bonds 483 boolean field fields boolean 344 boolean operations in queries 358 boolean operations on hit lists 383 box creation commands CAL 502 box manipulation commands CAL 507 boxes changing styles 319 creating 314 deleting 325 font 322 hiding or showing 321 moving 324 properties 318 resizing 325 selecting 324 style 318 bring to front command 325 browsing databases 338 browsing search results 475 browsing with the record tool 338 Btrieve
103. to move to record N the key for that record is looked up in the array and a new select statement is issued to retrieve only the corresponding record Thus Move Last takes no more time than Move Next There are tradeoffs between the two schemes e The new scheme takes time to retrieve the set of ID s during a database open or after a search or sort Normally this is quite fast 542 CS Oracle Cartridge Appendix E even for a large table and steps are taken to avoid repeating the operation unless neces sary A message on the status bar indicates when this caching process is taking place e In the new scheme moving from one record to the next is somewhat slower since each move involves a fast one hit search This is not very noticeable during list browsing but slows down multi retrieve operations such as filling table view Because of these drawbacks the new caching scheme is OFF by default To turn it ON for an Oracle connected form 1 Click the File gt Database menu command or otherwise bring up the Properties dialog 2 Go to the Oracle tab of the dialog 3 Check the Cache ID s for faster moves box 4 Click OK You will get an alert instructing you to 5 Save the form close it and reopen it This is currently necessary in order to reinitialize the database connection with the caching scheme Configuring via CF_SETTINGS table When you select a table in an Oracle database ChemBioFinder determines and displays
104. transactions on the server This new mode of operation requires a differ ent underlying technology based on Microsoft ActiveX Data Objects and a different philoso phy in some aspects of usage such as the han dling of lists and new features such as index management All of these are described in this document In ChemBioFinder Oracle e Searches are carried out on the server including structure searches e Search results are automatically deposited directly into tables in the Oracle database e Hitlists are not saved in files but to other tables in Oracle e Saved lists can be annotated and on restore can be selected from a pick list directory e When working with large databases you can choose a new mechanism which elimi nates certain slow operations associated with large record sets e g Move Last This is a user choice because there are trade offs involved e You cannot create an Oracle database but if you have the privileges you can create a table within one This causes import opera tions to work somewhat differently e To improve performance you can create indexes on selected columns Other more subtle differences are noted in the sections below Structure search speed is very fast in ChemBi oFinder The fast speed comes from two fac tors improvement of the SQL so that hits are added much faster to the hitlist table and an optimization of certain frequent operations and improved screening effici
105. view Adjust the height of any form by dragging the bar divider on the left to view the forms clearly Go to View gt Form View To retrieve all the records in your database double click Full List in the Explorer window ChemBioFinder amp BioViz 299 User Guide Name searching To find all compounds in the CS_Demo data base with molecular names starting with benz 1 Switch to the Form View if you are not already in it 2 Go to Search gt Enter Query TIP Although the tutorials describe the use of the Search menu you may find using the Search toolbar more convenient The icons on the tool bar match those you have already seen on the Search menu Clicking the Find icon is equiva lent to pressing the Enter key when you are ready to begin your search See Queries on page 357 for information on more advanced use of the Search toolbar The form is cleared so that you can enter a new query 3 Click the Molecule Name box and type benz 4 Press the Enter key 12 hits are returned with names starting with benz 5 Click View gt Data Table gt In Current Window The Table view appears Browse to verify that the molecular names are correct NOTE Notice that this search gave you ben zene but not bromobenzene The query you entered above is an anchored substring and only gives you strings starting with the indi cated substring For more information on how to specify te
106. when you save the form To rename a query 1 Point to the query and right click The context menu is displayed 2 Click Rename on the context menu The name Q1 is highlighted 3 Enter a new name and press the Enter key Changing the display color The color of the box next to the query name is the same color to be used to display the points should you plot the results You may change any query to any color so that the plots look the way you want To change the display color 1 Point to the query and right click The con text menu is displayed 2 Click Change Color on the context menu The color picker context menu appears 3 Select a new color and click OK The color in the box changes If you have plotted data with BioViz you will see that the points that correspond to the query also change color Child lists You can add a new query either by searching the Full List or searching another query When you create a new query from another one the result is a child list For comparison purposes it is often an advantage to create multiple child lists each from a single search attribute rather than one child list based on multiple attributes You can create a child list for only the cur rently selected list If you are not sure that the list you want is selected double click it Before you create a child list select Over Cur rent List on the Search menu Note that once selected Over Current List has a check ma
107. where the ester oxygen comes from the acid would be mapped like this oH e ai g Hoa Am o DN a OH a o Rx Figure 21 18 Alternate possible atom map for ester ification ChemBioFinder 12 0 uses atom to atom map information to determine reacting centers for reactions If only some atoms are mapped ChemBioFinder 12 0 uses that information and does not worry about the specific fates of the other atoms For example if you don t know or don t care about the mapping of some atoms you can leave them unspecified in the atom to atom map By default atom to atom mapping is not dis played within ChemBioFinder 12 0 To turn on this display select Atom to Atom Map on the Structure sub menu of the View menu For more information see Changing options with the view menu on page 454 NOTE For information about specifying atom to atom maps with Chem amp Bio Draw see the Chem amp Bio Draw User s Guide ChemBioFinder amp BioViz 367 User Guide Searching for reactants If you know what starting materials you are interested in but don t know their products you might perform a reactants query A reac tants query is very similar to a reaction search except that there is nothing to the right of the arrow For example consider the query e is Figure 21 19 Sample reactants query If you are doing a substructure search this finds any reactions in which maleic anhydride or a compound containing a
108. 0 seconds FONT changes the current font Any boxes created subsequently adopt this font Follow the keyword with a name from your Windows font list followed optionally by e Font size in points default is 8 e Style from the list below default is 0 or plain text ChemBioFinder amp BioViz 513 User Guide e Color three values for red green and blue each ranging from 0 to 255 default is 0 0 0 or black Font styles are sums of bold 1 italic 2 and underline 4 Thus a style value of 1 means bold 3 means bold italic 6 means italictunderline and so on SEEPTAB briefly displays the periodic table window then closes it The window will be displayed for the amount of time specified 1 decisecond 0 1 second If the duration is omitted it will be displayed for four seconds QUITECLOSE closes the active form This command is similar to FILE CLOSE but auto matically discards any changes instead of prompting the user what to do HIDETABLE closes the Table View window for the current form If a subform is active it returns the subform to form view SET allows you to modify basic ChemBio Finder settings including most of those found in the Preferences dialog and several that can not be accessed in any other way See the online help for a complete listing of parameters that can be SET CLEAN will attempt to standardize the bond lengths and angles of the current molecule It is the same as opening t
109. 0 7 75 score 0 18 406 Compound Profiles Chapter 24 Figure 24 2 A compound profile for MW LogP and IC50 A compound profile is useful as a visual indi cation of the quality of each compound As such it is most useful in table view where you can see and compare several profiles at once The highest benefit comes from using profiles in sort search operations You can pose one compound as the query and then sort the remaining ones by deviation from that query Creating a compound profile Profiles are displayed on the form in a special data box created with the Profile tool To create a Profile box The database connected to the form or subform you are working with must have at least one numeric field NOTE You can also include structure field in profile 1 Click the Profile tool on the Form toolbar 2 Drag a box on the form The Profile Wizard appears then click Next Profile Wizard ChemBioFinder Compound Profile Wizard Welcome to the Compound Profile Wizard A Compound Profile compares values of selected fields with user defined ideal values Each value is shown on a vertical band shaded to indicate regions of cost undesirability The ideal value is shown by the line in the middle Click Next to begin defining fields Cloge AW petivity score 2 20 dist 3 30 Define Field dialog is displayed Define a field Choose a field enter short name and value range Field
110. 1 Create a button on the form 2 Right click the button and click the Edit script context menu command The script editor window opens for script entry 3 Click OK when you have completed the script The script is executed when the button is clicked TIP You must toggle out of layout mode to use the button To create a script connected to a trigger event 1 Open the Box Properties dialog box and click the Form tab 2 Select an event in the Run script on box by clicking the check box next to it 3 Click the Edit The script editor window opens for script entry 4 Click OK when you have completed the script The script is executed when the event occurs To create a script linked to a subform table 1 Right click on the subform name to open the Subform Properties dialog box 2 Enter a name in the Table script text box then click the Edit button The script editor window opens for script entry 3 Click OK when you have completed the script The subform contents are displayed in hyperlink style blue underlined Clicking any link executes the script The script editor There is a single script editor for all scripts CAL and Python The contents change to match the script being edited This is a change from the CAL editor in earlier versions where you could have a separate window for each script The editor is modeless that is it stays on the screen when you switch to work in Chem
111. 2 0 window ChemBioFinder amp BioViz 375 User Guide e Click somewhere in the form outside the Structure box 3 Optional enter more query terms in the other data boxes for a combined search 4 Select or deselect the Search gt Substructure menu option as appropriate for your query NOTE The Similarity option is not available for reaction queries 5 Do one of the following to search e Click Search gt Find e Click the Find icon on the Search Toolbar The search proceeds as with simple structure searching Special structure searches The Find Structures submenu on the Search menu provides for several common types of structure searches can not be efficiently con ducted using regular means NOTE The Special Structure Searches feature is available in both Pro and Ultra 12 0 but not in Standard version As with other searches all of these searches operate within the current record set if the Over Current List option is in effect Otherwise the whole list is searched regardless of how many records are currently displayed Special struc ture searches are intended to apply to all data sources including Oracle but presently only work for MST sources The following figure 376 Queries Chapter 21 shows the menu options under Find Struc tures submenu Ele gdt View Tet Search Record Sgipts Online Window Help Empty Structures Reactions With Stereo Centers Missing Stereochemistry Charged Radica
112. 6 The label Name after the radio button From table updates to show your choice and the Auto link via check box becomes available NOTE An auto link cannot be set up if you are entering a fixed list of choices 7 Check the Auto link via box From the drop down menu choose the column of the subtable in this case Name under Chemist which is to be matched against the column ID NOTE The columns shown in the drop down menu should match the type of the fields to be linked i e if the ID is numeric then only numeric fields may be linked 8 The form box displays a chemist s name Multiple sort ChemBioFinder s multiple sort feature lets you rearrange the hitlist based on one or more form fields you specify For example you can first sort the list by Reg number and then further arrange the list in order of Full reg number Sorting by main form fields To sort the hitlist using fields in the main form 1 Click the Record gt Sort menu command The Sort Multiple window appears 2 In the Sort Multiple window select from the left pane the field by which you want to sort To sort by multiple fields select the fields in the order you want to sort 3 By default each field is sorted in ascending order To reverse the order right click the field name in the right pane and click Descending in the pop up menu To remove ChemBioFinder amp BioViz 437 User Guide a field right c
113. 7 Click the Form Properties OK The source of the data to display on the form is indicated but the form is still blank To access the data you need to draw some data boxes and indicate what data to show in each of those boxes Creating fields Whether you created a new database or are working in an existing one you can add or remove fields in the selected table You can choose from the following types of fields abe Text field Allows you to enter text such as names comments and references A text field is fixed in length and requires that you choose a maximum length width for any data item to be stored in the field If you enter a width of 50 then you can t store any item with more than 50 characters in that field You can specify widths of text fields as large as 254 characters If this is insufficient you need to create a Memo Rich Text field instead Because the text field width cannot be modi fied after a field is created it is often wise to err on the side of caution and make it longer than you need initially On the other hand larger field widths also create larger files and slower search times NOTE Non ASCI characters will not display correctly in a data table text field ChemBioFinder amp BioViz 343 User Guide Oo Integer field Used for whole numbers such as ID s All integers in ChemBioFinder 12 0 are long so can accommodate billions of values 232 of them 00 Double field Us
114. ASSWORD v default The PASSWORD command has the following arguments Part Description User variable to which the user s data is assigned variable default String presented as the default password Remarks If variable is omitted the text will be assigned to V1 Password entry example This example uses the MSG command to prompt the user for a password then the PASS WORD command to retrieve it After using the IF command to test whether the password is correct it either EXITs or continues with the rest of the script nter the secret msg Pleas password password 1 if v1 lt gt the secret password exit A Le geen CAL commands GETDATA syntax Reads the contents of a data box into a user variable GETDATA v box The GETDATA command has the following arguments Part Description variable User variable to which the text is assigned box Box identifier indicating the source of the text Remarks GETDATA accepts only boxes that contain text or data that can be represented as text including numbers formulas or dates You cannot GETDATA from a data box containing a structure or a picture ChemBioFinder amp BioViz 533 User Guide If variable is omitted the text will be assigned to V1 CAL commands PUTDATA syntax Copies the contents of a user variable to a data box PUTDATA box text The PUTDATA command has the following arguments
115. BioFinder 12 0 To close the script edi tor click OK or Cancel The editor has three modes e CAL for developing CAL scripts Use the Verify button to check syntax Run to test the script NOTE To work with CAL interactively do not use the script editor Use the command box that appears when you click the Scripts gt Command Line menu command e Python for editing Python scripts As in CAL mode you can view or edit a script and click Run to test it When you switch into this mode prompts are removed e Python Interactive for interactive devel opment of Python scripts In this mode you can enter Python commands and execute them one at a time or click Run to test the script The buttons on the script editor are as follows ChemBioFinder amp BioViz 463 User Guide e Verify checks a CAL script for syntax errors This button does not apply to Python e Run executes a script used for testing e Import loads a new script from a text file e Properties Opens a dialog box with two options save script internally with the ChemBioFinder 12 0 form or save script as an external text file e Help opens the CAL Help window or Python manual Interactive mode The Python Interactive Mode is modelled on standard Python environments such as IDLE and PythonWin In this mode e Type cfhelp for a page of tips and samples of ChemBioFinder 12 0 specific program ming e At ea
116. BioViz 515 User Guide modified the form in any way the File Close CAL commands SET syntax command will present an alert asking if the h the val f vari f that user wants to save changes while the QUIET ee oe e control the overall behavior of ChemBio CLOSE command will not Finder CAL commands HIDETABLE syntax SET section preference setting Closes the Table View window for the active The SET command has the following argu form active_form_definition ments HIDETABLE The HIDETABLE command takes no argu Part Description ments section String describing the general Remarks category of preference The Table View for the active form can be dis played with the Menu Command View Data preference String naming the preference Table to change If the active form is a subform the setting String describing new value HIDETABLE command will return it to form of preference view Values The values for section preference and value are Section Preference Description Values DISPLAY ATOM_LABEL_COLOR The color in which to display color atom labels that cannot be interpreted by ChemBio Finder The default is Purple DISPLAY ATOM_NUMS Whether or not to display Oor1 atom numbers on each atom The default is 0 do not display 516 CAL Commands Appendix D Section Preference Description Values DISPLAY ATOM_SPECIAL_COLOR The color of query atoms and color other atom
117. But Python is far superior to CAL in many ways e Python is a complete programming lan guage not just a set of commands It allows calls to system functions access to data bases OLE Automation file I O program flow control data structures object ori ented and structured programming and all other features offered by a modern lan guage e Python can be developed interactively in the ChemBioFinder 12 0 Script Editor a development environment similar to IDLE PythonWin and others This environment combines line by line execution with pro gram construction convenient for develop ment and debugging e Python scripts can operate ActiveX controls that is also available in ChemBioFinder 12 0 form boxes e Python communicates with ChemBioFinder 12 0 via OLE Automation allowing it to access documents record sets data form boxes structures CAL commands e Python in ChemBioFinder 12 0 is inte grated with ChemScript the chemical structure processing language from CambridgeSoft ChemScript is an extension to Python which allows carrying out detailed analysis or manipulation of mole cules reactions and models Creating a script A ChemBioFinder 12 0 form can contain a col lection of scripts both CAL and Python Each is connected to the form in one of three ways depending on how the script will be executed To create a script first decide how it will be called To create a script activated by a button
118. Data Box displays a data item or structure Use it to display any data from a database including text numbers dates molecules reactions or pictures It is the only box that allows you to edit data in the database Data boxes do not have labels but you can label them by adding a Frame or Plain Text You can also use the Data Box to display static data not from a database To draw a Data Box 1 Click the Data Box tool 2 On the form drag diagonally to create a box To specify what type of data is displayed in the box See Setting box properties on page 318 If the form already has a database open you can right click in the data box select Field and choose from a list of the available fields Creating frames The Frame tool allows you to create an enclo sure with a label surrounding a data box or group of boxes When you draw a new frame you are automatically prompted for a text label to be attached to it To create a frame 1 Click the Frame tool 2 On the form drag diagonally to create a frame A framed box appears with the label Data To change the label 3 Right click on the label and choose Label from the drop down menu The Enter the label dialog box appears 4 Type the label you want to attach to the frame 5 Click OK A fixed label appears on the frame To change a label 1 Right click on the edge of a frame and select Label 2 Enter the new label in the text box Another way to
119. Format and output the record data Our simple example just prints a line to the output window e Lines 16 17 Proceed to the next record e Lines 18 22 Objects created in a script must be freed before leaving Without this you may find it impossible later to exit ChemBioFinder An object can be freed by setting it to zero Rec 1 Name Bromobenzene For mula C6H5Br Rec 2 Name 3 Bromobenzoic acid Formula C7H5BrO02 Rec 3 Name 6 6 Dibromoindigo Formula C1l6H8Br2N202 Rec 4 Name 3 Bromophenol For mula C6H5BroO Caveats e Subforms are not supported by the CF Automation interface If you need to work with subform data you will have to use CAL for the time being e Running Python scripts cannot currently be interrupted Be warned before trying the above script on a long hitlist Once it starts running it will not stop until finished or until you kill ChemBioFinder in Task Man ager We are working on this problem e If after you have run a script you try to exit ChemBioFinder and it refuses to exit it means the script created a ChemBioFinder object and failed to release it Methods of communication There are two general methods of communi cating with other Windows applications such as Microsoft Excel by using a script within ChemBioFinder 12 0 or by using a Visual Basic procedure within the other application The following is an overview of each method Using scripts A ChemBioFin
120. IT ends the script immediately INTERACTIVE turns interactive mode on or off STEP toggles single step debugging mode on and off The table below shows examples of Script Only Command Command Action Sica a label IF VI provide an error message if the wee 1 MSG variable V1 is empty Empty value PAUSE 100 pause 10 seconds GOTO start go to specified label LOOP 10 begin loop to repeat ten times PAUSE pause the default time 2 seconds ENDLOOP return to LOOP statement until done NOTE Script commands are subject to change See the Readme for up to date infor mation CAL commands syntax Marks a line as a comment and not a com mand to be executed text The command has the following argument Part Description text String containing the comment Remarks The character must be the first character in a line to mark it as a comment This command is useful only in a script file and has no effect when entered on the Com mand Line command_line_definition CAL commands syntax Labels a line with the preceding or following text label or label The command has the following argument Part Description label Text to be used as a label Remarks This command is useful only in a script file and has no effect when entered on the Com mand Line CAL commands GOTO syntax Unconditionally transfers execution to a spec
121. If you want to then choose a specific directory for the Look In tab to open type the path in the Startup directory text This setting does not box or click to affect any query browse to a file in the properties Startup directory specify the number of most recently open files to show in the File menu type the number or click the Up and Down Arrows in the Number of recently used files to show on File menu box to set a whole number from zero to 10 open the last file you used when you start ChemFinder Office click Reopen last source on startup show all files in the directory tree click Show files in directory tree use the ChemDraw ActiveX control to draw and edit struc tures open ChemDraw to draw and edit struc tures click the ChemDraw style radio button click ChemFinder style radio button 3 Click OK The Preferences window closes Chem amp Bio Office 2010 User Guide 481 ChemBioFinder 482 ChemFinder Office Chapter 30 Structural Query Features To perform a substructure search in ChemBioFinder you must first draw the query structure itself Query structures can be drawn in many different programs but we recom mend using ChemDraw and this Appendix is focused on using ChemDraw to draw query structures For more information about the structure drawing and query capabilities of ChemDraw please consult the ChemDraw User s Guide
122. MoMeight Double MolWeight Dou XN ABSTRA Memo ABSTRACT Men RXN COMME Memo COMMENTS Men IRXN ATMOSP Text 3 ATMOSPHERE Text Mabe RXN TEMP Text 17 TEMP Text Mabe RXN TIMF Text 13 TIMF Text lt gt The Import dialog box scans the file to deter mine what data fields are present and how much space to allow for them in the database The number of records scanned is shown in the status bar If the input file is large the scan may take a while To interrupt the scan press the Esc key A message box appears to confirm whether you really want to stop The scan continues until you click Yes To abort the scan click Stop scanning NOTE You should let the scan go to comple tion so that all needed fields are created in the database before loading Using log files During the import ChemBioFinder 12 0 cre ates a log file of the actions taken The log file log is a text file that is created alongside the input file and overwrites any previous log file The log records data of your choice form the following options during the import e Errors Errors and warnings e General data Information about the input file and import process e Records processed Logs an entry for each record of the input file e Structures registered Logs an entry for each structure stored in the database e Data registered Shows each data item stored in the database e Database schema Shows input fields found and c
123. NOTE Choose Save to save the form Choose Commit Changes to save the data in your database Tutorial 4 Searching a database NOTE Select the Over Current List command and add it to the instructions ChemBioFinder 12 0 helps you organize and find information One way to find information is to browse through the database one record at a time This is a good way to see some of the information available However because data bases can be very big browsing is often ineffi cient Searching a database is like using the index of a book With an index you can quickly focus on the few pages you are interested in When you search a database you find only those few records that have the information you look for After you have this smaller collection a hit list you can then browse it much more effi ciently than you could the whole database ChemBioFinder 12 0 performs the following types of searches 298 Tutorials Chapter 17 e Text and structure searches demonstrated in Tutorial 4 e Reaction searches demonstrated in Tutorial 5 In this tutorial you will learn how to search substructures and text in the CS_Demo Data base This database is included with ChemBio Finder 12 0 as a sample database of approximately 300 organic and inorganic com pounds Opening the demo database To open the CS_Demo database 1 Start ChemBioFinder 12 0 and click the Existing tab on the Open dialog box If ChemBioFinder 12 0
124. NOTE The Open and Create Database buttons work with ChemBioFinder 12 0 databases only To access data in other types of databases use the Attach Table or the Oracle button if avail able For more information about data sources see Attaching tables from other applications on page 342 The Open dialog box appears ChemBioFinder amp BioViz 295 User Guide 6 Select CS_demo mdb ChemOffice 2010 samples folder and click the Open button The database opens and the Box Properties dialog box appears displaying the Database tab 7 Select a table A list of the tables in the database and the fields in each table are shown The field you select determines what type of data appears in the box you selected in step 3 Assigning fields to data boxes To display structures from the CS_Demo data base in a Structure Framed box on your form From the list of fields in the Box Properties dialog box select Structure and click OK The Structure field is linked to the Structure Framed box In the Structure data box the data of the Structure field for the first record in the CS_Demo database appears To assign fields to the other data boxes 1 Right click in the Molname Framed box and click the MoIname NOTE After you open a database and table the shortcut menu displays the database fields The Molname field in the database is linked to the Name box and the data for the first record appears in the Name box 2
125. OFF turn off append mode INPUT 2 prompt and get user input to enter new V2 data GETDATA 3 copy data from molname box molname to V3 PUTDATA mol store given string in molname name be box nzene LET 3 V1 sets V3 equal to the value v4 stored in V1 plus the value stored in V4 SUBSTR 2 stores cde in V2 abcdef 3 5 ChemBioFinder amp BioViz 531 User Guide CAL commands SETVAL syntax Assigns the specified string to a user variable SETVAL variable text The SETVAL command has the following arguments Part Description User variable to which the text is assigned variable text String that is assigned to the variable Remarks If variable is omitted the text will be assigned to V1 CAL commands READVAL syntax Reads the contents of a text file into a user variable user_variable_definition READVAL v filename The READVAL command has the following arguments Part Description User variable to which the text is assigned variable filename String containing the file name from which to read the text Remarks The complete file path c some long path TEMP TXT is necessary when reading files 532 CAL Commands Appendix D If variable is omitted the text will be assigned to V1 If the file is greater than 32K in size only the first 32K is read READVAL example This example uses the READVAL c
126. OK NOTE Use the field type Double to create a field containing real numbers such as 123 7 and 43 242 The data table tree displays your changes 9 Click the Form tab 10 Click the Generate form check box Click the Style button In the Form Generation dia log box make sure the check box for Struc ture in upper left of form is checked 11 Click OK in the Form Generation dialog box and again in the Properties dialog box The Mydb form is generated Check the field assignments in the data boxes 12 Right click in the structure data box There should be a check next to Structure indicating that the Structure field is linked to the structure data box 13 Right click in the Boiling Point data box There should be a check next to Boiling Point Adding records Now that you created new fields and assigned them to data boxes you can add data to your database This tutorial was written to demonstrate use of the Chem amp Bio Draw control the default structure mode Before you begin to add struc tures you might want to check whether Chem BioFinder 12 0 is set appropriately To check the current setting 1 Right click on the Structure data box and click Properties 2 In the Box Style section of the Box Proper ties dialog box select Chem amp Bio Draw style When Chem amp Bio Draw style is selected ChemBioFinder 12 0 defaults to the Chem amp Bio Draw control This allows you to edit structures directly
127. Part Description box Box identifier indicating the destination of the text text String containing the text to store Remarks If PUTDATA attempts to store text in a data box that contains a non text data type such as a number date or formula the text will auto matically be converted to the correct type CAL commands APPEND syntax Determines whether data in a user variableuser_variable_definition is kept if other data is being moved there APPEND value The APPEND command has the following argument Part Description value Value describing whether new data should be added to the end of existing data or whether it should overwrite the existing data 534 CAL Commands Appendix D Settings The settings for value are Setting Description ON New data is added to the end of existing data OFF New data replaces existing data Different form example This example shows how you can use a script to open a second form with some of the same fields as the original form but for example a different layout This same sort of procedure can be used to display related records if you do not want to use an explicit subform The APPEND SETVAL and GETDATA com mands build a search string based on the con tents of the link_field field on the original form The Menu Command File Open opens the second form or switches to it if it is already open Finally the Menu Command Search En
128. Possible hits C6H6 compounds with 6 carbons and 6 hydrogen atoms and no other elements C6NO compounds with 6 carbons no nitrogens plus any number of other elements C6 N1 3 compounds with 6 carbons and one to three nitrogen atoms plus any number of other elements Formula queries consist of element symbols and element counts or ranges The following rules apply e Symbols may be one or two letters Sym bols may be in upper or lower case if there are ambiguities the program resolves them according to rules described in Formula Input Rules on page 495 Capitalize the symbols properly and insert spaces between elements e Use the Periodic Table to enter formulas For more information see Periodic table on page 457 and Formula Input Rules on page 495 e Element counts are single integers or ranges two integers separated by a hyphen If a count is omitted it is assumed to be 1 e Ifthe formula query is preceded by for example C6H6 then the search requires an exact formula match containing no ele ments other than those indicated If there is no then the search is a partial match other elements may be present in the hits e Symbols may be repeated For example CH3CH3 is interpreted as C2H6 NOTE Formula searches are completely non structural CH3CH2OH matches both dimethyl ether and ethyl alcohol because both compounds have the same condensed formula C2H6O e Par
129. R current working directory CURR_TABLE current table name TE current date DA DTBA_NAME_L database full path Angle bracketed lt item gt is required bracketed item optional lt rect gt four integers left top right bottom lt box gt a point within box x y or a box name Box name a user assigned box name b field name casei Figure 29 15CAL help window TIP In ChemBioFinder 12 0 this window is resizable Creating a script To create a script 1 Create a button on a form 2 Label the button 460 Customizing ChemBioFinder 12 0 Chapter 29 3 Right click and click the Edit Script context menu command The CAL editor appears E CAL Editor Browse_button Browse script loop mols with short pause if SNUM_RECS lt 1 exit pause 2 endloop Import Properties Help Figure 29 16The ChemBioFinder 12 0 script editor 4 Type in your script commands or use the Import button to import an existing script 5 Click OK to create a new file TIP You can still create scripts in Notepad or another text editor if you wish Save the file with extension cfs in the C Documents and Set tings All Users Application Data CambridgeSoft ChemOffice 2009 Chem BioFinder System windows and C Program Data CambridgeSoft ChemOffice 2009 Chem BioFinderSystem Vista subdirectory if you want the name of the script to appear on the Scripts menu The
130. Relational Data and Subforms Chapter 23 3 Click somewhere in the form and drag to create a data box When you release the mouse button the Subform Properties dialog box appears By default newly created subforms are associ ated with the same database as the main form To use a different database as the data source for the subform 1 Click the Open Database button The Open dialog box appears Choose a database and click the Open but ton Select the table to be linked in this case Synonyms Click the Form tab Select the Generate form check box If you want to set the style click the Style button See Creating forms auto matically on page 311 for details on Form style Click the Subform tab The tab should con tain reasonable data Link To SYNONYMS subform SYN_ID Title Synonyms based on the choices made so far Choose Mol_ID from the Link from MOLT ABLE main form drop down menu NOTE To use the subform relationally to the main form the two forms must have one field in common This Linking Field must share the same data type text integer real as a field in the main form The fields do not need to have the same name Modify box properties as desired You may want to change the box title font or pres ence of scrollbars Click OK The new subform appears show ing one synonym 9 Optional double click in the subform to switch it to table view The Subform is connected to
131. Rs hit NOTE The data in this table is just for display It is not saved with the form The table will con tinue to be displayed when you toggle the Table view until you change the hit list by running another query or restoring the full list To sort an R Group Table 1 Right click the header of any R column R1 R2 etc 2 Click Sort Column gt command The options are e Ascending e Descending e Multiple Ascending and Descending sort by the molecu lar weight Multiple opens a dialog box that lets you sort by another parameter or group of parameters To set up a multiple sort 1 Select fields in the order in which you want them to apply 2 Right click selected fields to change the sort order ascending descending or to remove an unwanted parameter You can cut and paste R group cells containing either structures or text using the clipboard 340 Databases Chapter 19 R Group plots Once yov ve generated an R group table you can then plot the various substituent groups against any other plotable field 1 With the table view still displayed click the View gt BioVizPlots gt New 2 On the General tab click the X or Y vari able to display the drop down menu The R Group positions are now included in the menus and may be used like any other numerical field to create a plot Figure 19 16 Setting up an R Group plot General Display Analysis Dimension Variables C One variable Logsc
132. Show cutoff line is the pink line It describes the relationship between the den dogram an the cluster window Linear Log scale adjusts the attenuation of the tree by plotting the vertical horizontal node position on the scales In the Label frame click the drop down arrow and select the label to be displayed on the dendogram nodes or leaves Choose the Font for the label display Cluster Properties CS Clustering Figure 28 4 Cluster properties CS Clustering Dialog features e In the color frame Solid and Shaded speci The various actions that you can perform on fies how balls to be colored in the display the CS Clustering dialog to make the dendo For Shade By select the data type from the gram and cluster window look the way you drop down menu and choose a range of col want are as follows ors using a button at the end of the color gradient bar 1 Hover As you move mouse across the cluster dialog the nodes or the balls it e Ball Size adjusts relative sizes of the ball touches gets highlighted like the lines in e In Labels frame click the drop down dendogram are highlighted to red and the arrow and select the text to be displayed on ball in the Cluster window to blue the ball 2 Click As you move the mouse across the e Choose the Font for the label display two panes click on any node or ball This click will freeze the selected node or the ball color changes on freeze and you an easily move your mouse
133. Source C Display As CLOGP Value Range Weight 100 a Minimum 5 6 Maximum 13 79 r lt Back Cancel 3 On the Field page choose a numeric field from the drop down menu of Source e You may edit the name automatically entered in the Display As text box e You may edit the Value Range The default display is the actual low high values for the first 1000 records in the database e You may choose a log scale if no part of the Value Range is negative e You may weigh this profile relative to other profiles where 100 is important 0 is not 4 On the Profile Choose page choose a cost profile Profile Choose Choose a cost template Select a pattern to represent costs across the value range Bottom is ideal top is high cost A FAVA high butte high plateau high valley low butte low plateau Ideal within 1 V2 unacceptable above Y3 Example CLOGP lt Back Cancel Choosing from this gallery is just for convenience Any pattern you choose can be later modified to any other shape TIP As you click each profile a line of descriptive comments is displayed below the gallery window to aid your selection 5 On the Cost Profile page you may edit your profile See To change a cost profile on page 409 for details ChemBioFinder amp BioViz 407 User Guide 6 The Profile page of the wizard has an add another field check box that changes the Finish button to a Next b
134. String displayed as the static text Remarks When a new Static text box is created it adopts the current font settings These settings can be controlled with the FONT command After a static text box is created its contents can be changed with the SETTEXT command Text will wrap to fit within the dimensions specified If all text cannot be displayed within the bounds of the text box only the first part will be displayed However all text is still present and will appear if the box is resized to larger dimensions FONT and TEXT example This example uses the FONT command to set the font to be large bold and bright 24 point Arial bold in red then uses the TEXT com mand to create a short wide data box near the top middle of the form FONT Arial 24 1 255 0 0 TEXT 200 40 450 70 My Compound Database CAL commands PICT syntax Creates a new picture box on the active form PICT left top right bottom filename The PICT command has the following argu ments Part Description left Integer value representing the distance in pixels between the left edge of the box and the left edge of the active form top Integer value representing the distance in pixels between the top edge of the box and the top edge of the active form right Integer value representing the distance in pixels between the right edge of the box and the left edge of the active form bottom Integer value representi
135. Subtract hom L2 L1 Cancel Figure 21 30 The Restore Merge List dialog box 5 Select the integration option and click OK e Replace discards the current hit list and displays the records from the hit list you chose to open e Intersect displays only those records that appear in both the current hit list and in ChemBioFinder amp BioViz 383 User Guide the saved hit list This is a Boolean AND operation e Subtract displays only those records that are in the current hit list but are not in the saved hit list For example if the current list contains records 1 2 3 4 and 5 and the restored list contains records 4 5 6 and 7 then only records 1 2 and 3 will be displayed This is a Boolean NOT opera tion it shows the records in the current list that are not also in the restored list e Union displays all records in either the current list or the saved hit list This is a Boolean OR operation e Subtract from displays only those records that are in the saved hit list but are not in the current hit list This is the same as Subtract but with the order of the lists reversed The hit lists are integrated You can browse and save this new hit list just as any other hit list Drag and Drop list merge 1 Perform a search and save the hit list 2 Perform another search and save the list Two saved queries are shown in the figure below Explorer TE Queries HB Full List Q1 1
136. This guide contains information for the Chem BioFinder amp BioViz It assumes that you are familiar with the basics of your Windows oper ating system If you are not refer to your sys tem manual Some of the material describes tasks that must be performed in conjunction with other integrated CambridgeSoft products The material on the addins describes tasks that must be performed in conjunction with Micro soft Excel or Word If you are not familiar with these products please consult the relevant user s manual The chapters in this guide are organized by task They are intended to help you familiarize yourself with the ChemOffice applications and start using them as quickly and efficiently as possible New users should read the ChemBio Finder amp BioViz chapter to get an overview of the product and how it works The Tutorials chapter demonstrates most of the features of the application Perform the tutorials in the order they are presented Experienced users can skip to subsequent chapters which provide more detailed information Conventions The following notations are used throughout this guide ChemBioFinder amp BioViz 283 User Guide e The following symbol indicates that a fea ture is available in the Ultra version only ULTRA e The following symbol indicates that a fea ture is available in both Pro and Ultra ver sions but not in Standard version PRO Special formats CAUTION Cautions are us
137. To deselect click the command again 8 Drag over a section of the plot When you release the mouse button the scale expands to show the points selected While the initial view is the area you selected you may use the scroll bars to view any part of the plot at the expanded scale Clicking either the X or Y Zoom Button will return that axis to the original scale while leaving the other axis at the expanded scale Clicking Unzoom on the BioViz context menu will restore the original scale to both axes simultaneously You may repeat zoom that is zoom in on an area in an already expanded scale If you have performed multiple zooms the Zoom button acts as an Undo control reversing one step at a time Statistical analysis You can perform statistical analyses on plots using the Analysis tab on the BioViz Plot Prop erties dialog box The tab is available only for two variable plots ChemBioFinder amp BioViz 307 User Guide The following statistical parameters may be When you select curve fitting the R squared calculated value also becomes available for display The e Minima and maxima of the X or Y variable calculated values are displayed below the plot You may also display a linear quadratic or cubic least squares fit of the data points with Standard deviation of the X or Y variable or without a confidence interval of one to three standard deviations e Mean or median of the X or Y variable
138. a domain eliminates the need to per form the initial routine query or create a local database You only need to save the domain information by saving the form The next time you open that form you see only the domain A third advantage is that the sort order at the time of creation is preserved Sorting is a time consuming operation By using a domain you can sort once and save the preferred order To more information including how to create a domain see Saving query lists Minimize child tables on a single tab Whenever a subform appears on screen Chem BioFinder automatically updates the data from the server If you have a lot of subforms on a single tab ChemBioFinder must update all of them at once potentially slowing down your work So if you have subforms you need to see only occasionally put them on other tabs of the form so they will not be updated until you activate those tabs Remove plots that you are not using Plots that are visible all take at least some pro cessing and closing a plot window still doesn t remove it from memory If you have generated plots you no longer need use the View gt BioViz Plots gt Remove menu command to delete them then save the form ChemBioFinder amp BioViz 443 User Guide 444 BioSAR Chapter 27 ULTRA Clustering in BioViz Clustering in ChemBioFinder BioViz is a method for analyzing biological and chemical data It is smoothly integrated with ChemBio Finder database
139. a items do one of the following e Click the Commit button on the Add Record Toolbar e Click the Commit Changes icon on the Record Toolbar e Click Record gt Commit Changes e Perform another action such as moving to another record or printing The new record is added to the database NOTE Selecting Commit Changes or moving to another record if you have two or more records saves the data to the database Do not use File gt Save clicking File gt Save saves changes to the form layout not changes to data in the database Duplicating records You can create a new record by modifying an existing one To duplicate a record Click Record gt Duplicate Record You are in Add Mode and the form fills with data from the previously displayed record When you commit the changes you create a new record whose fields contain the data displayed Before committing the duplicate you can modify fields or structure and commit changes just as you would with any other new record NOTE When duplicating records only those fields that are visible on the form are dupli cated Data in fields present in the database but not visible on the form are not copied into the new record The new record has a new Mol_ID Undoing data entry Before committing a new data entry you can revert the contents of the form to its previous unmodified state To undo your changes do one of the follow ing e Click Record gt Undo Chang
140. a or tab delimited Because ChemFinder 12 0 uses the Access Jet database standard names of fields con trols and objects must conform to Access rules These are e May be up to 64 characters long e May include any combination of letters numbers spaces and special characters except a period an exclamation point an accent grave C or brackets e Must not begin with leading spaces e Must not include control characters ASCII values O through 31 ChemBioFinder amp BioViz 389 User Guide e Must not include a double quotation mark in table view or stored procedure names Importing structures ChemBioFinder 12 0 imports structure files directly into a database You can choose to replace the existing records append new records or merge the data eliminating dupli cates The general procedure for importing structures is 1 Use the File gt Import submenu to choose the type of structure file to import The Open Chemical Structures dialog box appears 2 Browse to a folder containing structures 3 Select a file or files using Ctrl click or Shift click and click the Open button The Data Import dialog box appears 4 Click the File button and select a database to import into NOTE You can also type ina name to create a new database file 5 Choose the type of import Overwrite Append or Merge If you have selected Merge click the Merge tab and choose the matching fi
141. a temporary delimited ASCII file By default all fields that appear in boxes on the current form except structure but including formula and molecular weight are written The second line instructs Excel to open the file Excel can automatically recog nize the file format as tab delimited The third line instructs Excel to auto size column widths 1 4 to fit their contents NOTE This example requires that the text export delimiter be set to TAB otherwise Excel may not read the file correctly To check this click the File gt Export menu command then open the Text Options tab of the Data Export dialog box You can include either or both of these scripts on the Scripts menu and you can activate them with buttons on the form To include a script on the Scripts menu give it a filename with extension CFS and place it in the ChemBio Finder 12 0 System directory or in the direc tory containing the ChemBioFinder 12 0 application To activate a script from a button label the button with a script filename or string which can be converted into a filename For example if TOEXCEL CFS exists in the ChemB ioFinder 12 0 System directory label a button ToExcel to start the script For more informa tion see Adding a button on page 317 468 Customizing ChemBioFinder 12 0 Chapter 29 Using Visual Basic The second method of communicating between ChemBioFinder 12 0 and other appli cations such as Excel is using OLE Au
142. across the dialog ChemBioFinder amp BioViz 449 User Guide To unfreeze the selection click on any empty space in any of the window get orig inal color Drag You can change the shape and size of the dialog Re project cluster When you move the pink dotted line up or down in the left win dow dendogram pane the cluster window right pane will change the diagram accordingly Show Properties Click the black arrow in the lower right corner of the cluster dialog You will see the properties of the dendo gram and the cluster 450 Clustering in BioViz Chapter 28 Right click On freezing any node ball you can easily perform actions on that particular node ball Right click on it it shows menu options Zoom Show structure window and Selection to list e Zoom It changes the size of the data dis play beneath the viewing window e Show structure window The highlighted or freezed node ball structure is displayed correspondingly e Selection to list It generates a hitlist of the selected node ball Customizing ChemBioFinder 12 0 You may customize ChemBioFinder 12 0 in the following ways e Customize display of your molecules fonts pictures and forms e Customize the Favorites tree e Design the toolbars to your specifications e Perform automated tasks such as interfac ing with Microsoft Excel or by using CAL the ChemBioFinder 12 0 Automated Script ing Language Setting preferences
143. act CambridgeSoft support at http www cambridgesoft com services for information on using the Automation inter face Scripting CAL ChemBioFinder 12 0 is equipped with its own scripting language the ChemBioFinder Auto mation Language CAL CAL is used to oper ate the program from the keyboard or to create custom scripts for automating simple opera tions such as switching between forms or send ing data to Microsoft Excel CAL scripts are stored in text files with their pathnames stored in forms In ChemBioFinder 12 0 you have the option of storing scripts directly in form files Scripts created in Chem BioFinder 12 0 are stored internally by default When you open a form which references exter nal script files you will be prompted to store the script internally If you choose to convert the external script files to internal the scripts will be saved when the form is saved and the original script files may be deleted Scripts originally saved as internal may be also be saved externally TIP You can save the form with a different name and the original will remain untouched in which case deleting the script files would not be a good idea If you choose to leave the form unmodified the alert will continue to show up every time the form is opened To suppress the prompt 1 Click the File gt Preferences menu com mand 2 Click the General tab 3 Deselect the Check for external scripts check b
144. age to a specified application Follow the DDE keyword with three arguments e The service name usually the name of the recipient application e The topic name a string recognized by the recipient identifying the nature of the mes sage It is typically SYSTEM e The command an instruction to the ser vice indicating what you want it to do OUTPUT_STR gives CAL access to the out put window used by Python where string writes a string into the output window fol lowed by a new line The command brings the window up on the first call if necessary The string need not be quoted even if it contains multiple words Details of these components depend on the ser vice you are addressing The table below shows examples of Program Execution Commands Command Action CALL execute script file located in myscript scripts directory Command Action DOS erase execute DOS command to junk delete a file file dat EXEC notepad execute Windows program myfile txt DDE CHEM3D send DDE message to quali CFWIN open fied service benz mol CAL commands CALL syntax Executes the specified CAL script CALL scriptname The CALL command has the following argu ment Part Description scriptname String containing the name of the CAL script file to execute Remarks If the CAL script file is in ChemBioFinder s standard search path only the actual file name BROWSE
145. ale Base Two variables x Mol_ID X Style Boiling _Point z Gibbs_Free_Energy oe Line chart Mol_Refractivity Scatter plot R group R1 C R group R2 R group R3 7 R group R4 Bins Plolr group RS oa Synonyms SYN_ID m l aS Eee J Locked Point limit 500 Cancel Figure 19 17 R Group 2 vs Molecular Weight The R Groups are along the X axis as shown in the preceding figure The structure on the upper right corner of the plot is the template Creating a database Instead of opening an existing database you may want to create a new empty one To create a new database using the automatic form generation technique See Tutorial 3 Creating a database on page 296 The follow ing procedure results in a simple database with one table for storing structures To create a database 1 Right click in the form and click Properties 2 On the Database tab click the Create Data base The Save As dialog box appears 3 Choose the directory to which you want to save the database 4 Specify a name for the database and click Save ChemBioFinder 12 0 creates the database con taining one table called MolTable with four fields E Structure E Formula e Molecular weight Mi Mol_ID The Mol_ID field corresponds to a column in the table where a numeric ID is automatically entered as each structure is registered The other fields represent information stored in th
146. alog box appears Figure 19 18 Select Data Source dialog box 4 From the Machine Data Source tab select the ODBC data source to access then click OK Select Data Source File Data Source Machine Data Source Data Source Name Type Description CAMBRIDGESOFT1 User User Oracle database dBASE Files User Excel Files User MS Access Database User New Machine Data Source is specific to this machine and cannot be shared User data sources are specific to a user on this machine System data sources can be used by all users on this machine or by a system wide service Cancel Help NOTE The ODBC data source dialog box shows all data sources known to ODBC including ChemBioFinder 12 0 Access and other file based data sources If you attempt to open one of these through the ODBC dialog you get an error message File based data sources must be opened using Open Database as described above If the ODBC data source dialog does not show the database you seek you may need to create a new data source You can do this using the New For details click the Help button in the ODBC dialog box 5 If you are prompted for a user name and password enter it If you don t know what name and password to use see your System Administrator 6 In the tree diagram click the table you want to attach then click OK The newly attached table appears in the tree diagram in the Form Properties dialog box
147. alphanumeric representation of different structural representations of the same structural formula canonicalization NOTE InChI is a registered trademark of the International Union of Pure and Applied Chemistry InChI Material in ChemBioFinder 12 0 is IUPAC 2008 All three commands place the data on the Clip board allowing it to be copied into other appli cations To copy a structure as a name or InChI string 1 Click in the Structure box to select it 2 Right click and click the Copy As gt Name or Copy As gt InChi submenu command 3 Paste the data into the other application using Ctrl V or the Edit gt Paste menu com mand Exporting an ASCII file Delimited text files may be the most universal file format used by non chemical applications In a delimited text file each line represents a record and all fields in the record are listed in order from left to right separated by some character such as a tab or a comma Individual records are separated by carriage returns ChemBioFinder 12 0 allows you to include a header line at the start of the file that lists the names of all of the fields It also allows you to append to or overwrite existing text files You can import a delimited text file saved by ChemBioFinder 12 0 into many other applica tions including spreadsheets and external data base systems Choose the csv file format to ChemBioFinder amp BioViz 395 User Guide export to spr
148. and connect it to a database You can create the form manually or automatically For more information see Connecting a data base to a form on page 295 e Database Wizard Helps you set up a data base connection From the Existing tab e Browse to an existing form in your file sys tem From the Recent tab e Open a form on the recently used file list You can choose whether the ChemBioFinder 12 0 startup dialog is displayed when ChemBi oFinder 12 0 opens by doing the following 290 The User Interface Chapter 16 1 Go to File gt Preferences 2 In the Preferences dialog box click the General tab 3 Select or deselect Show startup dialog If you choose to hide the ChemBioFinder 12 0 dialog box ChemBioFinder 12 0 will open a new blank form by default when you open the application To open the ChemBioFinder 12 0 dialog box when the preference is set to hide go to File gt New Using ChemBioFinder with databases ChemBioFinder 12 0 comes with the Microsoft Jet database engine ChemBioFinder 12 0 maintains its own table of chemical informa tion structure formula and molecular weight and relies on Jet to create a database system for managing the rest of the data The data created by Jet is stored in an MS Access database file MDB file If you have MS Access installed you can use it with the rela tional part of the database You can use ChemBioFinder 12 0 to add chemical structures to a database you
149. artridge brings up the appropriate Oracle parts of the process When you have opened an Oracle database note that some Properties dialog tabs show entries not available in ChemBioFinder 12 0 including e Database tab CS Oracle Cartridge version if any e Table tab Table owner name name of pri mary index if any e Field tab Oracle native data type name name of associated index if any When you open an Oracle database and select a table ChemBioFinder Oracle gathers infor mation about the columns If you open a table you know to contain structures and ChemBio Finder Oracle does not show a structure or formula or molweight column then it may be necessary to set up some configuration infor mation about the table For details see Con figuring via CF_SETTINGS table on page 542 Searching From the user s point of view searching in ChemBioFinder Oracle works basically the same way as in ChemBioFinder 12 0 you enter a query search then work with the hitlist Internally however the ChemBio Finder Oracle machinery is quite different There are three types of table involved in han dling hit lists All are created in your own tablespace One is global applying to all lists saved from any table others are connected to the particular table or view being searched e CF_HITLISTS The directory of all saved lists This table is created the first time any list is saved e SAVED_tablename All lists which h
150. ases created in English can be sorted correctly using the following languages e English e German e French e Portuguese e Italian e Modern Spanish If you want to sort text in a different language than the one in which the database was created perform the following procedure 1 Ona computer using the same language as the text you want to sort open MS Access 2 Open the MDB file you want to sort 3 Compact the database click Tools gt Data base Utilities gt Compact Database 4 After the database is compacted close MS Access The correct sort information is written into the database When you perform a sort in ChemBioFinder 12 0 the sort order will be correct Resetting the database To reset the database to its original state Click Search gt Retrieve All 354 Working with Data Chapter 20 Changing the database scheme You can create or remove fields or tables in an existing or new database as long as the data base is not read only and you have permission to modify it You may also attach or link tables from external data sources Use the Box Properties dialog box to perform the following procedures Do one of the following e Click File gt Database e Right click any empty space in the form window and click Data Source The Box Properties dialog box appears with the Database tab displayed To add a field 1 Click the Field tab 2 If there is more than one table select the table that w
151. atabases to find chemical structures so that you do not need to search manually Using ChemFinder Office you can browse the following types of files for chemical informa tion e MS Word documents e MS Excel spreadsheets e ChemFinder databases e ChemDraw files e SD files e Isis Draw files In addition to browsing ChemFinder Office can search files by e Chemical structure e Chemical formula e Molecular weight e Draw structures you want to find with the ChemDraw plug in ChemFinder Office can search for the whole structure a sub structure or a structure similar to the one you draw When searching by structure you can specify a search by e Substructure e Full structure e Similarity e Identity You can save frequently used collections of data sources documents and databases in Data Source Definition dsd files Instead of checking many data sources that you want ChemFinder Office to search Chem Finder Office can search one DSD file You can also generate and store combinatorial libraries from experiments performed with generic reactions For more information see CombiChem on page 495 ChemFinder Office helps you to build data bases by extracting information from various sources and exporting to another source The user interface UI ChemFinder Office is installed when you install ChemOffice Ultra The UI window titled Find Chemical Structures is shown in the following illustrati
152. ation methods found in ChemBio Finder 12 0 In addition you can use Access directly to operate on a ChemBioFinder 12 0 database A ChemBioFinder 12 0 molecule database consists of three components the structure storage files with file extensions MST and MSX the data storage files which include a Microsoft Access database file extensions MDB and LDB and the forms with file extension CFX used to view the structures and the data For more information see Database File Types on page 469 If you have Access on your system double clicking an MDB file in Explorer starts up Access and opens the specified database When you open a ChemBioFinder 12 0 data base in Access you will see the same tables as displayed in the ChemBioFinder 12 0 Database dialog box including the main structure table usually named MolTable but you will not see columns for structure formula or molecu lar weight These fields cannot be manipulated directly using Access The following are some of the operations you can perform on a ChemBioFinder 12 0 data base using Access Most of these capabilities are not available through the current version of ChemBioFinder 12 0 e Compress or repair the database e Change column field or names or formats e Change table names e Add or delete columns or tables e Import or export tables Load non structural data from various file types including delimited ASCII Excel or Word e M
153. ave been explicitly saved from a given table or view This is created the first time a list is saved e HITS_tablename All lists automatically saved after every search over a given table or view This table is created the first time a search or list operation is carried out and is deleted at the end of the session Here s what happens when you present a query to ChemBioFinder Oracle 1 If the query contains a structure it is con verted to a text representation and copied to a temporary table NOTE The table is called temp_queries It is created in the CSCartridge tablespace and removed as soon as the search is finished or interrupted ChemBioFinder 12 0 does not yet handle the case of multiple structure boxes where more than one contains a query 2 The query is converted to a SQL select statement Query components in form boxes are ANDed together just as in Chem BioFinder 12 0 where the structural parts are calls into the CS Oracle Cartridge struc ture search functions 3 The hits table is created if it does not already exist 4 A unique ID is assigned to the new list which will result from the search 5 The select statement is wrapped in a larger SQL statement which will cause the results to be deposited directly into the hits table 6 The SQL is executed 7 When the search is complete the results are new rows in the hits table Each row con tains the new list ID alongside the ID of a rec
154. bforms 399 Access relational data eee 399 Creating a subform 399 Working with subforms s 401 Searching a subform eeeeeeeeeees 402 Chapter 24 Compound Profiles scccesssseseees 405 Creating a compound profile 406 Editing a compound profile 408 Customizing oii cpeiechartendatiealeectetiealicees 411 Chapter 25 ChemBioFinder Oracle s0000008 413 SOUD oe e a eee 413 Opening an Oracle database 414 Searching ssesiissisiieii issis 415 SOINS irene onian deecseencceceeiesaes 416 Handling lists oseere 416 Setting Oracle preferences 417 ii Contents Updating and adding data 417 TANS ia teceracctenseeececeaenetnci 418 Lis so 0 11a een E 419 PD cred pstaadsaedgecd ee astara tee 420 Chapter 26 BRIO V 12 siviesscntcacsanssaccanscdescoeseanecaiscasnenntets 423 Changes in version 11 0 0 eee 423 Changes in version 10 0 0 eeeeeeeeeeee 424 Creating a plot ee 425 Statistical analysis sseeeeceeeeee 428 Plotting QUEIES 2322 5 sosiessrriaceosseneeesees 432 Changing the display cece 433 Chapter 27 BIOSAR scstaastiesconisonscascauscesttannrconsevnseenses 435 Subforms and autolinks 0 ee 436 IVT eS OTL koneen 437 Qu ry MtIStS aiecaseaeceeececenencenvanedacn eee 438 DOMAINS esercenti 441 Creating an mdb database 44 Chapter 28 Clustering in Bi0VIZ
155. bond of thick type For example here is an excerpt from the bond table of a molfile with relative bonds 4510000 2611000 lt bond 5 marked as UP 4711000 lt bond 6 marked as UP 488 Structural Query Features Appendix A M CFW 5 BOND_RELS lt overrides type of bond 5 to be UP THICK M CFW 6 BOND_RELS 6 lt same for bond The consequences of having a ChemBio Finder only tag are When any of the MDL file formats is saved from within ChemBioFinder the tag is written Reading these files back into ChemBioFinder will retain the thick bond types If a structure is drawn in ChemDraw and saved as MDL Molfile thick bonds are lost and are converted to normal hash wedge bonds This is not true if the file is saved as CDX If a structure is saved as molfile from ChemBioFinder reading it into ChemDraw loses the thick bonds Mol or SDFiles obtained from ISIS or other programs do not know about this tag and thus cannot convey thick bonds How ever such files may be edited by hand to include the ChemBioFinder tag An MDL file written by ChemBioFinder containing tags should in principle be read able by any program which can import such a file The unrecognized tags should simply be ignored Normalization Closed rings of alternating single and double bonds are normalized This is required to make their substituents equivalent Ortho dimethylbenzene is remains same whether there is a sin
156. c tion center indicators The arrow at the left indicates that you are looking for this substructure as a product 8 Press the Enter key You get 3 hits containing a product with a carbonyl ring that was formed during the course of the reaction O Figure 17 11 One of the product query hits Searching by reaction type In many cases you have some idea of both your starting materials and your products but are looking for some information on how to get from one to the other For example to search for reactions that reduce a carbonyl to an alcohol 1 Click Search gt Enter Query The form is cleared 2 Double click in the Structure box 3 Draw the following O A 5 we Figure 17 12 A reaction type query structure 4 Press the Enter key Browse through the 23 hits Each of the reactions found shows the transformation of a carbon oxygen double bond to a carbon oxygen single bond This hit list includes reductions of aldehydes acids and ketones O Search over list In this example you start with the previous list and search again to get only ketone reduction reactions To search over a list 1 If you are not continuing directly from the last example double click the previous query in the Query Tree to make sure it is the active hitlist 2 Click the Search gt Over Current List from the menu 3 Double click in the Structure box 4 Draw the following Je NOT O H NOT O H
157. c ture and the target structure do not match Most similarity searching on the other hand relies instead on the notion of molecular descriptors Each compound can be repre sented by a collection of qualitative terms that describe general aspects of the structure For example benzoic acid might be described as e organic acid e contains 6 membered ring e contains delocalized ring e contains C double bond O As you can see the descriptors can be very broad and they can overlap The set of descriptors used by ChemBioFinder is very large When you draw a compound ChemBioFinder compares it against all of the descriptors it knows about Some descriptors will be present in your compound and some will not Since each descriptor for a given compound is either Present or Not Present they are often stored as bits and another name for a compound s set of descriptors is its bitscreen Consider the following query and target com pounds Bitscreen Desc Name ATE TUTTE Tv TA HT Query 23 Q LE Q and T 17 QAT TT Wa QorT 30 QuT Both have similar numbers of descriptors pres ent the query has 23 while the target has 24 But are they close enough Complete structure similarity One of the hallmarks of a good similarity algo rithm is whether it is commutative That is two compounds should have the same similarity ChemBioFinder amp BioViz 497 User Guide value no matter which you compare to which T
158. car bon atom e Inorganics Finds structures lacking car bon e Salts Finds structures that can be consid ered as salts Rings Finds any of the following types of ring structures selectable from a submenu e Bridged Systems For example two rings share more than one bond e Spiro Systems For example two rings sharing just one atom e Fusion Systems For example structures with a ring fusion two rings sharing one bond e Highly condensed Rings sharing at least four bonds with others in the group where the group has at least seven rings e Necklace A ring bridging at least one other ring half its size or less e Polyhedra A group of rings each of which is fused to at least two others in the group ChemBioFinder amp BioViz 377 User Guide e Duplicates Locates all records whose structures duplicate at least one other If Clustered List is selected the query will be a list of duplicates only clustered together that is a sorted list This makes duplicates easier to compare but you cannot edit records displayed in a sorted list If Unique Structures Only is selected the query will be the same as the parent list but with only one unique copy of each duplicate structure NOTE The Duplicate search must be per formed in Full Structure mode If the Search type is set to Substructure you will get an error message reminding you to reset the search type preference to Full Structure
159. ce current list Furans Add to current list Listi furans xf list aniline by name and sss Intersect with current Ist list nonblank molnames Subtract from current lst List2 full list Restore Previous List is no longer dimmed after you have done a single search it is available and will return you to the full list This is true also in ChemBioFinder 12 0 Over Current List Omit From List and Find List work as before Setting Oracle preferences When you are working with an Oracle data base the Properties dialog contains a tab for Oracle settings Items currently in this tab are as follows Auto sort on Displays the default sort field All lists will be sorted in ascending order over this field if no other sort criterion has been specified At present the auto sort field is always the primary key and cannot be changed Primary key Names the primary key of the current table if any e Saved hits Displays the name of the table in which saved hitlists are stored for the current form if one has been created e Records per retrieve Sets the size of the ADO recordset cache that is the number of records brought to the client for each retrieve operation This value can be adjusted for better performance but in practice it does not have much effect e Cache ID s for faster moves Checking this box enables a new record retrieval scheme designed for more efficient browsing of large lists details are given in
160. ch new line the window shows the Python prompt gt gt gt After the prompt you can enter any Python command then press Enter The command is executed immediately and a new prompt is displayed on the next line e The first time you execute a command in the window there is a short delay while Python is initialized If it is not already visi ble the Output Window then opens show ing a ChemBioFinder header and the output of your command e Ifthe line you enter ends with a colon then it is taken as the beginning of a compound multi line statement After you press Enter the next line begins with the continu ation prompt and is indented The state ment is not executed until you press Enter twice in a row that is you must enter a 464 Customizing ChemBioFinder 12 0 Chapter 29 blank line to terminate the compound state ment e You can execute commands other than the one you just typed Position the cursor on any line and press Enter The command under the cursor is executed If the line is part of a compound statement the entire statement executes Afterwards you are not given a new prompt and the cursor does not move unless it was positioned at the end of the line in which case it inserts a new line and moves to it e If you copy text into the window it is not automatically executed You can execute pasted code a line at a time by positioning the cursor on each line and pressing Enter e If you switc
161. chemical database To open a database to associate with a form 1 Right click on the form and click Data Source The Form Properties dialog box appears ChemBioFinder amp BioViz 333 User Guide 2 Click Open Database The Open dialog box appears Open _ we Look in E samples o O csbr 54142 Ajisiccr moe ig iPScreen By isiccrsm_bachup mdb MyRecent ZB acrosase wos A mydb md Documents B AGROBASE_backup mdb ZJNCI_DEMO MOB 2 chem3D mdb B newtest mdd B cs_pemo moe B nianemo moe Desktop i cs_ DEMO _bachup mdb A pscreen mndb B cs_DemoPius mdb IZ 0EMO mdb iB reroctss moe PB Gennxns mdb B roctem os B ist_pemo wos My Computer amp Fie name MDB Open MyNetwerk Flesoftype Molecule DB mdb Place I Open as readonly My Documents le Figure 19 2 The Open dialog box 3 In the Open dialog box choose a database with an MDB file extension then click the Open button The Form Properties dialog box reappears with a data source tree displayed The CS_Demo database is shown below Form Properties Sr Database Table Field Form E MolTable fhe Molname E CS_DEMO 00 MoL_ID hiii Properties a Structure Name CS_DEMO E Formula Fie C Documents and Setting WH MolWeight Connect Jet 3 x Updatable Yes v lt gt Create Database Open Database Database Wizard Cancel Figure 19 3 The CS Demo database Form p
162. ck inside a subform you activate the miniature form inside the box and can work within it Below are examples of subform use e You have data that is associated in a one to many relationship For example you want to view a chemical structure together with its physical properties stored in a separate table e You are running a stockroom and you want to store package sizes and prices in the same place because they are related Each chemical may be available in lots of pack age sizes and you wouldn t want to re draw the structure every time you added a new package You can use a subform so the physical property information is entered once in the main form and the package sizes and prices are entered many times in the subform By linking these two data tables with a linking field you can make these tables relational one table can interact with the other The contents of a linking field are not important as long as they are different for each record in the main form Various forms of ID numbers are often used as linking fields As you browse through the main form corresponding records in the subform appear Creating a subform You create a subform place form objects on it and connect the subform to a database just as you do a regular form For detailed information on these procedures see Forms on page 311 For users of version 8 0 and earlier Creating and linking subforms in ChemBio Finder 12 0 was si
163. click in the structure data box and click the Save Structure context menu com mand The Save As dialog box appears 2 Choose the destination directory gt Type the file name and choose a file format 4 Click the Save The structure is saved to the indicated file You can read these files with any application that supports the specified file format NOTE To save most of the file types listed above you must have ChemDraw ActiveX Con trol Pro installed Using copy paste with structures You can copy structures and paste them into Chem amp Bio Draw or ISIS Draw You can also use the Copy As command to copy the structure as a text string The structure Copy As command has three options e The Name command invokes the CS Struct gt Name utility Struct gt Name gen erates systematic chemical names with proper CIP stereochemistry descriptors e The SMILES command creates a SMILES string A SMILES string is a standard way to describe a chemical structure in a line of text Several software packages use SMILES strings as a way to enter and store chemical structure information e The InChI command invokes the CambridgeSoft implementation of the IUPAC InChI algorithm The InChI algorithm takes a chemical structure and converts it into an alphanumeric string A key aspect of the InChI algorithm is that the generated string is independent of the way that a structure is drawn producing a consistent
164. control to store data in your ChemBi oFinder 12 0 database and add related numeri cal or textual data and comments You can use the Chem amp Bio 3D ActiveX control to view the structures The general steps for using ChemBioFinder 12 0 are as follows e Create a form e Create or open a database and link it to the form e Add or manipulate data e Perform a search These steps are described in the ChemBio Finder 12 0 Tutorials and in the detailed refer ence material in the manual The ChemBioFinder User Interface The ChemBioFinder 12 0 User Interface UI consists of menus toolbars and the form win dow The central part of the form window con tains the work space where you create and view structures and data The toolbars contain icons that change the way the pointer behaves or that perform actions corresponding to menu commands The components of the ChemBioFinder 12 0 UI are described below Screen Ele ment Description BioViz window Displays plotted data from ChemBioFinder 12 0 data bases Current list size Displays the number of records through which you are browsing Might be less than the total database size if you have recently performed a search Current record Displays the position within the current hit list of the record you are viewing Control box A data box containing an ActiveX control ChemBioFinder amp BioViz 285 User Guide Screen Ele
165. copies 398 You may also select a different printer than the default NOTE ChemBioFinder 12 0 defaults to printing a single page This is indicated by the option labeled Selection If for example you are printing in Form view and you set the layout in Page Setup to three per page you will print Importing and Exporting Data Chapter 22 the record selected and the next two records If your layout is one per page the default you will print only the selected record Note also that if a subform is selected the entire record with the subform is printed 9 Click OK when you have finished Relational Data and Subforms Subforms allow you to work with multiple data tables in a relational database You should be familiar with working with ChemBioFinder 12 0 forms and databases before proceeding to subforms Access relational data A subform is a special box within a form that behaves like a separate form file A subform is used to display information stored within a database but it usually displays data from a different database or different table within the same database than the main form A subform is usually linked to the main form so that retrieval of data in the main form also retrieves related records in the subform Like other types of boxes you can move select and resize a subform on the main form How ever you cannot select it by clicking inside it You must click the title bar When you cli
166. cord Next to display all of the records in the current list The PAUSE command keeps each record on screen long enough for people to see it loop rec next pause 2 endloop CAL commands PAUSE syntax Temporarily stops the script from executing PAUSE decisecs The PAUSE command has the following argu ment Part Description decisecs Amount of time to suspend script execution Remarks 10 decisec 1 second If the decisecs argument is omitted the script will be suspended for 2 seconds CAL commands EXIT syntax Immediately halts execution of a CAL script EXIT Remarks This command is useful only in a script file and has no effect when entered on the Com mand Line ChemBioFinder amp BioViz 539 User Guide 540 CAL Commands Appendix D PRO CS Oracle Cartridge Pre setup procedures Prerequisites for connecting ChemBio Finder Oracle to an Oracle database e ChemBioFinder Ultra e Oracle Client e Oracle OLEDB Provider ChemBioFinder Ultra We recommend Version 10 1 or newer Oracle Client We recommend version 9i or newer This is available as a free download from http www oracle com 1 Download and install the Oracle Client soft ware version 91 This is available free from Oracle Note that there are different versions for 32 bit 64 bit and Itanium systems The minimum install alone called Runtime is not adequate to provide support for ChemBioFinder
167. data boxes and may be formatted in the Box Proper ties dialog box Used to format text in Text and Memo fields Screen Ele ment Description Total database Displays the total number of size records in the current table Toolbars ChemBioFinder 12 0 has several toolbars to create and manipulate the ChemBioFinder 12 0 form and the database records it displays Toolbars are normally docked at the top and left side of the UI but they can be torn off and placed anywhere on the screen for your convenience You can view the toolbars dis played in the ChemBioFinder window through View gt Toolbars submenu You can also use the Toolbars submenu to customize the toolbars A description of toolbar customization is beyond the scope of this manual See Microsoft help for information on customizing toolbars Main toolbar The Main Toolbar contains the standard tools you find in most modern applications New Open and Save Cut Copy and Paste Undo and Redo Print and Help New Save Switch to Form Form Paste Redo Print Tabie val D amp 7 a a w 5 Open py J ndo Layout Database form ul MO wizard Figure 16 1 The Main Toolbar The three tools are e Layout Mode switches between Layout Edit Mode and View Mode When the Layout Mode button is depressed the Form ChemBioFinder amp BioViz 287 User Guide Toolbar is visible and an alignment grid appear on the form e Switch to Table swi
168. der 12 0 CAL script can com municate with other Windows applications using either of two commands EXEC o start an application and possibly pass information on the command line DDE to communicate using Dynamic Data Exchange with a DDE ready application Using EXEC is straightforward but limited You can start all Windows applications by this command Most can be passed a filename on the command line such that the specified file is opened or printed on startup A few appli cations can accept more detailed instructions Consult the application s manual for informa tion about how it can be operated using the command line If you have Visual Basic or similar program ming language you can extend the power of EXEC You can write an application using the advanced features of Visual Basic and then call the application from within ChemBio Finder 12 0 using the EXEC command Using DDE is more complicated You can operate most Microsoft Office components and many other programs to varying extents with DDE For example practically every com mand on the Excel menu can be executed by DDE The syntax is rather difficult but can usually be worked out by experimenting and consulting ChemBioFinder 12 0 help An example is given below DDE is the most direct way of using Excel to view data from ChemBioFinder 12 0 To use MS Excel to view ChemBioFinder 12 0 data 1 Start MS Excel You can start it manually using a CAL script
169. describes how ChemBio Finder interprets formulas and resolves these ambiguities Consider an example In entering a formula query you type cooh Most chemists recognize this as a carboxyl group carbon two oxygens hydrogen How ever it might be interpreted as cobalt Co oxygen hydrogen Similarly CLI might be carbon lithium or it might be chlorine iodine PHE might be phosphorus helium or since ChemBioFinder allows 3 character amino acid symbols as special atom types it might be phe nylalanine Phe One way to avoid ambiguity is to separate let ters with spaces For example the string c o cannot possibly be interpreted as cobalt Another way to avoid ambiguity is to enter for mulas using the Periodic Table instead of typ ing them ChemBioFinder allows free format input and attempts to make the most reason able interpretations of them by using the rules described below Rules If a symbol is properly capitalized first letter upper case followed by zero one or two lower case letters then the longest valid sym bol which matches is preferred Thus Phe matches phenylalanine rather than phosphorus Co matches cobalt Because of this rule if you properly capitalize all symbols no ambiguities will arise If symbols are not properly capitalized such as all lower case then with the exception noted below the shortest symbol which matches is preferred Thus co is ta
170. different record e Filters displays filter bars for those fields being used to modify the plot TIP In order to see some of the features described below you will need to tile the windows to view the form and the plot simulta neously Filters Filters can be used in two different ways e Filter a plotted variable to reduce its range e Filter on other variables to add other dimen sions to the plot To activate filters click the View gt Filter Window or use the context menu Right click menu for plots When the filter window opens Right click in it to select or deselect fields There is no limit to the number of filters that can be applied to a plot NOTE Filters act on all active plots not just the one displayed Autoscale When you filter a plot you may want to expand the scale to better display the remain ing points If you select Autoscale on the BioViz context menu the scale will readjust automati cally every time you adjust a filter Autoscale is a toggle that remains in effect until you can cel it Alternately you can make all of your filter adjustments without changing the scale then select Rescale to All Points on the BioViz context menu Zoom The BioViz zoom feature is a toggle activated from the BioViz context menu To expand a portion of a BioViz plot 7 Select Zoom on Drag on the BioViz context menu A check mark appears next to the command when it is selected
171. display all records from both lists Using atom lists Using the text tool in Chem amp Bio Draw you can enter in a structural query a list of possible atom types one of which must match in the target compound If you want to search for molecules containing a benzene ring with an ether amine or phos phane group a query might look like the fol lowing O N P Figure 21 31 Atom list query Atom types and bond types To broaden or narrow a search query you can define the properties of the atoms and bonds in a structural query These properties are defin able in Chem amp Bio Draw Pro using the Atom Properties and Bond Properties dialogs acces sible from the Structure menu See Structural Query Features on page 483 for more infor mation Suppose you want to find all molecules that contain a non oxygen chalcogenide bonded to ChemBioFinder amp BioViz 385 User Guide another atom not necessarily carbon You also want the bond type between the chalcogen and the other atom to be a single or double bond The query drawn in Chem amp Bio Draw Pro may look like this This atom may be any non hydrogen atom A si0 This bond may be single or double S Se Te wW This atom must be S Se or Te Figure 21 32 Specifying bond and atom types in a query The A label denotes that the atom may match any atom except hydrogen The indica tor near the bond indicates that the bond has been defined in
172. ds to the atom are single It also allows searches for atoms with at least one multiple double triple or aromatic bond The default value Undefined finds targets without regard to the hybridiza tion of the atom 492 Structural Query Features Appendix A This property is only meaningful in a substruc ture search With a substructure search the query 1 This atom is marked with the atom property Unsaturation must be present Finds any of 4 aE 2 0 OH Does not find any of OH T 0 Q IT O O Bond properties ChemBioFinder allows special properties to be assigned to bonds in a query These properties usually will only be meaningful during a search They generally serve to broaden or nar row the scope of the query Special bond types The table below describes the special bond types that ChemBioFinder allows Bond Type Description Aromatic target bond must be aromatic as defined by the Hiickel 4n 2 rule Any target can have any bond type here S D target must have a single bond or a double bond here Tautomeric same as S D D A target must have a double bond or an aromatic bond here S A target must have a single bond or an aromatic bond here Topology If Ring or Chain is chosen the target bond must or must not be in a ring respectively Reaction center The reaction center refers to those bonds that are directly affected
173. e To refine a search 1 Verify that the Search gt Over Current List menu option is selected 374 Queries Chapter 21 2 Do one of the following e Click Search gt Enter Query e Click the Enter Query icon on the Search toolbar ChemBioFinder 12 0 searches over the previously retrieved hit list If no hits are found a message appears asking whether to search over the entire database As long as the Over Current List switch is on each search further refines the current list Use the Retrieve All command to reset You may also use the Restore Previous List command which acts like a Back button Restore Previ ous List goes back one in the history including any Retrieve All s you might have done Entering a structural query To begin a structural query 1 Do one of the following to clear the form e Click Search gt Enter Query e Click the Enter Query icon on the Search toolbar 2 Do one of the following to place a structure into a data box e Double click in the structure box and edit with the Chem amp Bio Draw Control e Right click and click Edit in Chem amp Bio Draw e Right click and click Read Structure to open an existing molecule file e Use Edit gt Paste to insert a structure from the clipboard 3 Click Search gt Preferences 4 Click the Search Type tab 5 Select the appropriate options Optionally select options on the Details tab as well 6 Do one of the following e Click Search
174. e structural portion of the database linked to the assigned ID The Formula and Molecular weight data are automatically calculated from a structure These internal fields cannot be edited or deleted After creating a database you can create fields for storing other types of data It is not neces sary to create the entire set of fields before working with the database You may add more fields later Creating tables There is no limit to the number of tables a data base can contain You may want multiple tables in a database in order to manage rela tional data or simply to organize different col lections of information in the same place A table must contain at least one column When you create a new table ChemBioFinder 12 0 creates a numeric column called ID You can use this column to store integer data or delete it and replace it with your own columns Table names must e Begin with a letter e Not contain punctuation characters e Not be the same as a table already on dis play To create a new empty table 1 Right click in the form and click Properties The Box Properties dialog box appears 2 Click the Table tab The Table tab appears 3 Click the Create Table The Create Table dialog box appears 4 Type a name for the new table then click OK The table appears in the Data Source tree Deleting tables To delete a table from the database 1 Right click in the form and click Properties The Box Pro
175. e a field 1 Right click in the form and click Properties The Box Properties dialog box appears 2 Click the Field tab The Field properties appear 3 In the field list select the field to be deleted 4 Click the Delete Field 5 When prompted whether you want to delete the selected field click OK to delete or click Cancel to leave it unmodified CAUTION When you delete a field all data contained in the field is also deleted You are not warned explicitly about this Adding multiple structures You can include more than one structure on the same form by creating multiple structure col umns in a table Each structure column you create represents four types of data e The structure displayed as a diagram The Molecule ID which connects the struc ture to a record in a relational table The formula derived from the structure e The molecular weight derived from the structure To create multiple structure columns in a table 1 Click File gt Database The Form Properties dialog box appears 2 Create or open a database Click the Field tab 4 Select the Table in which you want to create new structure columns 5 Click the Create Field The Create Field dialog box appears ca 6 Select Structure from the Type drop down list An uneditable name is assigned to the field 7 Click OK Four new fields appear in the list and are named to belong to the same set of structure columns 8 C
176. e also exact search ing similarity searching see also normal searching SMD files 389 Sorting 429 sorting by subform aggregate Oracle 416 data 353 data tables 353 fields 353 formulas 353 from the data table 353 in reverse order 353 languages other than English 354 Oracle databases 416 structures 353 text 353 special atom types list of 489 special bond types 493 special structure searches 376 SQL searches 369 Statistical analysis 307 statistical analysis see BioV1z status bar 289 status bar description 287 stereochemistry 486 allenic 486 cis trans double bonds 486 octahedral 486 overview 363 queries 486 relative tetrahedral 373 487 search preferences 372 square planar 486 tetrahedral 486 trigonal bipyrimidal 486 stopping queries 374 Struct gt Name TM 395 structural query features 483 structure columns 345 display preferences 451 queries 360 registration options 453 searches 360 structure box description 287 structure field 341 344 structure mode 361 structure window 306 structure window description 287 structures adding 347 adding to non chemical database 345 as pictures 351 checking chemistry 351 chemically significant text 351 cleaning 350 copying as text strings 395 editing 349 350 entering 350 453 file formats 389 importing 390 query properties 483 ChemBioFinder amp BioViz 559 User Guide red highlighting in queries 368 374 scaling 452 sorting 353 structu
177. e area you want to examine and releasing the drag will cause the plot to zoom in on that area When unchecked dragging a rect angle selects the points within it without changing the scale You can use zoom to reset the scale even on Font Selects the font Different fonts may be used for the Comment X and Y axes Table 26 BioViz options Display tab Menu option Description Properties Opens the BioViz Proper ties dialog box Filter Window Opens a filter window See Filtering on page 430 locked displays Unzoom Resets the scale after a zoom or a series of zooms Rescale to All Scales the plot so that the Points visible points fill the plot window Autoscale Automatically rescales every time you change the list that is perform a search restore a list etc Locked Locks the display See Table 25 for details Copy Image Copies the plot to the Clip board allowing it to be pasted into other docu ments Table 27 Context menu options Table 27 Context menu options ChemBioFinder amp BioViz 427 User Guide Menu option Description Selection to List Creates a hitlist from selected data points The list is displayed in the Queries Tree and is treated and saved like any other search query You cannot use Restore Query on a list selected this way but you can use Restore List to retrieve the records Table 27 Context me
178. e dis played on the plot ChemBioFinder amp BioViz 423 User Guide 1 Right click in the plot then click the Prop erties context menu command The BioViz Plot Properties dialog box appears TIP You must right click either in the plot area or in the top border Clicking any other border brings up different context menus See Changing the display on page 433 for details 2 On the Display tab enter your legend in the Comment text box You may also enter a font and point size for the legend 3 Click OK to display the legend The default position for the legend is in the upper right corner of the plot After you have created it you may position it where you want by dragging it To remove the legend open the BioViz Plot Properties dialog box and delete the text in the Comment box Background color You can choose any background color you want for a chart A Color button on the Dis play tab of the BioViz Plot Properties dialog box opens a color picker dialog box Other changes Extended state saving Filter slider positions and colored by state of plots are now saved with the form Improved Filter display See Filtering on page 430 for details Improved statistical display See Statistical analysis on page 428 for details Improved Histogram bar coloring See His tograms on page 425 for details 424 BioViz Chapter 26 Changes in version 10 Removal of empty points
179. e for the most recent files opened Type in a number from 0 to 16 or press the up and down arrows to change the current value by one unit in the Recent file list size option on the General preferences tab H H H Brg h Figure 29 7Visualization of reaction centers 454 Customizing ChemBioFinder 12 0 Chapter 29 3 Changing options with the view menu Several structure display options can be set from the View menu including Atom Num bers Reaction Centers Stereochemistry and Atom Maps in reactions To display reaction centers Select the View gt Structure gt Reaction Centers menu option Qata Table gt FN B 0 E Continuous Forms u A g Foem view popoean emanan a EP Surch Views Ctr w Structure Refresh Bioviz Plots b E Periode Table Gid oa Atom Numbers Tanlharc gt Stereochemistry Figure 29 6Viewing reaction centers With reaction centers shown any bond that changes in the course of a reaction is colored Additionally any atoms that participate in reaction centers are circled if none of their adjacent bonds participate in the reaction center He 0 OH H3C To display atom to atom maps Click the View gt Structure gt Atom to Atom Map menu option With atom to atom maps shown equivalent atoms in reactants and products are colored the same SH oO H Se t 8 Figure 29 8Atom to atom maps These two preferences affect only the display of r
180. e string is taken as an anchored substring Thus if you search for benz it gets anchored to the left and returns words beginning with benz e Text strings may contain wild cards or Boolean operators Standard wild cards are and These characters are equivalent and hit any string Other wild cards are also possible If wildcards are present they override the above defaults NOTE Using wildcards or a in memo fields may lead to unexpected results This is because a memo field may contain formatting information surrounding the text you see so a search like benz may give no hits Using benz however will give the same results in a memo field as in a plain text field e A check box in the Search Preferences dia log allows you to request a full word ChemBioFinder amp BioViz 357 User Guide match When this box is checked a hit must contain the query as a complete word not embedded within a larger string e Boolean operators are NOT OR and AND They may be used to combine search terms within one field TIP Use NOT to search for empty fields Examples of queries Examples of queries Table 21 Entry Possible hits 90 values from 89 5 to 90 5 90 1 values from 90 05 to 90 15 values from 90 through 100 inclusive 90 100 gt 90 and lt 100 values from 90 through Numeric searches Searching numerical data allows you to
181. e the Selection tool to move the data boxes to where you want them in the form Using the form tools You must use the Form Tools toolbar to design a form Box creation commands are not avail able from the menu 314 Forms Chapter 18 To display the Form tools do one of the fol lowing e Click the Layout icon on the Main toolbar e Select the View gt Toolbars gt Form menu option The Form toolbar appears providing tools for you to create and edit a form Control Box Picture Subform Selection tool Frame check box ture Subform E Ae Checkbox Contro Box boi Fiame Figure 18 6 The Form toolbar Using the grid In a new form the snap grid is turned on by default This grid helps you align boxes on the form Turning on the grid forces objects to snap to the grid as they are drawn To toggle the grid on or off do one of the fol lowing e Click the Grid tool on the Form toolbar e Select deselect the View gt Grid menu option NOTE You can change the grid spacing using the Preferences dialog box See Setting prefer ences on page 451 Creating boxes A ChemBioFinder 12 0 form is composed of a collection of boxes that display data from the associated database or other information Each box displays one data item of the current record To create a data box use one of the tools on the Form toolbar NOTE The Form toolbar is not visible unless the Layout button is selected The
182. e you may find a molecule that interests you and want to find other related records The Find Current Molecule feature lets you perform a quick structural search of the struc ture currently being displayed on the form However this feature does not allow you to enter other search terms The type of structure search complete structure substructure and or similarity is determined by what you have selected in the Search menu To find the current molecule 1 Browse to the record containing the struc ture of interest 2 From the Search menu choose the type of structure search you want to perform 3 Do one of the following e Click Search gt Find Current Mol e Click the Find Current Molecule icon on the Search Toolbar ChemBioFinder 12 0 begins the search and displays the search status on the lower right corner of the status bar When the search is complete the form displays the first hit and the list you can browse is restricted to the records hit by the query Entering a reaction query The general procedure for creating a reaction query is very similar to creating a structural query 1 Do one of the following to clear the form e Click Search gt Enter Query e Click the Enter Query icon on the Search toolbar The form clears 2 Enter the query e Double click in the Structure box e The Chem amp Bio Draw Control appears Draw the structure or substructure or reac tion in the From ChemBioFinder 1
183. eactions Not checking the boxes means these types are displayed as all other atoms and bonds Favorites tree The Favorites Tree is a user constructed col lection of file system objects It may include folders subfolders ChemBioFinder 12 0 forms structure files and documents of all kinds Its purpose is to allow you to collect CH3 o CH3 et Q organize and access the data and documents you use regularly Axi Favorites ChemFinder Samples 0 AGROBASE CFW I CS_DEMO CFW DEMO CFW CF CF_old Exported items CS_DEMO doc CS5S_DEMO csv Database Queries Favorites Figure 29 9The Favorites tree ChemBioFinder amp BioViz 455 User Guide You can open items in the Favorites Tree from within ChemBioFinder 12 0 by double click ing them Table 29 Favorites tree options if the file is double clicking will a ChemBioFinder open it 12 0 form a ChemBioFinder execute it 12 0 script an SD or RDFile load it a ChemBioFinder 12 0 query restore it any other type of document open it in its source application There are two ways to add items to the Favor ites Tree e Drag one or more files from Windows Explorer into the Favorites window e Use the context menu To create a new folder in the Favorites Tree 1 Point to the parent folder The new folder will be a subfolder of this folder 2 Right click and click t
184. eadsheets and the txt format for general export NOTE In delimited text files structures are automatically exported as SMILES strings Exporting a Word file The export to MS Word option is similar to the other export options however a couple of points are worth noting e Export to Word is much slower than to other formats For this reason you should probably limit the use of this option to rela tively short hitlists e You can speed up the export by not export ing the structure field e Structures are exported as OLE objects and can be edited in Word with the Chem amp Bio Draw Control e If you should by accident begin exporting a large database you can terminate the export by bringing ChemBioFinder 12 0 to the front and pressing the Esc key Exporting to SDFile When you export to SDFile you are allowed to export subform fields Each subform field is exported to a separate record in the SDFile but separate subform records are concatenated into a single multi line text block 396 Importing and Exporting Data Chapter 22 To export subforms 1 Click the File gt Export gt SDFile menu com mand The Data Export dialog box appears 2 Click the Text Options tab and select the Export subform data check box 3 Return to the Export tab In the Field col umn of the Data Fields table all subform fields now appear with checks in the check box next to the field name Deselect any subform fields you do
185. earch is indicated by counters in the status bar at the bottom of the window When the search is complete the number of hits is displayed in the Current List Size win dow of the Status Bar and the form displays the first hit In a substructure search the matched portion of each molecule is high lighted in red You get 3 hits reactions in which an alkyl magnesium halide is consumed Browse the list of three hits as in previous tutorials Searching for products In the next exercise you search for information on a particular reaction product Searching for 302 Tutorials Chapter 17 products of reactions is very common in syn theses where you know what you are aiming for but you do not know how to produce it In this example we look for reactions that close a ring alpha to a carbonyl To perform a reaction product search 1 Click the Search gt Enter Query The form is cleared so that you can enter a new query 2 Double click on the Structure data box The ChemDraw control appears 3 Draw the following Pe 4 Switch to either selection tool Lasso or Marquee and select the single bond next to the double bond 5 Right click point to Topology and choose Ring 6 Select the remaining single bond 7 Right click and select Topology gt Ring Right click again and select Reaction Center gt Make Break Your structure should now look like this al a Figure 17 10 Product query with topology and rea
186. ectly from ChemBioFinder 12 0 without having to import or redraw them To read a structure from a file into a structure box 1 Right click in the structure box and click the Read Structure context menu command The Open dialog box appears 2 Choose the file to read 3 Click the Open The structure is read into the structure box The database is not affected by this operation until you choose Commit Changes or move off of the record Drag and drop You can drag certain types of files from the Windows Explorer or Desktop onto ChemBio Finder 12 0 The following table summarizes the ChemBioFinder 12 0 Drag and Drop options type of file sup comments ported file types e CDX e SKC e MOL e MST Structure Must be dropped into a structure box type of file sup commenis ported file types Graphic e WMF Must be dropped into e EMF fa picture box e BMP e GIF e PNG e TIF Form e CFW Does not need to be dropped onto an existing form Multiple files can be dropped at once but you cannot mix types as defined in column 1 of the table If several structure or graphic files are dropped at once they are loaded into suc cessive ChemBioFinder 12 0 records If only one is dropped you are asked if you wish to append the structure graphic in a new record or overwrite the existing record If more than five structures graphics are dropped an alert will ask you if you wish to
187. ecurity dialog box Security dialog available encounter all of the above options Database security 2 Click the plus sign next to Forms to dis play the options take the appropriate action Table 27 Forms security options If you want users to Then select open or create data bases Open create data base create forms Create new forms open forms Open other forms edit forms Save changed forms Table 27 Forms security options If you want users to Then select change the layout of a form Change form layout use all of the above options Forms 3 Click the plus sign next to Automation to display the options take the appropriate action Table 28 Automation security options If you want users to Then click access OLE automa tion writing and programming Allow CAL OLE Automationaccess NOTE Must be checked to enable export to Excel use scripts Can use scripts menu edit scripts Edit scripts use all of the above Automation options 4 Click the plus sign next to Edit to dis play the options take the appropriate action Table 29 Editing security options If you want users to Then click clear forms Clear delete relational and structural data Cut copy relational and structural data and multiple table rows to the clipboard Copy
188. ed 3 Click Search gt Find ChemBioFinder 12 0 begins searching The progress of the search is indicated by counters in the status bar at the bottom of the window When the search is complete the number of hits is displayed in the Current List Size win dow of the Status Bar and the form displays the first hit In a substructure search the matched portion of each molecule is high lighted in red NOTE You can also set search preferences on the Search tab of the Preferences dialog box For more information see Customizing ChemBioFinder 12 0 on page 451 In this search you get 122 hits of structures that contain an aromatic six membered ring The list you can browse is limited to the hits found in the search NOTE If a search gets no hits an alert appears and you are returned to the query mode with the query on display Combined searching In some cases you may want to combine struc ture searching with text searching to find a spe cific class of compounds For example you may want to find all compounds in the data base that have a benzene substructure and that have a molecular weight greater than 400 To perform a combined search 1 Click Search gt Enter Query The form is cleared so that you can enter a new query 2 Double click in the Structure box The Chem amp Bio Draw control appears 3 Draw benzene 4 Click the Molecular Weight box and type gt 400 5 Press the Enter key
189. ed for real numbers such as physical constants and unit prices Real numbers in ChemBioFinder 12 0 are double precision In ChemBioFinder 12 0 12 double fields can serve as ID fields Picture field Allows you to store a bit map file BMP GIF JPEG PNG or TIFF or Windows metafile WMF EMF such as a spectrum or experimental setup as a data item in a database A Picture box on a form may be used to dis play a static picture attached to the form such as a logo or it may be used to show pictures stored in the database which change as you move from record to record If you import a database containing pictures type Long Binary or BLOB they will be interpreted as pictures and the form generator will create a picture box for it Memo Rich Text field Used to display text Memo fields can be of any length Because memo fields are less structured searching them can be slower than searching a text field Additionally memo fields cannot be sorted To search for text 1 Right click in a memo or plain text field and select Find Text The Find Text dialog box appears 2 Enter the text and the match conditions 3 Click either the Forward or Backward to search 4 To search for the next occurrence do one of the following 344 Databases Chapter 19 e Click Find Next e Use the F3 key Memo fields can store Styled Text For more information see Styled text on page 352 ate field Allows you to store da
190. ed to warn you of situations that might cause a possible loss of data NOTE Notes are used to highlight important information TIP Tips are used to present information sup plemental to the main text Shortcut key sequences are indicated with a sign for example Use the command Ctrl H to toggle hidden Hydrogens and lone pairs 284 ChemBioFinder amp BioViz Chapter 15 A bold font is used to refer to the User Inter face for example Click File gt Save Additional information Additional sources of ChemOffice information are e The Quick Reference Cards e The Help system e CambridgeSoft Web Pages e http CambridgeSoft com services Quick reference card The ChemOffice Quick Reference Cards are located in the back of the printed manual The cards summarize ChemOffice Desktop appli cation commands and features Help system ChemOffice applications provide some or all of the following types of Help e Help An HTML reference guide e ToolTips Short descriptions of user inter face objects displayed by pointing e Status Bar The lower left corner of the screen displays useful information as you work The User Interface ChemBioFinder 12 0 is a database manage ment system that allows storage retrieval and searching of molecular structures text and numerical data You can create structures in either Chem amp Bio Draw or with the built in Chem amp Bio Draw ActiveX
191. efault in the Element Editor NOTE The data of the Periodic Table is stored in a tab delimited ASCII file called CS ChemB ioFinder 12 0 Custom Elements txt located in your ChemBioFinder 12 0 system directory It 458 Customizing ChemBioFinder 12 0 Chapter 29 can be easily edited with a text editor or spread sheet program if you want to change default data values Embedding ActiveX controls You can embed most windowed ActiveX con trols on a form For stand alone controls you can embed the control and use it immediately If the control needs programming or if you want the control to manage ChemBioFinder data you will need to customize its behavior using Python scripts To embed a control 1 Select the Control box tool on the Forms toolbar 2 Drag a rectangle on the form The Insert Control dialog box appears 3 Select a control from the list The control appears in the Control box Figure 29 14Adding a spreadsheet to a form NOTE Not all controls listed are suitable for use in a Control box but appropriate error messages should be displayed in such cases Customizing controls The behavior of an embedded control can be customized by adding Python scripts to the form to perform custom actions at given times The control can be accessed via the Automa tion interface through the Control property of the corresponding Box object which is obtained from the Boxes collection of the Doc ument object Cont
192. eft of form check box If you do not select this option the boxes are generated in the order they appear in the list 6 Select the Form style you want Then in the Form style section click If you want the boxes to be surrounded by a Framed frame be labeled above Titled be labeled to the left Labeled not be labeled Plain Table 18 1 Form style options 312 Forms Chapter 18 7 Use the thumb wheel arrows to select the number of columns from one to four in the Columns list 8 Use the Grid size drop down menu to choose the size and spacing of the boxes and grid as follows If you want the boxes Then for Grid to be Size choose larger and spaced Large further apart medium relative to the Medium Large and Small settings smaller and spaced Small closer together Table 18 2 Grid size options 9 Click the OK button in the Form Generation dialog box Your form settings are saved 10 Click the OK button in the Form Properties dialog box A warning dialog box appears allowing you to create a new form or replace the existing form Click No to create a new form Yes to replace the existing form ChemFinder Ultra 2 J Do you want the generated form to replace the existing one Click Yes to replace No to generate form in a new window I Don t ask me this again Figure 18 3 New form warning box Saving a form In most non database a
193. eld match options and logging options 6 Select the fields to be imported with the check boxes e Optional Double click the field name to change the name of the field field type and width in the Data Field Import dialog box e Optional Click the Logging tab to change details of the log file e Optional Click the Form Style tab to select the style of boxes that will be cre ated for new fields 390 Importing and Exporting Data Chapter 22 e Optional Click the Advanced tab to set the Advanced options Import only part of a file by setting the starting point You may indicate a starting point by line num ber byte number or record number Also select the version of the ChemBioFinder database to be created Versions back to 7 0 are supported In addition import structures only by selecting the check box and enter duplicate reagent values by checking the Store redundant reagents check box NOTE In SD and RD files reagents and catalysts are specified in each record ChemBioFinder 12 0 stores them in subtables Thus if the same reagent appears in more than one record ChemBioFinder 12 0 only needs to store it once You can over ride this default with the check box 7 When you have finished selecting your options click the Import button The struc tures are imported to the specified database Structure and reaction ChemBioFinder 12 0 allows you to import Structure Data files SDFiles and Reaction Data f
194. enclosure around a data box or group of boxes containing a label Picture box Displays a graphic Picture boxes may be either Fixed that is they remain the same for all records in the database and are linked to a particular graphic file or associated with a picture Field in which case there could be a different graphic in each record Profile box Displays Compound Profiles Framed data box A data box surrounded by a labeled frame Query indicator Displays QRY when you enter a search query 286 The User Interface Chapter 16 Screen Ele ment Description Read only indi cator Displays READ if the database is read only Record toolbar Contains icons for commands in the Record menu Click an icon to perform the command Search toolbar Contains commands in the Search menu Status bar Displays information about the item opened in the ChemBio Finder window Structure box Displays the chemical struc ture of the current record Structure window Displays the chemical struc ture of the selected or moused over point when a plot window is displayed May be displayed as tabbed with other windows Subform Displays relational informa tion from a different database or a different data table within the same database Text box Text Format toolbar Displays text Text boxes are Fixed text fields are displayed in text
195. ency that improves structure search speed in all CambridgeSoft products Setup Before you can make use of the ChemBio Finder Oracle your machine must be config ured as an Oracle client If you are already a user of the CS Oracle Cartridge you are proba bly all set If not you will need to enlist the ChemBioFinder amp BioViz 413 User Guide help of an Oracle administrator to set up the server and set you up as a client For ChemBioFinder 12 0 installation instruc tions see the readme txt included on the distri bution media Ideally ChemBioFinder Oracle should access any existing Oracle database in any format In practice there are some limitations See Pre setup procedures on page 541 for notes and recommendations about preparing an Oracle database for use with ChemBioFinder Oracle Opening an Oracle database To open an Oracle database 1 Right click in the form and click the Data Source context menu command to open the Database tab of the Box Properties dia log box 2 Click the Oracle Database button The CS Oracle Connection dialog opens NOTE The Oracle Database button is available to any user There is no check to see whether the machine is a valid Oracle client 3 Enter values for Host name User name and Password the same values you use to log in from any Oracle client OR e Choose a name from the drop down list of recently used items When you choose an item from this li
196. end to menu 477 settings 480 UI 471 cleaning structures 350 clearing forms 347 373 color preferences 452 color setting 323 combined searches see searching com bined combined searches see searching com bined commands add new record 347 bring to front 325 commit changes 348 350 351 current Record 289 current record 285 data source 333 342 delete record 353 enter query 373 Find 373 find current molecule 375 Find List 360 find text 344 first record 338 go to record 338 Intersect with current list 384 last record 338 next record 338 previous record 338 read structure 392 redo 353 replace current list 383 restore list 383 save list 383 Save Structure 394 548 Index search over list 303 send to back 325 undo changes 349 commit changes command 348 350 351 committing changes vs saving 313 committing new data 348 communicating with other applications us ing DDE 467 communicating with other applications us ing OLE automation 468 communicating with other applications us ing scripts 467 commutative principle 497 complete structure similarity see Tanimoto similarity compound profiles 405 creating 406 customizing 411 display preferences 409 dist 410 editing 408 score 406 search sort 410 concurrent access 336 connection table file format 389 controls embedding 458 counterions 351 create database button 341 create table dialog box 341 creating and editing tabs 318 boxes 314 boxes with frames 315 button
197. ent from the default in previous versions Domains The Domain feature in ChemBioFinder allows you to create a subset of a database Once cre ated a domain acts as if it is a full database Any database searches you perform are limited to only the domain Any hitlists you create will be added to the query tree as if you are work ing with the full database Creating a domain Before you create a domain you must run a query to define the subset of the database with which you want to work This subset becomes the domain TIP If you want your domain to have a partic ular order sort before creating the domain The order will be preserved for all subsequent use To create a domain 1 Select a query by double clicking on it 2 Click the Search gt Domain gt Set Domain to Current List menu command Query control display When you run queries in a domain they will not be displayed as child queries of the domain unless you select Over Current List on the Search menu and specify the domain as the active list Cancelling the domain If you no longer want to use a domain click the Search gt Domain gt Reset to Full Database command again to cancel it Creating an mdb database When working with a large Oracle based data base on a server it is sometimes convenient to store a subset of the database dataset as a local database ChemBioFinder local databases are Microsoft Access based file extension MDB so the e
198. ent list See Restoring a hit list on page 383 for details Restore List apply the query s color to a plot of the intersection of the selected query with the current list This is the same as single click on the query choose a different query icon color from the color picker dialog Color On Plot Change Color TIP Double clicking the root item Full List has the same effect as choosing Retrieve All from the Search menu modify the query and or rerun it Restore Query goes to Query mode and displays the struc ture You may modify the query then rerun it manually Restore Query The Queries context menu When you right click on a query you display a menu with commands to manage the query if you want to then choose repeat the search using the Rerun selected query This is the same as double clicking on the query save the query to a separate file with extension cfq Save Query mark the query so it will be saved as named when the form is saved This has no effect unless the Query Saving preference has been set to Discard unnamed queries See Saving and restoring lists on page 382 Keep ChemBioFinder amp BioViz 381 User Guide if you want to then choose delete the selected query from Remove the tree The next time you save the form this query will be lost If you delete by mistake you can clo
199. entheses may be used to group elements and apply a count to the entire group For example CH2 3 is interpreted as C3H6 e Spaces or non alphanumeric characters other than parentheses are ignored Date searches Dates might be used to track individual reac tion runs purchasing histories and so on Searching dates is very similar to searching numerical data Ranges are specified using a hyphen between the values at either end of the range Ranges may also be indicated using inequality opera tors lt gt together with the AND operator Dates are always displayed according to the preferences set in the operating system s Inter national control panel but need not be input in that format The following table shows query examples Table 23 Entry Possible hits Apr 11 1971 the exact date April 11 1971 March 31 1971 any date in the second July 1 1971 quarter of the year 1971 gt 4 11 71 any date after April 11 gt 4 11 71 1971 or on April 11 1971 ChemBioFinder amp BioViz 359 User Guide Find list Use the Find List command to retrieve records having specific values in any non structure field Type parameters into the Find List box as fol lows e Ifthe column you search is an integer type you can use hyphens to indicate ranges e Ifthe column you search is a number or text type you cannot use hyphens to indicate ranges you must search for an exact match NOTE To sea
200. erlap Chem amp Bio Office 2010 User Guide 479 ChemBioFinder If you want to then click If you want to then click require that any reaction center present in the query overlap with reac tion centers in the target This preference applies only to reaction searching Hit must overlap reaction center allow hits to contain molecular fragments in addition to that which was hit by the query Extra fragments may be present in hit allow uncharged carbon atoms in the query to match charged carbon atoms in the target Charged atoms in the query must always match charged atoms in the target regardless of this setting Match any charge on carbon allow uncharged atoms in the query to match charged atoms in the target Charged atoms in the query must always match charged atoms in the target regardless of this setting Match any charge on heteroatom allow a query drawn as absolute hash wedge bonds to hit a target stored as relative Absolute center hits relative 480 ChemFinder Office Chapter 30 Relative tetrahedral stereo match a relative relation ship between tetrahedral stereocenters Changing ChemFinder Office settings You can change ChemFinder Office settings so that ChemFinder Office appears the way you want You can customize the way the ChemFinder Office window appears with the items on the View menu You can change some
201. ers you can use wildcards or specify a numerical range When structure searching you can search by sub or full structure search for an exact match simi larity or tautomerism and specify how stereo chemistry will be matched You can also combine structure searching with text or numerical searching A Find Structure com mand performs duplicate error isotopic label and other special structure searches The chapter describes the different types of searches and how to set up and manage searches It concludes with some examples of advanced techniques Text searches ChemBioFinder 12 0 like all databases sup ports text searching You can search any alpha numeric field for strings of text Use text searching for example to find chemical names or comments in a reference field For text searches ChemBioFinder 12 0 inter prets the query then passes it as Structured Query Language SQL to the relational data base The following rules apply to these queries e When searching a normal text or memo field a plain text string is taken as an unanchored substring if you are not doing Full Word search An asterisk is added automatically at each end of the string and the hits include any string con taining the search string Thus if you search for benz it gets converted to benz and returns benzene and fluroben zene e When searching a normal text or memo field with wildcard th
202. es on page 318 tabs see Creating and editing tabs on page 318 and security see Securing forms on page 327 You can edit your form at any time see Edit ing forms on page 324 and Changing form layout on page 327 The first step in designing a form is selecting the database and deciding which fields to include Creating forms automatically Use the Form Generation dialog box to create a form or change the layout of an existing form In the dialog box you choose the form style and properties from pre defined options To begin creating a new form 1 Right click on a blank area of the current form and select Data Source The Form Properties dialog box appears 2 In the Form Properties dialog box select the Form tab ChemBioFinder amp BioViz 311 User Guide 3 Select the Generate form check box then click the Style button The Form Generation dialog box appears In the left panel all the fields are selected by default Form Generation 7 g 3 pi amp Choose fields to be included C Titled C Labelled 00 aa 0 Plain eR aed Medium v J Structure in upper left of Form Subforms Figure 18 2 The Form Generation dialog box 4 Deselect those fields in the Choose fields to be included section that you want to exclude from the form 5 To have a Structure box in the upper left corner of the form select the Structure in upper l
203. es e Click the Undo Changes icon on the Record Toolbar After you commit the changes they cannot be undone Editing data Modifying the data in a database is performed by directly changing the data items on the form and committing those changes NOTE The Formula and MolWeight fields are automatically calculated by ChemBioFinder 12 0 from the Structure field and cannot be edited by the user The MOL_ID field is also set automatically by ChemBioFinder 12 0 and cannot be edited To edit data Click the data box whose data item you want to edit If you click on a Structure data or a picture box it is highlighted If you click on a data box containing alphanumeric data a cursor appears in the data box To edit alphanumeric data 1 Replace it with the text or number you want 2 Do one of the following e Click Record gt Commit Changes e Click the Commit Changes icon e Move to a different record NOTE Moving to a different record always commits changes first Editing structures You can edit structures by using the Chem amp Bio Draw drawing tools You can also neaten the appearance of a structure by cleaning it up The Clean Structure command is used to neaten the appearance of molecules by regularizing bond lengths and angles Since the degree of change required cannot be determined a priori the Clean Structure command begins gently You may need to repeat the command to get the changes you wish Fo
204. et compound Unlike exact searches similarity searches do not highlight matched portions of the target compounds Similarity searching matches gen eral structural features and not specific atoms and bonds so highlighting specific areas would not be appropriate You can adjust the degree of similarity from 0 to 100 necessary to produce a hit by using the slider on the Search Type tab of the Prefer ences dialog box Structure modes The term Structure Mode refers to whether the query defines a substructure of the com pounds in the database being searched or the full structure In this context it is important to note that full structure does not mean the same as exact When you specify the Exact search type the structure mode is always full structure but you may choose the full structure mode with any of the three search types See Full structure searches on page 362 and Exact searches on page 361 for more details Substructure searches A substructure search finds structures that con tain the query plus any additional attachments at the open positions This is the default search mode The substructure is highlighted in red in the hit list structures Using the ChemDraw ChemBioFinder amp BioViz 361 User Guide ActiveX toolbar you can attach different fea tures to a query such as atom lists and variable bond types to perform a narrower or broader search For more information ab
205. f data you need to export Click the Export button Once data is exported STATISTICA is launched and the data is imported into STATISTICA There after the analysis tools available in STA TISTICA can be used to analyse the exported data NOTE Structure fields are not exported because STATISTICA can not process structure fields Printing You can print out all or part of your database To print a database 1 Before printing decide if you want to print a table view or a form view Set ChemBio Finder 12 0 to the appropriate view Click the File gt Print Setup menu command In the Print Setup dialog box set the printer paper size default US Letter and page orientation desired Click OK when you have finished TIP Settings in this dialog box affect the Page Setup so it s best to start here Click the File gt Page Setup menu command In the Page Setup dialog box set the mar gins and units cm inch layout and other options e The Header option prints the file path at the top of the page e The Footer option prints the date time and record number at the bottom of the page Click OK when you have finished Click the File gt Print Preview menu com mand to check the settings Click the File gt Print menu command or the printer icon on the main tool bar The Print dialog box appears ChemBioFinder amp BioViz 397 User Guide 8 Set the print range and number of
206. f seconds to wait for a response to a DDE transaction The default is 30 seconds ChemBioFinder amp BioViz 521 User Guide Section Preference Description Values OPTIONS EXPLICIT_METAL_H Whether or not to require that O or 1 metals have hydrogens drawn implicitly If this parameter is off ChemBioFinder will automatically add hydrogens to fill each metal s minimum valence This parameter can be set manually in the General tab of the Prefer ences dialog The default is 1 require explicit drawing OPTIONS EXPORT_HEADER ASCII value of the delimiter 0 255 to use when exporting delim ited text files This parameter can be set manually in the General tab of the Prefer ences dialog The default is 9 tab OPTIONS LOAD_LAST_FORM_ON_ Whether or not to load the 0 or 1 STARTUP last active form file the next time ChemBioFinder is launched The default is O do not load 522 CAL Commands Appendix D Section Preference Description Values OPTIONS OPTIONS NON_INTERACTIVE VALIDATE_VALENCE Whether or not to suppress Oor 1 non critical dialogs Princi pally useful when ChemBio Finder is being used unat tended such as over the WWW It is not recom mended to have this option on when using ChemBio Finder directly The default is 0 interactive mode Whether or not to providea Oor 1 warning when attempting to enter a substance containing
207. f the Properties dialog box Just click the button labeled Font 294 Tutorials Chapter 17 3 Click the Frame tool 4 Place the pointer at the corner of the upper right data box and drag to create a border around the group of three data boxes The Enter the Label dialog box appears 5 In the Enter the Label dialog box type Frame and click OK The label appears above the box To place a picture in your form 1 Click the Picture tool and drag in the form The Open dialog box appears 2 Browse to a graphic file then click Open NOTE ChemBioFinder 12 0 supports EMF WMF BMP GIF JPG PNG and TIF formats The picture appears in the area you dragged in the form Editing data boxes To edit one or more data boxes you must first select them 1 Click the Selection tool 2 To select the upper left box click it A selected data box is designated by four black squares at its corners NOTE You can click an empty space in the form with the Selection tool to deselect the box To select multiple boxes Press the Shift key and click in each box TIP You can also select multiple boxes by Click dragging a rectangle around the box You can Select all the boxes on the form by choosing Edit gt Select All The frame and the box behave as one object when you select move resize or delete To separate them into two objects 1 Click inside the Framed box to select it 2 Go to Edit gt Bring to
208. figu ration it should hit only that if it represents a mixture it should hit any of the components If you choose Same in the stereo search choices you are requesting that whatever ste reochemistry is specified in the query must match that of the target If the query has rela tive bonds and RTS is activated a hit must have the same relationship between centers You can use the following three flags in searches based on relative stereochemistry e Abs Refers to the Absolute flag It matches the exact stereoisomer as drawn Example gt NH e Rel Refers to the Relative flag It matches the exact stereoisomer as drawn or its enantiomer Example PA ChemBioFinder amp BioViz 487 User Guide e Rac Refers to the Racemic flag It matches a mixture of the exact stereoisomer as drawn and its enantiomer Example ool MDL file formats All bond styles available in ChemDraw are retained in CDX files The same is not true of major MDL structure files MolFiles SDFiles and RDFiles In these formats only three ste reo bond types are available hash wedge or either squiggly bond thick bonds are not rec ognized This presents a problem for the ChemBioFinder user wishing to import or export structures having relative stereocenters ChemBioFinder addresses this problem by using a proprietary tag in the file recognized only by ChemBioFinder The tag is BOND_RELS and is applied to every stereo
209. find information such as boiling points and molecu lar weights Ranges are specified using a hyphen between the values at either end of the range For numerical searching the query is a decimal value or range If a single value is given the number of significant digits determines the precision of the search A hit is any value that rounds off to the query 358 Queries Chapter 21 Entry Possible Hits Will Not Hit 100 inclusive benz Benzene Benzoic Bromobenzene gt 90 and lt 100 values from 90 through acid 100 exclusive benz OR Benzene Benzoic Azobenzene Molecular formula searches bromo acid Bromoben zene Dibromo Formula searching allows you to search molec benzene ular compositions Searches can be inclusive exact designated with an equals sign or with benzene Benzene Benzoic acid the element range you specify Benzene dg ChemBioFinder 12 0 allows formula searching Bromobenzene based on special atoms such as A Q X and M The definitions for these atom types can overlap For example the structure BiC13 will be hit by the query AX3 and it will also be hit by the query A4 However it will not be hit by the query A4X3 even though it does indeed have 4 atom that match A and 3 atoms that match X The following table shows query examples Table 22 Entry Possible hits C6H6 compounds with 6 carbons and 6 hydrogen atoms plus any number of other elements Table 22 Entry
210. from your Windows font list size String containing the size of the font in points style String containing the style in which to display the font as described in Settings T String containing the red component of the font color in the range from 0 to 255 g String containing the green component of the font color in the range from 0 to 255 b String containing the blue component of the font color in the range from 0 to 255 Settings The settings for style are Setting Description 0 Plain text 1 Bold 2 Italic 3 Bold and italic Setting Description 4 Underline 5 Bold and underline 6 Italic and underline 7 Bold and italic and underline CAL commands SEEPTAB syntax Displays the Periodic Table window then closes it SEEPTAB decisecs The SEEPTAB command has the following argument Part Description decisecs Amount of time to display the Periodic Table window before closing it Remarks 10 decisec 1 second If the decisecs argument is omitted the Peri odic Table window will be displayed for 4 sec onds CAL commands QUIETCLOSE syntax Closes the topmost form immediately without checking to see if it has been modified QUIETCLOSE The QUIETCLOSE command takes no argu ments Remarks This command is similar to the Menu Com mand File Close However if the user has ChemBioFinder amp
211. g Color On Plot from the tree context menu causes points on the plot to be recolored The recolored points are those which are on both the selected list and the plot ted one You may color more than one list at a time When a list is colored on the plot its item in the queries tree is shown with a check mark clicking it a second time uncolors it and removes the check mark Synchronization of plots Multiple plots attached to a form are synchro nized If you select mouse over a point in one plot the same point is highlighted in all other plots and the related structure is displayed in the Structure Window This behavior is slightly modified if one of the plots is a histogram You must select not mouse over a histogram bar to highlight points in other plots Mousing over a point in a line or scatter plot will highlight the point in the center of the corresponding histogram bar 200 160 120 77 80 41 40 0 Count 0 24 0 49 0 74 0 365 0 615 0 Figure 26 15 Synchronized histogram Changing the display Once you have selected data points and pro duced a plot there are several options for mod ifying the display e Changing Colors to change the color of a plot a Open the Queries pane of the Explorer window b Right click a list and click the Change Color context menu command c Select a new color from the color menu e Selection and Zooming to select a part of
212. g box click Dis able The Validate Security dialog box appears NOTE This form only appears if you entered a password when you enabled security See Setting security options on page 327 4 Enter your password then click OK Security is disabled and the defaults are reset Security Disabled appears in the lower left corner of the Form Security dialog box Overriding security In order to edit security options you must tem porarily remove security In this case you should use the Override option rather than the Disable option To temporarily disable security 1 Right click in the form and click Properties 2 In the Form tab of the Form Properties dia log box click Security The Form Security dialog box appears 3 In the Form Security dialog box click Over ride Security The Validate Security dialog box appears NOTE This form only appears if you entered a password when you enabled security See Set ting security options on page 327 4 Enter your password then click OK You are allowed to edit the security options Security Overridden appears in the lower left corner of the Form Security dialog box 5 When you have completed your changes click Override Security to toggle security back on Security Enabled appears in the lower left corner of the Form Security dialog box ChemBioFinder amp BioViz 331 User Guide 332 Forms Chapter 18 Databases You work wit
213. g multiple structures 345 clearing 373 creating automatically 311 creating manually 313 editing 324 moving 346 ChemBioFinder amp BioViz 551 User Guide saving 313 setting security 327 vs databases 292 forms creating and saving 295 formula field 341 formula input rules 495 formula searching see searching formula searching by 474 formulas input rules 495 sorting 353 FoxPro 342 fragments in full structure searches 371 searching 362 frame tool 315 framed box tool 315 framed boxes 315 framed boxes creating 315 framed boxes description 286 frames 315 frames creating 315 framing pictures 452 free sites in queries 491 full structure searching 362 full structure searching see also substruc ture searching full strucuture searching 362 G G groups see alternative groups general properties 483 general preferences 453 generic groups see alternative groups generics hitting in queries 371 go to record command 338 grid 314 spacing 452 552 Index tool 314 H headers delimited text files 395 help CAL 460 hiding annotations 452 data boxes 321 histogram plots 306 425 hit any charge on carbon 371 hit any charge on heteroatom 371 hit lists boolean operations 383 current 289 intersecting 384 joining 384 merging 383 replacing 383 restoring 383 saving 383 saving as text files 383 hydrogens in queries 484 hydrogens added to structures 351 ID queries 360 identity searching see exact searc
214. gle or double bond between the two substituted ring atoms In a substructure non tautomeric query the following query O O will get the following hits and will NOT hit the following Ow O O en O Table 31 Normalized query Changing the scope of a search When preparing a chemical structure to be used in a query there are two ways to broaden or narrow the scope of the search e Specify atom or bond properties e Specify atom or bond Special Types In general properties narrow a search and spe cial types may either narrow or broaden the search Atom properties ChemBioFinder allows special atom properties to be assigned to an atom in a query These properties are usually only meaningful during a search They generally serve to broaden or narrow the scope of the search Special atom types ChemBioFinder recognizes six special atom types that can match any one of a predefined set of elements e A matches any non hydrogen atom e Q matches any heteroatom non hydrogen non carbon e R matches any atom including hydrogen Also used to indicate a link node See Link nodes and multivalent Rs on page 386 for details A link node may be any number of atoms including zero e X matches any halogen F Cl Br I At e M matches any metal atom shaded in the periodic table below Figure A 1 Metals in the periodic chart ChemBioFinder amp BioViz 489 User Guide Atom lists As with
215. gt BioViz Plots submenu or from the data field context menu Existing plots can be dis played when not visible or removed from the form with the View menu You may create a plot based on any numerical field in the data base The following options are available e Line plots with one or two variables e Scatter plots with one or two variables e Histograms X axis variable only Single variable plots A single variable plot displays a Y coordinate variable vs the record number To create a single variable plot 1 Point to BioViz Plots on the View menu 2 Select New to open the BioViz Plot Proper ties dialog box re BioViz Plot Properties General Display Dimension Variables One variable C Two variables Style C Line chart Scatter plot C Histogram l Locked Logscale Base a Ce Bins Plot name BioVizPlot1 Point limit 500 Figure 17 15 Plot properties 3 Click One Variable in the Dimension box The X coordinate is grayed out and the Analysis tab is not displayed 4 Select any numerical field from the drop down menu for the Y coordinate 5 Enter a name for the plot optional TIP Note the Point Limit field on the lower right side of the Properties dialog box in Figure above Plotting a large dataset can be very slow As a safely precaution the default is set to 500 meaning only the first 500 points in the dataset will be plotted On most compu
216. gt Find e Click the Find icon on the Search Toolbar The status bar counters indicate search prog ress When the search is complete the form displays the first hit The list you can browse is limited to the hits For Normal or Exact searches the hit portion of each molecule is highlighted in red If a search doesn t find any hits you are returned to query mode TIP You can change the highlight color in the preferences dialog For example to show no highlighting choose black as the highlight color See Color preferences on page 452 for more information Using the current molecule as a query As you browse through a database you may submit any structure on the screen as the struc tural query Often you use similarity or sub structure searches see above with this type of query to find related compounds To use the current molecule for a query 1 Using the Record commands go to the record containing the structure that you want to use as a query 2 Click Search gt Current Mol As Query All boxes of the form are cleared except the structure so that the molecule on display can be used as part of the query You can then continue with the query as if you had drawn the structure from scratch Finding the current molecule The Find Current Molecule command located in the Search menu and on the Search toolbar is similar to the Current Mol as Query com mand discussed above As you browse through the databas
217. h data within ChemBioFinder 12 0 by entering it into a database editing it and interfacing with Chem amp Bio Draw and Chem amp Bio 3D You can perform all of these functions on data using the commands in the menus or you can use the buttons in the Record toolbar for most of these functions First Goto Last Undo Omit Record Record Record Changes Record Adda Commi Delete Record Record Record Changes Record Figure 19 1 Database functions on the Record toolbar Selecting a database A ChemBioFinder 12 0 form does not store data directly but is simply the window through which you look at data When creating a form you need to specify the source of the data to display A form displays data from a single table in a database To specify the data source for a form you must open or create a database and then select a table If you want to view data from more than one table you must create a form for each table Typically you create a main form for one main table and a subform for each other table For more information See Relational Data and Subforms on page 399 You can connect a database to the form before creating boxes or any time after If the form is already connected to a database you can change the database or the data source If the form has boxes with fields connected to them then the boxes automatically connect to fields of the same name in the newly opened data base Opening an existing
218. h from interactive to standard Python mode all prompts are removed and the text is shifted left Line by line execu tion is then disabled and you can edit the text freely The output window The output window is a dockable window for displaying output from scripts The window comes up automatically the first time it is needed The text in the window is not editable but can be copied to the Windows Clipboard for pasting into other applications Standard keyboard accelerators such as select all Ctrl A or copy Ctrl C can be used To generate output in the window from a CAL script use the OUTPUT_STR command OUTPUT_STR string or phrase which echoes string or phrase into the win dow followed by a carriage return The string should not be quoted The string goes through the CAL translator and may be modified with regard to spacing or internal quoting To prevent translation and have the string taken verbatim precede it with a backslash character OUTPUT_STR use this as written Output from a Python script uses the same mechanism To copy text or clear the output window Right click anywhere in the window and choose the desired command from the context menu Programming in Python A description of the Python language is beyond the scope of this manual However to learn more about Python you will find numer ous books and Internet resources on Python as well as the Python Help file This section cov ers programming to
219. have developed If your database was developed in Microsoft Access you can open it in ChemBi oFinder 12 0 The database model A database is a collection of information In ChemBioFinder 12 0 the information is orga nized into increasing levels of complexity At the simplest level is the data item itself for example a molecular weight value Structure Formula MolWeight C21H300966246 Hyd C1SH3002 290 44 Andr Figure 16 6 A data item in the database At the next level is a field a group of data items defining one type of data Fields are gen erally set up once and rarely modified Structure Formula Hol eight C21H3005 62 46 C1SH300P 290 44 C21H3002 314 462 CI BH17NZ gt g 326 Figure 16 7 A data field in a database At the next level is the record a set of data items one for each field defining a single entry MOL_ID Structure Formula Hoy 157 C21H3005 362 4t C1SH3002 290 4 Figure 16 8 A record in a database A collection of records is a table A table is defined by a set of fields and a set of records which grows as entries are added In spreadsheet terminology e A data item is found in a cell e A field corresponds to a column e A record corresponds to a row e A table corresponds to a worksheet A database is a storehouse for tables possibly one possibly more than one A database con taining only one table is known as a simple or flat or flat file
220. he ChemBioFinder 12 0 Automation Language CAL 2 Click the Button tool on the Form toolbar 3 On the form drag to draw a button The Enter the Label dialog box appears ChemBioFinder amp BioViz 317 User Guide 4 Enter a label The text can be descriptive Click to browse and does not have to correspond to the name of the script 5 Click OK For more information about using a button to run a script See Using scripts on page 467 Adding a subform The Subform tool is used to create a subform box to display data from a related data table See Relational Data and Subforms on page 399 for more information Adding a profile The Profile box tool creates a profile box on a form Compound profiles are a new feature in ChemBioFinder 12 0 See Compound Pro files on page 405 form more information Adding a control The Control box tool is used to embed an ActiveX control in a form You can use this to display a calendar spreadsheet chart spec trum picture web link and so forth See Embedding ActiveX controls on page 458 for more information Creating and editing tabs If you have a large number of fields in a data base you can access information more easily and make the form less cluttered by using tabs to divide a long form into smaller parts con tained on separate tabs To create tabs on a form Right click an empty part of a form and select Add Tab context Two tabs appea
221. he New Folder con text menu command 3 Type in a new name for the folder To add an item to a folder 1 Point to a folder 2 Right click and click the New Item context menu command A File dialog box opens 456 Customizing ChemBioFinder 12 0 Chapter 29 3 Browse to the file you want to add select it and click the Open button The item is added to the folder To rearrange items or folders in the tree Drag the item to a new location To resort a folder or subfolder alphabetically Right click on the folder and click the Sort Folder context menu command Toolbars ChemBioFinder 12 0 lets you format your tool bars You can Customize the toolbars by drag ging buttons on or off To open the Customize dialog box Click the View gt Toolbars gt Customize menu command The Customize dialog box appears Customize Commands Toolbars Keyboard Menu Options Categories Commands O New oe Open Close Save Save As Add to Favorites Description Figure 29 10Customizing toolbars To add an option to a toolbar that is already in the ChemBioFinder 12 0 window 1 Click the Commands tab in the Customize dialog box 2 Locate the command and drag an option from the Commands window to a toolbar in the ChemBioFinder 12 0 window The option appears where you drop it on a toolbar You can delete a button by dragging it off the toolbar To return a toolbar to the default set
222. he Preferences dialog The default is 33023 purplish DISPLAY SHOW_AAMAP Whether or not to highlight Oor 1 matching mapped atoms in a reaction in color This param eter can be set manually in the Display tab of the Prefer ences dialog The default is 0 do not high light DISPLAY SHOW_H_CHARGED_AT Whether or not to display 0 or OMS implicit hydrogens on all atoms bearing a charge or radical The default is 1 display DISPLAY SHOW_H_ON_HET Whether or not to display 0 or implicit hydrogens on all heteroatoms This parameter can be set manually in the Display tab of the Prefer ences dialog The default is 1 display 520 CAL Commands Appendix D Section Preference Description Values DISPLAY SHOW_H_TERM_C Whether or not to display implicit hydrogens on all terminal carbons This parameter can be set manu ally in the Display tab of the Preferences dialog The default is 0 do not display O or 1 DISPLAY SHOW_RXN_CENTER Whether or not to highlight reaction centers This param eter can be set manually in the Display tab of the Prefer ences dialog The default is 0 do not high light 0 or 1 OPTIONS OPTIONS CFW_METAFILES DDE_TIMEOUT Whether to generate pictures using ChemBioFinder or using ChemDraw when copying a structure to the clipboard The default is 0 use Chem Draw to generate 0 or 1 0 60 Number o
223. he compound you want to use as your base 2 Right click in the Profile data box then click the Compound Pro file gt Search Sort gt Sort relative to current context menu command ChemBioFinder 12 0 sorts the database 410 Compound Profiles Chapter 24 3 For easiest comparison switch to Table View Profile score ea eS a EEF E Figure 24 4 Profiles in the table view The dist value in the profile displayed in red at the bottom of the chart changes when you sort Before sorting it matches the score value After sorting it displays the deviation of that compound from the base If you sort relative to a compound then that compound gets dist 0 since it defines the reference point The dist value for other compounds will increase as they become less similar to the base You can also sort relative to the ideal value In this case the dist value for each compound is the same as its score and the records are ordered on that basis TIP To reset the database right click in the Mol_ID field and click the Sort Col umn gt Ascending context menu command Example Do the following 1 In the CS Demo database create a profile with one field Molweight and a cost pro file such that values below 100 are ideal and above 100 increasingly bad 2 Browse through the compounds Benzene mw 78 falls in the ideal region so it has a cost of zero and a score of zero Buckyball fullerene mw 800 falls way ou
224. he full structure Tanimoto similarity test is commutative It compares the number of descriptors they have in common in the inter section of the query and the target to the num ber of descriptors they have in total in the union of the query or the target The ratio of these two values is known as a Tanimoto coef ficient and is always a value between 0 and 100 QnT OUT Tanimoto Coefficient For the two compounds above the Tanimoto coefficient is 17 30 or about 57 This is not very similar Although ChemBioFinder will allow you to specify any Tanimoto value down to 0 for most cases you will likely be look 498 Similarity Rules Appendix C ing for compounds that have Tanimoto coeffi cients of 90 or higher Substructure similarity Unlike full structure similarity substructure similarity is not commutative you are compar ing a portion of one structure against the entire other structure and so it does matter which you compare to which In considering substructure similarity ChemBioFinder finds what percent age of descriptors in the query are also present in the target This value will always be at least as large as the complete structure Tanimoto coefficient for the same two compounds and usually it will be larger The two compounds above are 17 23 or about 74 similar by substructure similarity For a given coefficient value a sub structure similarity search will always return all of the hits in a full str
225. he hits table The resulting list is ready to browse save export etc NOTE Text searches in Oracle are case sensi tive You will get different hits from the query benz than from Benz 544 CS Oracle Cartridge Appendix E Index Symbols in query 359 parentheses symbol 359 query operators parentheses 359 in query 369 Numerics 1D plot 304 2D plot 306 3D properties 363 3D searching 363 3D structure display 320 A A any special atom type 489 Access attaching tables from 342 manipulating MDB files 469 multi user 336 read only 336 secured 337 Access database opening 335 accessing relational data using subforms 399 ActiveX control 481 ADD indicator 347 ADD indicator description 286 ADD indicator when displayed 289 add new record command 347 adding buttons 317 checkboxes 317 data 347 data box menu 321 fields 343 menu to a data box 321 pictures 316 plain text 316 records 289 297 347 scroll bars 321 structures 347 tables 354 403 adding multiple structures to forms 345 adding structures to non chemical databas es 345 aligning objects 326 aligning and distributing objects 326 alternate groups searching with 363 alternative groups attachment point symbol 365 defining 364 description 363 anchored substring text queries 357 AND operator hit lists 384 AND operator queries 358 359 368 annotations showing 452 ASCII file exporting 395 assigning fields
226. he molecule in Chem Draw and selecting the Clean Up Structure command The arguments are optional HELP displays a list of all valid CAL com mands The valid parameter types are listed for each command as is a brief description GET retrieves a value from the ChemBio Finder ini file Follow the keyword with a vari able name and the section and item number of the value you want to retrieve SOUND plays a wav file you specify 514 CAL Commands Appendix D SYSMETRIC retrieves the specified system metric into a variable The table below shows examples of General Commands Command Action MSG Click display message wait for OK to con click eimie FONT Times change font to red 12 point 12 1 255 0 0 Times bold Gn WAL 4 amp place the value of item num ber 5 in section 4 into the variable V1 SOUND play the sound in the files beep wav beep wav CAL commands MSG syntax Displays a message in a dialog box and waits for the user to dismiss the dialog MSG message The MSG command has the following argu ment Part Description message String displayed as the message in the dialog box CAL commands FONT syntax Changes the current font size style and color used for all subsequent box creation FONT fontname size style r g bj The FONT command has the following argu ments Part Description fontname String containing the name of a font
227. he target to produce a hit If the stereochem istry of the query is unspecified it will only hit targets which do not specify stereochemistry The only variable in an exact match search is whether or not it is tautomerically flexible The Details tab in the Preferences dialog box is unavailable for Exact searches Similarity searches A Similarity search finds targets that look like the query Similarity searches are by their nature fuzzy What looks like means is obviously subject to interpretation and depends on the application In medicinal applications the drug absorption properties are relevant Ina toxicological context the metabolism is of interest For database queries the similarity in functional groups is what is measured A quan titative measure of similarity know as the Tan imoto algorithm after its discoverer is calculated For more information see Appen dix ChemBioFinder C Similarity searches may be either full or sub structure In a substructure similarity search there is no penalty if the target contains extra non similar aspects In a Full Structure similar ity search the results are guaranteed to include all hits you would obtain from a substructure search with the same query Usually they include additional hits For this reason similar ity searches are useful if you have a general idea of the types of compounds you are look ing for but don t have a precise conception of the targ
228. hing implicit hydrogens 492 in queries 492 on metals 453 implicit hydrogens added to structures 351 importing data 389 duplicate reagents from RD or SD files 390 from a specified location 391 hit lists 383 log files 391 partial RD or SD files 390 RDFiles 390 SDFiles 390 security settings 330 structure data and reaction data files 390 structures 390 structures only from RD and SD files 390 text files 393 importing and exporting data 389 396 inequality symbols in query 359 integer fields 344 intermediates in queries 368 Intersect with current list command 384 ISIS Graphic files 389 ISIS Sketch files 389 isotopes 485 L labels editing 315 fixed 315 320 fonts 322 live 320 labels formatting 289 languages other than English sorting 354 last record command 338 layout tool 314 link node 386 linking subforms to main forms 399 live labels 320 LN link node special atom type 386 489 locking plots 426 427 log files 391 logon database 337 M metal special atom type 489 main form description 286 main toolbar description 286 managing queries 380 mapping atoms in reaction queries 367 Markush structures 351 matching stereochemistry 372 mathematical operators in CAL commands 530 MDL file format 488 MDL molfiles 389 MDL rxnfiles 389 memo fields 344 menu bar description 286 menu commands CAL 499 menu adding to data box 321 minus symbol in query 359 models viewing with Chem3D 351 modif
229. hrough your database and to interact with other applica tions such as Chem amp Bio Draw and Chem amp Bio 3D You create forms using the Form toolbar The Form toolbar only appears when you select ChemBioFinder amp BioViz 293 User Guide Layout mode The Layout Mode tool is on the Main toolbar so before you begin look at the View gt Toolbars submenu and make sure there are check marks next to both Main and Form Edit For information about each tool see Creating forms manually on page 313 Creating data boxes Data and structures from a database are dis played in boxes To create a data box 1 On the Main toolbar click the New Form Tool A new blank form appears 2 If the Form toolbar is not visible click the Layout mode tool on the main toolbar 3 In the Form Tool Click the Data Box tool 4 In the form window click drag diagonally to create a box 5 Draw two more boxes in the same way You will edit them in later steps A frame a framed box and a text box are dif ferent types of boxes and require a label To draw a Framed Box 1 Click the Framed Box tool and drag diago nally to create a framed box A box labeled Data is created 2 Right click on Data and select Label The Box Text or Label dialog box appears In the Box Text or Label dialog box type Frame Box and click OK The label appears above the Framed Box TIP You can change the font of the label from the Box tab o
230. ht Descriptive statistical analysis dean X 161 52 Variance X 95 98 Mean Y 533 46 Variance Y 137 16 Version I1 plot R208 Sees BP A K 800 Molecular Weight Figure 26 8 Displaying Statistical Analysis Results You may choose from linear quadratic or cubic curve fitting A confidence interval of one to three standard deviations may also be displayed Both descriptive statistics and the curve fit update dynamically when the record set changes or filters are applied NOTE Curve fitting gives incorrect results if one of the axes is logarithmic For example you do a linear fit on the original data and then transform that fit to the log plot thereby creat ing a curve Once you have created a plot you might want to clean up the display There are two ways to do this sorting the data on a field and using filters Sorting The standard ChemBioFinder 12 0 sort feature is the first step in cleaning up a graph You may sort into ascending or descending order There are two ways to sort a dataset on a given field e Right click in the field box and click the Sort context menu command ChemBioFinder amp BioViz 429 User Guide e Display the Data table view and double click on the table header of the field you want to sort Filtering BioViz filters limit the display of a variable by trimming either end of the range that is you can eliminate high points
231. i fied line in the current script GOTO label The GOTO command has the following argu ment ChemBioFinder amp BioViz 537 User Guide Part Description label String indicating the destina tion line Remarks The label must be correctly specified with a CAL This command is useful only in a script file and has no effect when entered on the Com mand Line GOTO example This example allows the user to batch enter several new compounds and input one field for each It starts with a MSG command to tell the user what to do Then it has a line starting with a colon that serves as a label to start the loop The INPUT command gets the name of the new entry from the user The IF command tests to see if the user entered a blank string and EXITs the script if so After the Menu Command Record Add creates a new record the PUTDATA command enters the user s string into the molname field Closing the loop the GOTO command jumps execution back to the start label msg Enter new compound names Enter a blank name when complete start input 1 if Svl exit record add putdata molname v1 goto start CAL commands IF syntax Conditionally executes a command depending on the value of an expression 538 CAL Commands Appendix D IF variable operator value command or IF variable operator value command ELSE command ENDIF The GETDATA command has the following arguments
232. ies Chapter 21 Click the Alternative Group query tool Drag with the tool in an open part of the page to create an area large enough to draw the alternative groups Type a title in the Alternative Group Title box The title must match the atom label in the parent structure but we ll use R in this example 1 Title box Figure 21 9 Adding a title to an alternative group 8 Draw the substructure fragments in the Alternative Group box Use the single bond tool to define a fragment and the text tool atom HotKeys or Nicknames to create atom labels for each variable Figure 21 10 Adding the alternative groups 9 Add the Attachment Points a Click the diamond shaped Attachment Point tool on the Chemical Symbols pal ette b Click the open atom position on each substructure fragment TIP Alternatively the HotKey period can be used to add attachment points o Cl CH OH Ph Figure 21 11 Completed alternative group query NOTE In the above procedure the parent structure was drawn then the R Group table was added In fact the order doesn t matter You may create the R Group table first then draw the parent structure In either case as soon as a generic atom label in the structure matches the group title in the R Group table a hollow attachment point symbol appears next to the label in the parent structure 10 Type Ctrl W to return to ChemBioFinder 12 0 The
233. igure 21 12 Reaction center example By default ChemBioFinder 12 0 considers reaction centers whenever you search for reac tions ChemBioFinder 12 0 assumes that any 366 Queries Chapter 21 atoms and bonds that change in the query must be part of the reaction center of the target For example F Cl se does not hit a ao S N E FA Eidi Cl F Doai O Figure 21 13 Query does not hit because it does not contain the reaction center when the Reaction query must hit reaction cen ter preference is selected Even though there is a C F bond in the target reactant and a C CI bond in the target product these bonds do not participate in the reaction which really affects another part of the compound If you deselect the Reaction query must hit reaction center preference this query hits the target above When creating reaction queries it is important to consider what sort of information you are really looking for Suppose you want to con vert n decanal to n decanol A N Z ANZ N i a SAS MA So A IN A A AN Pa ONS NN SA A v OH Figure 21 14 Reduction of n decanal Are you really interested only in these two compounds You might be interested in any reaction that converts a straight chain aldehyde to the alcohol H H Pr OH H H Figure 21 15 Generic aldehyde reduction query Since the corresponding n octanal n octa nol reaction would probably occur under very similar c
234. ile does not exist it will be created otherwise it will be overwritten For File Save if the path is omitted from the file name the file will be saved in the current directory Example 1 LOOP Example This example uses the LOOP command and the Menu Command Record Next to display all of the records in the current list The PAUSE command keeps each record on screen long enough for people to see it loop rec next pause 2 endloop Example 2 Different Form Example This example shows how you can use a script to open a second form with some of the same fields as the original form but for example a different layout This same sort of procedure can be used to display related records if you do not want to use an explicit subform The APPEND SETVAL and GETDATA com mands build a search string based on the con tents of the link_field field on the original form The Menu Command File Open opens the second form or switches to it ifit is already open Finally the Menu Command Search Enter Query enters search mode the PUT DATA command enters the search string gen erated earlier in the script and the Menu Command Search Find executes the search append off setval 1 append on getdata 1 link_field append off file open d chemfndr otherform cfx search enter query putdata link_field v1 search find Example 3 Saving Compounds Example This example uses the LOOP ENDLOOP commands and the Menu Command Rec
235. iles RDFiles directly into a database Since these files contain both structures and data ChemBioFinder 12 0 creates fields in the database to accommodate the incoming data In RDFiles incoming data may be hierarchical and complex When loading RDFiles ChemB ioFinder 12 0 converts the data to a relational form creating new tables as necessary and generating linking data NOTE When importing RD files boxes and subforms are created and positioned automati cally If you have a blank form when you import ChemBioFinder 12 0 creates boxes on the main form If you have a form with boxes when you import new boxes are created on tabbed forms You can import with a form linked to a data base a blank form or no form If you import with no form ChemBioFinder 12 0 creates a new form Selections you make on the Form Style tab of the Data Import dialog box deter mine what the form will look like To import structure and reaction data files 1 Use the File gt Import submenu to choose the type of structure file to import The Open dialog box appears 2 Choose the file to import and click the Open The Data Import dialog box appears Data Import E Import Logging Form Style Advanced Input file EN EE AEA K A P N E E A N Stop scanning Scanning input file Data Fields Input Field Type Width Output Column Typ A MS Structure Structure Structure Strur abe RXN Formula Text 88 Formula Text 00 RxN
236. ill contain the new field 3 click the Create Field The Create Field dialog box appears 4 Replace the default name New_Field select a data type and adjust the field width optional Click OK when you have fin ished To delete an existing field 1 Select a field 2 Click the Delete Field A warning box comes up asking if you really mean to delete a field 3 Click Yes to delete the field CAUTION All data entered in the field will be lost as soon as you click the YES button To add a table 1 Click the Table tab Do one of the follow ing 2 Click the Create Table 3 Enter a name in the Create Table dialog box The new table is created with a default field named ID To remove a table 1 Select a table 2 Click the Delete Table 3 Click YES in the warning box CAUTION All data in all fields in the table will be lost To attach a table from another database 2 Click the Table tab Click the Attach Table The Attach Table dialog box appears Select the type of database MS Access or Oracle ODBC For MS Access browse to the MDB file containing the table Select a table and click OK ChemBioFinder amp BioViz 355 User Guide 356 Working with Data Chapter 20 Queries You can search the database by querying any field or combination of fields You can specify a chemical structure and or text as the query When searching text or numb
237. in the Structure data box in ChemBioFinder 12 0 ChemBioFinder 12 0 style opens Chem amp Bio Draw in its own window for editing Now you are ready to begin adding records to your database 3 Deselect the Layout tool to hide the Form toolbar 4 Double click in the Structure box The Chem amp Bio Draw appears TIP If your default is Chem amp Bio Draw Style you can open Chem amp Bio Draw by right clicking in the structure box and selecting Edit in Chem amp Bio Draw 5 Select the benzene tool and draw benzene on the structure box 6 Click anywhere outside the Structure data box to enter the structure in the data box Benzene appears in the Structure Data box ChemBioFinder 12 0 calculates the molecular formula and assigns an ID number of 1 7 Click the MolName box and type Benzene 8 Click the Boiling Point box and type 80 1 9 Go to Record gt Commit Changes create the new record You entered the first record in your database The size of your database is indicated in the Status Bar Enter two more records ChemBioFinder amp BioViz 297 User Guide 1 Go to Record gt Add New Record 2 Add a record for n Pentane with bp 36 1 3 Repeat step1 and then add a record for Cyclohexane shown below with a bp 80 7 NOTE After you have two or more records in your database you can commit changes by moving to a different record using the Record tools 4 Click File gt Save
238. in which the command resides menuitem Stringstring definition containing the name of the specific command within the menu param Stringstring_definition containing additional infor mation required by the command Settings The settings for param vary depending on the specific menu command Most menu com mands use no param and ignore it if present 500 CAL Commands Appendix D The following commands accept a value for param and suppress the appropriate dialog if it is present Command Param File Open Name of the file to open File Save Name of the file to save Record Go to Index of the destination record within the current list current_list_definition Search Substruc ON or OFF corresponding to ture the checked unchecked state of the menu Search Simi ON or OFF corresponding to larity the checked unchecked state of the menu Search Match ON or OFF corresponding to Stereo the checked unchecked state of the menu Remarks Menu commands need not be spelled out in full you can enter just enough letters to iden tify the menu option For example to execute the Record next command you can enter rec n For File Open if the file to be launched is in ChemBioFinder s standard search path only the actual file name CS_DATA is required Otherwise the complete file path c some long path CS_DATA CFX is neces sary For File Save if the specified f
239. ing up room on the form The Queries Tree in the Explorer Window gives you an easy way to track multiple hitlists To create a new plot view an existing plot or delete a plot use the BioViz Plots submenu of the View menu Plots are saved with the form and will come back when it is opened though they may be hidden Changes in version 11 User customizable styles Point shapes You can select one of six shapes for data points square circle triangle diamond cross or star Selected or moused over points retain the same display as in earlier versions the selected point is displayed as a double hollow red circle and points being moused over pointed at are displayed as red solid with a black circle Point shape selection is from the Display tab of the BioViz Plot Properties dialog box Axes You can set both the content and the font used for each axis The default X and Y labels are the names of the fields plotted but you can now enter any text in any font to override the default You may also choose whether or not to display the X and or Y grids by using the check box next to each label TIP Labels are sticky that is the labels used for the previous plot are the defaults for the next plot created If you entered axis labels for Plot I and want to use default labels for Plot 2 you must go to the Display tab to delete the label entries when you create Plot 2 Legend You can add a legend or comments to b
240. inting 397 products in queries 368 searching for 366 profile box description 286 profiles see compound profiles program execution commands CAL 510 Python 462 Python interactive mode 464 Python script creation 463 Q Q heteroatom special atom type 489 QRY indicator 289 QRY indicator description 286 queries anchored substring 357 atom lists 385 490 atom not lists 490 atom properties 483 atom properties in 489 atom types 385 483 bond properties 493 bond types 385 483 booleans 358 charges 485 context menu 381 creating from BioViz plot 309 dates 359 entering 289 369 373 exact structure 362 finding current structure 375 formulas in 358 free sites 491 full structure hydrogens in 484 ID 360 identity 361 implicit AND between fields 358 368 implicit hydrogens 492 ChemBioFinder amp BioViz 555 User Guide inequalities 359 intermediates 368 isotopes 485 multiple fields 368 multiple fragments 362 multiple substructures 387 no highlighting 375 numbers in 358 overlapping fragments 371 plotting with BioViz 309 precision 358 products 368 progress display 368 374 radicals 485 ranges 358 359 reactants 368 reactions 366 red highlighting 368 374 refining 374 similarity 361 similarity rules 497 special atom types in 489 special bond types 493 SQL 369 stereochemistry 363 486 stopping 374 structural similarity 361 structures 360 subforms 402 submitting 373 substituents 484 490 tuning 372
241. is already running click File gt New to open the dialog box or access CS_Demo directly from the Favorites tab of the Explorer Window 2 Navigate to the C Documents and Set tings All Users Application Data CambridgeSoft ChemOffice2009 Che mBioFinder Samples 3 In the Samples directory select CS_demo cfx and click the Open button The CS_Demo database opens in ChemBioFinder 12 0 Before you begin searching open the Explorer window if it is not already open 4 Go to View gt Explorer Window 5 Click the Queries tab TIP The default set in the Preferences dialog box is to save all queries listed in the Queries tree If you don t want to save a particular query delete it before closing the form Formula searching To find compounds in the CS_demo database with six carbons and one or two nitrogen atoms 1 Click Search gt Enter Query The form is cleared so that you can enter a new query 2 Click in the Formula box and type C6N1 2 3 Press the Enter key The Status Bar indicates that 12 hits were retrieved from the 285 records in the database The Queries tree in the Explorer window dis plays one query as a child of the full list Queries are saved with the form and can be reviewed at any time For more information see Managing queries on page 380 There are three methods for browsing the search results In the Form View Use the Record menu commands or toolbar to go through the records
242. is omitted it is assumed to be 1 SETVAL puts the specified text into a variable READVAL reads the contents of a text file into a variable WRITEVAL copies the contents of a variable to a file INPUT displays a text input dialog accepts data from the user and stores it in a variable An optional prompt string is displayed in the box when it appears PASSWORD is the same as INPUT but dis plays all characters as asterisks GETDATA retrieves the contents of a form box as long as it is not a structure into a variable see above for how to identify a box PUT DATA copies specified text into a form box Form names are case sensitive Be sure to use the same case as the form box name into which you want to store data TO_CANON retrieves the contents of the cur rent structure as a canonical string or puts the canonical string on the clipboard FROM_CANON generates a structure from the canonical string TO_SMILES retrieves the contents of the cur rent structure as a smiles string FROM_SMILES generates a structure from a smiles string 530 CAL Commands Appendix D APPEND determines whether data in a storage location is kept if other data is being moved there This setting is also consulted when you do a File Export to SD or delimited text file APPEND ON causes any subsequent data movements to append new data to old APPEND OFF causes old data to be overwrit ten This applies to all variable commands except PUTDATA The defa
243. ists in 416 indexing 419 loading 418 opening a database 414 searching in 415 setting preferences 417 setup 413 updating and adding data 417 using CAL with 420 Oracle Cartridge configuration via CF_SETTINGS table 542 fast move caching scheme 542 pre setup procedures 541 ordering objects 325 other applications attaching tables from 342 other applications communicating with us ing DDE 467 other applications communicating with us ing OLE Automation 468 other applications communicating with us ing scripts 467 Output window 464 output window description 286 overlay 309 overlay with scatter plots 432 overriding security 331 P Paradox 342 password for secured forms 337 periodic table 457 484 picture box description 286 picture boxes creating 316 picture fields 344 picture tool 316 pictures 316 framing 452 of structures 351 preferences 452 saving 317 saving ChemDraw drawings as 351 searching 351 updating 317 plain text tool 316 plot properties point limit 305 plots histogram 306 single variable 304 two variable 306 plotting options 304 portal database 346 precision in numerical queries 358 preferences color 452 date display 359 display 451 general 453 grid spacing 452 picture display 452 recent file list size 454 registration 453 search details 370 search type 369 setting 451 stereochemistry 372 structure display 451 tuning 372 preferences in ChemFinder Office 481 previous record command 338 pr
244. itor 6 Click OK to return to the form The script will automatically be executed at the specified event 7 Click OK in the Box Properties dialog box 8 Save the form if you wish to keep the changes Python A Python interpreter is embedded in ChemBio Finder 12 0 the language components reside outside ChemBioFinder 12 0 as well as avail able from within it and appear to be built in In the same way you can develop complex mac ros inside Microsoft Word or Excel using Visual Basic you can develop scripts inside ChemBioFinder 12 0 using Python The Output window facilitates Python in ChemBioFinder 12 0 The script editor is used with either CAL or Python It s default config uration is Python interactive About Python Python is a full featured cross platform pro gramming language used to develop applica tions controls DLLs command line utilities and so forth The language is Open Source maintained and supported by a large commu nity of developers Python is available in ChemBioFinder 12 0 in the same ways as CAL In both cases a script can be connected to and activated from a but ton form trigger event or hyperlink in a subform table 462 Customizing ChemBioFinder 12 0 Chapter 29 e be developed and executed in command mode one line at a time e provide direct access to data in boxes on the ChemBioFinder form be saved to an external file or stored inter nally in the form
245. k box appears in the form 4 Right click in the box and click Properties 5 In the Box Properties dialog box select the picture field you want to link to the box and click OK The picture field item appears in the box To read in a picture file or to replace a picture in a Picture Box 1 Right click a picture and click Read File The Open dialog box appears 2 In the Open dialog box select the file you want to display in the Picture Data Box then click the Open The new picture is displayed in the Picture Box NOTE If the Picture box is linked to a Picture field you must click the Commit changes tool to save the picture in the database To save a file from a Picture Data Box 1 Right click on the Picture Box and select Save File 2 In the Save As dialog box type a file name then click the Save The picture is saved Adding a check box The check box tool allows you to add check boxes to your form A check box can be assigned to either a Boolean or an Integer field To add a check box 1 Click the check box tool 2 On the form drag an area large enough for the text next to the check box The Enter the label dialog box appears 3 Type in the text and click OK 4 Right click and select a Boolean or Integer field from the field list to assign to the check box Adding a button Buttons on the form are used to activate scripts To place a button on a form 1 Write a script using t
246. k structures in database dialog box The following properties can be checked e Ambiguous stereochemistry Flags struc tures with ambiguously drawn tetrahedral or double bond stereochemistry Not cor rectable e Valence charge Flags structures contain ing an atom with an impossible valence or charge Sometimes correctable e Net charge present Flags structures con taining a net charge This option is not checked by default because it is not nor mally useful Not correctable e Unrecognized atoms Flags structures containing an atom that was not inter preted by ChemBioFinder 12 0 Such atoms typically have atom type R with a greyed text label containing question marks Not correctable e Mass imbalance Flags reactions in which the molecular formulae of reactants is different from products Not correct able e Doubly drawn atoms Flags structures in NOTE The 3D not scaled in Angstroms feature which two atoms are very close together and at least one of which lacks a label Also to qualify as a doubly drawn pair the combined valence of explicit bonds must not exceed the capacity of either atom You get this sort of structure when attempting to draw a bond from an exist ing atom but miss and accidentally create a new atom Chem amp Bio Draw flags these cases with a wavy red box 3D not scaled in Angstroms Flags struc tures with Z coordinates or 3D not scaled in Angstroms Such structures will
247. ken as carbon oxygen instead of cobalt The exception is if two characters represent a valid two letter symbol and also a valid one letter symbol followed by an invalid one then the two letter symbol is favored Thus cI is not taken as carbon followed by the invalid symbol L but instead is taken as chlorine Examples There is an easy way to experiment with for mula interpretation use the Periodic Table Type a formula into the text box at the bottom then click anywhere outside that box ChemBi oFinder interprets the formula and redisplays it with correct capitalization ChemBioFinder interprets some ambiguous formulas as follows Formula ChemBioFinder Interpretation cooh COOH ChemBioFinder amp BioViz 495 User Guide Formula ChemBioFinder Interpretation Cooh CoOH cnosi CNOSI cNoSi CNoSi bru BrU bru BRu 496 Formula Input Rules Appendix B Similarity Rules A common situation is that you are not looking for a specific compound but any compound that is close enough will do ChemBioFinder uses the Tanimoto equation to determine if compounds are similar You can specify how similar in the Searching tab of the Preferences dialog Exact searching relies on the notion of an atom and bond table a specific set of atoms joined to each other in a certain order by a given set of bonds If some atoms or bonds are missing added or different the query stru
248. ks the main form and subform Clicking in either form activates it To test this 1 Click anywhere outside the subform box and browse your database using the Record tools As each molecule record of the MolTable is displayed the subform shows the first matching ID from the Synonyms table 2 Click inside the subform box Now when you browse you are browsing only the entries in the subform To display all of the synonyms 1 Toggle out of Layout mode Double click in the subform box to switch to Table view Save and close the file 1 Click File gt Save 2 Click File gt Close Congratulations You have completed the ChemBioFinder 12 0 Tutorials Forms You use forms to interact with information in a database A ChemBioFinder 12 0 form is com posed of data boxes for viewing or modifying data items such as structures numbers text or pictures A form can also contain subforms for relational access to different data tables and different databases You can create a form in the following ways e Automatically using the Form Generator dialog box e Manually using the Form tools e With the Database Tree The example below shows a form displaying a single record of information from a database 2 4l Figure 18 1 Form showing a single record Creating a form consists of creating a layout see Creating forms manually on page 313 and setting box properties see Setting box properti
249. le 30 If your script Then does not appear in the Scripts menu type call and the name of your script in the Enter Script Command dialog box then click Execute 4 Press any key except Escape to execute the command and go to the next command As each step is encountered it is displayed in the status line 5 Press the Esc key to stop debugging the script 6 Type step off in the Enter Script Command dialog box to exit the debugging mode Trigger scripts Trigger scripts run in response to certain pre defined events A trigger script can for exam ple automatically load a box with data calculated from the contents of another box whenever you move to a new record You access a trigger script from the Run script on listbox in the Form tab of the Properties dia log box The listbox shows the available trig ger events and allows you to create edit enable or disable scripts for each event To run a script on an event 1 Right click in the form and click the Prop erties context menu command 2 Click the Form tab 3 Click the check box of the desired event in the Run script on list box If an event is not checked no script will run on that event even if one is available ChemBioFinder amp BioViz 461 User Guide 4 Click the event name to highlight the row of the listbox Clicking in a check box does not select the row 5 Click the Edit button to write or edit the script in the CAL Ed
250. le field 1 Connect your form to the CS_Demo data base On the form there are four fields Mol_ID Molname MolWeight Structure and Formula ChemBioFinder amp BioViz 445 User Guide In this section clustering is performed on Mol Weight NOTE You can perform clustering on any numeric or structure field 2 Perform search on C6 You will get 42 hits TIP Perform analysis on fairly small set of records otherwise the display becomes cumber some 3 Right click the MolWeight box and then click Cluster by MolWeight It takes few minutes for the operation to per form as it gathers the data perform clustering and data projections then calculates the display co ordinates You will get screen as shown below displaying the results of clustering operation W CS Clustering Figure 28 1 CS Clustering dialog In the above figure the display is divided into two parts On the left is the dendogram a standard graph for displaying the results of the clustering operation Each point along the 446 Clustering in BioViz Chapter 28 baseline leaf represents one of the input records In the clustering figure you get 42 hits and 42 of them are evenly spaced along the x axis A horizontal line above the base represents a node or a merge of the two objects under neath it The position of the node under y axis is prop
251. le to display 3 Click OK The box display is fixed Adding a data box menu You can add a menu containing a list of choices to a data box so you can choose an item from it to appear in the data box To add a menu 1 Right click on a data box and click Proper ties The Box Properties dialog box appears 2 On the Box tab click the With drop down choices check box The Choices tab appears 3 Take the appropriate action Table 20 Menu list options If you want to Then click use a list from a From table and database table as follow the instruc the data box menu tions at the bottom of the dialog box create your own list Fixed list of choices for the data box and follow the menu instructions at the bottom of the dialog box Table 20 Menu list options If you want to Then click use a list from a database table and add your own items a From table A list appears b Click Fixed to the data box list of menu choices and edit the list 4 Click OK to close the dialog box then click in the data box A button appears in the lower right corner of the box when you click in the box 5 Click the button to display the menu 6 Select any item on the menu the text appears in the top left corner of the box and the button disappears Click within the data box to make the button reappear Adding a scroll bars Scroll bars are used to accommodate lengthy data when
252. lick on the data box and connect it to the ID field to be retrieved In this example connect the form box to the Chemist_ID field 3 To connect the box to the ID field right click on the box and choose Properties Box Properties dialog box appears 4 Check the option With choices or auto link Checking this will automatically brings up the Choices tab Box Properties Database Table Field Form Box Choices Fromtable Chemists Name Fixed list of choices Structure E Formula WF MolWeight Murphy EER MOLNAME Rubenstein be CORP_ID S fabe DATE fhe memo 00 Chemist_ID FB Chemists Dill Jones pt Auto link will replace the retrieved data with the matching 00 1D value from the column selected above Choose the field She Name below which is to match on MolT able Mol ID Autotink via ID I Hide menu Cancel In the Choices tab e Ifthe Auto link via box is unchecked the dialog lets you define a set of choices for data input e If the box is checked then you have to define both a set of input choices and an auto link connection TIP To prevent the drop down choice menu from appearing check the Hide menu box This applies only if you have set up auto link 5 Select the From table radio button In the data source tree locate the subtable and click the column of data to be displayed in the box in this case Name under Chem ists
253. lick the field and select Remove 4 Click OK when finished Sorting by subform fields Just as in the main form you select in the sub form the fields you want and the order you want them to be sorted You also indicate which value in each field you want ChemBio Finder to sort by the minimum value the max imum average of the values or the sum To sort the main form using subform fields 1 Click the Record gt Sort menu command 2 In the Sort Multiple window select from the left pane the subform field by which you want to sort the hitlist The subform field is displayed in the format subform name field name To sort the hitlist by more than one field select the fields in order of priority 3 To reverse the order in which values will be sorted right click the field name in the right pane and select Descending in the pop up menu 4 Also in the pop up menu select the value in the field you want ChemBioFinder to sort by max min average or sum The default is Min 5 Click OK when finished Query hitlists The Queries tab in the Explorer window main tains a list of search queries from the current 438 BioSAR Chapter 27 and previous sessions Queries are associated with forms So the query hitlist is saved when you save the form Viewing the query list When you open an existing form the tree updates to show only the queries for that form The Explorer Window must be visible to view the Queries
254. linear spline Cost Profile high plateau IC50 0 56 Figure 24 1 IC50 profile The cost profile is designed by the user to reflect their opinion of what constitutes a good value for a property The user can adjust the cost profile to reflect how unhappy they would be when a compound deviates from the ideal value by changing the range of values at zero and the slope of the line to one For example a user might want a drug candi date to have a good solubility in units of ChemBioFinder amp BioViz 405 User Guide mg ml and good biological activity in units of nm They might be willing to sacrifice some activity to get better solubility so the cost function for solubility would be adjusted to penalize any deviation from some ideal range more severely than the corresponding cost function for activity The default display preference is to have white regions in the bars represent ideal values darker regions increasing deviation from the ideal The normalization function permits properties of different types to be compared A score the total deviation from ideal of all fields is dis played Each property can be assigned a weight to adjust its effect on the overall calculation The score is the same for a given compound regardless of whether or not you ve done a sort or where the compound appears within a hitlist A bad compound has a high score MolVeight LogP cost wt 0 00 0 0
255. llowing e From the Look In tab select files to search e From the File menu select Open or choose a file name from the most recently used list of files For more information about opening files to search through see Searching DSD files on page 476 3 Click New Search Click Edit Structure The ChemDraw plug in tools palette appears Selecting appropriate ChemDraw tools click in the Structure window and draw the structure you want to search for Structure Look In Search Options N ZZ N Figure 30 2 Drawing a query structure For more information about using the ChemDraw plug in see the ChemDraw User s Guide Alternately you can select a structure from ChemDraw or from a ChemFinder database and paste it in the Structure window using the right click menu Chem amp Bio Office 2010 User Guide 473 ChemBioFinder 7 Click Find Now NOTE If the Find Now button is grayed out you have not selected a file or directory to search Click the Look In tab and make a selection To search for other properties or more than one property at a time 1 Click New Search 2 Take the appropriate action ChemFinder Office shows all of the files with the structure that you specify in the Hit List window shown below Each entry in the Hit List is a record or a hit If you want to search for then in the Structure window a specific molecular weight type a
256. low points or both from the display Filters can be set for either or both plotted variables You may also filter the dataset on other variables up to a total of 31 filters per chart l x Right click to choose filtering fields 100 94 1004 62 Boiling_Point 1004 62 788 40 sf gocesescsccceccossccococoscocos assess seessecsccecossccestecassosmecescorecscconsvessecescossocees 27811 501 34 75298 100462 Boiling 278 11 651 51 903 152 Boiling Old filter style Figure 26 9 Filter sliders 430 BioViz Chapter 26 Filters ate set in the filter window If the window is not visible check the box next to Filter Window on the View menu When a filter is set e All plots associated with a given form are affected unless the plot is locked before applying the filter e Points missing a value for a given field are hidden whenever the filter for that field is visible The range is displayed in black below the slider and the set points in red above the slider Filter name is centered rather than on the right Operation of the sliders is unchanged Right click to choose filtering fields 93 04 1004 62 0 00 Boiling _Point 1004 62 22 99 790 41 22 99 MoMeight 906 81 Molname Benzene Partition Coe 2 142 Polar_Surfac 0 Figure 26 10 Filter window stacked with details and structure windows To activate a filter Right click in the Filter window and select a variable from the list When you view
257. ls With Isotopic Labels Query Structures Ready ali of 286 ab 206 Figure 21 25 Find Structure menu These are generic searches made without entering any query information The options are e Empty Structures Locates records con taining no structure It is equivalent to spec ifying a molecular weight of zero in a regular search It is provided because the latter method is a bit obscure e Reactions Locates structures that are reactions The same effect can be achieved by entering a bare arrow as a structure query e With Stereo Centers Finds structures con taining tetrahedral stereochemistry e Missing Stereochemistry Finds structures with atoms capable of tetrahedral or double bond stereochemistry but drawn as unspecified e Charged Finds one or more atoms with a charge e Radical Finds one or more atoms with a radical e With Isotopic Labels Retrieves records containing a structure with an atom that either has a mass number or has an Isotopic Abundance attribute Query Structures Locates structures with any generic variability such as atom types R A M Q X Alkyl Aliphatic EDG EWG bond types single or double etc variable charge element lists C N O ring bond count etc 3D Locates structures that could be tar gets in a 3D search These are structures scaled in Angstroms and having Z coordi nates Both conditions must be met Struc tures that meet o
258. m with multiple subforms into an Excel spreadsheet you must take precautions to get all of the sub forms correctly exported This is because the exporter normally uses only the field names and the BioSAR subforms show the same set of fields from different assay tables On export they will collide and the data will not come over correctly To prevent this ChemBioFinder 12 0 has an option on the Text Options tab of the Data Export dialog box Prefix output fieldnames When this box is checked the output names will match the input names which are prefixed for subform fields Tips for optimizing performance When working with a large data base or multi ple forms you will want to ensure that you can still work efficiently To do so there are a few techniques you can use to improve ChemBio Finder s performance even when you are working with a lot of data Use domain linked forms Using a domain offers a significant speed advantage compared to working with the full database If you choose Retrieve All after per forming some queries you will get only the domain as the full database Since the domain is typically much smaller than the database it was created from the query and restore com mands are executed much faster Another advantage is that the domain is non volatile that is the view remains on the server until you delete it If you routinely work with a particular subset of a large database creating
259. maleic anhydride substructure is consumed or transformed Searching for products If you know the desired end product but not how to get there you can do a products query A products query is similar to a reaction search except that there is nothing to the left of the arrow For example consider the query Figure 21 20 Sample products query If you are doing a substructure search this finds any reactions in which bicyclo 2 2 1 hep tane or a compound containing this substruc ture is produced Searching for intermediates Rarely you may be looking for reactions for which you only know something about an 368 Queries Chapter 21 intermediate An Intermediate Search is very similar to a normal reaction search except that there are arrows on both sides of the target structure For example consider the query y R C C 0 Figure 21 21 Sample intermediates query This finds any reactions containing the Ketene structure shown as an intermediate NOTE ChemBioFinder 12 0 cannot predict products or intermediates of reactions It finds this information only if it is already present in the database Combined searches You can combine structure searching with text searching to find a specific class of com pounds For example you may want to find all compounds in the database whose names end in mycin and whose structures contain a phenyl ring Because you are entering multiple queries in different data boxe
260. mands apply to the contents of the active data box To select an object on a form Click the Selection tool on the Form toolbar then click an object on the form to select it A highlight appears around the object indicating that it is selected To select multiple objects on a form 1 Click the Selection tool on the Form tool bar 2 Do one of the following e Press the Shift key and click on the multi ple objects e Drag the Selection tool around the boxes you want to select To select all the objects in the form Click Edit gt Select All Moving objects Use the Selection tool to move data boxes or other objects to a different place on a form To move objects on a form 1 Click the Selection tool on the Form tool bar 2 Select the object to move 3 Drag the object to a different place NOTE To move a subform you must drag the title bar of the subform not its contents If an object is nearly in the right place you can nudge it to get it exactly aligned To move an object one pixel at a time 1 Select the object you want to move 2 Press an arrow key in the direction you want to move the objects The objects move one pixel in the direction of the arrow key Resizing objects Use the Selection tool to resize a data box or any other object on the form NOTE You cannot resize more than one object at a time or simultaneously resize a box and its frame unless you create a framed box using
261. molecular weight g in the Find Chemical Structures Data Source File Edit View Record Search SendTo Help Fan Z M4 0 BAF Structure Look In Search Options New Search N NH3 A Substructure Full Structure Similarity Identity Formula l C8H12N2 Edit Structure Name In Folder File Size Total Hits Type YINFOCHEM C C Program Files Ca 8 704 250 2 ChemFinder NcI_DEMO C C Program Files Ca 7 168 500 2 ChemFinder NIADEMO CFW C Program Files Ca 10 752 38 1 ChemFinder lt M gt Ready rec 5 list 5 db 788 Figure 30 3 Data source window with hit list 8 Use the forward and back arrows on the Record Search toolbar to navigate through the hits If ChemFinder Office finds no hits a warning message appears To refine your search so that ChemFinder has a greater possibility of finding hits use the Search Options tab Searching by multiple properties You can search for a chemical structure chem ical formula molecular weight or any combi nation of these properties simultaneously 474 ChemFinder Office Chapter 30 Mol Wt text box a molecular weight type arange of within a range molecular weights g with lt or gt in the Mol Wt text box a chemical formula type a chemical formula in the Formula text box more than one crite enter the appropriate rion structure criteria form
262. mplified in version 8 5 ChemBioFinder amp BioViz 399 User Guide Users of previous versions should note the fol lowing changes e There is now a single dialog box which sets properties of both the subform box and its subform You set all of the details in one place in a single operation In the new dialog box the Database Table and Field tabs reflect the data source of the subform not the parent form The database tree control in the dialog box also shows subform data source You can use the Explorer window to display the tree control of the parent data source if they are differ ent As before the Form tab shows properties of the subform while the Subform tab shows properties of the box and the linkage between the subform and its parent e When creating a new subform you get the same dialog box by clicking within the sub form as by clicking on the box header For convenience the dialog box comes up automatically whenever you create a new subform box After you have created a subform the sub form tool is deselected This prevents the frequent mistake of drawing a subform box then trying to draw a data box within it and getting another subform Creating a subform manually To create a subform 1 Start ChemBioFinder 12 0 and open or cre ate a form The form should have at least one data box and be linked to an existing database Click the Subform button on the Form tool bar 400
263. ms ChemNMR ChemProp Htmi ChemDrawtelp chm hemFinder samples Cet Acx2000IndexA cfw Acx2002ZIndexA cfw AcxSC2000IndexA c AcxSC2002IndexA c AGROBASE CFW CS_DEMO CFW DEMO CFW FeFOCTSS CFW y Files of type Sources clw doc xs cdx chm mol ske Figure 30 1 Files and data sources tree NOTE You can set Preferences to keep the file names hidden in the directory tree For more information see Changing preferences on page 481 2 In the Select files of type box use the drop down menu to choose types of files in which to search e You can select all data sources or files with the following extensions e cdx and mol e doc and xls e CFX e sdf 3 Click the box next to the file s or data source s that you want to search For example you want to find a specific ben zene file you saved However you are not sure what part of ChemDraw you saved it in Click the ChemDraw box and all of the ChemDraw files are searched When you have selected your data sources return to the Structure window by clicking the Structure tab Searching by chemical structure You can find chemicals based on their struc ture with ChemFinder Office NOTE Any search method that you use in ChemFinder you can also use in Chem Finder Office To search by chemical structure only 1 Open ChemFinder Office The Find Chemical Structures Data Source window appears 2 Do one of the fo
264. n and the top edge of the active form filename Name of the CAL script file to display in the button Remarks If the CAL script file is in ChemBioFinder s standard search path only the actual file name BROWSE is required Otherwise the com plete file path c some long path BROWSE CFES is neces sary When a new button is created it adopts the current font settings These settings can be controlled with the FONT command By default the name of the CAL script file for example BROWSE is shown on the button This can be changed with the SETTEXT com mand BUTTON example This example uses the BUTTON command to create a button near the bottom of the form and assign to it the REGISTER CFS script in the same directory as the form BUTTON 50 300 200 330 Register CAL commands SUBFM syntax Creates a new subform on the active form SUBFM left top right bottom The SUBFM command has the following argu ments Part Description left Integer value representing the distance in pixels between the left edge of the subform databox and the left edge of the active form top Integer value representing the distance in pixels between the top edge of the subform databox and the top edge of the active form right Integer value representing the distance in pixels between databox and the left edge of the active form the right edge of the subform bottom Integer value representing the
265. n a form containing data and retrieve a small hit list 3 Click the File gt Export gt Other menu com mand The File Export dialog box appears 4 Click the Text Options tab 5 Choose the Other option and specify a delimiter 6 Click the Export button to save the choice and carry out an export ChemBioFinder amp BioViz 393 User Guide 7 Go back to step 1 of the import procedure to begin the import again TIP Once you have specified a delimiter it will be remembered and you will not have to repeat this operation The input file scan also determines the names and types of the data fields in the input file Field names must appear in the first line of the file in the correct order separated by the same delimiter as the data items Field types are determined by examining all the data in each column using the same rules as for SD import if all items in one column are integers then the field type is set to integer and so on Widths of text fields are set to accommodate the largest item in the file Exporting data You can create a new SDFile RDFile ASCII text or MS Word file by exporting records from an existing database Text files can be saved in text txt format or in the Comma Separated Value csv format readable by most spreadsheets When you export a file all records in the current hit list are exported You can include or exclude fields to be exported from a checklist The Data Expor
266. n is deselected The default is 100 DISPLAY MOL_HIGHLIGHT_COLO R The color in which substruc color ture search matches are displayed This parameter can be set manually in the Color tab of the Preferences dialog The default is Red 518 CAL Commands Appendix D Section Preference Description Values DISPLAY NET_OUTSIDE Whether or not to move Oorl bracketed text to the outside where possible in the display of net reaction changes in molecular formulas and molecular weights The default is 1 move to outside DISPLAY NET_RXN_CHANGE Whether or not to display net 0 or 1 reaction changes in brackets in molecular formulas and molecular weights The default is 1 display changes DISPLAY PICTURE_BACKGROUND The background color of color Picture boxes This param eter can be set manually in the Color tab of the Prefer ences dialog The default is White DISPLAY QUERY_BOND_COLOR The color in which bonds color with query properties should be displayed This parameter can be set manually in the Color tab of the Preferences dialog The default is Green ChemBioFinder amp BioViz 519 User Guide Section Preference Description Values DISPLAY RXN_CTR_COLOR The color in which reaction color centers should be high lighted if highlighting is turned on This parameter can be set manually in the Color tab of t
267. n the Password box NOTE Use ofa password is optional 5 To enforce Workgroup Security in an MS Access Workgroup Administrator database ChemBioFinder amp BioViz 327 User Guide you must specify a Workgroup Information File Take the appropriate action NOTE Enforcing workgroup security is optional Table 25 Workgroup naming options If you want to Then enter a work group file name Type the name of the MS Access Workgroup database in the Work group Information File box browse for the Click File and select the workgroup file _ file The following steps refer to the options in the Enable Disable section of the dialog box 1 Click the plus sign next to Database Security to display the options take the appropriate action Table 26 Database security options If you want users then select to be prompted to log on with a username password to open a form Password to open form use a username pass Logon to MS word to log on to the Access database MS Access database MDB files 328 Forms Chapter 18 Table 26 Database security options If you want users to then select be prompted to log on to a database with a username pass word when the form is open Prompt for data base logon use a username pass word to open the molecule database MST files Protect molecule database be able to access the Form S
268. n the Validate Security dialog box type your username and password and then click OK If the form you access includes a secured molecule database the Database Logon dialog box appears ChemFinder Molecule Database Security Enter the Usemame Password and MS Access Cox Workgroup file required to open this database Usemame Cancel Password peoo Workgroup Information File Ea Figure 19 7 ChemBioFinder 12 0 Molecule Data base Security dialog box 2 Type your user name Password and Work group Information File name if applica ble then click OK The form opens ChemBioFinder amp BioViz 337 User Guide Browsing databases You can browse a database using the buttons on the Record toolbar First Goto Last Undo Omit Record Record Record Changes Record Previous Next Adda Commit Delete i Record Record Record Changes Record Figure 19 8 Browse functions on the Record toolbar To Browse e Click First Record to display the first record in the database e Click Previous Record to display the record before the currently shown record e Click Next Record to display the record after the currently shown record e Click Last Record to display the last record in the database NOTE The current record number is displayed in the Status Bar Go directly to a specific record as follows 1 Click Record gt Go To Record The Record Number dialog box appears 2 Type the number of
269. nally by the name of a table in angle brackets In ChemBioFinder 12 0 it can now take just the table name and causes the form to become attached to a dif ferent table in the current database as if you had brought up Properties and clicked a different table name Example OPENDB lt CHEM_STRUCTS gt causes the current form to be connected to the table CHEM_STRUCTS e STATMSG command displays a message on the status bar Format STATMSG lt mes sage gt Example STATMSG Search is now in progress e SEARCH SAVE LIST RESTORE LIST work with Oracle Normally you can follow either of these commands with the name of a file in ChemBioFinder Oracle you can instead provide a list name ChemBioFinder amp BioViz 421 User Guide 422 ChemBioFinder Oracle Chapter 25 ULTRA BioViz With BioViz you can identify trends and cor relations in your data and within subsets of your data without the extra step of exporting to another application You can have as many plot windows as you like each showing a dif ferent visualization of data from the current form BioViz is designed to be used with the Struc ture Window and the Queries Tree While not necessary to creating visualizations they offer considerable convenience when working with plots Before working with BioViz go to the View menu and activate the Structure and Explorer windows The Structure window gives you a way to display structures without tak
270. nd more records later 6 After importing you should create a pri mary key and index see Indexing on page 419 To append to an existing table follow the pro cedure above except e Step 1 You can start with an existing form instead of a blank one e Step 2 You should select the target table When you do there will be no need to edit the table name in Step 5 Indexing As every Oracle administrator knows a key to good performance is to index certain columns so that searches over them become fast look ups If you intend to create load or manage tables then you are an administrator and need to know something about indexing ChemBio Finder Oracle provides a few tools to assist you There are two types of index of interest to ChemBioFinder Oracle e Structure indexes Any column containing structures should have an index created by the CS Oracle Cartridge If there is no index searching is still possible but very slow e Primary keys A table containing a column of structures should also have a column of unique record identifiers for use in various list handling operations Preferably this column is of type INTEGER and is desig nated as the primary key of the table ChemBioFinder 12 0 provides information about these indexes and allows you to create or recreate them if necessary To create a structure index 1 Right click on the structure box of an Ora cle connected form and choose Proper ties
271. nder amp BioViz 319 User Guide graphics such as rectangles and orbitals are not transferred nor does ChemBioFinder 12 0 consider their chemical implications To choose how to view structures 1 Right click in a structure data box and choose Properties The Box Properties dialog box appears 2 On the Box tab in the Box Style section select the structure format to view from the menu Table 19 Structure box format options If you want to Then choose edit in the Structure Structure Chem amp Bio box using the Chem Draw style amp Bio Draw Control edit in Chem amp Bio Structure ChemBio Draw Finder style Structure Chem amp Bio 3D style insert 3D images Viewing structures in Chem amp Bio 3D format Unlike the Chem amp Bio Draw and styles Chem amp Bio 3D style is view only You cannot edit the structures in Chem amp Bio 3D style To activate the Chem amp Bio 3D Control Double click in the 3D Structure Box Click outside the box to deactivate the control To rotate the structure Drag in any direction in the box Unlike in Chem amp Bio 3D you do not have pure locked X or Y axis rotation but you can approximate them by dragging horizontally or vertically 320 Forms Chapter 18 The Chem amp Bio 3D Control displays different context menus depending on whether you Right click while pointing to the model or while pointing elsewhere in the Struc
272. ne a search See the Chem amp Bio Draw User s Manual for information on how to add 3D properties to structures NOTE The 3D Properties feature is available in Both Pro and Ultra 12 0 but not in Standard version Searching with R groups ChemBioFinder 12 0 supports queries using R tables including multiple R tables Queries containing large numbers of R groups or large numbers of R values are not advisable how ever because ChemBioFinder 12 0 pre pro cessing expands the query substituting all combinations from the R group table s Alternative groups Instead of submitting multiple queries on structures that share a common substructure you can submit a single query with the parent structure and variable functional groups or substructures The parent structure is drawn ChemBioFinder amp BioViz 363 User Guide with attachment point s that refer to a list of alternative groups that you define Figure 21 8 Alternative groups Defining an alternative group To define an alternative group 1 Click the query icon to begin the search 2 Right click in the structure window and click the Edit in Chem amp Bio Draw TIP You want to open Chem amp Bio Draw because you will need more space than the structure window provides Chem amp Bio Draw opens to a new page 3 Draw the parent compound 4 Label the atom where the alternate groups will attach with a generic label such as R 364 Quer
273. ng the distance in pixels between the bottom edge of the box and the top edge of the active form filename Name of the Windows meta file to display in the picture box Remarks If the Windows metafile is in ChemBio Finder s standard search path only the actual file name and extension BUTTRFLY WMF is ChemBioFinder amp BioViz 505 User Guide required Otherwise the complete file path c some long path BUTTERFLY WMP is necessary PICT example This example uses the PICT command to cre ate a large picture field toward the right of the form and display in it the BUTTRFLY WMF picture in the ChemBioFinder System direc tory PICT 300 100 500 300 buttrfly wmf CAL commands BUTTON syntax Creates a new button on the active form BUTTON left top right bottom filename The BUTTON command has the following arguments Part Description left Integer value representing the distance in pixels between the left edge of the button and the left edge of the active form top Integer value representing the distance in pixels between the top edge of the button and the top edge of the active form right Integer value representing the distance in pixels between the right edge of the button and the left edge of the active form 506 CAL Commands Appendix D Part Description bottom Integer value representing the distance in pixels between the bottom edge of the butto
274. nge hasn t changed just its location Plotting queries When you perform queries see Queries on page 357 and have one or more hitlists 432 BioViz Chapter 26 attached to your form the BioViz plot displays the results of the current hitlist You can dis play overlays by selecting hitlists rather than making them current For example the following figure shows results of a screening test relative to a control SDs Above Control 0 500 1000 1500 2000 2500 Record i Figure 26 14 Screening test results To remove outliers more than 2 5SD from the control e Search for lt 2 5 and gt 2 5 in the SDs Above Control field e The plot displays the results for the hitlist NOTE By default the hits are shown on the same scale as the original list which may cause them to cluster in one sector of the window If this happens right click the plot and choose Rescale to All Points or Auto scale Rescale to All Points operates on the current datapoints only Auto scale sets a switch so that all subsequent searches and list operations will automatically rescale the plot To display the results of an overlay on the full list 1 Open the Queries pane of the Explorer Win dow 2 Double click on the Full List to make it the current list 3 Click the query to select it for display over the current list CES S i be Selecting a list by single clicking in the queries tree or choosin
275. nly one of these conditions can be found by using the Check structures search NOTE The 3D feature is available in both Pro and Ultra 12 0 but not in Standard version Classes Provides the following search options selectable from a submenu e Hydrocarbons Finds structures with Car bon and Hydrogen only If there are more than one fragments they must all be hydrocarbons e Aliphatics Finds structures with a carbon carbon bond or methane and no rings e Alicyclics Finds structures having a car bocyclic ring that is not aromatic or antiar omatic e Aromatics 4n 2 Finds structures con taining one or rings with a 4n 2 electron system Includes pyrrole and charged rings e Antiaromatics 4n Finds structures con taining one or more rings with a 4n elec tron system e Aromatics Cyclically alternating Finds structures containing one or more rings that have 4n 2 bonds distributed as alter nating single and double bonds This is the criterion for delocalized used since ChemFinder 10 e Natural products Finds structures con taining a carbon and at least nitrogen or oxygen e Alkaloids Finds structures with MW gt 200 and containing carbon and basic nitrogen e Heterocycles Finds structures having a ring containing a heteroatom e Metals Finds structures containing a metal bond e Organometallics Finds structures contain ing a metal carbon bond e Organics Finds structures having a
276. not of much use during the execution of a CAL script but can be a quick syntax aid when entered into the ChemBio Finder Command Line File commands READMOL filename READPICT boxname filename WRITEMOL filename WRITEPICT boxname filename WRITETEXT filename READMOL and WRITEMOL operate on the current molecule These commands will work only if there is at least one structure related box structure formula or molweight on the form and you are positioned to a valid entry in the database READMOL reads a specified structure file and replaces the current molecule in the form WRITEMOL saves the current molecule to a specified structure file if the file ChemBioFinder amp BioViz 527 User Guide doesn t exist it is created otherwise it is over written For both READMOL and WRITE MOL the format of the file is determined by its extension for example benzene cdx is a ChemDraw file READPICT and WRITEPICT transfer pictures into or out of picture boxes where boxname is the name of the picture box on the form and filename is a pathname to a graphics file with extension bmp jpg gif png emf or wmf WRITETEXT exports the current list as delim ited text with whatever delimiter is specified in the Preferences dialog The table below shows examples of File Com mands Command Action READMOL benz mol read specified file to become current molecule write current molec
277. nts Up to 2 Finds any of PDS CH Does not find any of 9 p Substituents free sites The Substituents Free Sites property specifies the maximum number of additional substitu ents that may be present on an atom This prop erty is only meaningful in a substructure search TIP Specifying Free Sites 0 is a quick way to indicate that you want no further substitution at a site Target structures will match the query structure as drawn with no additional ligands With a substructure search the query with free sites property 2 1 1 This atom is marked with the atom property Substituents Free Sites 2 Finds any of anaes ChemBioFinder amp BioViz 491 User Guide Does not find any of 8 Implicit hydrogens This atom property may have either of two val ues Allowed default or Not Allowed If implicit hydrogens are Not Allowed the atom must be fully substituted in the target This property is only meaningful in a substruc ture search NOTE This atom property does not affect the display of implicit hydrogens only their pres ence in a search For more information about displaying implicit hydrogens see Setting preferences on page 451 Unsaturation Sometimes it is useful to specify that an atom must or must not be attached to unsaturated aromatic double or triple bonds ChemBio Finder allows searches for atoms whose unsat uration Must Be Absent all bon
278. nu options Statistical analysis You can perform statistical analysis on BioViz plots When you specify two variables a third 428 BioViz Chapter 26 tab appears on the BioViz Properties dialog box BioViz Plot Properties General Display Analysis Dimension Variables One variable Logscale Base Two variables x MolWeight E Style Line chart Y Boiling_Point 2 Scatter plot im c Bins Plot name MW vs BP A nO Z Wed T Locked Point limit 500 Figure 26 6 The Analysis tab appears when two variables are specified For descriptive statistics minimum maximum mean median and standard deviation can be calculated for both X and Y variables R Squared is available only when curve fitting is chosen BioViz Plot Properties General Display Analysis Descriptive Statistics Curve Fitting IV Show Curve Fitting Linear Minimum X C Quadratic C Cubic Standard Deviation X Minimum Y Maximum Y Mean Y Median Y Confidence Interval o standard errors Cms mor NOTE R square is available when curve fit ting is selected Figure 26 7 BioViz Analysis In Version 12 results of descriptive statistics are displayed on the plot Version 10 plot 1200 1000 800 Boiling 6004 4004 200 0 160 320 480 640 800 Molweig
279. o the exported dataset e In the Data Export dialog box select a path and file name for the new database Use the File button to browse for a loca tion e Inthe lower half of the dialog box all data fields are selected for inclusion in the 442 BioSAR Chapter 27 exported database by default Clear the appropriate check boxes to deselect fields you want to omit e Check the field names to ensure each one complies with Access database rules If necessary edit the field name by double clicking it e On the Text Options tab select a delimiter and other options you want to include subform data empty records and headers You also have an option to save structures in CDX or CDXML format 4 After you have made your selections click the Export button Importing the cfxml file Once you have saved the dataset in CFXML format you must bring it back into ChemBio Finder to save it as an MDB file NOTE To avoid conflicts with field name type definitions close the master database before importing and open a blank form 1 In a blank form click the File gt Import gt CFXML menu command and open the file The Data Import dialog is displayed 2 Select deselect the fields you want to import and the options you want to apply to the file 3 After you make your selections click the Import button Your dataset is imported into an Access database Exporting to an Excel spreadsheet When you export a BioSAR derived for
280. oesssesssocssoosso 497 Complete structure similarity 497 Substructure similarity eee 498 Appendix D CAL Commands ccscccscsscscssessesees 499 CAL Del Darsena RA 499 Menu commands ssseeeeeeeeeeeeeee 499 Box creation commands 008 502 Box manipulation comman4d 507 Program execution commands 510 General command6s eceeeeeeees 513 File commands esseere 527 Variable commandsS cesses 529 Environment variables c0 535 Script only commands cee 536 Appendix E CS Oracle Cartridge ssccsesecssees 541 Pre setup procedures ceeeeeeeees 541 Fast move caching scheme 542 Configuring via CF_SETTINGS table542 SeEArcChiNg seisis niina 543 MU cuncurnnannan 545 ChemBioFinder amp BioViz iii User Guide iv Contents What s New ChemBioFinder has long been the preferred tool for storing chemical structures physical properties notes tables of data and charts based on that data ChemBioFinder introduces a variety of improvements and new features not found in earlier versions New Features Classes This is new menu item within the Find Struc ture submenu under the Search menu The Classes menu provides a submenu with various items for performing searches For more infor mation see Special structure searches on page 376 By date modified This is anew men
281. olumns generated The log file for an RDFile import additionally presents an overview of the data table hierar chy within the RDFile You can choose whether to create the log file or not If you choose to create the log file you can save it with a different name or append to an existing log file ChemBioFinder amp BioViz 391 User Guide Importing from a specified location You can start an import from an arbitrary loca tion in an SDFile or RDFile such as a byte or line number To set the location from which to import 1 Click the Advanced tab of the Date Import dialog box 2 Select the appropriate options Data Import Import Logging Form Style Advanced Start reading at beginning C line C byte C record ChemFinder 9 0 v Ignore text import structures only Output database version M Store redundant reagents Table 24 To start from Click the beginning of the beginning SDFile or RDFile a specified line line and type the line number number a specified byte byte and type the number byte number a specified record record and type the record number 3 Click Import 392 Importing and Exporting Data Chapter 22 Reading a structure In addition to importing ChemBioFinder 12 0 can read files of any of the supported structural formats For example if you have structures stored in Chem amp Bio Draw format you can open them dir
282. ommand to assign the contents of a file to a variable This might be the first step for example in writing the data to a database READVAL d reports status txt CAL commands WRITEVAL syntax Copies the contents of a user variable to a text file WRITEVAL v filename The WRITEVAL command has the following arguments Part Description User variable from which the text is obtained variable filename String containing the file name in which to store the text Remarks The complete file path c some long path TEMP TXT is necessary when saving files If the specified file does not exist it will be created otherwise it will be overwritten WRITEVAL example This example uses the WRITEVAL command to write the contents of a variable to a text file WRITEVAL 2 f formulas mydata txt CAL commands INPUT syntax Displays a text input dialog accepts data from the user and stores it in a variable INPUT variable input The INPUT command has the following argu ments Part Description variable User variable to which the user s data is assigned input String presented as the default input Remarks If variable is omitted the text will be assigned to V1 CAL commands PASSWORD syntax Displays a text input dialog accepts data from the user and stores it in a variable Each char acter entered by the user is displayed as an asterisk to conceal its identity P
283. on Selecting files to search Use the File menu or the Look In tab to tell ChemFinder Office where to look for struc tures Chem amp Bio Office 2010 User Guide 471 ChemBioFinder Selecting files from the file menu Use the File menu to look for a structure in a specific file or data source 1 From the File menu choose Open The Open dialog box appears 2 Select a file or data source you want to search by doing one of the following e In the File Name text box type the name of the file to search e Use the directory tree in the Open window to browse to a file to search 3 Click Open When you select a single file the first structure in the file appears in the Structure window as soon as you open the file You can browse through the file using the forward and back arrows in the Search Record toolbar Selecting files with the look in tab Use the Look In tab window to search for a structure in multiple files The Look In tab window shows all the documents and data bases data sources on your mapped network CD ROM floppy and hard drives You can select entire folders to search or multiple indi vidual files by using the check boxes next to the file names To look for a structure in specific files or data sources 472 ChemFinder Office Chapter 30 1 Click the Look In tab The files and data sources appear in a tree directory Structae Look In Search Options oa a r Fo ChemDraw ChemOraw Ite
284. on carbon atoms in the query to match charged atoms in the target NOTE Charged atoms in the query must always match charged atoms in the target regardless of this setting Hit any charge on heteroatom Run a search that ignores differences merely due to salt state and presence of solvents e Ignore salts and solvents e Hit any charge on hetero atom On carbon e Permit extra neous frag ments in full structure searches Allow uncharged carbon atoms in the query to match charged carbon atoms in the target NOTE Charged atoms in the query must always match charged atoms in the target regardless of this setting On carbon Allow fragments in the query to overlap share one or more atoms in the target Query fragments can overlap in target Require that any reac tion center present in the query overlap with reaction centers in the target This preference applies only to reaction searching Reaction query must hit reaction center Prohibit generic struc tures from hitting any other structures in a query Generics hit only generics Allow hits to contain molecular fragments in addition to the structure hit by the query Permit extraneous fragments in full structure searches Require full word text matching If you do not check this box the query will hit any matching text frag ment Text match full word only
285. onditions it is a reasonable thing to look at Generally you want to use substruc ture queries that include little beyond the reac tion center in question when you are searching for reactions NOTE ChemBioFinder 12 0 supports several query properties to allow you to specify exactly how a bond participates in a reaction center For more information about these properties see Setting search details preferences on page 370 Atom to atom mapping The second most important part of reaction searching is the atom to atom map You can specify maps in Chem amp Bio Draw where they are stored as part of the data about a reaction Maps are used during searching to resolve cer tain types of structure search hits Atom to Atom mapping does not affect the search result when a query reaction is done with or without reaction map Consider a simple esterification reaction OH a O Figure 21 16 Esterification example Does the ester oxygen come from the acid or the alcohol You specify the fate of individual atoms through an atom to atom map In real ity the ester oxygen in this reaction originates in the alcohol so the atom to atom map looks like this fa I B HoA a N p oH a So a ei Ren O a O OHa 0 asd Figure 21 17 Atom map of esterification By matching numbers across the arrow you can see where atoms move during the course of the reaction The other reaction not observed experimentally
286. onfiguration To specify this centers must be drawn with stereo bonds and the entire structure marked Abs CHIRAL e A racemic mixture of the drawn configura tion and its mirror image This is drawn as above but without the Abs CHIRAL mark e An unmarked structure representing unknown stereochemistry or a mixture of all possible stereo isomers e A given relationship between centers That is a known orientation of the substituents with respect to each other rather than a known absolute configuration To specify this centers are drawn not with the stan dard hashed and wedged bonds but with thick stereo bonds If these options are checked in the Search tab of the Preferences dialog then any stereo chemistry indicated on the query must be matched by the target For more information on changing searching preferences see Set ting search details preferences on page 370 3D Properties 3D queries are particularly useful in pharmaco phore searching where you are looking for a particular 3D relationship among atoms and bonds for example in a series of potential receptor ligands You can create a 3D query in Chem amp Bio Draw Pro by adding geometries lines planes etc and constraints specified as ranges to a query structure For example you might specify that two atoms must be between 4A and 5A apart or that two planes must be separated by 80 100 ChemBioFinder 12 0 can then use these properties to refi
287. onment variables SINDEX SRECNO SNUM_RECS SDTBA_NAME_ LONG SDTBA_NAME__SHORT SFORM_NAME_ LONG SFORM_NAME_SHORT SCFW_DIR SFORM_DIR SSYSTEM_DIR NOTE To view a complete list of variables click Help on the Enter Cal Command dialog box ChemBioFinder provides several variables to allow you to retrieve information about the current ChemBioFinder environment They cannot be set directly but are modified as a consequence of other commands For example the menu command Record Next increments the current RECNO by 1 The table below shows examples of Environ ment Variables Command Action SETVAL 1 SRECNO V1 now equals the number of the current record ChemBioFinder amp BioViz 535 User Guide Command Action SETVA i vi V1 now equals total SNUM_RECS number of records in the current list SETVAL ee V1 now equals for SDTBA_NAME_ example c ChemBio LONG Finder mydb mdb SETVAL ve V1 now equals for SFORM_NAME_ example mydb SHORT SETVAL V1 V1 now equals for SSYSTEM DIR example c chem fndr system Script only commands text i label label GOTO label IF vl op v2 stmt IF vl op v2 lt stmt s gt ELSE lt stmt s gt NDIF OOP count NDLOOP PAUSE dseconds EXIT INTERACTIVE ON OFF STEP ON OFF Be oe Script only commands are usef
288. onnect the new fields to boxes by right clicking on the appropriate data box and choosing the field from the context menu field list Non chemical databases If you opened a database that you created using a program other than ChemBioFinder 12 0 and you want to add structures to it you can create structure fields in any modifiable non attached table To create a structure field 1 Open a database 2 Right click and select Properties 3 In the database tree click the table to which you want to add structures 4 Click the Field tab 5 Click the Create Field The Create Field dialog box appears 6 Choose Structure from the Type drop down list then click OK ChemBioFinder amp BioViz 345 User Guide You do not provide a name or other details when you create Structure columns ChemBio Finder 12 0 automatically creates four columns and names them These columns contain no data until you enter structures into the data base Backing up databases To back up the current ChemBioFinder 12 0 database 1 Click File gt Copy Database A Save As dialog box appears By default your copy is named YourDatabase_copy cfx 2 Rename your copy if you wish select a location and click OK A complete set of ChemBioFinder 12 0 database files is created in the selected location Moving databases ChemBioFinder 12 0 saves only the definition of the form and information for connecting to the database in the CFX file
289. opening Chem amp Bio Draw to create and edit structures e Structure Chem amp Bio 3D style as above but defaults to display 3D structures To set the box style 1 Right click in the data box you want to change and click Properties The Box Properties dialog box appears 2 Choose the box style from the Box Style drop down menu 3 Click OK Viewing structures You can display structures in a structure box in three styles e ChemBioFinder e Chem amp Bio Draw Chem amp Bio 3D In ChemBioFinder style the Chem amp Bio Draw application opens when you want to edit struc tures or create a query This mode of opera tion was used in all earlier versions of ChemBioFinder1 1 0 In Chem amp Bio Draw Style you edit directly in the structure box using the Chem amp Bio Draw Con trol This mode of operation was introduced in ChemBioFinder 8 The Chem amp Bio 3D style is a display only for mat that allows you to rotate and analyze struc tures within a ChemBioFinder 12 0 structure window See the Chem amp Bio 3D User s Man ual for information on using the Chem amp Bio 3D Control The Chem amp Bio Draw format displays more graphically rich drawings than the ChemBio Finder 12 0 format However ChemBioFinder 12 0 does not use all of the Chem amp Bio Draw drawing features when searching For exam ple textual annotations are ignored and R group tables are not recognized Certain ChemBioFi
290. ord Next to step through each record in the current list For each record it builds a unique file path based on the current INDEX using SETVAL and APPENDVAL commands Finally it saves each compound to disk with the WRITEMOL command Since the file path ends in cdx this script saves all of the compounds in Chem Draw format append off loop setval 1 c mydir appendval 1 Sindex appendval 1 cdx writemol v1 rec next endloop Example 4 GOTO Example This example allows the user to batch enter several new compounds and input one field for each It starts with a MSG command to tell the user what to do Then it has a line starting with a colon that serves as a label to start the loop The INPUT command gets the name of the new entry from the user The IF command tests to see if the user entered a blank string and EXITs the script if so After the Menu Command Record Add creates a new record the PUTDATA command enters the user s string into the molname field ChemBioFinder amp BioViz 501 User Guide Closing the loop the GOTO command jumps execution back to the start label msg Enter new compound names Enter a blank name when complete start input 1 if Svl exit record add putdata molname v1 goto start Box creation commands DBOX coords fieldname RAME coords text EXT coords text ICT coords filename UBFM coords RROWBOX coords RAMEDBOX coords fieldname
291. ord Toolbar Text format toolbar The Text Format Toolbar contains standard text formatting tools that you can use when entering or editing information in data and text database The first displays the word READ fields when you are using a read only database such as one that is on a CD ROM a read only form file or if you have selected Open as read only Text Format Toolbar Arial 10 BLUx x AZ B on the open file dialog box The second indicator displays the word ADD 4 z 31 z a when you are entering a new record s 11 The third displays QRY when you are entering Figure 16 5 The Text Toolbar a query 1 Font To hide or show the Status Bar 2 Point size Select or deselect View gt Status Bar an More UI features 4 Italics F Uang Style button for text and frame boxes Ue The Box Properties dialog makes the Style but Te SUpeisenpt ton available for frames and plain text labels 8 Color This button opens the Box Style dialog box 9 Left alignment where you can set frame type printability and 10 Center alignment other display characteristics a tl Read only structure box option 12 Bullets The Box Style dialog has a check box Box is The status bar read only This applied to text numeric data While you move among records counters in boxes and structure boxes If you mark a struc the lower right corner of the window change to ture box read only the structure cannot be indicate the current record the cur
292. ord from the searched table 8 The final list is prepared by a join selecting rows from the main table which have record ChemBioFinder amp BioViz 415 User Guide ID s matching those of the new list in the hits table The resulting list is ready to browse save export etc NOTE Text searches in Oracle are case sensi tive You will get different hits from the query benz than from Benz Sorting Certain sort operations require a ChemBio Finder 12 0 system table CF _SORT that may not exist in your current form If the table does not exist you will be alerted the first time you attempt such a search in an Oracle data base To create the CF _SORT table 1 Open a new form then click the File gt Data base menu command The Form Properties dialog box opens 2 On the Database tab click the Oracle Data base button 3 Log in as the owner of the schema where your ChemBioFinder 12 0 system tables are located Typically this will be ChemBio Finder NOTE If you do not have privileges to log in as this user consult a system administrator 4 Click the Oracle tab of the dialog box then click the Prepare Schema button ChemBioFinder 12 0 will create the one new table needed without modifying any of the others NOTE If this button is dimmed it means you are not logged in as the owner of the current schema 416 ChemBioFinder Oracle Chapter 25 5 Go back to your original f
293. orm 1 Press the Shift key and click the objects to align 2 Use the Edit gt Align submenu to take the appropriate action Table 23 Object alignment options If you want to line Then choose up along the top edge of the first Top object you place on the form middle of an object Vertical Center in a vertical line bottom edge ofan Bottom object left edge of an Left object middle of an object Horizontal Center in a horizontal line right edge of an Right object The form objects line up according to your choice To space objects on a form evenly 1 Press the Shift key and click the objects to distribute 2 Use the Edit gt Distribute submenu to take the appropriate action Table 24 Object spacing options If you want to space Then choose objects evenly between the outer boxes of the form Vertically left and right of the Horizontally form The form objects are spaced according to your choice Changing form layout Changing a form layout is the same as auto matically creating a new form When you have created a new form you can use it to replace the old form or save it as an alternate form See Creating forms automatically on page 311 for details Securing forms You can control the options available to users of your forms by setting the security options You can also provide the database connection information used to log on
294. orm and repeat the sort TIP You may have to click Refresh Session Data on the Oracle tab before the sort will work Subform value aggregate In an Oracle database ChemBioFinder 12 0 allows sorting the main list over subform field aggregate values If for example you have a subform showing a column of test values where there are multiple records in the sub form for each main record you can sort the main hitlist based on the sum or average of the set of test values for each record To sort by aggregate 1 Click the Record gt Sort menu command to bring up the Sort Multiple dialog box 2 Click a subform value in the left hand box to sort by 3 In the right hand box right click the Fxn column and choose a function from the popup menu MIN MAX AVG or SUM 4 Click OK The hitlist is sorted by the selected value s NOTE AVG and SUM are available only for numeric fields MIN and MAX can also be used for text fields Handling lists There are differences between ChemBioFinder 12 0 and ChemBioFinder Oracle in working with hitlists Save List does not bring up a file dialog in ChemBioFinder Oracle instead it presents a dialog in which you enter a name and a line of comments for each list Restore List presents a dialog in which you choose from the available saved lists see screen shot below CS Oracle Restore List List Name Comments 1 2 3 1 1 2 Listi benzenes G Repla
295. ortional to the distance between its chil dren where distance is the measure of similar ity between two objects Thus the node just above the baseline connects pairs of com pounds with very similar in this case usually identical molecular weights On the right is the cluster window which pro vides another way of viewing the data The cluster window screen depends on the position of the dotted pink cutoff line across the dendogram Every node directly below the line is represented as a single ball in the cluster window with its size scaled to the number of leaves it contains Thus a large ball represents a large group of compounds with similar molecular weights where the smallest ball is a single compound of a weight all its own By moving the cut off line up and down you vary between a coarse grained view with few clus ters to a more detailed view with many To modify the cluster dialog click the black drop down arrow in the lower right corner See Dendogram Properties on page 448 and Cluster Properties on page 449 for more information Clustering on multiple fields To perform clustering on multiple fields you need to create a profile box which contains user defined set of fields and conditions for comparing data records See Creating a com pound profile on page 406 After the profile box is created on the form save the form Structure 2527 230 55 i 1 i CLOGP MolVeight HOF
296. ource such as a data CD Instead of accessing the read only source directly you can create a portal database a local writable database with attachments to the external tables of interest The portal looks and behaves just like the target database but with out the limitations ChemBioFinder 12 0 creates a portal database when needed For example if you are using a database CD perform a search and attempt to sort by formula a message appears that offers to create a local database attach the current table save the form and proceed with the sort If you create the local database you can use the new form to get the data with full function ality and performance Working with Data Entering data You enter data into a database by adding a new record Adding a new record consists of three steps e Clearing the form e Adding new data e Committing the new entries Clearing the form To begin adding a new record 1 Create a form and link it to a database For more information see Creating forms manually on page 313 The form should contain all the data boxes you want to view and edit The boxes should be assigned to their appropriate fields 2 Do one of the following e Click Record gt Add New Record e Click the Add Record icon on the Record Toolbar 3 All of the boxes in the form are cleared to prepare for entering new data The Status Bar is updated to show that you are in record addition mode
297. out what query features you may use and how these features affect a search see Changing the scope of a search on page 489 NOTE In searching substructures ChemBio Finder 12 0 finds the substructure query regardless of its orientation or drawing presen tation in the targeted molecules Bonds shown in bold above are actually highlighted in red in ChemFinder 12 0 Full structure searches A full structure search finds structures that completely match the query If you do not specify stereochemistry or use generic atom or bond labels you may get more than one hit You may also get more than one hit if there are duplicates in the database For more informa tion see Stereochemistry on page 363 and Exact searches on page 361 Fragment searches You can draw more than one structure or struc ture fragment in your substructure search query In the Details tab of the Preferences dia log box you may allow fragments to overlap in the target structure For example if you perform the following sub structure query with Query fragments may over lap in target selected OH nar a Figure 21 5 Fragment query 362 Queries Chapter 21 The hit list will include the following SF Sa Figure 21 6 Example of substance hit in a fragment query The dot indicates an atom shared between the two fragments The hit list will not include this molecule if the overlap option is deselected Tautomeric searches
298. ove quantities of data from one column or row to another e Carry out complex queries on non struc tural data Permanently change the sort order of a table For more information about these actions please consult the Microsoft Access User s Guide Do not add or delete records to the MolTable within Access because the data component of the database will become out of synchrony with the structure component Database File Types ChemBioFinder 12 0 databases are supported by a library called MstLib This library con tains a number of files for supporting the struc ture column In addition ChemBioFinder 12 0 uses additional screening files for improving performance of search operations ChemBioFinder amp BioViz 469 User Guide The following table lists the various file types used by ChemBioFinder 12 0 Extension Purpose MST Structure Storage MSI Screen Traditional MSX Screen Traditional MSF Screen Full Exact MSK Screen Skeletal MSS Screen Similarity MS3 Screen 3 D MSH Screen Hash CFW ChemBioFinder Form CFX ChemBioFinder Form CFS ChemBioFinder Script MDB MS Access database LDB Locks on database NOTE When MSS extension is missing the MSX extension is used but the quality of the search is lower 470 Customizing ChemBioFinder 12 0 Chapter 29 ChemFinder Office Overview ChemFinder Office lets you search data sources documents and d
299. ox then click OK To execute CAL commands 1 Click the Scripts gt Command Line menu command The Enter CAL Command dialog box appears 2 Type in a single CAL command Click the Help button to see CAL Scripting Help 3 Click the Execute button to run the com mand You can keep entering commands one by one 4 When you have finished running com mands click the Done The Command drop down list contains previ ously entered commands To rerun a previously entered command 1 Select the command from the list 2 Click the Execute button For detailed information about the command language see CAL Commands on page 499 ChemBioFinder amp BioViz 459 User Guide Getting CAL help To display information about the CAL script ing language Click the Help button in the Enter CAL Command dialog box The CAL Scripting Help window appears containing commands variables and syntax notes W CAL Scripting Help Command Arguments Description AAMAPS ONIOFF _display don t display colored AA map ACTIVATE lt subformbo direct subsequent input to subform ADDRECORD COUNT Append one or more empty records APPEND ONIOFF set append mode on off default toggle APPENDVAL v lt text gt append text to specified variable ARROWBOX rect launches moving arrow Variable Description CHIRAL 1 current mol is marked chiral 0 not chiral CLIPBOARD text from Windows Clipboard CURR_DI
300. perties dialog box appears 2 Click the Table tab The Table tab appears ChemBioFinder amp BioViz 341 User Guide 3 In the data source tree select the table to delete 4 Click the Delete Table A dialog box appears giving you the option of completing the deletion or cancelling 5 Click Yes to delete the table The table and all data it contains are immediately deleted from the database CAUTION You cannot undo a deleted table Before you delete a table create a backup copy of the data base to prevent accidental loss of data For more information see Backing up databases on page 346 Attaching tables from other applications You can use ChemBioFinder 12 0 to add chemical structures to a database you have already developed If your database was devel oped in Microsoft Access you can open it directly in ChemBioFinder 12 0 can also work with data from other file based databases such as dBASE and xBase clones but in this case you must open or create a ChemBioFinder 12 0 database and attach the table to link to tables in the data source After you attach a table it appears and functions as if it were part of your local ChemBioFinder 12 0 database The procedure you use depends on whether the tables you want to attach are from a file based Access FoxPro dBASE or non file based Oracle database system Attaching files from a file based database To attach a file based database table 342
301. pics with specific applica tion to ChemBioFinder Python operates on your data through the ChemBioFinder OLE Automation interface This interface provides external access to a library of the objects you work with in Chem BioFinder application document form recordset fields boxes and others The inter face is documented on the ChemBioFinder SDK site You may find it more convenient however to use an object browser to see the library in its current form To illustrate we will develop an example Python script Suppose you have a form open you perform a search and get a hitlist You would like to generate a report that contains a set of records in formatted blocks showing spe cific data items You can perform this task using the script shown below You can copy and paste the script into the Script Editor to try it or use it as a template ChemFinder Python script Gener ate Report Created Wednesday November 01 2006 10 55 AM Loop records printing name and Formula From win32com client import GetAc tiveObject cfapp GetActiveOb ject ChemFinderll Application cfdoc cfapp ActiveDocument cfrset cfdoc Recordset namefield cfdoc Fields mol name fmlafield cfdoc Fields for mula recno 1 cfrset MoveFirst while not cfrset EOF molname cfrset Value name field index formula cfr set Value fmlafield index print Rec
302. ppli cation Use the items in the Send To menu to send files to these applications e MS Word e MS Excel e CS ChemFinder e CS ChemDraw e ChemACX Com Search To send a file to another application 1 In the Data Source Find Chemical Struc tures window click the Send To menu The Send To menu appears 2 From the Send To menu choose an applica tion to send a file to The Send To box dialog box appears NOTE When you send files to Chem ACX Com The Send To dialog box does not appear The structure associated with the file is sent directly to ChemACX Com 3 From the Molecules section select one of the following If you want to Then click send the structure displayed in the Structure window Send current mole cule send all the struc tures listed in the Hit List Send all molecules in current hit list 4 From the Document section select one of the following if available If you want to then click send structures to a new untitled docu ment in an applica tion send structures to a document you already have open in an application Send molecule s to a new document Send molecule s to a currently open document 5 In the Document section select the name of the file from the drop down list if neces sary If the text box in the Document section is not available skip this step Chem amp Bio Office 2010 User Guide
303. pplications including Chem amp Bio Draw and Chem amp Bio 3D you edit data on the screen but your changes are not made permanent until you click File gt Save or type Ctrl S In database programs such as ChemBioFinder 12 0 your changes are automatically and per manently saved to the database when you switch records This is committing the changes You then have the opportunity to revert to the original data by clicking Record gt Undo Changes The File gt Save menu command refers only to changes made on the form itself such as the position of boxes Choosing the File gt Save menu command has no effect on changes you make to data stored in the database Saving a form also saves subforms and changes that you make to subforms After you create a form you can save it When you retrieve the saved form it automatically opens a connection to the database defined in the forms To save a form as cfx file 1 Click File gt Save To save the form under a new file name use File gt Save As The Save dialog box appears 2 Choose the directory in which you want to save the form type a filename and click the Save button ChemBioFinder 12 0 saves the form with a CFX extension NOTE While saving if you select All Files in the Save as type dialog box you will see files with msf and msk extensions A file with the extension msf is a multiple sequence file A file with msk extension is a mask file Creating fo
304. proceed Dropping one or more form files opens the forms without affecting the current form and database Importing text You can import comma or tab delimited text files The Import Delimited Text command uses the same dialog and has most of the same features as Import SDFile Delimited text DT differs from SD files in that e DT files cannot contain structures e DT files are not as well defined and require interpretation in order to determine field names and delimiter type To import text records into a new database 1 Open a new blank form 2 Click the File gt File Import gt Delimited Text menu command 3 In the File Open dialog browse to select the input file e The input file is scanned to determine the field delimiter If the file extension is csv the delimiter is taken to be comma If the extension is txt the first few lines of the file are examined for the presence of com mas or tabs If one or the other is found it is taken as the delimiter If not an alert is pre sented e This alert will appear in two cases e The input file contains only a single col umn The alert can be ignored click OK e The input file has some delimiter between fields other than tab or comma In this case you must specify the delimiter using the File Export dialog box To specify the delimiter using the Role Export dialog box 1 Click Cancel to dismiss the alert and abort the import 2 Ope
305. r a database opens in read only mode e Ifthe component files extensions CFX MDB LDB MST MSX have read only attributes e Ifthe files are on read only media such as CD ROM 336 Databases Chapter 19 e If you select Read only in the File Open dialog box when you open a form or data base When you open a read only database the fol lowing conditions apply e READ appears in the status line e You can not modify data in text or structure boxes NOTE If only the form CFX file is set to read only READ does not appear on the status line and the database can be modified Multi user access If a database resides on a network more than one ChemBioFinder 12 0 user may access it at the same time Each user can view print or modify records independently of the others The following table shows how the type of user affects the other users in the group Table 19 1Multi user access User type Affect on other users Multiple readers User actions do not affect in read only each other access Multiple writers All users can read and write in normal access A user may see another user s edits If two users try to edit the same area at the same time one is alerted that the database is tempo rarily locked Table 19 1 Multi user access User type Affect on other users One writer The writer in normal multiple readers access is not affected by the readers The readers in read only access
306. r in the lower left corner of the form Clicking on the second tab will present you with a new empty form To rename a tab 318 Forms Chapter 18 1 Right click the tab and click Rename Tab The Tab Name dialog box appears 2 Type a name for the tab and click OK The new name appears on the tab To remove a tab Right click the tab and click Delete Tab context The tab is removed Setting box properties Use the Box Properties dialog box to set ChemBioFinder 12 0 form attributes includ ing data source display type font and box style To open the Box Properties dialog box Right click on a data box and click Properties The Box Properties dialog box appears NOTE The Properties option is only avail able in Layout mode Setting data box styles Use the Box Properties dialog box to change the style of a data box on a form For example you can change a data box to a frame or pic ture The Box Style menu only shows applicable styles for each field For example you cannot show a real number in a Picture For information about field types See Creat ing fields on page 343 Choose from the following styles e Data Box displays alphanumeric data Can display multiple lines of data e Frame displays alphanumeric data Can display a single line of data e Plain Text displays alphanumeric data Text data can be displayed in multiple lines Use Ctrl Enter to start a new line Yo
307. r more details about how the command works see Structure Clean Up in Chapter 4 Advanced Drawing Techniques of the Chem amp Bio Draw User s Guide Before committing a data entry you can revert to the previous unmodified record by choosing Undo Changes from the Record menu To edit structural data 1 Do one of the following ChemBioFinder amp BioViz 349 User Guide e In Chem amp Bio Draw mode Double click the structure box The Chem amp Bio Draw Control appears e In ChemBioFinder 12 0 mode Double click the structure box Chem amp Bio Draw opens and the structure appears in the From ChemBioFinder 12 0 window e Ineither mode Right click in the structure box and click Edit in Chem amp Bio Draw Chem amp Bio Draw opens and the structure appears in the From ChemBioFinder 12 0 window 2 Edit the structure 3 Click in the ChemBioFinder 12 0 form or close the Chem amp Bio Draw window by typing Ctrl W when you are finished 4 Click Record gt Commit Changes Click the Commit Changes icon or move to a differ ent record The changes are stored To clean up a structure 1 Right click in the box containing the struc ture and click Clean Structure 2 To save the cleaned up structure do one of the following e Click Record gt Commit Changes e Click the Commit Changes icon Working with structures using Chem amp Bio Draw Enter or edit Chem amp Bio Draw structures in data boxes of the
308. rch for a list of records using partial text a wildcard search or range of numbers do a search on the relevant field e Ifthe column you search is a text type you must use quotes around any item that con tains commas For example you must type 1 2 Pyran as 1 2 Pyran e You may save a list as a text file and retrieve it later with the File button To find a list 1 Click Search gt Find List The Find List dialog box appears 2 Choose a field from the Column menu 3 Paste or type a list of field parameters into the Find List text box 4 Click OK The list of matching records is retrieved Structure searches You can search a ChemBioFinder 12 0 data base by sub or full structure To define your search more precisely use the query functions in Chem amp Bio Draw These are described in Chapter 9 of the Chem amp Bio Draw User Manual 360 Queries Chapter 21 and in Structural Query Features on page 483 in this manual ChemBioFinder 12 0 matches structures in three ways e Search type Normal Exact Similarity e Structure mode sub or full structure Tautomerism x yes substructure tautomerism no normal structure mode full structure tautomerism amp Search type pe yes exact structure mode full structure tautomerism substructure similarity _ structure mode full structure Figure 21 4 Structure search tree Search types ChemBioFinder 12 0 supports three structure
309. rch frequently To save a list of directory paths 1 Open Notepad or some other ASCII text editor 2 Type the directory or database paths you want to search 3 From the File menu in Notepad choose Save As The Save As dialog box appears 4 In the File Name text box type a name for the file and include a dsd extension For example type a File Name like search dsd 5 Click Save 6 Close Notepad Searching DSD files To search for a structure in a DSD file 1 From the ChemFinder Office File menu choose Open The Open dialog box appears 2 In the Files of type text box select Data source definitions dsd from the drop down menu 3 In the File Name text box type the dsd file name or select the file from those listed 4 Click Open The first structure associated with the last saved version of the dsd file appears in the Structure window 5 Click New Search ChemFinder Office clears the Structure window 6 Click Edit Structure and draw a structure to search for 7 Click Find Now ChemFinder Office searches through the files specified in the DSD file Any hits appear in the Hit List Sending a file to another application You can send a structure or a file of structures like SDF files to another application You can cut a single structure from an application and paste it into another or you can send more than one structure directly into another a
310. rders the records by increasing C H N count for compounds containing carbon followed alpha betically by any other elements Formulas for compounds without carbon are sorted in alpha betical order Sorting by text fields such as molecular name sorts the records alphabeti cally After sorting the database must be reset to its original state before you can update it NOTE You cannot edit records sorted by for mula or molecular weight However if you attempt to sort on one of these fields ChemBio Finder 12 0 offers to set up a database a portal database which allows the operation For details see Attaching tables from other appli cations on page 342 To sort on a field e In the Form View right click in the field you want to sort by and click Sort gt Ascend ing or Sort gt Descending Inthe Data Table View double click on the table header of the field you want to sort by The table is sorted in ascending order by the column you selected Double clicking again will sort in descending order TIP There is also a context menu option for sorting in Data Table view Right click in a col umn and choose Sort Column ChemBioFinder amp BioViz 353 User Guide Sorting in languages other than English Text that you sort must be in the same lan guage as the default language of the system on which the database was created or an incorrect sort order can occur The ChemBioFinder 12 0 sample datab
311. re index except that you carry it out on a field of type Long This creates an index on the 420 ChemBioFinder Oracle Chapter 25 field and also designates it as the primary key It will fail unless the column already contains unique non null values NOTE A new button Set As Structure may appear if you have selected a certain type of column This is an advanced feature described in Configuring via CF_SETTINGS table on page 542 TIP If you want to create a primary key but don t have a column of unique integer values you can create one using a CAL script For example assuming you ve already created a column and form box called ID loop putdata ID Sindex record commit record next endloop CAL Some new features have been introduced into ChemBioFinder 12 0 Automation Language CAL to support Oracle Some are not specific to Oracle but of general utility e SQL command When you are connected to an Oracle database you can pass any SQL command which does not return records The format is simply SQL lt command gt where the command is not quoted Example SQL create table mytable id inte ger CURR_TABLE variable This variable con tains the name of the table connected to the current form This works whether or not you are in Oracle Example MSG Current table is SCURR_TABLE e OPENDB allows change of table Normally this command takes the name of a database followed optio
312. rences Structure registration options To have ChemBioFinder 12 0 present an alert when attempting to enter a structure with an atom in a non standard valence state Click the Check valences check box in the Registration section To have ChemBioFinder 12 0 confirm when you are about to modify data in the database Click the Ask to commit changes check box in the Registration section ChemBioFinder 12 0 opening options You can set ChemBioFinder 12 0 to open with the ChemBioFinder 12 0 Opening dialog box or to open the last form you were using To set the options for what ChemBioFinder 12 0 displays when it starts up 1 On the General preferences tab Table 28 Startup options If you want to then start with the check the box next to opening dialog box Show startup dialog start by opening the check the box next to last form you used Reopen last form ChemBioFinder amp BioViz 453 User Guide Table 28 Startup options If you want to use a default script then check the box next to Check for external scripts change which window is on top in the Explorer window select an entry from the Explorer tab drop down menu select a different theme select an entry from the Frame style drop down menu 2 Click OK Setting the recent file list size You can set the number of files you opened recently that ChemBioFinder 12 0 shows To set the list siz
313. rent list size edited except in query mode and the total size of the database The lower left corner of the window displays help for Automatic frame label updates menu items and other information The label of a framed box is updated if you When you first open a form the current list change the field it displays size equals the total database size The total database size changes only when you add or Themes delete records If you search to find a subset of Themes let you customize the UI style to your the entries in the database then the current list preference Options include WinXP Office size changes to indicate the number of hits in 2003 Office 2007 and Whidbey See Chem the search BioFinder 12 0 opening options on page 453 To the left of these counters are three other for more information indicators that show the general status of the ChemBioFinder amp BioViz 289 User Guide Resizable dialog boxes The Box Properties Plot Properties Data Import and Data Export dialog boxes and the script editor can be resized allowing you to see more in text windows tree controls and so forth The position and size is remembered during the current ChemBioFinder 12 0 ses sion Opening ChemBioFinder 12 0 In default mode ChemBioFinder 12 0 opens with the ChemBioFinder startup dialog This dialog lets you From the New tab e Blank Form Open a blank form to create your own e Database Connection Open a blank form
314. res importing only 390 style box changing 319 style definition 426 styled text 352 subform fields exporting 396 subform description 287 subforms changes in ChemFinder 9 399 creating 400 data table 402 linking fields 399 overview 399 searching 402 switching between forms and data ta bles 402 tutorial 310 using scripts 403 subforms tutorial 309 submitting queries 373 substituents 484 exactly 490 free sites 491 in queries 484 490 up to 490 substructure searches 361 substructure searching 300 substructure searching see also full struc ture searching substructure searching see also similarity searching substructure similarity 498 supported file formats 389 synchronization 433 y tables 560 Index adding 354 403 creating 341 deleting 341 tabs creating and editing 318 tabs renaming 318 Tanimoto similarity 497 tautomers searching for 362 temporary database 346 tetrahedral stereo center hits 373 text as structures 351 creating 316 customizing 322 fields 343 format toolbar 322 352 sorting 353 styled 352 text box description 287 text boxes formatting 289 text files importing 393 text format toolbar description 287 themes 289 themes selecting 454 toolbars customizing 456 form 288 main 287 record 288 search 288 text 352 text format 288 tools alternative group 364 attachment point 365 data box 315 frame 315 framed box 315 grid 314 layout 314 picture 316 plain te
315. rk next to it You are now ready to create a child list query The following sample procedure describes how to create a child list by searching for car boxyl structures 1 Click the Query icon to put the form in query mode ChemBioFinder amp BioViz 439 User Guide 2 Double click in the Structure window The ChemDraw toolbar appears 3 Using the bond tool create a carboxyl structure 4 When you have finished creating the struc ture click outside the Structure window 5 Click the Search button The new list is created as a child of the previ ous list Explorer 2 Queries Full List S E Q1 1003 Molweight lt 250 Q2 110 555 query C2 Database Queries Favorites BioSAR Figure 27 17 In this example Q1 is a child list of a parent list named MW Filter Creating multiple child lists You can run similar queries each with differ ent attributes and displayed as a child of the parent query Queries Full List MW Filter 1187 BioSAR list 91 E Q1 807 Molweight lt 70 I o3 178 Molweight lt 40 M Q4 848 Molweight gt 50 Database Queries Favorites BioSAR 440 BioSAR Chapter 27 Figure 27 18 Several child lists of the parent list MW Filter To create another child list you must first select the parent list To select the parent do either of the following e Double click the parent list e With a child list selected click Restore Pre vious Li
316. rms manually You create a form and define it by using the Form tools to create objects and the Box Prop erties dialog box to set the form properties To create a new form do one of the follow ing e Click File gt New e Click the New File icon on the Main Tool bar To create form with the database tree The Database Tree is the same familiar tree as in the Database Properties dialog showing the tables or views and columns of the currently open database When you open or activate a form or subform or change databases the tree updates to display the current database and expands to show the columns of the currently selected table To view the Database Tree if it is not visible 1 Select the View gt Explorer Window menu option 2 Click the Database tab To use the Database Tree to build a form 1 Open a new form ChemBioFinder amp BioViz 313 User Guide 2 Right click on the form and select Data Source 3 Click the Open Database on the Database tab 4 Browse to a database and click the Open 5 Click OK in the Form Properties dialog box The Database Tree displays the database Figure 18 4 Creating a form with the database tree 6 Double click the Structure field in the Data base Tree A structure box appears in the upper left of the form Figure 18 5 Structure box created from the database tree 7 Continue double clicking the other fields 8 Us
317. roperties 4 Click the OK button The database is associated with the form 334 Databases Chapter 19 Selecting the data to display You indicated the source of the data to display on the form but the form is still blank To see the data you need to indicate what data to show in each box You can use the Box Proper ties dialog box as described in See Setting box properties on page 318 To choose the data box to display 1 Right click in a box or frame then click Field The Field properties appears 2 From the data source tree select the field to display Box Properties Database Table Field Fom Box suuctue Properties Name Structure Type Table lt Create Field Figure 19 4 Selecting a field in the database tree 3 Click the OK button The field data is displayed in the box If you use this method with a framed box the box label will remain unchanged If you want to use the field name as the box label you can do it in one step as follows 1 Right click in a framed box 2 Select the field name from the list at the bottom of the right click menu The frame receives the field name and the data is displayed in the box CS_DEMO i Properties Data Source Field ChemBioviz Plot Cluster by MolWeight Sort gt Mol_ID Structure Formula MolWeight Molname Calculate Property gt Figure 19 5
318. ry must match those in the target Uncharged atoms in the query may or may not match charged atoms in the target depending on the state of the appropriate check box in the Search tab of the Preferences dialog The valence of a charged atom is taken to be the valence of the isoelectronic neutral atom With a substructure search the query with charge or radical Nt Finds any of om H OH NH2 H Ta Rr Does not find any of OH OH H OH H Isotopes Isotopic labels specified in the query must match the target Unlabeled atoms in the query match unlabeled or isotopically labeled atoms in the target Additionally D is treated inter changeably with H and T is treated the same 3 as H With a Substructure Search the Isotopic query D So BC ChemBioFinder amp BioViz 485 User Guide Finds any of 7N ee a 2H s5 Ar CHa D D Does not find any of AN HO 13CH3 S 3CH3 Ho N Stereochemistry Stereochemistry specified on the query must match the target if the relevant Match Stereo item is selected in the Search tab of the Prefer ences Stereochemistry is specified at a tetrahe dral site by using stereo bonds up down either Stereochemistry about a double bond is specified by the geometry of the drawing ChemBioFinder cannot currently interpret other stereochemistry types allenic square planar octahedral etc and ignores them dur ing a search 486 Structural Quer
319. s To set acolor 1 Click the button corresponding to the inter face element you want to change The color dialog box appears 2 Select the new color 3 Click OK TIP Some users prefer not to see red high lighting because it masks the atom colors You can change the highlight color on the Color tab of the Preferences dialog box Selecting black will effectively cancel highlighting leaving atoms to display in their normal colors Structural query matching Search Type Search Details and Tuning help you define a query to give the kind of hits you are looking for The settings are discussed in the chapter on queries under Search types on page 360 Setting search details preferences on page 370 and Tuning on page 372 General preferences The general preferences let you set e Recent file list size e Startup defaults e Frame styles e Query save defaults To set the general preferences 1 Click the File gt Preferences menu com mand The Preferences dialog box appears 2 Click the General tab The General tab appears Preferences x Display Colu Search Type Detals Tuning General s Regatiaton N Recent fle ist sze 6 i W Check valences Ask to coment changes I Use Queey Add Window Al Startup Show startup dialog Reopen last loma W Check for extemal scripts E xplorer tab Favores Frome style Whedbey zj Pisces Caine Figure 29 5Setting general prefe
320. s there is an implicit AND condition between data items in different fields To perform a combined search 1 Do one of the following to clear the form e Click Search gt Enter Query e Click the Enter Query icon on the Search toolbar 2 Enter the structural query if any 3 Enter the text and or numeric queries in the appropriate boxes 4 Do one of the following e Click Search gt Find e Click the Find icon on the Search Toolbar Combined searching example Suppose you want to find all molecules in the CS_Demo database that contain a benzene ring and which have names related to penicillin 1 Click Search gt Enter Query 2 Draw a benzene ring 3 Enter penicillin in the Molname field 4 Check that the Search gt Substructure option is selected 5 Click Search gt Find You get 2 hits of molecules whose names con tain penicillin and whose structures have an aro matic ring of six carbon atoms NOTE Inacombined search progress reports are given only during the structure search part When the counters at the bottom of the screen are advancing structures are being searched You can press Esc to end a search during the structure searching You cannot end a search during the SQL searching by pressing Esc SQL searches SQL Structured Query Language can be used to create powerful searches The details of the language are not discussed here Queries beginning with a backslash are taken as s
321. s and Settings Style af ra I Open database read only Security I Do not ask to upgrade pt Run script on C Open fom C Move to new record O Enter query aaa ceos i Figure 18 9 Form properties dialog box ChemBioFinder amp BioViz 323 User Guide 3 Take the appropriate action Table 22 Background color options To set the back Click ground color of the the Form Back ground database form the Query Back ground query form The Color dialog box appears Figure 18 10 The Color picker dialog box 4 Select a color 5 Click OK The Form or Query Background changes to reflect the color you choose To set the default background color 1 Click File gt Preferences The Preferences Dialog Box appears 2 Click the Color tab 3 On the Color tab click the Form Back ground 4 In the Color dialog box select a color and click OK The color you choose becomes the default form background color Editing forms You can move or resize boxes and other objects on your form with the Selection tool and the items in the Edit menu Selecting objects on a form Use the Selection tool to choose data boxes and other objects on a form that you want to move resize or delete 324 Forms Chapter 18 When the selection tool is active the Edit menu commands apply to the boxes them selves When the selection tool is not active the Edit Menu com
322. s and forms and presents to the user visually appealing highly interactive dis play Features e One click clustering over current hitlist on any numeric field or structure box e Multi dimensional clustering via compound profile allows detailed specification of fields and conditions e Fast new clustering and projection algo rithms from the core chemistry group e Resizable zoomable two pane display showing dendrogram and cluster visualiza tion e Drop down control panels for display and behavior customization e Unique cluster window allows visualization by adjustable partitioning of dendrogram tree e Dendrogram tree may be oriented in any direction Sliding adjustment varies dendrogram node spacing between linear and log scale e Shaded coloring may be applied to clusters based on value of a selected field e User choice of text labels may be applied independently in each pane e Tooltips provide full information about nodes and clusters e Intuitive highlight and selection mecha nisms are synchronized between the two panes Selected set of nodes or clusters can be con verted with one click to ChemBioFinder hitlist e Pop up structure window displays struc tures and data of highlighted nodes Structure clustering based on Tanimoto similarity between structure screens Working with Clustering This section describes the steps for carrying out clustering operations Clustering on sing
323. s appli cation filename Remarks If the file to be launched is in ChemBio Finder s standard search path only the actual file name CHEMDRAW is required Other wise the complete file path c some long path CHEMDRAW EXE is necessary The EXEC command starts a program but does not return from it in order to return to ChemBioFinder you need to use the Task Manager or click in the ChemBioFinder frame window EXEC example This example uses the EXEC command to start Microsoft Excel The first line starts with an asterisk and so is not executed It serves only to make the example more readable for the user RUNEXCEL CFS script to start Excel EXEC co msoffice excel excel ex CAL commands DDE syntax Sends a Dynamic Data Exchange message to a specified application DDE timeout servicename topic command The DDE command has the following argu ments Part Description timeout An optional time in seconds to try establishing the connection servicename String containing the identi fier of the recipient applica tion often but not always the application name topic String identifying the nature of the message command String containing instructions to recipient application indi cating what you want it to do Remarks DDE commands are highly specific to each application Please consult the documentation for the desired recipient application for infor
324. s case font changes apply only to the current selection within the text e When you are editing in a regular data or structure box Font changes apply to the entire contents of the box e When you are in form edit mode with the selector tool active and one or more boxes are selected Font changes apply to all 322 Forms Chapter 18 selected boxes except frames around data boxes Customizing fonts All labels on ChemBioFinder 12 0 objects can be edited to your specifications You can edit any label s font font style size and color To set the font for a label 1 Click on the label to select it 2 Right click and select Properties 3 On the Box tab of the Box Properties dia log box click Font The Font dialog box appears 4 Set the text font style size and color The sample area previews the font 5 Click OK to commit the changes NOTE To change the color of the atom labels in the structure box you must use the Periodic Table See Periodic table on page 457 Customizing numbers Using the Box Properties dialog box you can specify how numeric data is displayed in forms you can customize the following properties e Currency symbol e Decimal position e Scientific notation To specify the numeric format 1 Right click in a data box containing numeric data and click Properties The Box properties dialog box appears 2 Click Format The Numeric Format dialog box appears N
325. se and reopen the form without saving rename the query Rename When the Query Saving prefer ence has been set to Discard unnamed queries this has the same effect as Keep for all queries at the same Sort Folder depth in the tree sort alphabet ically by name You also use the context menu to display the Query Properties dialog box In this dialog box you can modify the query name add a comment or change the color used in plots Text entered in the Comments box will replace the standard description displayed along with the number of hits Query Properties X Name S55 query CS0 comments Co i co Hts 3 Tabie MoT abie SELECT Moiname Mol _JO Strutture A ox FROM MolT able WHERE Mol_ID IN 46 63 86 93 94 108 118 119 121 1 Corcel Figure 21 28 The Query Properties dialog box 382 Queries Chapter 21 Domains If you are browsing a list other than the full data base you can make it seem that the database con sists only of the current child list Click Search gt Domains gt Set Domain to Current List The current list acts like a full database For example a Retrieve All command will retrieve only this list without selecting Search Over Current List searches will go over it only etc To reset searches to the full database Click Search gt Domains gt Reset to Full Database NOTE Set Domain to Current List remains in effect until cancelled If you save the form it will
326. see Structural Query Features on page 483 Chem amp Bio Draw allows you to draw many objects that have no chemical meaning These include boxes circles arrows orbitals and others It also allows you to assign non chemi cal styles color to objects that have chemical meaning ChemBioFinder 12 0 ignores these properties and stores only objects with chemi cal meaning in structure fields To store a Chem amp Bio Draw drawing exactly as drawn store it as a picture You can copy and paste a Chem amp Bio Draw drawing into a Picture field Figure 20 2 Form with picture field NOTE Objects stored in a Picture field have no chemical significance and cannot be searched Viewing models using Chem amp Bio 3D ChemBioFinder 12 0 also provides access to the Chem amp Bio 3D Control This means a Structure data box can be designated as Chem amp Bio 3D style To view the molecular model for a structure 1 In the Database pane of the Explorer win dow double click the Structure field to add another Structure field to the form 2 Right click in the field and click Properties ChemBioFinder amp BioViz 351 User Guide 3 In the Box Style section select Structure Chem amp Bio 3D style from the drop down menu The Structure field displays a 3D structure Figure 20 3 Form with 3D structure field To rotate the model or modify the display dou ble click in the field The default tool is the
327. st it automatically fills in the user name and the password if Save password was checked when the item was created NOTE The first time you bring up the Oracle Connection dialog box there is no list of recent items so ChemBioFinder 12 0 offers to create one for you If you accept it generates a list of 414 ChemBioFinder Oracle Chapter 25 all available hosts as found in the file tnsnames ora created during Oracle client configuration e The database is opened and the list of tables displayed NOTE The list of tables shown in the tree consists of all tables and views owned by the current user plus those to which the user has been granted certain privileges To see the details you can turn on SQL tracing while a database is being opened 4 Proceed as you would for any ChemBio Finder 12 0 database click to select the table you want to display set other desired options and check the box on the Form tab if you want to generate a form automati cally The Oracle tab of the dialog described in Setting Oracle preferences on page 417 The features on this tab are mainly for advanced users and do not require adjustment NOTE The Oracle tab appears in the Properties dialog only when an Oracle database is open 5 Click OK The database opens in a display form if you requested one The Database Wizard can also be used to open an Oracle database A button on the Wizard labeled CS Oracle C
328. st on the Search menu or toolbar You can verify that you have selected the par ent list by viewing the status bar information With the parent list selected you can add another child list to your query at 1 of 1187 db 38547 Figure 27 19 The value 1187 in the status bar indicates that the parent list in figure 5 has been selected 38547 is the number of entries in the full list Merging lists with drag and drop In some situations you might want to merge two lists using drag and drop The result is a new list that has attributes based on the merged lists 1 Select a list and drag it onto another list The Restore Merge List dialog opens 2 Select the type of merge you want in the Restore Merge List dialog box 3 Click OK A new list is displayed with the merged criteria you selected Restore Merge List L1 current list Replace use L2 4 5 hit s EHB C Intersect L1 and L2 L2 C Subtract L1 L2 3 5 hit EN Boles C Union L1 L2 Subtract from L2 L1 Cancel Figure 27 20 Restore Merge List dialog Saving query lists When you transfer data to ChemBioFinder 12 0 from BioSAR Browser ChemBioFinder 12 0 opens a file of type bsbxml and creates a form to simulate the BioSAR setup At the same time it restores whatever hitlist was in effect in BioSAR In ChemBioFinder 12 0 the BioSAR hitlist is automatically saved when you save close and reopen a file This is differ
329. stogram plot in the BioViz plot properties dialog box the plotting axis switches to X and the Bins section becomes available Each bin in a histogram is labeled with its high low cutoff points Note also that the data for the bin is displayed in the status bar as you mouse over it When you overlay queries the histogram bins display the partial membership of the selected queries within the bars of the histogram ue d u4 4 S mees me sot erten o mim e m ezma 1 ee ae Satse ee co v reer so more aie n urne oar eson Figure 26 5 Histogram display with overlaid queries Plot options BioViz options are available from the Bio Viz Properties dialog box and from the context right click menu Some of the context menu ChemBioFinder amp BioViz 425 User Guide commands repeat options in the Properties dia log box Dialog Option Description Dimension Number of variables plotted One and two dimensional plots are currently supported Table 25 BioViz preferences General tab Style Currently supported plot styles are Line Scatter and Histogram Bin By number Sets up n bins evenly spread across the whole range of values n must be lt 500 By size Sets up bins of size n The number of bins will be as many as are necessary to cover the range Dialog Option Description Locked Locks the display When the display is locked the following have no effect
330. structure and the R Group table appear in the structure window 11 Continue the query as usual ChemBioFinder amp BioViz 365 User Guide Reaction searches You can search and store reactions In a reac tion one or several compounds reactants are transformed into other compounds products Individual reactants or products are separated from each other with plus signs The reactants are separated from the products with an arrow Reactions may have multiple steps for exam ple A gt B gt C gt D Here A is the reactant and D is the product B and C are intermediates for the complete reaction A multi step reaction is actually a shorthand notation for many related reactions In the example above B is an intermediate for the complete reaction but it is also a reactant rela tive to C or D It is also a product relative to A The complete reaction implies many sub reactions such as B D and A gt B Reaction centers The most important part of a reaction is the part that actually changes from the reactants to the products This part which probably includes a number of atoms and bonds is called the reaction center For example only the bold bond in the figure below and the two atoms on either side is part of the reaction center The rest of the structure is unchanged from the reactant to the product Q OH J I JON FO cl Pa on FO F
331. t dialog box is similar to the Data Import dialog box It gives you options for file naming and file type selection and lets you select which fields will be exported If you save to an existing file you have the option to replace or append the records The Text Options tab of the dialog box con tains options relevant to both text file export and structured text export It also has an option 394 Importing and Exporting Data Chapter 22 Prefix output filenames relevant to Oracle subform data and an option to select only the fields on the current tab for tabbed ChemBio Finder 12 0 forms To export a file 1 Use the File gt Export submenu to select the output file type The Data Export dialog box appears 2 Type a name and path for the file or click the File button and browse to an existing file 3 Select deselect the fields you want to export 4 Click the Text Options tab and choose appropriate options NOTE Choosing Comma delimited does not automatically set the file type Text files txt may be either tab delimited or comma delimited If you want to export in the Comma Separated Value csv format you must name your file accordingly either by typing the name or selecting the file type from the Save As dialog box 5 Click the Export button The file is exported Saving structures Saving structures is similar to exporting them without the fuss To save the structure on display 1 Right
332. t formula data box formu created above SETFIELD 21 change field for formula data box to molweight molweight CAL commands DELBOX syntax Deletes a data box frame static text box pic ture box button or subform the active form DELBOX box 508 CAL Commands Appendix D The DELBOX command has the following argument Part Description box Box identifier indicating the box to delete Remarks The DELBOX command is a shortcut for FORMEDIT ON followed by SELECT fol lowed by the Menu Command Edit Clear The DELBOX command deletes only the box not its actual contents For example deleting a button does not delete the CAL script file from your disk CAL commands SETFIELD syntax Connects a database field to an existing data box or a CAL script name to an existing but ton or replaces one already connected SETFIELD box fieldname The SETFIELD command has the following arguments Part Description box Box indicating the target fieldname String containing the data base field name if the target is a data box or CAL script name if the target is a button to assign to the target CAL commands SETTEXT syntax Attaches a text string to a frame text box or button or replaces one already attached SETTEXT box text The SETTEXT command has the following arguments Part Description box Box identifier indicating the target
333. t in ChemBioFinder and creat ing a form 3 Add a row containing the table name col umn name and a column of type PICTURE Searching Here s what happens when you present a query to ChemBioFinder Oracle 1 If the query contains a structure it is con verted to a text representation and copied to a temporary table NOTE The table is called temp_queries I is created in the CSCartridge tablespace and removed as soon as the search is finished or interrupted ChemBioFinder does not yet handle the case of multiple structure boxes where more than one contains a query 2 The query is converted to a SQL select state ment Query components in form boxes are ANDed together just as in ChemBioFinder where the structural parts are calls into the CS Oracle Cartridge structure search func tions 3 The hits table is created if it does not already exist 4 A unique ID is assigned to the new list which will result from the search The select state ment is wrapped in a larger SQL statement which will cause the results to be deposited directly into the hits table 5 The SQL is executed When the search is complete the results are new rows in the hits table Each row contains the new list ID alongside the ID of a record from the searched table 6 The final list is prepared by a join selecting rows from the main table which have record ChemBioFinder amp BioViz 543 User Guide ID s matching those of the new list in t
334. tance in pixels between the bottom edge of the box and the top edge of the active form fieldname Database field name defini tion that will provide the data that is displayed in the data box Remarks When a new box is created it adopts the cur rent font settings These settings can be con trolled with the FONT command You can assign a fieldname even if there is no data source for the form If a data source is assigned at a later point and a field within that data source has the same name as assigned to the data box the data box will automatically display the contents of that field ChemBioFinder amp BioViz 503 User Guide After a box is created its field name can be changed with the SETFIELD command DBOX and FRAME example This example uses the DBOX command to cre ate a short wide data box near the top left of the form and display the Formula field within it It then uses the FRAME command to label the data box with a slightly larger frame DBOX 10 20 210 50 Formula FRAME 5 5 215 55 Formula CAL commands FRAME syntax Creates a new frame on the active form FRAME left top right bottom text The FRAME command has the following argu ments Part Description left Integer value representing the distance in pixels between the left edge of the frame and the left edge of the active form top Integer value representing the distance in pixels between the top edge of the
335. tches between Form View and Table View e Database Wizard activates the Database Wizard to connect a database to a form Form toolbar Use the Form Toolbar to create a new form or to add an object to an existing form ee ww wwe wc c ween cw cn tence wenn ween cence n cece cen cencncccccncescesceey Selection Check bax Contro Box n Frame Picture Subform i OE PE LTT A Le KA VEEE j boa ar J xli oo to hint a 3 fe anc nc ccc cc Sac i acres rs Data T Profile Box FramedBax Sutton Bax id Figure 16 2 The Form Toolbar NOTE The Form toolbar docks on the left side of the ChemBioFinder 12 0 window by default but can be docked anywhere or torn off as shown The tools are described in Forms on page 311 288 The User Interface Chapter 16 Search toolbar The Search Toolbar contains the tools you need to query the database and work with the hitlists that the query produces Enter Retrieve Previous Restore Find ne All Query List List Find Find Current Save List Restore Molecule Previous List Figure 16 3 The Search Toolbar Record toolbar The Record Toolbar contains the tools you need to browse a database or hitlist It also has tools for adding deleting and changing records First Goto Last Undo Omit Record Record Record Changes Record R cord Tog lbar Id 4 E gt bi p Previous Next Adda Commit Delete i Record Record Record Changes Record Figure 16 4 The Rec
336. ter 18 Table 31 Searching security options If you want users to Then click use all of the above options Searching 7 Click the plus sign next to Update records to display the options take the appropriate action Table 32 Update security options If you want users to be able to Then click update database records Update records add database records Add new records delete database records Delete records 8 To allow users to import data SDFiles or RDFiles select Import data 9 To allow users to export data including delimited text files select Export data 10 Click the plus sign next to Print to dis play the options take the appropriate action Table 33 Printing security options If you want users to Then click print a single record only Single record Print several records Several records Use print preview mode Print preview Table 33 Printing security options If you want users to Then click perform all of the above Print functions To complete setting security 1 Click Enable 2 Click OK The options you choose are applied to the form Disabling security To disable security and reset defaults 1 Right click in the form and click Properties 2 In the Form tab of the Form Properties dia log box click Security The Form Security dialog box appears 3 In the Form Security dialo
337. ter Query enters search mode the PUT DATA command enters the search string gen erated earlier in the script and the Menu Command Search Find executes the search append off setval 1 append on getdata 1 link_field append off file open d chemfndr otherform cfx search enter query putdata link_field v1 search find CAL commands APPENDVAL syntax Concatenates a new string to the end of an existing user variable APPENDVAL v text The APPENDVAL command has the follow ing arguments Part Description User variable to which the text is concatenated variable text String that is concatenated to the variable Remarks APPENDVAL is a shortcut designed to make it easier to build string values It is the same as setting APPEND ON doing a SETVAL and then restoring APPEND to its original state If variable is omitted the text will be assigned to V1 Saving compounds example This example uses the LOOP ENDLOOP commands and the Menu Command Record Next to step through each record in the current list For each record it builds a unique file path based on the current INDEX using SETVAL and APPENDVAL commands Finally it saves each compound to disk with the WRITEMOL command Since the file path ends in cdx this script saves all of the compounds in Chem Draw format append off loop setval 1 c mydir appendval 1 Sindex appendval 1 cdx writemol v1 rec next endloop Envir
338. ters this will take no more than a few seconds To plot a larger dataset reset this value as necessary 6 Click OK The Plot appears in a new window 7 Click the Notes tab to view addition infor mation For example points will not be plotted if they are missing Y values This is reported in the Notes Alternate context menu procedure To produce a single variable scatter plot right click in a numerical field point to BioViz Plot ChemBioFinder amp BioViz 305 User Guide and click ID Plot Properties Data Source Field BioViz Plot E OnX Axis Sort gt On Y Axis ai 1 D Plot Mol_ID Reset X Y Structure Fiker Window Formula v MolWeight Moinanme Calculate Property gt Figure 17 16 data field context menu Histogram plots A histogram plot is a variation of a single vari able plot where the X coordinate is the vari able value and the Y coordinate shows the count in each histogram cell To create a Histogram plot 1 Click BioViz Plots gt New on the View menu 2 Click the One Variable radio button in the Dimension box of the Bio Viz Plot Properties dialog box 3 Click the Histogram radio button in the Style box 4 Click either the Number or Size radio button in the Bins box and enter a value optional e Number sets how many bars will appear in the plot e Size sets the number of data points per bar 5 Select any numerical field from the drop down menu for the X coordinate
339. tes The dates are displayed according to the set tings in the Windows Regional Settings control panel RSstructure field cConsists of four fields a numeric ID stored in the relational database plus three fields Structure Formula Mol Weight that take data from the ChemBio Finder 12 0 structure database files M Boolean Used with check boxes When searching Boolean fields you can only search for ON This is because ChemBioFinder 12 0 automatically clears all fields when activating the Queries form You can create more than one set of structure fields in a table Each is assigned a unique set of names and each refers to its own ID column in the table although all structural data is taken from the same structure database files To create a field 1 Right click in the form and click Properties The Box Properties dialog box appears 2 Click the Field tab The Field properties appear 3 Click the Create Field The Create Field dialog box appears 4 In the Name box type a name 5 In the Type box choose a data type from the drop down menu 6 For text fields only type a width number of characters in the Width box or use the thumb wheels to select a value 7 Click OK The name of the new field appears in the data source tree Deleting fields Just as you can create any field and assign it to a data box at any time you can modify the database by deleting fields from the selected table To delet
340. the BioViz Plot Properties dialog box The plot is locked to a given dataset Note that filters will be locked as well Expand the plot to view individual data points Select Zoom on Drag on the BioViz context menu Dragging over a section of the plot enlarges it rather than selecting the points Change the color of the data points In the Queries control select Change Color on the Queries context menu Note that you cannot change the color of the Full List only of daughter lists The data points are displayed in the color you select Plot multiple datasets overlay With the Full List selected click Color on Plot on the Queries context menu for each query you want to overlay Alternately click the query or the colored box next to it A check mark appears in the box next to the query name and the data points are displayed in the color assigned to the query Tutorial 7 Working with subforms Subforms allow you to display relational data If you have a database containing two or more data tables and these data tables share a com ChemBioFinder amp BioViz User Guide 309 mon linking field then you can display data from both tables Whenever the value of the linking field changes in the main form the sub form only displays those records from its table which have the same value in the linking field You can also use subforms to display data from different databases
341. the Structure box The new or edited structure is now displayed but has not yet been added to the database Click Record gt Commit Changes then click the Commit Changes icon or move to a different record The changes are stored With a few exceptions you can store any chemically meaningful structure or reaction that can be drawn in Chem amp Bio Draw Within Chem amp Bio Draw you can confirm that a struc ture is chemically meaningful by selecting it and using the Structure gt Check Structure menu command For more information see the Chem amp Bio Draw User s Guide Two exceptions are e ChemBioFinder 12 0 does not support importing molecules with multiple or vari able points of attachment such as ferrocene e ChemBioFinder 12 0 does not recognize bare heteroatoms For example if you draw the following structure N Chem amp Bio Draw reports an illegal valence when you choose the Check Structure command ChemBioFinder 12 0 automatically infers hydrogen atoms to main group elements as necessary to fill their lowest acceptable valence The structure above is registered in as methylamine CH3NH Structures and reactions drawn with query properties are generally meaningful only in the context of a query Query structures can be stored in a ChemBioFinder 12 0 database but they are not treated as Markush structures and are not guaranteed to be hit by all valid search queries For more information
342. the above action Subform plots A third type of view is the plot view You can use BioViz to create a 1 D 2 D or histogram plot of any numerical field s of the data table connected to the subform To create a subform plot You must be working with a form that has a subform with at least one column of numeric data 1 Click the subform box to activate it 2 Click the View gt Subform Plot View toggle The BioViz Plot Properties dialog box appears 3 Set up the plot See Creating a plot on page 425 for more information NOTE For 2 D plots both numeric fields must be in the data table associated with the subform data box The plot appears in the subform data box Subform plots have less functionality than reg ular BioViz plots While mousing over a point will highlight it selection filtering and color ing are disabled Since selection is disabled subform plots are always in zoom on drag mode Use Control W to toggle between the form table and plot views The Switch to Table tool only toggles between form and table as does double clicking in the subform TIP The subform remains selected until you click the main form so you can only browse in the subform If a plot is displayed browsing does nothing If you toggle the main form to table view when a subform plot is displayed the plot is dis played as a graphic rather than an active plot Using scripts in subforms You can specify
343. the current form OPENDB c data mydb mdb Variable commands SETVAL v text READVAL v filename WRITEVAL v filename INPUT v prompt PASSWORD v default GETDATA v box PUTDATA box text FROM_CANON str CLIPBOARD TO_CANON v CLIPBOARD ROM_SMILES str TO_SMILES v APPEND ON OFF APPENDVAL v text INCREMEN v DECREMEN v LET v v op v wn UBSTR v lt str gt lt from gt lt to gt CAL has nine variables called V1 V2 V9 These are temporary storage locations you can use to move information between form boxes and other data sources Variable names can be substituted in any CAL command Any item shown in italics in a com mand description may be replaced by the name of a variable prefixed with a dollar sign For example MSG message may be either MSG An explicit message a message explicitly coded into the script or MSG V2 a message taken from variable 2 at run time ChemBioFinder amp BioViz 529 User Guide You may concatenate variables and variables and literals together in CAL commands You must add both a leading and trailing dollar sign to the variable name For example MSG V2 V1 Displays a message box with the value of V2 immediately followed by the value of V1 Most commands for manipulating variables take an optional variable number as the first argument If the number
344. the database you chose In this example when a record is retrieved in the main form its Molname is used to search the Synonym field of the Synonyms table of CS_Demo The subform displays the hits from this search Subform generator Automatic subform generation is part of auto matic form generation see Creating forms automatically on page 311 To generate a subform 1 Right click on a blank area of the current form and click the Data Source context menu command The Form Properties dialog box appears 2 In the Form Properties dialog box select the Form tab 3 Select the Generate form check box then click the Style button The Form Generation dialog box appears 4 Click the Subforms button The Subform Generation dialog box appears 5 For each subform you want to include a Choose a field in the Link from box to specify the linking field of the parent form b Expand the table you want to display in the subform in the Link to box and select the linking field of the subform c Click the Add button to append the selected subform to the list being gener ated 6 When you have added all subform links click OK to close the dialog box and return to the Form Generation dialog Change existing subform layout You can use the Form Generator to automati cally change the overall layout of an existing subform To change the layout of an existing subform 1 Right click on the title bar of the
345. the queries for that form Each time you carry out a search or list opera tion a new query is generated in the tree A name is assigned to the query and it is dis played in the tree along with the size of the list number of hits and a brief description The generated name is Q lt n gt where nis a sequential number and indicates that the query has not been named or marked for sav ing CAUTION Depending on your preference settings unnamed queries may be automatically dis carded See Saving and restoring lists on page 382 for details To activate the Queries tree control 1 Click the View gt Explorer Window menu option 2 Click the Queries tab on the Explorer win dow to display the Queries tree Queries are listed as children of the database displayed as Full List When you select Search Over Current List from the Search menu before performing a query it is displayed as a child of the previous list The current list is indicated with a frame around the colored box 7 database E o1 16 555 query full list BLo2 24 Molweight E OF ommon B os5 1 555 query Current List marked with a frame Search over Current list query child list Database Queries Favorites Figure 21 27 The Queries tree To restore a query Double click a query if you want to then choose merge the hits of the selected query with the curr
346. the record within the current list to display and click OK The specified record is displayed NOTE Record numbers are temporary refer ring only to positions within the current list in its current sort order For example if you have 338 Databases Chapter 19 done a search that found ten hits then the only valid record numbers are 1 10 If you want to move to a specific absolute location in a data base you must run a search for a value in a field that identifies that location The data table Sometimes browsing through a data record set is more convenient if the data is presented in tabular format NOTE You cannot add or modify records while viewing data in a table To display data in a table Click View gt Data Table gt In Separate Window or type Ctrl T A list window containing the fields and records in the form appears Figure 19 9 Data Table view in a separate window To display a particular record in the form Click the record s entry in the list window By default the fields in the Data Table are dis played in the order in which they were created To reorder the columns in the Data Table 1 Click one of the column headers to select the column T Taai Liege Figure 19 10 Column selection indicator in the Data Table view 2 Drag the header to a new position The cursor changes to the icon shown below The new position is indicated with a red vertical line Figure
347. there is limited space for the data box To add a scroll bar 1 Right click a data box and click Properties The box properties dialog box appears 2 In the Box style section select the With scroll bars check box 3 Click OK The scroll bar appears on the bottom right in the data box Hiding data boxes You can show or hide boxes when switching between query and browse mode For example you can hide non searchable data boxes during query entry or show only those data boxes that display information useful for query entry ChemBioFinder amp BioViz 321 User Guide When you are in form layout mode all boxes are visible regardless of the setting To hide data boxes 1 Right click on the box and click Properties 2 In the Box Style area select the Hidden in Browse Mode check box or the Hidden in Query Mode check box 3 Click OK 4 Deselect the Layout Mode to view the results Customizing text Use the Text Format toolbar to customize text fonts sizes styles colors and alignment in form boxes All of the standard text formatting options are available To display the Text Format toolbar Select the View gt Toolbars gt Text Format menu option The Text Format toolbar appears NOTE Text copied from a word processor such as Microsoft Word retains its styles when pasted into a Rich Text box The text format toolbar is active e When you are editing a memo field in a rich text box In thi
348. this case in the Bond Proper ties dialog of Chem amp Bio Draw you specified that the bond type may be single or double S D Finally by entering S Se Te enclosed in brackets you specified that one of these ele ments must match in the target molecules Searching fullerenes A search of fullerenes can illustrate the restric tions you can place on a formula search Sup pose you want to find all fullerenes containing 20 to 80 carbon atoms but you also do not want to include large organic molecules The formula query could be C20 80 HO By designating zero hydrogen atoms you exclude hydrocarbons from the hit list By clearly capitalizing the elements and spacing the query you avoid searching ambiguities 386 Queries Chapter 21 although there were no ambiguities in this example Link nodes and multivalent Rs A link node is a placeholder for zero or more unspecified atoms It is especially useful when searching for targets with any of several ring sizes or chains substituted in particular ways at either end While link nodes are traditionally divalent ChemBioFinder 12 0 places no con straints on the upper limit of the range Multi valent R and A atoms are functionally similar to link nodes They may be thought of as higher valent link nodes Q Rio we cd Chahe Figure 21 33 Link nodes The traditional representation of a link node is CH2 but this is misleading because any atom type can substit
349. tings 1 Click the Toolbars tab in the Customize dia log box The Toolbars tab appears and shows all of the toolbars that currently appear in the ChemBioFinder 12 0 window Customize Commands Toolbars Keyboard Menu Options Toolbars Main Toolbar ViMenu Bar Reset All Record Toolbar Search Toolbar Text Format Toolbar Figure 29 11 2 Click the toolbar you want to return to default settings and then click the Reset button The toolbar in the ChemBioFinder 12 0 window changes to the default settings To return all the toolbars to the default set tings 1 Click the Toolbars tab in the Customize dia log box The Toolbars tab appears and shows all of the toolbars that currently appear in the ChemBioFinder 12 0 window 2 Click the Reset All button Periodic table ChemBioFinder 12 0 features a periodic table for data display and formula entry Selecting an element displays physical and historical data To display the Periodic Table window 1 Click the View gt Periodic Table menu option Periodic Table 8 Oxygen Mass 15 9994 Electroneg y 3 44 Valencefs PA Discovered by Priestley 1774 Tij V Cr Co Ni Nb Figure 29 12 2 Click an element to display its name mass and other properties in the top box and to display its symbol in the bottom edit box B
350. toma tion ChemBioFinder 12 0 is an OLE Automation server meaning that it offers a collection of data management capabilities to outside programs capable of communicating with OLE objects While this collection is cur rently fairly small it is adequate for a variety of data retrieval and search tasks This feature allows you to write a custom Visual Basic pro cedure that directly retrieves and manipulates data from ChemBioFinder 12 0 The general procedure for accessing ChemBio Finder 12 0 data from within a Visual Basic script is as follows 1 Create a ChemBioFinder 12 0 Document object typically passing a filename so that you open a form complete with its database connection 2 Use methods of the Document object to move through the database search and access data Document methods include some that access Field objects used to query the data in the database and Mole cule objects for accessing details of molec ular structures For more information see the CambridgeSoft SDK web site http www cambridgesoft com services docu mentation sdk Using Microsoft Access The methods described above for communicat ing between ChemBioFinder 12 0 and Excel apply also to Access You can start Access using the EXEC command You can send it DDE commands contained in a CAL script although Access provides fewer capabilities with DDE than does Excel Or you can write programs using Access Basic that rely on the OLE Autom
351. traight SQL and passed directly to the database as the WHERE clause of the SQL query These must contain column names and punctuation as dictated by SQL For example a valid query might be molname like benz and bpoint gt 200 A straight SQL query may be entered in any box of the form which contains non structural data The SQL query is not associated with the box in which it is entered Query procedures Searching includes the following steps e Setting the search type preferences Struc ture searches only e Entering the query in the form e Submitting the query to the search engine To perform a search use the Search menu or the corresponding tools in the Search toolbar Enter Retrieve Previous Restore Find Quey Al Quern List List pe en Find FindCurent Save List Restore Molecule Previous List Figure 21 22 The Search toolbar The following procedures describe searching with the Search menu You may use the Search toolbar instead for most procedures Setting search type preferences You can set preferences for the type of struc ture for which you want to search To set Search Type preferences ChemBioFinder amp BioViz 369 User Guide 1 Select Preferences from the Search menu The Preferences dialog box appears with the Search Type tab displayed Preferences Display Color Search Type Details Tuning General A Bibstricture Ae Full Structure 2
352. tside the ideal so it has a high cost and a score of 1 3 Right click in the profile box 4 Click the Compound Pro file gt Search Sort gt Sort relative to ideal con text menu command 5 Click the Switch to Table icon to make it easier to compare the profiles The compounds are ordered by dist value from 0 00 to 1 00 Note that the score and dist values are the same 6 Browse to bromobenzene mw 157 The score for this compound is not ideal It will be approximately 0 1 depending on how you set the profile TIP You can sort by Molname or MW to find the compound more easily 7 Click the Switch to Table icon again to return to form view 8 Right click in the Profile data box then click the Compound Pro file gt Search Sort gt Sort relative to current context menu command 9 Switch back to Table View are browse the results Bromobenzene is at the top of the list Other compounds with similar scores follow Note that the score and dist values are no longer equal Customizing The gallery of cost profile templates shown in the Cost Profile Chooser dialog box was designed to help you get started Some are based on user experience other chosen to pro vide the most common cost profile patterns As you work with the compound profiler you will develop your own templates and may want to substitute them in the chooser The templates are taken from files stored in the ChemBioFinder system profiles folder
353. ture Box Either can be used to change the display mode To change the display method one 1 Double click in the 3D Structure Box to activate the Chem amp Bio 3D display 2 Point to an atom or bond in the model and Right click 3 Select a display mode from the Display Mode submenu Method two 1 Double click in the 3D Structure Box to activate the Chem amp Bio 3D display 2 Right click anywhere in the 3D Structure Box but not on the model itself 3 Select a display mode from the View gt Model Display gt Display Mode submenu For more information on the Chem amp Bio 3D Control see the Chem amp Bio 3D User s Man ual Setting fixed and live data In the Box Properties dialog box you can des ignate whether the data source is fixed or from a field Fixed data is attached to the form and does not change as you browse Data from a field is stored in the database and is different for each record As you browse the record dis play updates according to the contents of the field To specify live data for a data box 1 In the Box tab select the field to associate and then click the Field radio button 2 Click OK The box display updates as you change records To specify fixed data for a data box 1 In the Box tab select the field to associate and click the Fixed radio button 2 Type a label in the text box If you choose a structure or picture field click the browse tool to browse to the fi
354. types not listed in the Periodic table The default is Purple DISPLAY BOND_NUMS Whether or not to display Oor 1 bond numbers on each bond The default is 0 do not display DISPLAY BOND_SPACING Spacing between double 0 100 bonds as a percentage of bond length The default is 12 DISPLAY FONT_ADJUSTMENT A correction to the font size 50 80 of atom labels based on a structure s average bond length More specifically the font size of atom labels is nominal value FONT_ADJUSTMENT 10 0 average bond length The default is 20 DISPLAY FORM_COLOR The background color of the color form This parameter can be set manually in the Color tab of the Preferences dialog The default is Grey ChemBioFinder amp BioViz 517 User Guide Section Preference Description Values DISPLAY FRAME_PICTURES Whether or not to display 0 or 1 borders around pictures This parameter can be set manu ally in the Display tab of the Preferences dialog The default is 1 display DISPLAY GRID_SPACING The spacing in pixels 0 100 between hash marks on the grid This parameter can be set manually in the Display tab of the Preferences dialog The default is 10 pixels DISPLAY MAX_BND_LEN The scaling factor by which 10 500 the maximum bond length is modified This value is only applicable when the Fit to box optio
355. u item that appears within the Find Structure submenu under the Search menu For more information see Special structure searches on page 376 Clustering This is a new tool for ChemBioFinder bio visual chemist See Clustering in BioViz on page 445 for more information ChemFinder amp BioViz 281 User Guide 282 What s New Chapter ii ChemBioFinder amp BioViz About ChemBioFinder 12 0 ChemBioFinder 12 0 is a database manage ment system for anyone who works with chemical information It provides a place to store chemical structures physical properties notes tables of data and charts With ChemBi oFinder 12 0 you can quickly find and orga nize your data About BioViz BioViz is a visualization add in for ChemBio Finder 12 0 that allows you to plot numeric data in ChemBioFinder 12 0 databases You can identify trends and correlations in your data and within subsets of your data without exporting to another application You can have as many plot windows as you like each show ing a different visualization of data from the current form ChemBioFinder 12 0 amp BioViz collaborates with the following CambridgeSoft products to help you perform specific tasks Chem amp Bio Draw Lets you draw two dimensional structures and reactions Chem amp Bio 3D Lets you draw three dimen sional structures Chem amp Bio Draw Excel Allows you to export data to Excel About this guide
356. u set the field size when you create the field up to a maximum of 254 characters e Picture displays Windows metafile data Pictures are scaled to fit within picture boxes with fixed height to width ratios e Formula displays any kind of text but num bers are subscripted Formulas are pre sented in modified Hill order as follows If a substance contains both carbon and hydrogen the carbons are listed first fol lowed by the hydrogen atoms followed by other elements alphabetically by element symbol If a substance contains carbon the carbons are listed first followed by other elements alphabetically by element symbol Otherwise all elements are listed alphabeti cally by element symbol e Button used to create buttons to actuate scripts Buttons display button labels e Rich Text displays styled data in multiple lines Use Ctrl Enter to start a new line You can format the text with the Text For mat toolbar If the data in a field contains rich text markup characters are displayed e Structure Chem amp Bio Draw style displays chemical structures or reactions Reactions are laid out for best fit with the box and the layout may change if the box is reshaped The box defaults to using the Chem amp Bio Draw Control to create and edit structures but you can reset the preference For more information See Setting preferences on page 451 e Structure ChemBioFinder style as above but defaults to
357. ub form and the main form simultaneously To search a subform 1 Click the Search gt Enter Query menu com mand to clear the subform and main form TIP You can also click the Enter Query icon on the Search Toolbar or type Ctrl F 2 Enter a query in the subform data box See Queries on page 357 for details on enter ing queries 3 Click the Search gt Find menu command If the subform is linked to the main form the hit list contains the main form records related to the matches in the subform search You can browse and save this hit list just as you would a hit list from a main form search If the subform is not linked to the main form it behaves independently of the main form and is searched separately Viewing subform data in a table If you have more than one record in the sub form associated with a single record in the 402 Relational Data and Subforms Chapter 23 main form it may be more convenient to view the subform as a table while you browse through the main form The table view shows you the complete list of related records for each entry in the main form To display a subform in Table view e Select the subform and do one of the fol lowing e Double click on a record in the table e Click the View gt Data Table gt In Current Window menu command e Type Ctrl T e Click the Switch to Table tool A table view of the records in the subform appears To return to the Form view repeat
358. ucture similarity search and will often return additional ones as well CAL Commands ChemBioFinder Automation Language CAL is a set of commands that control many Chem BioFinder operations You invoke CAL commands in either of two ways e Interactively Type commands and exe cute them one at a time on a command line e Scripts Use ASCII files containing a series of CAL commands to be executed automatically in sequence Arguments to commands consist of numbers and text strings You can enter a text string without punctuation unless the argument is not the last one on the command line and contains multiple words or spaces In this case you must enclose the argument in quotation marks CAL help Information about the CAL command and variables is available in the CAL Scripting Help window To access CAL Help 1 From the Scripts menu select Command Line The Enter Cal Command dialog box appears 2 In the Enter Cal Command dialog box click the Help The CAL Scripting Help window appears W CAL Scripting Help Command Arguments Description AAMAPS ONIOFF display don t display colored 44 map ACTIVATE lt subform bo direct subsequent input to subform ADDRECORD COUNT Append one or more empty records APPEND ONIOFF set append mode on off default toggle APPENDVAL v lt text gt append text to specified variable ARROWBOX rect launches moving arrow Variable Description
359. ul only in script files not interactive CAL An asterisk is used to mark a line as a com ment and not a command that should be exe cuted 536 CAL Commands Appendix D Labels and GOTO give a mechanism for jump ing backwards or forwards in a script A label may be any text string starting or ending with a colon It may appear anywhere in the script Prior to ChemOffice 2005 it had to appear prior to any GOTO that referenced it IF is a standard conditional statement It com pares two values according to an operator and then executes its final statement if the result is true In the IF ELSE format it executes the ELSE statement when the IF statement is false Valid operators are Table 32 lt gt lt gt LOOP begins a section of code that will exe cute repeatedly until ENDLOOP is reached By default the number of times the code exe cutes is equal to the number of records in the current list but you can provide a specific count in the LOOP statement TIP ENDLOOP can be used anywhere within a loop clause to mean continue to the next iteration Example LOOP RECORD NEXT IF HAS_MOL 0 ENDLOOP ENDIF CLEAN ENDLOOP In this example if a record has no structure the program goes to the next record and skips the CLEAN PAUSE temporarily stops the script from exe cuting for a specified number of tenths of a second If no number is given the duration of the pause is 2 seconds EX
360. ula or molec ular weight NOTE When you search by chemical structure formula and molecular weight ChemFinder Office uses all the criteria together The information about each property adds to the search criteria of the other properties 3 Click Find Now a ChemFinder Office shows all of the files with the properties that you specify in the Hit List window below the Struc tures window b If ChemFinder Office finds no hits a warning message appears c To refine your search so that Chem Finder has a greater possibility of find ing hits use the Search Options tab To expand your search use the Look In tab For more information see Refining your search on page 478 Browsing search results You can view the search results in the Hit List The Hit List displays all of the files in which your search found matching structures File Size D INFOCHEM C C Program Files Ca 8 704 NCI_DEMO C C Program Files Ca 7 168 NIADEMO CPW C Program Files Ca 10 752 Figure 30 4 A ChemFinder Office hit list To view the search results To view the entire Hit List use the scroll bars e To display each hit in a given file in the Structure window select the file in the Hit List and use the arrows in the Search Record toolbar lq 4 gt gt i Figure 30 5 The Search Record toolbar e To display the actual file double click on a file name in the Hit List or right click and select
361. ule to specified file WRITEMOL saved mol WRITETEX export current list to a text Diemen file PENDB R E RE dbname RETABLE tablename TABLE tablename TABLE tablename REFIELD fieldname ELFIELD fieldname SORT D fieldname OGOaANnNnDUDAO Oracle database commands SQL lt SQLStatement gt SOLSELECT v lt SQLSelectStatement gt 528 CAL Commands Appendix D OPENDB opens a standard molecule database Specify a pathname to the MDB file or a name from the ODBC Data sources list When con nected to an Oracle database OPENDB takes a table name instead of a database name You can specify the mode of database opening e R read only e E exclusive e RE read only and exclusive CRETABLE creates tables in the current data base DELTABLE deletes tables in the current data base SELTABLE selects a table form the current database and makes it the current working table for subsequent field actions CREFIELD creates fields in the current table in the current database You can specify the field type and width in the CREFIELD com mand The default text field is 50 characters wide DELFIELD deletes fields in the current table in the current database SORT sorts the database contents on the speci fied field The default sorts the database in ascending order You can specify descending order with D SQL allows SQL to be passed directl
362. ulel cdx molecule2 cdx and molecule3 cdx 5 Click Save If you send a file to ChemFinder ChemFinder opens and the file you save appears as a form If you send a file to ChemDraw a warning appears to tell you the path of the file you saved Refining your search You can refine your search so that you have a greater chance of finding the structure you want Use the Search tools and the Search Options tab to change your query to refine your search To refine your search 1 From the Search menu choose Restore Pre vious Query or click 2 Change your query with the Search Options 3 Select the files and data sources you want to search 4 Click Find Now ChemFinder Office shows all of the files with the structure that you specify These files appear in the Hit List window below the Data Source Find Chemical Structures window If ChemFinder Office finds no hits your search may be too narrow and you should broaden your search options Using the search tools Some ChemFinder tools used to refine your search can also be used in ChemFinder Office To use the search tools e From the Search menu or Search toolbar take the appropriate action If you want to then click begin a new search Enter Query search for the current properties chemical structure chemical formula molecular weight Find Current Query see all the records in the search including records without a match to
363. ult at program startup is APPEND OFF APPENDVAL is a shortcut designed to make it easier to build string values It is the same as setting APPEND ON doing a SETVAL and then restoring APPEND to its original state TIP The difference between APPEND ON and APPENDVAL is that APPENDVAL does not add a carriage return to the string being appended whereas APPEND ON does If you want to insert a carriage return at the end of the string use APPEND ON INCREMENT adds 1 to the value of a vari able Use INCREMENT in loops DECREMENT subtracts 1 from the value of a variable Use DECREMENT in loops LET allows you to perform mathematical oper ations on variables that contain integer or real number values Only one operator per line is supported It recognizes the following opera tors e for addition e for subtraction e for multiplication e for division SUBSTR extracts a substring from a variable The extracted substring extends from a speci fied character to the end of the string or from The table below shows examples of Variable one specified character to another Commands Command Action SETVAL some store text in V1 exc SETVAL 2 store text in V2 other text READVAL 9 read text from file into V9 tmpdata txt APPEND ON turn on append mode WRITEVAL append contents of V1 to file QUICIOUNE 5 Exc SETVAL 2 append text to contents of V2 append me APPEND
364. umeric Format Unformatted C Currency Fixed point C Scientific 2 H decimal places Sample 123 45 Cancel Figure 18 8 The Numeric Format dialog box 3 Select the appropriate option Table 21 Numeric format options If you want to dis Then click play a varying number of Unformatted decimal places a currency symbol Currency and select the symbol from the drop down menu the currency symbol to the right of the number Symbol on right when a currency symbol is selected a standard floating point value with a selected number of decimal places Fixed point and select the number of decimal places the numbers displayed in scien tific notation Scientific and select the number of decimal places An example of the format you select is shown in the Sample area of the dialog box 4 Click OK The format is applied to the current data box Setting color You can set the following color options e The form background color e The color of the form in query mode e The default background for all forms To set the form background and form query colors 1 Right click in a data box and click Proper ties The Box Properties dialog box appears 2 Click the Form tab to display the Form properties Box Properties SS ce pEMO Database Table Field Fom Box MolTable 0 molo Structure F Formula VE M MolWeight She Molname im C Document
365. ute for the link node For this reason represents link nodes as R R without a repeat count can match any number of atoms including zero Although any atom type of a target atom matches a link node you can impose two restrictions the on the link node e Unsaturation e Ring topology Using Chem amp Bio Draw s Atom Properties menu to apply either of these properties to the link node restricts the range of target atoms to the specified topology For example specifying the link node to be aromatic would give the following results Query Results Will hit Br Me we ae C a OO L Figure 21 34 Results of a link node query Searching more than one substructure A substructure search may contain more than one substructure unit Suppose you want to find all compounds in the CS_Demo database which contain a benzene substructure and another substructure unit containing chlorine bonded to any atom A structure query as drawn in Chem amp Bio Draw would look like this A CI Figure 21 35 Structure query with two substructures You should get five hits Browse the hits By specifying the query as above you obtain hits such as benzyl chloride shown below where the substructure units are not connected H CI H Figure 21 36 Benzyl chloride hit by query with two substructures The substructure units can overlap they can share a common atom Examples of this over lap are shown below
366. utton Click Next to repeat the procedure for each profile you want to add When you have added all of your profiles click the Finish button The profiles are displayed in the data box Cost Profile Edit the cost profile To edit drag points or right click points or lines Cost Profile low walley CLOGP 1 57 To add a new profile Right click in the editor window then click the Add Field context menu command To delete a profile 1 On the Profile tab click one of the profiles to select it 2 Right click in the editor window then click the Remove Field context menu command To change the order of the profiles 408 Compound Profiles Chapter 24 Editing a compound profile You can edit any of the characteristics of a compound profile with the Compound Profile Editor To edit a profile Double click in the profile data box The Compound Profile Editor appears 1 On the Profile tab click one of the profiles to select it 2 Right click in the editor window then click the lt Move Left or gt Move Right context menu command To change the field associated with a profile 1 On the Profile tab click one of the profiles to select it 2 Click the Field tab Change the Source with the drop down menu Change any of the other variables as required 3 Click the Cost Profile tab and select a new profile NOTE You must select anew profile when you change the source field If you forget you will
367. xported dataset must take into account Access naming rules and limitations Access database rules Because ChemBioFinder 12 0 uses the Access Jet database standard names of fields con trols and objects must conform to Access rules These are e May be up to 64 characters long ChemBioFinder amp BioViz 441 User Guide e May include any combination of letters numbers spaces and special characters except a period an exclamation point an accent grave C or brackets e Must not begin with leading spaces e Must not include control characters ASCII values 0 through 31 e Must not include a double quotation mark in table view or stored procedure names Creating a local copy of a database If you frequently use a set of data that never changes consider exporting the data as a local ChemBioFinder database Having a local data base often makes many common tasks run faster tasks such as browsing searching plot ting and analyzing Creating a local database requires two steps 1 Exporting the dataset as a CFXML file and 2 Importing the file back into ChemBio Finder Once you import the file save it as a CFX file It will then be available for you to use whenever you need it Exporting the dataset To export a dataset 1 Run a query to create the dataset 2 Click the File gt Export gt CFXML menu com mand The Data Export window opens 3 Select the options you want to apply t
368. xt 316 record 338 topology 493 transferring information to other computers 346 trigger scripts 461 Tutorial 6 Creating a BioViz chart 304 two variable plot 306 U understanding forms and databases 292 undo 325 undoing changes 352 undoing data entry 349 uniform bond length 452 union with current list 384 unsaturation 492 unsaturation in queries 492 username for secured forms 337 using atom lists 385 ChemFinder with databases 290 current molecule as a query 375 form tools 314 grids 314 keyboard shortcuts 452 log files 391 periodic table 457 scripts 467 scripts in subforms 403 Visual Basic 468 V valence charged atoms 485 checking 453 non standard state 453 unfilled 484 variable commands CAL 529 view format for structures selecting 319 viewing models with Chem3D 351 results 374 structures 319 structures in Chem3D format 320 viewing subform data in a table 402 Visual Basic 468 W Windows metafiles 315 316 317 WMF file format 317 Word files exporting 396 working with multiple hit lists 384 subforms tutorial 309 Working with Clustering 445 working with structures using ChemDraw 350 working with subforms 401 X X halogen special atom type 489 zoom 433 zoom on drag 427 ChemBioFinder amp BioViz 561 User Guide 562 Index
369. xt changes you can revert to the previous unmodified state To undo your changes do one of the follow ing e Click Edit gt Undo e Click the Undo icon on the Main Toolbar After you commit the changes they cannot be undone Redoing changes When you undo an action the Redo command becomes active You can reverse the effect of the Undo command by choosing the Redo command To redo the last action performed do one of the following e Click Edit gt Redo e Click the Redo icon The last action undone is reinstated Deleting data You can delete the contents of individual fields by using the Delete or Backspace keys You cannot delete a structure formula molecular weight or Mol_ID To delete an entire record 1 Move to the record that you want to delete using the Record commands or toolbar 2 Do one of the following e Click Record gt Delete Record e Click the Delete Record icon The record is permanently removed NOTE You can delete multiple records if you use the Table view Sorting data You can sort the database by most types of data in a form Sorting on the Mol_ID field the molecular weight field or any other numeric field arranges the current list in increasing or decreasing numeric order according to that field Sorting on the structure field arranges the list by increasing number of atoms contained in the structure Implicit hydrogens are not counted Sorting on the formula field o
370. xt searches see Text searches on page 357 300 Tutorials Chapter 17 Numerical searching To search in the CS_Demo Database for com pounds with molecular weights between 90 and 100 1 Switch to the Form View if you are not already in it 2 Click Search gt Enter Query The form is cleared so that you can enter a new query 3 Click in the Molecular Weight box and type 90 100 4 Press the Enter key You get 11 hits with molecular weights between 90 and 100 5 Go to View gt Data Table gt In Current Window The Table view appears NOTE A molecular weight query is a decimal value or range The precision of the search depends on the number of significant digits entered For more information on molecular weight searching see Numeric searches on page 358 Substructure searching To enter a query and search for a substructure 1 Click Search gt Enter Query The form is cleared to allow you to enter your search terms The status indicator in the status bar is changed to remind you that you are in query mode and the color of the form may change 2 Double click in the Structure box A blue box is displayed around the Structure box and the Chem amp Bio Draw control appears 3 Draw benzene To set the correct options for a substructure search 1 Select the Search gt Substructure menu option if it is not already selected 2 Deselect the Search gt Similarity menu option if it is select
371. y Features Appendix A When evaluating a possible match the follow ing rules are applied e Unspecified stereochemistry a plain bond may match any stereochemistry either a wedged hashed bold or a plain bond Specific bond types need not match as long as the overall stereochemistry at a given atom does match Implicit hydrogens are taken into consider ation in both the query and the target if doing so helps to determine the chirality of a stereocenter With a full structure search and the Match Tet rahedral stereo option selected the query with stereochemistry HO Finds any of HO TH N OH N OH HO o BA O N 2 OH Does not find any of HO o vi OH H OH HO i OH Relative tetrahedral stereochemistry Relative Tetrahedral Stereochemistry or RTS specifies a given relationship between the cen ters That is a known orientation of the substit uents with respect to each other rather than a known absolute configuration To specify this centers are drawn not with the standard hashed and wedged bonds but with thick bold stereo bonds Relative and absolute configurations may be registered separately in ChemBioFinder and can be distinguished by various search options The basic ChemBioFinder search philosophy can be summarized as follows a more specific query is a more precise request and should get fewer hits than a more general query If the query represents a particular absolute con
372. y clicking different elements and numbers sequentially you can create a molecular for mula in the bottom editable text box You can then paste this formula into the form for a for mula query To copy a formula from the Periodic Table to the form 1 Drag the text to copy and then press Ctrl C 2 Click OK in the Periodic Table window to close it 3 In the form click the formula box into which you want to paste the text and press Ctrl V ChemBioFinder amp BioViz 457 User Guide To display data about the selected element in the Element Editor do one of the following e Display the desired element and click the display box at the top of the Periodic Table window e Double click the desired element button Element Editor Atomic Number Symbol Name Mass daltons Electronegativity Valence State s Melting Pointe 1538 BoiingPoint C 287 loniz Pot kd mol 7625 Density g cm 3 Psa Discoverer Prehistorie Figure 29 13 The Element Editor displays properties of the selected element The color of the element is shown in the periodic table for that element and in any structure data boxes in which that element is present Cancel To change the color of an element 1 Click the Color button in the Element Editor 2 Select a color from the Color dialog box and click OK 3 Click OK in the Element Editor To reset an element s color to the default Click Revert to D
373. y from CAL SQLStatement is a SQL statement that returns no results It is therefore useful for data manipulation operations Available only when connected to an Oracle database SQLSELECT returns a one row recordset It is useful for calculations or lookups v is the name or number of a variable to receive the results of a Select statement SelectStatement is a SQL Select statement designed to retrieve a single result If v is omitted results go in V1 Available only when connected to an Oracle database If you omit the password from the connection string and you will be prompted for it when running the command The table below shows examples of Database Commands Command Action RETABLE E x creates a new table MyTable DELTABLE j deletes a new table MyTable CAL commands OPENDB syntax Opens a database and assigns it as the Data Source of the active form OPENDB dbname The OPENDB command has the following argument Part Description dbname String containing the file name of a database which could be a MDB file or a name from the ODBC Data Sources list Remarks If the file to be launched is in ChemBio Finder s standard search path only the actual file name CS_DATA is required Otherwise the complete file path c some long path CS_DATA MDB is neces sary OPENDB example This example uses the OPENDB command to assign a new data source to
374. ying data 349 Mol_ID field 341 molecular formula queries see searching for formulas molecular formula searches see searching for formulas molecular weight field 341 molecular weight searching by 474 moving boxes 324 objects 324 moving forms and databases 346 MS Access see also Access MS Access workgroup information 327 MSI molfile 389 multiple structures adding to forms 345 multi step reactions 366 ChemBioFinder amp BioViz 553 User Guide multi user access 336 name searching 300 new form creating 313 new record indicator description 286 next record command 338 non file based databases attaching 342 normal searching 360 normal searching see also exact searching normal searching see also similarity searching numbers customizing 322 numeric format 322 numeric searches 300 358 O objects aligning 326 deleting 325 distributing 326 spacing 326 ODBC adding structures to existing sourc es 345 ODBC selecting data sources 342 OLE automation communicating with oth er applications 468 OLE automation overview 468 open database button 334 open last form on startup 453 opening databases 333 336 existing chemical databases 333 hit lists 383 secured MS Access databases 335 opening a database tutorial 295 opening options see preferences options 425 OR operator hit lists 384 554 Index OR operator queries 358 Oracle attaching tables 342 case insensitive query matching 372 handling l
375. you to ChemBioFinder 12 0 basic functions You may want to use the Quick Reference card while you perform the tutorials We recommend performing the tutorials in the sequence they are presented because each tuto rial develops on and refers to the previous ones Sample databases The Samples directory located in the Che mOffice 2010 samples folder contains several small databases forms and sample scripts The Cs_Demo database contains about 300 structure covering a range of structural types The database contains two tables that are visi ble using the form Cs_Demo cfx This is the form used in the following tutorials Demo cfx is a simpler form which displays only the main table of the same database CAUTION We recommend you make a working copy of the database before experimenting with it If you make changes to the data or structures in the database the examples in the tutorials may no longer give the documented results To copy the Cs_Demo cfx database Open Windows Explorer Create a folder for the database copies Select all Cs_Demo files Right click then click Copy Select the folder you created for the data base copies 6 Right click then click Paste i ee You can now experiment with adding modify ing and deleting data in the copies with no effect on the Cs_Demo database Tutorial 1 Creating forms Forms let you to display your data in a custom ized format to browse and search t
376. your search Retrieve All search for the struc ture currently displayed in the structure window but ignore any other search properties like molecular weight Find Current Struc ture restore the previous search so you can modify the search criteria Restore Previous Query For more information about the Search tools see the Searching chapter in the ChemFinder User s Guide Refining your query You can refine your ChemFinder Office search with the Search Options To use the Search Options 1 Click the Search Options tab The Search Options window appears Structure Look In Search Options Similarity Match tetrahedral stereo Match double bond stereo Fragments may overlap Hit must overlap reaction center Extra fragments may be present in hit Match any charge on carbon Match any charge on heteroatom Absolute center hits relative Relative tetrahedral stereo Lida id ida so Figure 30 6 Search options 2 Take the appropriate action If you want to then click require that the tetrahe dral stereochemistry of the target structure match that of the query struc ture Match tetrahedral stereo require that the double bond stereochemistry of the target structure match that of the query struc ture Match double bond stereo allow fragments in the query to overlap share one or more atoms in the target Fragments may ov

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