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Lead Discovery 5.1

1. Lead Discovery 5 1 For the Better Stat Structure Column Element x Source columns al Add gt Name Alias Path BASE64 CDX tel Data source COETEST MOLTABL lt Remove Expression NVL CsCartridge highlight 1 1 Data type IClob Source columns Add gt Name Alias Path BASE64 CDX rA Data source COETEST MOLTABL lt Remove CsCartridge MoleculeContains 1 structure highlight yes 1 2 ContentType chemical Ac cdx Edit Save As Save To de activate structure hit highlighting for a CSCartridge 1 If you are using CSCartridge and do not want to active the structure hit highlighting feature the following expression must be entered in the Expression field 1 2 Select Clob as the Data type of the column element Comment A filter is not required 3 Inthe Properties section click amp to show the column properties controls 4 Click Add gt Enter the mime type for the Structure Column as the Content Type property value Copyright 1998 2013 CambridgeSoft Corporation a subsidiary of PerkinElmer Inc All rights reserved 14 of 43 j gt PerkinElmer Lead Discovery 5 1 For the Better 5 Click OK The column property displays in the properties list 6 Click Save Start Structure Retrieve search StructureSearch SimilartySearch MolSim SimilartyFiter StructureFiiter Structure Column Element x Alias Path tol D
2. Structure Retrieve search StructureSearch SimilartySearch MolSim SimilarityFiter StructureFiter Filter Element x Source columns Add gt Name Alias Path BASE64 CDX 41 Data source COETEST MOLTABLE BASE lt Remove Expression CSCartridge MoleculeContains 1 to_clob structure SIMILAR YES SIMTHRESHOLD similarity_lower 1 1 sre 4 5 Creating Information Links Three information links are required to use the structure search functionality e For retrieving structures based on the list of identifiers e For substructure search Copyright 1998 2013 CambridgeSoft Corporation a subsidiary of PerkinElmer Inc All rights reserved 23 of 43 j gt Perkin Lead Discovery 5 1 For the Better 4 5 1 For similarity search Retrieving Information Links To create information links for retrieving structures Note You must always create this information link If you want to apply both similarity searches and substructure searches this information link is used as the retrieve link for both search types provided that all three information links use the same property prefix 1 2 oo O 0 NAg In the Information Designer click New and select Information Link The Information Link tab opens In the Elements tree select the column element that you created for the column containing identifiers of chemical structures Click Add gt The selected element is added to the Elements
3. e Information link to use for structure hit highlighting The information links required for a structure search always come in pairs of one retrieve link and one structure search link These two information links must have a matching prefix on their defined properties The definition of the elements including specification of certain properties and prompts is required to make the search and retrieve functionality in Lead Discovery work Read more about this in the following chapters The resulting tree structure in the library should look like the following one gf SimilaritySearch Structures gf SubstructureSearch U SimilarityFilter basen YY SubstructureFilter sal 345 COMPOUND ID WAY MOLFILE if 34 MOLSIM All these configurations are performed using the Information Designer tool See the following chapters for details To reach the Information Designer 1 Select Tools gt Information Designer The Information Designer opens Copyright 1998 2013 CambridgeSoft Corporation a subsidiary of PerkinElmer Inc All rights reserved 9 of 43 j gt Perkin Lead Discovery 5 1 For the Better 4 3 Defining Column Elements Define the column elements to use when creating the required information links Column Containing Property Name Property Value Chemical structures ContentType chemical x mdl molfile chemical x mdl chime chemical x daylight smiles chemical x cdx Unique identifiers of the lt prefix gt Column s
4. Start Structure Retrieve search Information Link x Add gt Path StructSearch_HL ID OXY Structure Struct Search_HL Structure lv _Move Down Down Prompt Type Mandatory Max Selections Values Move Down gads Parameter Name Data Type Value Type structure Undefined Single value it Properties test Cartridge CSCARTRIDGE i Ej SQL Save As Save Data i Note This Retrieve Search Information Link is for use with the Structure Viewer ONLY It cannot be used to directly add a data table from an Information Link File gt Add Data Tables gt Add gt Information Link Copyright 1998 2013 CambridgeSoft Corporation a subsidiary of PerkinElmer Inc All rights reserved 28 of 43 j gt Perkin Lead Discovery 5 1 For the Better 4 5 2 Creating Substructures Search Information Links To create an information link for the substructures search 1 D RE es In the Information Designer click New and select Information Link The Information Link tab is opened In the Elements tree select the column element that you created for the column containing identifiers of chemical structures Click Add gt The selected element is added to the Elements list on the Information Link tab In the Elements tree select the filter element that you created for the substructure search Click Add gt The selected element is added to the Elements list on the Information Lin
5. Value Structure Help OK Cancel Copyright 1998 2013 CambridgeSoft Corporation a subsidiary of PerkinElmer Inc All rights reserved 24 of 43 j gt Perkin Lead Discovery 5 1 For the Better Note While the second part of the property name is pre defined and you must assign it without changes for the structure retrieval link this is Retrieve you can use an arbitrary prefix for the element properties for example LeadDiscovery One set of elements as shown in the Configuration Overview chapter should always use one and the same property prefix If you want to configure alternative information links you can create more than one set of elements e g to set up information links running against different data tables However each set of elements should always use its own property prefix 15 Click OK The link property displays in the properties list Copyright 1998 2013 CambridgeSoft Corporation a subsidiary of PerkinElmer Inc All rights reserved 25 of 43 Lead Discovery 5 1 Information Link Alements 345 COMPOUND ID Remove i pay MOLFILE 134 MOLWT EA F_DATE COMPOUND Value Structure 16 Click Save The Save As dialog appears 17 Select where you want the invitation link saved 18 In the Name field type a name for the information link for example Structures j gt PerkinElmer For the Better 19 In the Description field type text describing the purpos
6. a subsidiary of PerkinElmer Inc All rights reserved 6 of 43 j gt Perkin Lead Discovery 5 1 For the Better htto www cambridagesoft com services EnterpriseSupport KnowledgeBase SystemRequirements fid 230 Tip For more information about creating and configuring information links refer to the following sections of the TIBCO Spotfire User s Manual Information Links Data Sources Folders Column Elements Filter Elements Copyright 1998 2013 CambridgeSoft Corporation a subsidiary of PerkinElmer Inc All rights reserved 7 of 43 j gt Perkin Lead Discovery 5 1 For the Better 4 1 Prerequisites Before you start configuring the information links for Lead Discovery you must complete the following tasks 1 Setting up the data sources Enter the information required to connect to the structure databases through the Data Source tab in the Information Designer The Connection URL template for an Oracle JDBC driver is as follows jdbc oracle thin lt host gt lt port gt databaseName lt database gt For an Oracle DataDirect driver the template to use is jdbc tibcosoftwareinc oracle lt host gt lt port1521 gt SID lt sid gt Add your own host name port number and database name to the specified locations The chemistry cartridges require the following settings on the Data Source tab under Connection initialization e For Symyx Direct MDL o Version 6 0 or later Select 1 f
7. can use an arbitrary prefix for the element properties for example LeadDiscovery One set of elements as shown in the Configuration Overview chapter should always use one and the same property prefix If you want to configure alternative information links you can create more than one set of elements e g to set up information links running against different data tables However each set of elements should always use its own property prefix Copyright 1998 2013 CambridgeSoft Corporation a subsidiary of PerkinElmer Inc All rights reserved 18 of 43 PerkinElmer Lead Discovery 5 1 For the Better 10 Click OK The column property displays in the properties list MOLSIM Column Element Source columns Name Expression molsim 1 structure similanty_type v Description v Filter Group By A Properties Property Name Lead Discovery Column Similanty Score 11 Click Save 12 Click to select the folder where you want to save the column element 13 Type a descriptive column name for example MOLSIM The column is saved in the library and is shown with an icon denoting its type in the Elements tree Cartridge CambridgeSoft CSCartridge CsCartridge Similarity 1 Symyx Direct Cartridge MDL molsim 1 structure similarity_ type Accelrys Accord Chemistry ChemistryMatches 1 sssConst MatchTanimoto Cartridge structure 100 ChemAxxon JChem Oracle 1 jchem jc_dissimilarity 1 C
8. list on the Information Link tab In the Elements tree select the column element that you created for the column containing chemical structures Click Add gt The selected element is added to the Elements list on the Information Link tab Tip In this information link you can add other columns from the database These columns display when you create a new data table from a list of search results Ensure the check box in the Retrieve column of the Elements list is selected for both elements In the Description field type a description of the information link optional In the Prompts section click to show the prompting controls Click Add Comment If you have included more columns than the required ones the Add Column dialog displays In that case select the identifier column and click OK The identifier column is added to the Prompts list on the Information Link tab 10 Set Prompt Type to Values 11 Ensure the Mandatory box is cleared 12 In the Properties section click to show the information link properties controls 13 Click Add to add the information link property 14 Type lt prefix gt Retrieve for the Property name and Structure for the Value in the Add Information Link Property dialog This property specifies that the information link will be shown among the available links in the Configure Structure Connection dialog Add Information Link Property Property name LeadDiscovery Retrieve
9. Desain In the Description filed type a description of the filter Click Save The Save As dialog displays Click to select the folder where you want to save the filter element Type the filter name for example SimilarityFilter Click Save The filter element is saved in the library oo SO Cartridge Search Expression CambridgeSoft CSCartridge CSCartridge MoleculeContains 1 Copyright 1998 2013 CambridgeSoft Corporation a subsidiary of PerkinElmer Inc All rights reserved 22 of 43 P gt Perkin Lead Discovery 5 1 For the Better to_clob structure SIMILAR YES SIMTHRESHOLD similarity_lower 1 Symyx Direct Cartridge MDL molsim 1 structure similarity_type BETWEEN similarity_lower AND similarity_upper Accelrys Accord Chemistry ChemistryMatches 1 sssConst MatchTanimoto structure 100 Cartridge BETWEEN similarity_lower AND similarity_upper ChemAxxon JChem Oracle jchem jc_dissimilarity 1 jchem jcf molconvert structure Cartridge smiles au lt 1 similarity_lower 100 IDBS ChemXtra Cartridge C IDBSCHX8 SIM 1 structure C IDBSCHX8 IDBS_MOLECULE TANIMOTO 0 gt similarity_lower 1 00 GGA Bingo Bingo Sim 1 structure tanimoto gt similarity_lower 100 If you are using CSCartridge the following expression must be entered in the Expression field CSCartridge MoleculeContains 1 to_clob structure SIMILAR YES SIMTHRESHOLD similarity_lower 1 1 Start
10. EST MOLTABLE M1 WHERE CSCartridge MoleculeContains M1 BASE64 CDX structure FULL NO 1 AND lt conditions gt Retrieve links with no highlighting SELECT mi TDY AS ID T1 M AS STRUCTURE FROM CSCUSER TESTSTRUCTURES T1 WHERE lt conditions gt Retrieve links with highlighting SELECT Mi MOT ID AS ID NVL CsCartridge highlight 1 M1 BASE64 CDX AS STRUCTURE FROM COETEST MOLTABLE M1 WHERE CsCartridge MoleculeContains M1 BASE64 CDX structure highlight yes Copyright 1998 2013 CambridgeSoft Corporation a subsidiary of PerkinElmer Inc j gt Perkin For the Better Below are examples of what the resulting SQL from the specified information links might look like for different All rights reserved 41 of 43 Lead Discovery 5 1 1 2 AND lt conditions gt 6 2 GGA Bingo Similarity search SELECT aL MOL ID AS MOLID Bingo Sim S Ls SMLLES 2structure tanimoto AS SIMILARITYSCORE FROM CORTEOIT SEFCOMPOUNDS S1 WHERE Bingo Sim Sl SMLuRS structure tanimoto gt similarity lower 100 AND lt conditions gt Retrieve links SELECT obe MOL ID AS MOLID S1 SMILES AS SMILES Bingo Molfile S1 SMILES FROM COETEST SFCOMPOUNDS Sl WHERE lt conditions gt Substructure search SELECT Sle MOT LD AS MOLID Bingo Molfile 51 SMILES FROM COR TE
11. Edit button select the check boxes for the above mentioned license functions and click OK 3 4 Web Player Considerations If Lead Discovery is going to be used by Spotfire Web Player users you also need some preparations to the Spotfire Web Player server Copyright 1998 2013 CambridgeSoft Corporation a subsidiary of PerkinElmer Inc All rights reserved 5 of 43 j gt Perkin Lead Discovery 5 1 For the Better 1 Use the upgrade tool to upgrade the Web Player server with the new packages See the TIBCO Spotfire Web Player Installation Manual chapter Deploying Extensions and Upgrades for more information 2 The authors of Spotfire analysis documents have control over which chemistry renderers are used for each visualization feature or application panel The specific renderer s designated in the analysis document will be used by the Web Player Server to deliver chemical structure images to the end user s web browser The Web Player end user does not need to have a chemistry renderer installed However any renderers that may potentially be used in analyses documents must be installed on the Web Player server Note A ChemDrawActivexX Enterprise installer is provided with the Lead Discovery distribution It should be installed on each Web Player server because the ChemDraw renderer is automatically delivered to all Lead Discovery users The Web Player will only make use of the provided ChemDrawActivexX control It is not sufficie
12. Enter a version number and a description for the deployment for instance 5 1 and Spotfire with Lead Discovery and click OK o0 et oO Copyright 1998 2013 CambridgeSoft Corporation a subsidiary of PerkinElmer Inc All rights reserved 4 of 43 j gt Perkin Lead Discovery 5 1 For the Better 3 3 Setting up Licenses All Lead Discovery users must have certain license functions enabled in order to use the all new functionalities like viewing structures opening SDFiles exporting data to SDFiles and conducting a structure search If you are using anonymous preconfigured authentication then the preconfigured single user that has been set up must have these license functions You can configure licenses from the Spotfire Administration Manager At present the following license functions are relevant for Lead Discovery 3 3 1 Access to Extensions this license function is needed in order to use any extension to TIBCO Spottfire Accord this license function is needed for a user to be able to change the settings for chemical structures in the Spotfire visualizations using the Accord Chemistry Control renderer ChemDraw this license function is needed for a user to be able to change the settings for chemical structures in the Spotfire visualizations using the ChemDraw renderer and editor ChemlQ this license function is needed for a user to be able to change the settings for chemical structures in the Spotfire visualizations usi
13. S T SECOMPOUNDS SL WHERE oingo sub S1 SMILES structure Wak AND lt conditions gt 6 3 Accelrys DataDirect Cartridge Previously MDL Similarity search SELECT T1 CDBREGNO AS CDBREGNO molsim Il CTAB structure similarity type AS SIMSCORE FROM IOLO IL oLORC2D MOL IL WHERE molsim I1l1 CTAB structure oTRUCTURE STRUCTURE similarity type j gt Perkin For the Better BETWEEN similarity lower Copyright 1998 2013 CambridgeSoft Corporation a subsidiary of PerkinElmer Inc All rights reserved 42 of 43 Lead Discovery 5 1 AND similarity upper AND lt conditions gt Retrieve links SELECT I1 CDBREGNO AS CDBREGNO molfile I1 CTAB AS MOLFILE FROM TSlS LSLSRC2D MOL I1 WHERE lt conditions gt Substructure search SELECT I1 CDBREGNO AS CDBREGNO FROM TSIS IGISRCZ2O0 MOL I1 WHERE sss I1 CTAB structure 1 AND lt conditions gt j gt Perkin For the Better Copyright 1998 2013 CambridgeSoft Corporation a subsidiary of PerkinElmer Inc All rights reserved 43 of 43
14. The link property displays in the properties list Copyright 1998 2013 CambridgeSoft Corporation a subsidiary of PerkinElmer Inc All rights reserved 29 of 43 P gt l PerkinElmer Lead Discovery 5 1 For the Better structure String unformatted Single value LeadDiscovery Search Subsinuctune 20 Click Save The Save As dialog appears 21 Select where you want to save the information link 22 Inthe Name field type a name for the information link for example SubstructureSearch Copyright 1998 2013 CambridgeSoft Corporation a subsidiary of PerkinElmer Inc All rights reserved 30 of 43 j gt Perkin Lead Discovery 5 1 For the Better 23 In the Description field type text describing the purpose of the information link optional Comment It is useful to note that this information link is used in the Structure Search tool only not to retrieve any data directly into TIBCO Spotfire which might help to avoid confusion among end users 24 Click Save The new information link is added to the library Other users can access this new information link If you are using CSCartridge an additional Information Link property must be added 1 Inthe Properties section click to show the information link properties controls 2 Click Add to add the information link property 3 Type lt prefix gt Cartridge for the Property name and CSCartridge for the Value in the Add Information Link Property dialog This property sp
15. To create a substructure search filter 1 Inthe Information Designer click New and select Filter The Filter Element tab is opened Copyright 1998 2013 CambridgeSoft Corporation a subsidiary of PerkinElmer Inc All rights reserved 20 of 43 j gt Perkin Lead Discovery 5 1 For the Better In the Data Sources tree select the column containing chemical structures indexed by the cartridge to use in the filter condition Click Add gt The selected column is added to the Source columns list on the Filter Element tab Define the following filter condition in the Expression field sss 1 structure 1 Where sss is the Symyx Direct MDL substructure search operator and structure is the parameter for the query structure Comment See the table below for a description of the search expressions to use on other cartridges Source columns Name Expression sss 21 structure 1 Paim k iw Description In the Description field type a description of the filter Click Save The Save As dialog displays Click to select the folder where you want to save the filter element Type a descriptive filter name for example SubstructureFilter Click Save The filter element is saved in the library CSCartridge MoleculeContains 1 structure FULL NO 1 sss 1 structure 1 ChemistryMatches 1 sssConst MatchSub structure jchem jc_compare 1 structure t s stereoSearch n 1 SSS 1 structur
16. arch for structures and also to connect to large structure databases through the tools of Lead Discovery it is necessary to set up information links and filters with a set of specific properties using the Information Designer Please follow the instructions below carefully to ensure that all functionality will be available Chemical structures loaded into Spotfire in ChemDraw s native file format CDX CDMXL are supported for chemical rendering chemical searching and exporting This content in data tables will be displayed natively in renderers that support the format ChemDraw or converted to MOLfiles or SMILES for renderers that do not offer support Query molecules will be extracted from renderers that support the format ChemDraw and sent unchanged to cartridges that support the format or converted to MOLfiles or SMILES for cartridges that do not When defining Information Links for Structure Query it is necessary to add a new property lt prefix gt Cartridge to the Information Link When this property is set to CSCartridge the native cdx format is preserved Instructions for configuring this property are included in the respective sections below Note Make sure that one or more of the supported structure data sources are installed at your site The current release of Lead Discovery supports a number of different Oracle cartridges For more information about the supported cartridges see Copyright 1998 2013 CambridgeSoft Corporation
17. artridge jchem jcf molconvert structure smiles au 100 Copyright 1998 2013 CambridgeSoft Corporation a subsidiary of PerkinElmer Inc All rights reserved 19 of 43 j gt PerkinElmer For the Better Lead Discovery 5 1 IDBS ChemXtra Cartridge SIM 1 structure IDBS_MOLECULE TANIMOTO IDBS_MOLECULE DELETE_HANDLE 100 GGA Bingo Bingo Sim 1 structure tanimoto If you are using CSCartridge the following expression must be entered in the Expression field CsCartridge Similarity 1 Stat Structure Retrieve search StructureSearch SimilartySearch MolSim Column Element x Source columns or Add gt Name Alias Path BASE64 CDX 41 Data source COETEST MOLTABLE BA Expression CsCartridge Similarity 1 Data type Clob v E Yv v Filter v Group By A Properties test Column SimilarityScore Delete 4 4 Creating Filter Elements Create filter elements with descriptive names to apply when creating information links 1 Substructure search filter 2 Similarity search filter The information below is an example of how to set up the filter elements for a Symyx Direct MDL cartridge If you are using another cartridge the expressions entered will be different See the tables below each step instruction or the documentation from your cartridge provider for more information about valid expressions WHERE statements 4 4 1 Creating Substructures Search Filters
18. aseeeeeeeeessaeaaeees 10 4 4 Creating Filter ElOMICING wscisisiicsciidenniis taivieciiiaden nbs trnhcaniesdeambancevienahcttn vtantrdhenns ddamiancedsaansaltvetiencdniesken 20 4 5 Creating Information Links inacssdscnicssisiavliatn nda aintaassadvemaicedaweasdeelvtubdriaveunsd2sicuiandsvsmtenalsnntemncaneuends 23 4 6 Verifying the Configuration cccccccccccccsseeeeceeceeeeeceeecaeeeeeeesseaeeeeeeseeaeeeeeesaeaseeesessaaseeeessnaeeeees 38 5 Testing the Installation sc teeaseete adit estas canteen eiaaaateie alas et dane origami whan eetasa deri oniedum td doce aiceeaea adc tencehcasees 38 5 1 Verifying the Installation se eatanitenadsnieneasicasanek dann me usnicnalleadtamwaksxiiamaateselaianiedrisimisecdshaustesniaxmeahddsamiuisdakaustts 38 De PADIS GIN AE E TE A ATE A E E A T EE E A E E E A 41 61 CambridgeSoft CSCartridge ccccccccccccssssssecccceeeceeeeseeecceeeeeseeeeeseceeeeeesseaeseeeceeeeessaaeeeeeeeseesaaas 41 o2 GOA BIOO gee eee een N EEDS ee eer eee 42 6 3 Accelrys DataDirect Cartridge Previously MDL cccccccssseeeeeeeeeeseeeeeeeeeeeeeeesaaeeeeeeesaaeeees 42 Copyright 1998 2013 CambridgeSoft Corporation a subsidiary of PerkinElmer Inc All rights reserved 2 of 43 For the Better j gt Perkin Lead Discovery 5 1 For the Better 1 Introduction This guide explains how to install and set up Lead Discovery modules at your site These modules provide the following extensions to the TIBCO Spotfire co
19. ata source CSCUSER TESTSTRUCT Content Type chemical Ac cdx Note The returned Content type is chemical x cdx when using the CSCartridge with no highlighting 4 3 2 Adding Structure Identifier Elements To add a column with structure identifiers In the Information Designer click New and select Column The Column Element tab is opened In the Data Sources tree select the column leaf node containing identifiers of chemical structures Click Add gt The selected element is added to the Source columns list on the Column Element tab In the Description field type your own description of the column In the Properties section click G to show the column properties controls Click Add to add the column property Type lt prefix gt Column for the Property Name and ID for the Value in the Add Column Property dialog ACM S e w Vo Copyright 1998 2013 CambridgeSoft Corporation a subsidiary of PerkinElmer Inc All rights reserved 15 of 43 j gt Perkin For the Better Lead Discovery 5 1 Add Colurnn Property Property name Lead Discovery Column Value Help e _ Cancel Note While the second part of the property name is pre defined and you must assign it without changes for the identifier column this is Column you can use an arbitrary prefix for the element properties for example LeadDiscovery One set of elements as shown in the Configuration Overview chapter should always use one and the same prop
20. ation There are some initial steps you must perform when deploying Lead Discovery on a Spotfire Server These are 1 Deploying the distribution package 2 Setting up licenses on Configuring information links 4 Verifying the configuration Please follow the instructions in this guide carefully 3 2 Deploying the Distribution Package Note For additional details on deploying new packages refer to the TIBCO Spotfire Deployment and Administration Manual To deploy the extension package to the server 1 Open the Administration Console located at http spotserver spotfire administration where spotserver is the name of one of your Spotfire servers in a web browser 2 Log in as a Spotfire Admin Select the Deployment tab Select the Environment to which you want to deploy Lead Discovery Rw Note The Environment you select must have a functioning TIBCO Spotfire deployment Click Add The Add to Deployment dialog appears Click Browse The File Upload dialog appears Browse to the LeadDiscovery spk file you want to include in the deployment Click OK in the Add to Deployment dialog to upload and add the file to the distribution The list of packages is updated with the contents of the file 9 Click Validate in the lower left corner to make sure the deployment is not damaged or corrupted in any way 10 Click Save in the lower left corner to save and publish the deployment The Save Deployment dialog appears 11
21. ave The new information link is added to the library Other users can access this new information link Copyright 1998 2013 CambridgeSoft Corporation a subsidiary of PerkinElmer Inc All rights reserved 35 of 43 j gt Perkin Lead Discovery 5 1 For the Better If you are using CSCartridge an additional Information Link property must be added 1 Inthe Properties section click to show the information link properties controls 2 Click Add to add the information link property 3 Type lt prefix gt Cartridge for the Property name and CSCartridge for the Value in the Add Information Link Property dialog This property specifies that the information link will be shown among the available links in the Configure Structure Connection dialog Add Column Property mx Property name LeadDiscovery Cartridge Value CSCARTRIDGE Help Cancel 4 Click OK The link property displays in the properties list Copyright 1998 2013 CambridgeSoft Corporation a subsidiary of PerkinElmer Inc All rights reserved 36 of 43 Lead Discovery 5 1 Stat Structure Retrieve search StructureSearch SimilartySearch Information Link Add gt Path StructSearch_HL MolSim EE J 345 iD StructSearch_HL ID W Similarity Filter Struct Search_HL SimilarityFilter Values Retrieve a lt lt TEE Mandatory Max Selections Move Up Prompt Type Move Down PEI ii Parameter Name Data Typ
22. e IDBS_MOLECULE IGNORE_STEREO 1 Copyright 1998 2013 CambridgeSoft Corporation a subsidiary of PerkinElmer Inc All rights reserved 21 of 43 j gt Perkin Lead Discovery 5 1 For the Better GGA Bingo bingo sub 1 structure 1 4 4 2 Creating Similarity Search Filters To create a similarity search filter 1 Inthe Information Designer click New and select Filter The Filter Element tab opens 2 Inthe Data Sources tree select the column containing chemical structures indexed by the cartridge to use in the filter condition 3 Click Add gt The selected column is added to the Source columns list on the Filter Element tab 4 Define the following filter condition in the Expression field molsim 1 structure similarity_type BETWEEN similarity_lower AND similarity_upper Where molsim is the Symyx Direct MDL similarity search operator extracting similarity values for chemical structures structure is the parameter for the query structure similarity_type is the parameter for the similarity search type similarity_lower is the parameter for the lower limit of the similarity rate range and similarity_upper is the parameter for the upper limit of the similarity rate range Comment See the table below for a description of the search expressions to use on other cartridges Sat miair Fier Filter Element x Source cohwnns Expression moans l Astrocture tsmlanty hype BETWEEN Aeemndanty lower ANC
23. e similanty_lower Integer Undefined test Search Similarity CSCARTRIDGE SQL Save As Save Value Type Single value Single value it j gt PerkinElmer For the Better xX i Note When setting an Information Link for Similarity Search Lead Discovery will convert the query molecule to MOLfile of SMILES before using it to replace the structure marking However if you set lt prefix gt Cartridge to CSCartridge then it will know that the cartridge can support structure in CDX format and it will not convert it Copyright 1998 2013 CambridgeSoft Corporation a subsidiary of PerkinElmer Inc All rights reserved 37 of 43 j gt Perkin Lead Discovery 5 1 For the Better 4 6 Verifying the Configuration In the Elements tree the elements columns filters and information links you created display in the tree For example SimilaritySearch Structures SubstructureSearch T SimilarityFilter YY SubstructureFilter 45 COMPOUND_ID mY MOLFILE 4 34 MOLSIM 5 Testing the Installation Perform the following procedures to verify the installation 5 1 Verifying the Installation The following five procedures ensure proper installation 5 1 1 Opening an SDFile To open an SDFile 5 1 2 Click Open on the toolbar or select File gt Open Browse to the SDFile and click Open You will see the table containing the fields of the SDFile including structures Expo
24. e of the information link optional 20 Click Save The new information link is added to the library Other users can access this link If you are using CSCartridge an additional Information Link property and parameter must be added Copyright 1998 2013 CambridgeSoft Corporation a subsidiary of PerkinElmer Inc All rights reserved 26 of 43 P gt Perkin Lead Discovery 5 1 For the Better P NODE DE e In the Properties section click to show the information link properties controls Click Add to add the information link property Type lt prefix gt Cartridge for the Property name and CSCartridge for the Value in the Add Information Link Property dialog This property specifies that the information link will be shown among the available links in the Configure Structure Connection dialog Add Column Property exa Property name LeadDiscovery Cartridge Value CSCA4ATRIDGE Help Cancel Click OK The link property displays in the properties list In the Parameters section click to show the parameters controls Click Refresh The structure parameter appears in the parameters list Select the structure parameter and click Edit The Edit Parameter dialog displays Set the Data Type to Undefined and the Value Type to Single value Click OK Copyright 1998 2013 CambridgeSoft Corporation a subsidiary of PerkinElmer Inc All rights reserved 27 of 43 PerkinElmer Lead Discovery 5 1 For the Better
25. earch from the pop up menu The Structure Search dialog displays Comment You can also select Tools gt Structure Search from the main menu Select one of the alternatives under Search for lf the Parameters button becomes available click on it to edit the parameters available for the selected search method Comment If you select Similarity search you must enter a threshold value in the Similarity Search Parameters dialog The higher the threshold the shorter is the hit list If you want to import a structure from a file click Import Structure The Open dialog appears Select the file you want to import and click Open The structure from the file displays in the Structure Search dialog If required click Edit Your selected structure editor launches If you have access to more than one editor you can select which one to use Edit the structure and click OK for ChemDraw or Transfer for Symyx Draw MDL Please refer to the documentation for your current structure editor for more details Select the information link to use for the search in the Search in drop down list If required limit the search to the current list of identifiers Copyright 1998 2013 CambridgeSoft Corporation a subsidiary of PerkinElmer Inc All rights reserved 39 of 43 j gt Perkin Lead Discovery 5 1 For the Better 5 1 5 Comment This option is only available when performing the search from the Structure Viewer and when any list except for the Ma
26. ecifies that the information link will be shown among the available links in the Configure Structure Connection dialog Add Column Property Ss Property name LeadDiscovery Cartridge Value CSCARTRIDGE Help Cancel 4 Click OK The link property displays in the properties list Copyright 1998 2013 CambridgeSoft Corporation a subsidiary of PerkinElmer Inc All rights reserved 31 of 43 P gt PerkinElmer Lead Discovery 5 1 For the Better Start Structure Retrieve search Structure Search Information Link Add gt Path Retrieve StructSearch_HL ID Y StructureFilter StructSearch_HL Structure Filter IV Move Up lt Remove v Join path a iM Prompt Type Mandatory Max Selections Values i Move Up Move Down A g gt MT Parameter Name Data Type Value Type structure Undefined Single value ull Properties test Search Substructure test Cartridge CSCARTRIDGE th SQL Save As Save Open Data i Note When setting an Information Link for Substructure Search Lead Discovery will convert the query molecule to MOLfile of SMILES before using it to replace the structure marking However if you set lt prefix gt Cartridge to CSCartridge then it will know that the cartridge can support structure in CDX format and it will not convert it 4 5 3 Creating Similarity Search Information Links To create an information link for the
27. erty prefix If you want to configure alternative information links you can create more than one set of elements e g to set up information links running against different data tables However each set of elements should always use its own property prefix Copyright 1998 2013 CambridgeSoft Corporation a subsidiary of PerkinElmer Inc All rights reserved 16 of 43 j gt Perkin Lead D ISCOVErY 5 1 For the Better 8 Click OK The column property displays in the properties list COMPOUND_ID Column Element Source columns Name Alias CDOBREGNO Data type Integer Description Filter Group By 5 Properties Property Name Lead Discowery Column 9 Click Save 10 Click to select the folder where you want to save the column element 11 Type a descriptive column name for example COMPOUND_ID The column is saved in the library and is shown with an icon denoting its type in the Elements tree 4 3 3 Creating Similarity Score Elements The information below is an example of how to set up the similarity score column element for a Symyx Direct MDL cartridge If you are using another cartridge the entered expressions will be different See the table below this step instruction or the documentation from your cartridge provider for more information about valid expressions To add a column with similarity score values 1 Inthe Information Designer click New and select Column The Column Element
28. ick Add The identifier column is added to the Prompts list on the Information Link tab 12 13 14 Set Prompt Type to Values In the Parameters section click Y to show the parameters controls Click Refresh Four filter parameters appear in the parameters list Parameter Name Data Type Value Type similarity lower Single value similanty_type String Single value similanty_ upper String Single value structure String Single value Comment In this example a Symyx MDL cartridge has been used For other cartridges some of the parameters above may be missing Select the similarity_lower parameter and click Edit The Edit Parameter dialog displays Set the Data type to Integer and click OK Select the similarity_upper parameter and click Edit The Edit Parameter dialog displays Set the Data type to Integer and click OK Select the structure parameter and click Edit The Edit Parameter dialog displays Set the Data type to Undefined and click OK In the Properties section click to show the information link properties controls Click Add to add the information link property Type lt prefix gt Search for the Property name and Similarity for the Value in the Add Information Link Property dialog This property specifies that the information link will be shown among the available Similarity search links in the Structure Search dialog Copyright 1998 2013 CambridgeSoft Corporation a subsidiary of PerkinElmer Inc All righ
29. j gt PerkinElme For the Better Lead Discovery 5 1 Installation Guide Powered by TIBCO Spotfire Last Updated April 10 2013 j gt Perkin Lead Discovery 5 1 Table of Contents 1 MUO CU eect eect e cena cpenteee E E once sadsene oes hoes E A ER 3 FC OCU SIC S E E A E E N E E A N E O sain E E E 3 PTS et Niet HO N eaei sgocercctens saan seesqnsee nares E E EE TEA E E T 4 3 1 Installation Overview cccccecccseecccseeeeceeeeecaeeeeseuceseauceceaeeeseueesseucessaueessaeeesseeeseueesseueessueeesseeesags 4 3 2 Deploying the Distribution Package ccecccccssseececeeeeeecaeeeeeseeeeeecseeeeesaeseeeessaueeessageeessaneeeesaaes 4 3 3 Setting up Licenses visicccccenecasccbeacenseeicdovactentewecsiesonessedliquseelsasenectdendewnedcceaqsedl qneawhe caused aaneeseeteveeacnes 5 3 4 Web Player Considerations ccccccccssssssecccceeeeeeeeseeecceeeeeaeeeseceeeeesssaeeeeeeeeeeessaaasseeeeeeeeseaaaseses 5 4 CZOMMOUL AUON sison aaan naaa aa ject aseateeisnactetededbeaeadeustsGgueeeuaiessnactesodusieabegsuesedactantabensastetaceate 6 4 1 PFEreQuiSiteS ccccccsssccccceseeecceeseecceeseeecsaececseuseeeseaseeecsaeeecseaececseaseeessageeessageeeeseeeeesseseeessaneees 8 4 2 Configuration Overview cccccccccecceseeeeecceeeeeesaaeeeuceeeeeeeaeeaeeeeeeeeeesseeaeeeceeeesesaeaaseeeeeeeessaaaaeeeeeeees 9 4 3 Defining Column ElOMent ccccccsseseeecceceeeeaseeeeeeceeeeeeeaeeesecceeeeessueaesseeeeesessae
30. k tab Ensure that the check box in the Retrieve column of the Elements list is selected for the structure identifier column element In the Description field type a description of the information link optional In the Prompts section click to show the prompting controls Comment You must add a prompt step on the identifier column This is required for limiting the search to a list instead of searching against the entire database when performing a structure search 9 Click Add The identifier column is added to the Prompts list on the Information Link tab 10 Set Prompt Type to Values 11 Ensure the Mandatory box is cleared 12 In the Parameters section click to show the parameters controls 13 Click Refresh The structure parameter appears in the parameters list 14 Select the structure parameter and click Edit The Edit Parameter dialog displays 15 Set the Data type to Undefined and click OK 16 In the Properties section click to show the information link properties controls 17 Click Add to add the information link property 18 Type lt prefix gt Search for the Property Name and Substructure for the Value in the Add Information Link Property dialog This property specifies the information link is shown among the available Substructure search links in the Structure Search dialog Add Information Link Property Property name LeadDiscovery Search Value Substructure 19 Click OK
31. l PerkinElmer Lead Discovery 5 1 For the Better Column Element Source columns Alias TE motile 21 Data type Clob Description Filter Group By A Properties Property Name Content Type chemical x mdl molfile 11 Click Save 12 Click to select the folder where you want to save the column element 13 Type a descriptive column name for example MOLFILE The column is saved in the library and is shown with an icon denoting its type in the Elements tree To activate structure hit highlighting for a CSCartridge When performing a chemical substructure search the resulting structures can be returned with the query molecule highlighted To activate substructure highlighting requires the modification to the Chemical Structure Element settings as described below Chemical Structure Element is used to retrieve structures It is called by the search structure search similarity and it can also be used by the Structure Viewer to retrieve a structure In certain cases it is not possible to highlight the substructure because there is not an exact match Copyright 1998 2013 CambridgeSoft Corporation a subsidiary of PerkinElmer Inc All rights reserved 12 of 43 j gt Perkin Lead Discovery 5 1 For the Better For example if a similarity search results with a 70 degree of similarity the resulting structure may not contain the exact substructure used for the search In this case the substructu
32. ng the ChemlQ renderer ChemistryViewer this license function is needed to open the Structure Viewer from the menu and toolbar in new analyses ExportToSDF this license function is needed for a user to be able to reach the Export to SDFile functionality from a Spottire table visualization ExportloCDExcel this license function is needed for a user to be able to reach the Export to ChemDraw for Excel functionality from a Spottire table visualization Marvin this license function is needed for a user to be able to change the settings for chemical structures in the Spotfire visualizations using the MarvinSketch renderer and editor SDFParser this license function is needed to open an SDFile in a new analysis Structure Filter this license function is needed to open the Structure Filter from the menu and toolbar in new analyses StructureSearch this license function is needed to reach the structure search functionality Symyx Draw MDL this license function is needed for a user to be able to change the settings for chemical structures in the Spotfire visualizations using the Symyx Draw MDL renderer and editor Configuring License Functions To configure license functions ee el Start Spotfire and log in as an administrator Select Tools gt Administration Manager Select the Groups and Licenses tab Click on the Licenses tab in the right hand pane For each group of users that will use Lead Discovery click the
33. nt to install any other version of ChemDraw on the Web Player 3 Using Lead Discovery with the Web Player requires the use of a renderer that supports the Operating System the Web Player runs on Check the system requirements for the renderer before installing For renderer system requirements please refer to the respective renderer provider 4 The chemistry renderers run on the Web Player Server in a dedicated 32 bit process You must therefore install a 32 bit compatible version of the renderers even if the Web Player Server OS runs on 64 bit processor 5 For some renderers it may also be important to consider the user account under which the renderer runs For example a renderer may require running under a designated user account which has been setup with appropriate environment variables and file system access When installing renderers pay attention to whether they are installed for use by a specific user or by all users of the system The user account under which the renderers will execute is indirectly controlled by the Identity of the account used to run the Microsoft Internet Information Services Application Pool associated with the TIBCO Spotfire Web Player Refer to IIS administration documentation for modifying the Application Pool Identity By default the application pool will run as the built in NETWORKSERVICE Windows account 6 It is recommended that you Stop IIS before installing renderers to the Web Player 4 Configuration To se
34. nterprise chemistry renderer It will be automatically installed and activated on the client computers during the first use of Lead Discovery It is therefore not necessary to independently install ChemDraw on the client computers in order to render chemical structures in Lead Discovery The automatic installation of the ChemDraw renderer should not interfere with pre existing ChemDraw installations on the client computer However Lead Discovery will not make use of pre existing versions of ChemDraw Tip Tasks 1 and 2 are explained in detail in the TIBCO Spottfire Installation and Configuration Manuals and TIBCO Spotfire Deployment and Administration Manual Copyright 1998 2013 CambridgeSoft Corporation a subsidiary of PerkinElmer Inc All rights reserved 3 of 43 j gt Perkin Lead Discovery 5 1 For the Better 3 Installation This chapter explains the installation procedures for installing Lead Discovery 5 1 3 1 Installation Overview The actual features and functionality of Lead Discovery are implemented in software packages These packages are bundled into a distribution which must be deployed on the TIBCO Spotfire Server and Web Player Server When the end users start Spotfire on their computers they will log into the Spotfire Server and download the deployment locally automatically downloading any newer or added packages Depending on the licenses that are enabled for each user varying features may appear in each user s applic
35. on 5 Select Clob as the Data type of the column element Comment For other cartridges this element may be of the Blob data type See the documentation from your cartridge provider for details on what data type your data source or the expression used returns The Information Designer automatically displays the returned data type from the data source when you add a single column to the column element tab but it is not updated as you add an expression 6 Inthe Description field type your own description of the column 7 Inthe Properties section click to show the column properties controls 8 Click Add to add the column property Copyright 1998 2013 CambridgeSoft Corporation a subsidiary of PerkinElmer Inc All rights reserved 10 of 43 j gt Perkin Lead Discovery 5 1 For the Better 9 Type ContentType for the Property name and chemical x mdl molfile for the Value in the Add Column Property dialog Add Column Property Property name Content Type Value chemical 4 lt ndl moffile ss atone Note No prefix is allowed for the property name of the structure column Comment The value must be a MIME type string as defined in the table above Make sure that the content type matches the output from the expression defined above 10 Click OK The column property displays in the properties list Copyright 1998 2013 CambridgeSoft Corporation a subsidiary of PerkinElmer Inc All rights reserved 11 of 43
36. or each folder in the library Create a new folder for the elements required for configuring the information links for Lead Discovery or add these elements to an existing folder Tip For more details about folders in the Spotfire library refer to section Folders of the TIBCO Spotfire User s Manual Copyright 1998 2013 CambridgeSoft Corporation a subsidiary of PerkinElmer Inc All rights reserved 8 of 43 j gt Perkin Lead Discovery 5 1 For the Better 3 Combining tables by creating joins If you want to work with data from different database tables you first need to create joins Tip For more details about joins in Spotfire refer to section Joins of the TIBCO Spotfire User s Manual 4 2 Configuration Overview To configure Lead Discovery you must define a coherent set of elements 1 Define column elements from the columns of the database tables which return e Chemical structures e Unique identifiers of the structures e Similarity scores for chemical structures 2 Create filter elements used for each search algorithm e Substructure search filter e Similarity search filter These filter elements correspond to the WHERE statements in the resulting SQL used to retrieve the results from a search 3 Create information links e Information link to use for retrieving structures based on the list of identifiers e Information link to use for substructure search e Information link to use for similarity search
37. ration Structure Connection dialog displays Comment You can also select View gt Structure Viewer from the menu Select the columns in the analysis containing molecular structures and identifiers You can retrieve the structures from an information link Note Lead Discovery expects the ID column to uniquely identify a structure so that no two structures have the same value of ID If several structures have the same value in the ID column only one of them will display in the Structure Viewer To indicate this the shown structure is marked as ambiguous Click OK The Structure Viewer displays Mark or highlight compounds in a visualization When there are no marked rows the structure from the currently highlighted row in the data table displays in the Structure Viewer pane of the Structure Viewer and its identifier displays in the List Content pane When there are marked rows the structures from the marked rows display in the Structure Viewer pane and their identifiers display in the List Content pane When you highlight a marked row its corresponding identifier and structure is highlighted in the Structure Viewer and List Content panes Searching for Compounds in the Structure Database To search for compounds in the structure database i oo In the Structure Viewer or in a table visualization with structures click to activate the compound on which you want to base the search Right click the structure and select Structure S
38. re functionality Ability to open an SDFile and view its fields in the table visualization including the molecular structures Ability to export data to an SDFile or a ChemDraw for Excel file Ability to use the Structure Viewer to view the structures create export and import ID lists Ability to use the Structure Filter to filter a data table based on structure Perform an R Group Decomposition on a substructure search Note The Structure Viewer and Structure Filter are not available in the Web Player e Ability to search on structures using the similarity and substructure search algorithms of the supported chemistry cartridges e For more information about system requirements for Lead Discovery see htto www cambridgesoft com services EnterpriseSupport KnowledgeBase SystemRequirements fid 230 2 Prerequisites This Installation Guide explains the steps required to deploy and set up Lead Discovery based on the assumption that you have previously performed the following tasks 1 Installed the Spotfire Server at your site 2 Deployed the core Distribution Package and Installation Documentation to the Spotfire Server 3 Installed one or more of the supported structure renderers on the client computers For more information about supported renderers and editors see http www cambridgesoft com services EnterpriseSupport KnowledgeBase SystemRequirements fid 230 Note Lead Discovery 5 1 includes a dedicated ChemDrawActiveX E
39. re will NOT be highlighted Comment The Structure Hit Highlighting is only supported by CSCartridge s oo 5 In the Information Designer click New and select Column The Column Element tab opens In the Data Sources tree select the column leaf node containing chemical structures indexed by the cartridge Click Add gt The selected element is added to the Source columns list on the Column Element tab In the Description field type your own description of the column Enter the following in the Expression field NVL CsCartridge highlight 1 1 9 In the Filters section click to show the filter controls In the Data Sources tree select the column leaf node containing chemical structures indexed by the cartridge Click Add gt The selected element is added to the Source columns list on the Column Element tab Enter the following in the Expression field CsCartridge MoleculeContains 1 structure highlight yes 1 2 10 11 12 13 In the Properties section click to show the column properties controls Click Add gt Enter the mime type for the Structure Column as the Content Type property value In the example shown below chemical x cdx is entered Click OK The column property displays in the properties list Click Save Copyright 1998 2013 CambridgeSoft Corporation a subsidiary of PerkinElmer Inc All rights reserved 13 of 43 j gt PerkinElmer
40. rked Rows list is selected in the Lists drop down of the Structure Viewer When you start a structure search from table visualization without activating the Structure Viewer or if the Marked Rows list is selected the Data Source option is the only option presented in the Limit search to drop down Specify the name for the resulting list Click OK Structures in the database that match the search criteria display in the Structure Viewer Structure Viewer pane A new ID list is added and displayed in the List Content Pane Selecting the Renderer To change the renderer used to display structures in the Structure Viewer 1 2 3 In the Structure Viewer pane of the Structure Viewer panel or popover right click the structure Select Renderer from the menu Select the renderer to use Comment You can switch renderers if you have more than one of the supported renderers installed on your machine Copyright 1998 2013 CambridgeSoft Corporation a subsidiary of PerkinElmer Inc All rights reserved 40 of 43 Lead Discovery 5 1 6 Appendix CambridgeSoft CSCartridge Similarity search SELECT CsCartridge Similarity 1 AS MOLSIM Mie MOL IDT AG LD FROM COETEST MOLTABLE M1 WHERE CSCartridge MoleculeContains M1 BASE64 CDX to cloor str ctuUre y SIMILAR YES SIMTHRESHOLD similarity lower ti 1 AND lt conditions gt Substructure search SELECT Milks Moly IDT AS ID FROM COET
41. rom dual o Version 5 0 or earlier Select cdcaux ctenvinit schema dbname from dual Replace schema dbname with the name of your schema and database e For Accord Select 1 from dual e For CambridgeSoft CSCartridge Select 1 from dual e For JCHEM Select jchem_core_pkg set_password lt schema password gt from dual e For ChemXtra Select 1 from dual e For GGA Bingo Select 1 from dual Tip Do not terminate the above initialization SQL statements with a semicolon The Information Designer tool may add such a semicolon during the save operation When editing the information link you may need to remove the added semicolon in order to avoid invalid character Oracle errors caused by a double semicolon at the end of the initialization SQL Tip For more details about data sources in Spotfire refer to section Data Sources of the TIBCO Spottire User s Manual Note To configure the information links for Lead Discovery successfully and to be able to view and search structures you need to know the columns in the database tables which store the following information e Chemical structures e Unique identifiers of the structures 2 Creating folders for storing elements and set permissions Information links and the elements that are used for creating them are stored in the library Different groups of users can be given different levels of access to the data by specifying what permission level each user group should have f
42. rting Data from Visualizations To export data from visualization 1 2 i Right click a table with structures and select Export to SDFile Select whether to export all rows marked rows or filtered rows only e All rows export every row in the data table regardless of filtering e Marked rows export the marked rows only e Filtered rows export the rows remaining after filtering only Select the column containing structures from the drop down list Comment The SDFile format supports only one structure per record You can select any column in the table that contains structures The first column containing structures is displayed as the default choice Use Add Remove and Remove All to select the columns to export with the structure Use Move Up and Move Down to specify the order of columns in the SDFile Click OK Copyright 1998 2013 CambridgeSoft Corporation a subsidiary of PerkinElmer Inc All rights reserved 38 of 43 j gt Perkin Lead Discovery 5 1 For the Better re 8 5 1 3 In the Save As dialog specify a filename and where you want to save the file Click Save Reaching the Structure Viewer To reach the Structure Viewer 1 9 1 4 Select a table visualization that contains structures Comment If you have not previously opened the visualization with structures the Structure Viewer button and the corresponding menu item may be inactive Click Structure Viewer in the toolbar The Configu
43. similarity search Copyright 1998 2013 CambridgeSoft Corporation a subsidiary of PerkinElmer Inc All rights reserved 32 of 43 j gt Perkin Lead Discovery 5 1 For the Better N On o p e 9 11 15 16 17 18 19 20 21 22 23 In the Information Designer click New and select Information Link The Information Link tab is opened In the Elements tree select the column element that you created for the column containing identifiers of chemical structures Click Add gt The selected element is added to the Elements list on the Information Link tab In the Elements tree select the column element containing similarity values for chemical structures Click Add gt The selected element is added to the Elements list on the Information Link tab In the Elements tree select the filter element that you created for the similarity search Click Add gt The selected element is added to the Elements list on the Information Link tab Ensure that the check box in the Retrieve column of the Elements list is selected for the structure identifiers and similarity values column elements In the Description field type a description of the information link optional _ In the Prompts section click to show the prompting controls Comment You must add a prompt step on the identifier column This is to limit the search to a list instead of searching against the entire database when performing a structure search Cl
44. tab opens 2 Inthe Data Sources tree select the column leaf node containing chemical structures indexed by the cartridge 3 Click Add gt The selected element is added to the Source columns list on the Column Element tab Copyright 1998 2013 CambridgeSoft Corporation a subsidiary of PerkinElmer Inc All rights reserved 17 of 43 j gt Perkin Lead Discovery 5 1 For the Better 4 Inthe Description field type your own description of the column 5 Type the following expression in the Expression field molsim 1 structure similarity_type Where molsim is the Symyx Direct MDL similarity search operator extracting similarity values for chemical structures structure is the parameter for the query structure And similarity_type is the parameter for the similarity search type Comment See the table below for a description of the search expressions to use on other cartridges select Real as the Data type of the column element In the Properties section click to show the column properties controls Click Add to add the column property Type lt prefix gt Column for the Property Name and SimilarityScore for the Value in the Add Column Property dialog O oN D Add Column Property Property name Lead Discovery Column Value Similarity Score Note While the second part of the property name is pre defined and you must assign it without changes for the similarity score column this is Column you
45. tructures Similarity scores for chemical lt prefix gt Column SimilarityScore structures Note If the column contains cdxml structures select chemical x cdx for the Content Type value Details for defining these column elements follow below 4 3 1 Defining Chemical Structure Elements The information below is an example of how to set up the column element containing chemical structures for a Symyx Direct MDL cartridge creating a molfile structure column If you are using another cartridge or another MIME type the entered expressions will be different See the documentation from your cartridge provider for more information about valid expressions To add a column with chemical structures In the Information Designer click New and select Column The Column Element tab opens In the Data Sources tree select the column leaf node containing chemical structures Click Add gt The selected element is added to the Source columns list on the Column Element tab If you are accessing a Symyx MDL cartridge type the following in the Expression field molfile 1 w N gt If you are accessing an IDBS ChemxXtra cartridge type the following in the Expression field CONVERT _MOLECULE 1 IDBS_ MOLECULE MOLFILE Comment For other cartridges leave 1 in the expression field and proceed to the next step If you want to convert the column to other MIME types please see the documentation from the cartridge provider for more informati
46. ts reserved 33 of 43 j gt Perkin Lead Discovery 5 1 For the Better Add Information Link Property Property name LeadDiscovery Search Value Similarity Cre Cera Note While the second part of the property name is pre defined and you must assign it without changes for the similarity search link this is Search you can use an arbitrary prefix for the element properties for example LeadDiscovery One set of elements as shown in the Configuration Overview chapter should always use one and the same property prefix If you want to configure alternative information links you can create more than one set of elements e g to set up information links running against different data tables However each set of elements should always use its own property prefix 24 Click OK The link property displays in the property list 25 Again click Add to add another information link property 26 Type LeadDiscovery StructureSearch ParameterType for the Property name and the expression corresponding to the chosen cartridge found in the table below for the Value This property ensures that the correct Parameters dialog in the Structure Search is available for the chosen cartridge Add Information Link Property openly name LeadDiscovery Structure Search Parameter Type Value LeadDiscovery Symyx Direct Similarity Search Hep OK Canca ia CambridgeSoft CSCartridge LeadDiscovery CSCartridge SimilaritySearch S
47. ymyx Direct Cartridge MDL LeadDiscovery SymyxDirect SimilaritySearch Accelrys Accord Chemistry LeadDiscovery Accord SimilaritySearch Cartridge ChemAxxon JChem Oracle LeadDiscovery JChem SimilaritySearch Cartridge IDBS ChemXtra Cartridge LeadDiscovery ChemxXtra SimilaritySearch GGA Bingo LeadDiscovery Bingo SimilaritySearch Note If you do not perform steps 26 and 27 in this list a default Parameters dialog is used Copyright 1998 2013 CambridgeSoft Corporation a subsidiary of PerkinElmer Inc All rights reserved 34 of 43 PerkinElmer Lead Discovery 5 1 For the Better 27 Click OK The link property displays in the properties list Qat SenilartySearch Information Link x Somarts i Add Bomen Path Reteave Move Up lt Remove EET MOLSIM Uses J Move Down 345 COMPOUND_ID Asers J Ede v Join path Desonption S Filters A Prompts Cohsnny Prompt Type Mandatory Max Selections Add Move Lip Move Down 28 Click Save The Save As dialog appears 29 Select where you want to save the information 30 In the Name field type a name for the information link for example SimilaritySearch 31 In the Description field describe the purpose of the information link optional Comment It is useful to note that this information link is used in the Structure Search tool only not to retrieve any data directly into TIBCO Spotfire which might help to avoid confusion among end users 32 Click S

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