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ICEdit Manual

1. Ctrl O Opens a file Ctrl S Saves the current structure s or reaction to a file in icf format Ctrl A Selects all objects within the drawing area Ctrl Z Undoes the last operation Ctrl Y Redoes the last undone operation Ctrl D Duplicates the selected object s Ctrl G Merges multiple selected chemical objects Ctrl H Ungroups a selected group of chemical objects Chapter 3 General Information ICEDIT Manual 23 4 4 1 Description of Standard Edit Buttons Standard buttons are provided by the applet and the Windows application Various edit and template buttons are provided in the button bar The chosen edit or template button is highlighted Selected molecule atom or bond templates can be used to draw the particular object into the drawing area by mouse click Selected edit buttons can be used to carry out the particular operation Please find below a detailed description of all template and edit buttons Standard Edit Buttons LJ Clear screen Deletes all objects from the drawing area Keyboard shortcut CTRL N Delete object The object s atom bond molecule text you are selecting with your mouse will be deleted If you draw a rectangle all objects within that area will be deleted Keyboard shortcut DEL Undo last operation Undoes the last operation Keyboard shortcut CTRL Z Redo last operation Redoes the last undone operation Keyboard shortcut CTRL Y r
2. ICEdit_JavaScriptEditor pdf Chapter 1 Introduction ICEDIT Manual 6 1 4 ICEDIT Java Applet 1 4 1 Functionality IS SE IO OJO OJO SON SE Dio IG y E ZADO Edit and template button bars Drawing area BBA OBES Description of the current button al am i t Benzene Fig 3 The ICEDIT Java applet The ICEDIT Java applet is an Internet browser based query editor for the input of chemical structures and reactions The easy integration in any desktop or web application makes IC EDIT an ideal tool to create queries for searching through structure and reaction databases It is downloaded on the fly and therefore it does not have to be installed on the user s computer The Java applet does not have access to the clients file system and hence it does not have the full functionality of the IC DIT Windows application Chapter 1 Introduction ICEDIT Manual 7 1 4 2 Enhanced ICEDI T Java Applet The enhanced ICED T applet is an enriched version of the Java applet that offers additional functionalities like full superatom support Due to the fact that the standard Java applet does not have access to the clients file system a system managed by a Servlet container like Apache Tomcat is necessary Please contact us for further information 1 4 3 System Requirements Supported Browsers Internet Explorer 5 5 or higher Firefox Windows Mac OS X Opera and Safari Mac OS X Software
3. e The configuration of standard edit and drawing buttons toolbars e OLE Server functionalities Integration in MSOffice and other OLE interfaces e General Programming Interfaces API s e Additional clipboard formats e ICRENDIT e Add in for MS Excel e CEDIT as ActiveX Control ICEDITOCX Chapter 13 Technical Documentation ICEDIT Manual 59 13 1 Copyright ICEDIT is using rdkit Copyright c 2006 201 1 Rational Discovery LLC Greg Landrum and Julie Penzotti All rights reserved Redistribution and use in source and binary forms with or without modification are permitted provided that the following conditions are met Redistributions of source code must retain the above copyright notice this list of conditions and the following disclaimer Redistributions in binary form must reproduce the above copyright notice this list of conditions and the following disclaimer in the documentation and or other materials provided with the distribution Neither the name of Rational Discovery nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS AS IS AND ANY EXPRESS OR IMPLIED WARRANTIES INCLUDING BUT NOT LIMITED TO THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED IN NO EVENT SHALL THE COPYRIGHT OWNER OR C
4. from the Windows clipboard into your drawing area Keyboard shortcut CTRL V Delete Deletes the currently selected atom s or bond s Keyboard shortcut DEL Expand Superatom Expands a selected superatom Contract Superatom Contracts a selected superatom Create Superatom Creates a self defined superatom Create Chiral Flag Creates a chiral flag on the selected molecule s Please refer to chapter 8 for further details Group Merges multiple selected chemical objects Ungroup Ungroupes a selected group of chemical objects Create No Structure Opens the Create No Structure dialog window to create a No Structure label Please refer to chapter 10 for further details on No Structures Color Provides the opportunity to change the color of the selected object s Please note The three object methods Copy Object s Paste Object s and Duplicate Object s do only work within ICED T Therefore they cannot be merged with the Windows methods Copy and Paste Chapter 3 General Information ICEDIT Manual 22 3 3 Keyboard Shortcuts The following keyboard shortcuts are supported by the IC EDIT Windows application Ctrl C Copies the selected object s into the Windows clipboard Ctrl V Pastes the object s from the clipboard Ctrl B Transfers the object s to the calling application only available if IC EDIT is called from another application Ctrl N New window clear screen
5. 4 iM Molecular Weight 78 1134 i Nominal Mass 78 0000 iw Exact Mass 78 0469 i Elemental Analysis C 92 26 H 7 74 Fig 4 Molecule Values dialog window Chapter 3 General Information ICEDIT Manual 16 By using the drop down list Decimals the number of decimal places can be adjusted 1 4 The calculated values can be pasted in the drawing area using the Paste button Not required information can be deselected and will not be transferred into the drawing area InChI InChiKey Calculate Calculates InChls and InChlKeys of all or the selected objects single molecules multiple molecules and parts of structures InChl 1Ss C6H6 c1 2 4 6 5 3 1 h1 6H iw InChikey UHOVONZIYSORNE UHFFFAOYSA N Comment Fig 5 InChI dialog window The calculated values can be pasted in the drawing area using the Paste button Not required information can be disabled and will not be transferred into the drawing area SMILES Calculate Calculates SMILES and Canonical SMILES of all or the selected objects single molecules multiple molecules and parts of structures cicocect if Canonical SMILES ctec ecc Fig 6 SMILES dialog window The calculated values can be pasted in the drawing area using the Paste button Not required information can be disabled and will not be transferred into the drawing area Atom Numbers Show To enable automatic atom numbers select Atom Number
6. 5 Select Use this tool either to select a single object or a group of objects in a rectangle The selected objects can then be moved drag with your mouse deleted or copied using either the context menu the menu bar or the appropriate keyboard shortcuts Select object Use this tool to select whole objects at once Click on a specific object as soon as it is marked by a red frame to select the complete object The selected objects can then be moved drag with your mouse deleted or copied using either the context menu the menu bar or the appropriate keyboard shortcuts Chapter 4 Description of Standard Edit Buttons ICEDIT Manual 24 Rotate selected objects Use this tool to rotate the selected objects either clockwise or anti clockwise Add reaction plus Adds a reaction plus to the drawing area gt Add reaction arrow Adds a reaction arrow to the drawing area Please note Only one arrow per reaction is supported Complex schemes will be supported in future ER Map atoms Adds mapping numbers to the atoms you select In order to do so please click on the two atoms you want to map at the reactant and product side of the reaction Please note Only mappings of reactant atoms with product atoms are supported Furthermore only atoms of the same atom type can be mapped Example OH NH gt Remove mappings from atoms and reaction center information from bonds Click single atoms bonds or draw a rectangle to
7. a whole object or parts of it please choose the select button and draw a rectangle covering the desired bonds and or atoms and or objects To select one or multiple bonds and or atoms please click on all desired atoms and or bonds while the shift button is pressed down Or choose the Select Object button to select whole objects at once Scale Objects To scale one or more objects please select first the objects and then use the double headed arrow in one of the four corners of the selection frame to change the size of the objects Chapter 5 Drawings ICEDIT Manual 31 5 3 Edit Atoms You can change the atom symbol of a selected atom by using the keyboard Please insert an atom label and press enter The input of atom symbols is not case sensitive Please note after drawing a bond the atom at the end of the bond is selected automatically This feature facilitates the input of different atom types by simple drawing a bond typing the atom label and pressing enter The keyboard input of charge and isotopes is supported as well e Fora charged atom please insert an atom symbol the amount of charge and the charge type respectively e g S2 e For isotopic information please insert the isotope number and the atom symbol respectively e g 2H In addition you can change an atom symbol using the Edit Atom dialog window To open the dialog window please use either the template button Draw an atom the context menu Edit A
8. or changes an existing bond into an up stereo bond An additional click on it changes the direction of the wedge Please note The orientation of up wedges is important for the automatic detection of the stereochemistry e g in case of query features Chapter 4 Description of Standard Edit Buttons ICEDIT Manual 27 4 2 3 Draw down wedges or change existent bonds to down wedges Draws a new down stereo bond or changes an existing bond into a down stereo bond An additional click on it changes the direction of the wedge Please note The orientation of down wedges is important for the automatic detection of the stereochemistry e g in case of query features Pp Draw a chain Draws a chain of C C single bonds Standard Atom Buttons E Draw an atom Use the dialog window to define atom properties and atom query features After having done the selection OK please click in the drawing area to place the atom Draw an atom Atorn properties Charge op Isotope oft A Radical Valence ott H auer atom subsitiioncount on 3 ringbondenunt or gt Reaction Stereo aff Reaction center aff No Implicit Hydrogens Unsaturated atom Exact change Exact valence Aromatic atom E z Fig 9 Draw an Atom dialog window Chapter 4 Description of Standard Edit Buttons ICEDIT Manual 28 Atom properties Use this dialog window to define charge isotope information radical informat
9. to place the atom N Draw nitrogen atoms Draws a nitrogen atom or converts an existing atom into a nitrogen atom After selection click in the drawing area to place the atom Chapter 4 Description of Standard Edit Buttons ICEDIT Manual 29 4 2 4 Lo Draw oxygen atoms Draws an oxygen atom or converts an existing atom into an oxygen atom After selection click in the drawing area to place the atom s Draw sulfur atoms Draws a sulfur atom or converts an existing atom into a sulfur atom After selection click in the drawing area to place the atom Others Draw text Activates the text input cursor within the drawing area at the selected position Draw Brackets Draws a pair of brackets Please refer to chapter 9 for further details IC MAP Automap the reaction Mapping numbers and reaction center information will be added automatically to a drawn reaction To remove the mapping and reaction center information please use the Remove mappings button from the button bar x The Automap the reaction button automatically maps all possible atoms and automatically adds reaction centers whereas the Map atoms button 4 allows the manual input of mapping numbers see above Please note The Automap the reaction button is only available if the automap functionality is included in your license Please contact us for further licensing information iceditsupport infochem de Standardiz
10. 4 2 4 2 1 4 2 2 Standard Templates Click in the drawing area to transfer the selected template By clicking on the desired attachment point at an already existing structure within the drawing area the template will be connected at the chosen attachment point y0049080d094000890 The ICEbDIT Windows application provides a large number of additional templates via the Templates dialog window Templates Open Standard Bond Buttons Draw single bonds or change existent bonds Adds a single bond Either click on a free spot within the drawing area or drag a bond between two atoms With additional clicks on a single bond you can convert it into 1 a double one additional click ii a triple bond two additional clicks iii a single bond again three additional clicks Please note It is only possible to convert a double bond to a triple bond if the valence on the C atoms is not exceeded If the valence is exceeded a single bond is drawn instead In this case a triple bond can be drawn using the Draw triple bonds button or the Edit Bond dialog Draw double bonds or change existent bonds to double bonds Draws a new double bond or converts an existing bond into a double bond 4 Draw triple bonds or change existent bonds to triple bonds Draws a new triple bond or converts an existing bond into a triple bond Draw up wedges or change existent bonds to up wedges Draws a new up stereo bond
11. A molecule containing a self defined superatom can be copied saved or exported like any other usual molecule However the self defined superatom is not added to the internal list of superatoms Therefore it is not stored for future use and must be newly created each time it is used Currently the storage of self defined superatoms as user defined templates is not yet supported but will be supported in a future version Chapter 7 Superatoms ICEDIT Manual 48 8 Chiral flag A chiral flag is used to mark the stereochemistry of the labeled molecule as absolute To add the chiral flag please select the molecule you want to label as chiral and use the context menu Create Chiral Flag The labeled molecule is now marked with the text box chiral To remove the chiral flag please delete the text box chiral The stereochemistry is no longer marked as absolute Example File Edit Object Chemistry Templates Options 7 5EC ESSE EEGs OAA Edit Bonds Edit Atoms oe Object s CL E Create Chiral Flag Os Chapter 8 Chiral flag ICEDIT Manual 49 Result 3 Infochem Chemistry Edit File Edit Object Chemistry Templates Options 7 Defoe oi Ho ajolololalolajelolek chiral Chapter 8 Chiral flag ICEDIT Manual 9 Brackets 90 To draw a bracket please select the bracket 11 button from the left hand side of the template menu and draw a pair of brackets into the drawin
12. ICT Manual Structure and Reaction Editor Version 3 0 1 Spring 2014 Table of Contents 1 INTOdU CIN nai 1 lo OVEN rs at 2 hz IGEDITFWINIOWS APPICALMON sein cajon 3 1 2 1 FUNCION Ina E AN arta EA N 3 122 System Requirements 4 ls SED Java Scriot Oink E 5 14 WCEP JAVA A e o ha eal le ted 6 1 4 1 FUNCION Iaido titi 6 1 42 Enhanced ICEDIT Java Applets 7 TASC Sy REA UMSS lab cree cet 7 1 4 AppletParamete Said aaa diodo tio 7 tS ICREND To dilata ect 8 1 5 1 A O O cinendead ameceatetanasears 8 1 5 2 System REQUIFEMENIS ccccceececccescecceseeecseuceccceuseeeseuseeecsaseesseseeessuseeessageeessegeeesssseesssageees 9 2 ICEDIT SO ida as Era asa 10 21 UM ICE MANS o el de lee bdo di 10 3 General INTOLMAtON idilio aa aaa aaa 11 Sa Description ate We AU Bai da 11 3 1 1 Fle a AY AA Pu een ac cam eande uct ets Nanak dale aed enmaanets uteieteacaes 11 O A A PP ere ee ee 13 A A 8 67 eel gO ene a or eee ee ee eee oe eee eo eee eee eee 14 A RP 15 Soleo Templates SMENU s a tado 18 JEG Options Men da a a A a De a ante 19 A cate a e ae hal ult cou atta oll ad tae 20 32 AGOMEXT MENUS o ta o nia 21 3 3 Keyboard Snoop 22 4 Description of Standard Edit Buttons ccccessseesseeeeeeeseeeeeeeesseeeeeeeesseeeeeeeesseeeseoensseeeseoenseeesseoneas 23 AT Standard EqiP Buin ia E E siete 23 Ag olanda d temblar deca 26 4 2 1 Standard Molecule Templates aa 26 J22 Standard Bond DUMON
13. Java Runtime Environment JRE 1 1x or higher Please note JavaScript must be enabled 1 4 4 Applet Parameters the width of the applet window in logical units the height of the applet window in logical units Off default On Hetero On Hetero or Terminal On All Chapter 1 Introduction ICEDIT Manual 8 1 5 ICRENDIT 1 5 1 Functionality ICRENDIT is a small Java applet primarily used to render one or more chemical structures in an HTML document An editing functionality is implemented by connecting to an IC EDIT installation at the client side It is based on the full application and therefore all IC EDIT application functionalities like the full support of superatoms templates general setting display features etc are supported ICRENDIT can be used to integrate chemistry into a browser application either only with display functionalities renderer component or with full display and editing functionalities editor component Example of the renderer component Only display copy save and version functionalities are supported Save OH Display Version Example of the editor component All display and edit functionalities are supported Copy pa Load Ho Paste OH Display Version Chapter 1 Introduction ICEDIT Manual 9 1 5 2 System Requirements Supported Browsers Internet Explorer 5 5 or higher Firefox Windows and Opera Software Java Runtime Environment JRE 1 5x or
14. ONTRIBUTORS BE LIABLE FOR ANY DIRECT INDIRECT INCIDENTAL SPECIAL EXEMPLARY OR CONSEQUENTIAL DAMAGES INCLUDING BUT NOT LIMITED TO PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES LOSS OF USE DATA OR PROFITS OR BUSINESS INTERRUPTION HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY WHETHER IN CONTRACT STRICT LIABILITY OR TORT INCLUDING NEGLIGENCE OR OTHERWISE ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE Chapter 13 Technical Documentation ICEDIT Manual 60 ICRENDIT is using com4j Copyright c 2003 Kohsuke Kawaguchi All rights reserved Redistribution and use in source and binary forms with or without modification are permitted provided that the following conditions are met Redistributions of source code must retain the above copyright notice this list of conditions and the following disclaimer Redistributions in binary form must reproduce the above copyright notice this list of conditions and the following disclaimer in the documentation and or other materials provided with the distribution THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS AS IS AND ANY EXPRESS OR IMPLIED WARRANTIES INCLUDING BUT NOT LIMITED TO THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED INNO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT INDIRECT INCIDENTAL SPECIAL EXEMPLARY
15. OR CONSEQUENTIAL DAMAGES INCLUDING BUT NOT LIMITED TO PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES LOSS OF USE DATA OR PROFITS OR BUSINESS INTERRUPTION HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY WHETHER IN CONTRACT STRICT LIABILITY OR TORT INCLUDING NEGLIGENCE OR OTHERWISE ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE Chapter 13 Technical Documentation ICEDIT Manual 61 14 Customer Support Please contact us to receive technical support or license information INFOCHEM GESELLSCHAFT FUR CHEMISCHE INFORMATION MBH Landsbergerstrasse 408 V D 81241 Munchen Germany Phone 49 0 89 583002 Fax 49 0 89 5803839 Email iceditsupport infochem de For general information about InfoChem products see the InfoChem homepage at http www infochem de Chapter 14 Customer Support
16. S sessen ee anane a aneen a ad 26 423 Standard AOM BUNNS sesiis e 27 A a a E seomaenestyeaties 29 5 Drawings iia 30 sn a ee me eee ee meer 30 de Sea OD 10 Ic en mene ane en rte dd ia 30 53 Ed AMS err ne ee ee eer 31 94 ONG S ag tats Sees FP veda ebsdnsenteed tees aatseaet wed se ciabntt waceune stds bat temcowes eae 32 Do e 33 5 5 1 Group or Ungroup Chemical ODjSCts rnern a i aA a ai i 33 O Display Foro iaa 34 5 6 1 General Sel a a A oie 34 562 ION ron O Aa 40 TS csecac esha cicte hc tiae tc iecaieatem cate iven sae cee uacaca uate vuwueeaa uetowceabieateuaeine di uasietevestnaess 44 7 1 A A a a a r ela copes yeaa Tere tiuanne aes copie 44 T2 SE IPPASTINGG SUD CTALOMS e Sau od Sees 46 Chiral TAG sacs ieee e O OS OO dni vodebiluaiudNwucesuceuucnd dmeucubuataad dns 48 CUS aoni a a a 50 10 NOS UCU oia ias 54 Ll Userdelined Template risien ia ica 56 12 OLE SErVer FUN CUON AOS ius uy 57 12 1 Integration In MS OM CC aeaa ie edito a 57 13 Technical DOCM oa 58 13 1 COPY Mist lali aos 59 WA CUStOomer UID DON ase siete aetecacees neaseutacesaseseasacenacesesuee sess eucuccssececsess 61 ICEDIT Manual 1 Introduction ICEDIT is a powerful chemical structure editor which is available as i Windows application as ii HTML5 based JavaScript editor as ili applet for all platforms supporting Java and as iv enhanced Java applet for web applications Furthermore the integration of IC EDIT in ICRENDIT al
17. dit Brackets from the Brackets context menu You can edit 1 the bracket type ii the bracket style or iii add display features to the brackets Edit brackets Bracket type Generic Bracket style Display square Fig 23 The Edit brackets dialog window Edit the Bracket Type The default bracket type is Generic You can change the bracket type from Generic to Multiple group and SRU e Bracket type Generic A pair of brackets is graphically drawn No repeating factor is displayed and no repeating factor will be interpreted chemically e Bracket type Multiple Group You can enter any integer beginning with 1 The multiple group information will be interpreted chemically e Bracket type SRU You can enter any value number range or free text The SRU information is displayed but will be not interpreted chemically For example The clamped part is not multiplied if the SRU value is set to 2 However if the Multiple group value is set to 2 the clamped part is multiplied Edit brackets Edit brackets Bracket type Repeat count Bracket type SRU label Multiple group 1 n Bracket style Display Bracket style Display square square Fig 24 The Edit brackets dialog window Chapter 9 Brackets ICEDIT Manual 53 Edit the Bracket Style The two bracket styles square and round are supported by the IC EDIT applicati
18. e the structure Standardizes the selected molecule or reaction in accordance with to InfoChem s standardization rules For further details please refer to the document Standardization Rules available on the download area of the InfoChem homepage http www infochem de Please use the back button to restore your previously drawn structure reaction if the standardization does not meet your requirements Please note The standardization button is only available if the standardization functionality is included in your license Please contact us for further licensing information iceditsupport infochem de Chapter 4 Description of Standard Edit Buttons ICEDIT Manual 30 5 9 1 9 2 Drawings To draw atoms or bonds click the corresponding button to activate the drawing mode You can change the alignment of atoms bonds or templates by dragging the object into the desired direction before releasing the mouse button Select the corresponding template button to draw rings and click once into the drawing area for one ring To fuse rings click on an existing ring bond To connect rings as spiro molecules click on a ring atom and drag the object into the desired direction before releasing the mouse button Otherwise the two rings will be automatically separated by a single bond Please note Rings and bonds will be fused automatically if the distance between two rings or bonds falls below a certain threshold Select Objects To select
19. ect Menu Group Merges multiple selected chemical objects by creating a group Keyboard shortcut CTRL G Ungroup Ungroups a selected group of chemical objects Keyboard shortcut CTRL H Chapter 3 General Information ICEDIT Manual 15 3 1 4 Chemistry Menu Superatoms Expand all Expands all identified superatoms Superatoms Contract all Contracts all identified superatoms Superatoms Show Info Opens a document in PDF format containing the supported superatoms Supported Aliaslist Molecule Values Calculate Calculates molecule values of all or the selected objects single molecules multiple molecules and parts of structures The following molecule values are supported e Formula e Molecular Weight The calculation is based on the natural atomic weight of the element unless an isotope is specified explicitly In this case the atomic mass of the specified isotope is used e Nominal Mass The calculation is based on the atomic mass of the most abundant isotope unless an isotope is specified explicitly In this case the atomic mass of the specified isotope is used The atomic mass is the rounded exact mass of the element e Exact Mass The calculation is based on the exact atomic mass of the most abundant isotope unless an isotope is specified explicitly In this case the atomic mass of the specified isotope is used e Elemental Analysis Molecule Values x x C6 H Decimals
20. g surface by using the mouse cursor Please note The distance between the pair of brackets can be adjusted later on by selecting and moving a single bracket However the height of the brackets cannot be adjusted later on This feature will be supported in future Therefore please make sure that the height is fitting before releasing the mouse button Molecules can only be interpreted correctly if the brackets are drawn properly The following types of brackets are supported e A pair of brackets covering a complete molecule e A pair of brackets covering a section in between a molecule Please note Both brackets of a pair must cross a bond of the molecule in this case Example D Infochem Chemistry Editor File Edit Object Chemistry Templates Options OLER Janceo DO Cb allowed hot allowed E e Chapter 9 Brackets IC EDIT Manual 51 You can edit delete or color a bracket by using the Brackets context menu To open the Brackets context menu please move the mouse cursor above one bracket until a red frame appears You can now open the Brackets context menu by right clicking Example iC Infochem CI memistr Y Editor pe E1 gt x l Fie Edit Object Chemistry Templates Options mAHGELROUQOHMEE Px ie ZAARA Edit Brackets Delete Brackets Copy Color E e N ol s Chapter 9 Brackets ICEDIT Manual 52 Edit Brackets To edit a pair of brackets choose E
21. he selected multiple items are now grouped and will be treated as a solely object visible at the selection frame which is covering all objects belonging to the created group Ungroup To ungroup a group of multiple chemical objects please select the desired group and use either the context menu option Ungroup the keyboard shortcut Ctrl H or the item Object Ungroup from the main menu Please note Multiple objects that are grouped act as one solely object Example 3 Infochem Chemistry Editor File Edit Object Chemistry Templates Options 7 Ola gt gt Ela l gt xr P lt is JAJIO OOOO lo jojo y Ungrouped grouped A Le Chapter 5 Drawings ICEDIT Manual 34 5 6 Display Features The following display features are supported e Display of implicit hydrogen labels Per default all implicit hydrogen labels are hidden You can change the show hydrogen labels option via the General Settings dialog to show implicit hydrogen labels On All On Hetero or Terminal or On Hetero atoms e Color for atoms bonds and text You can change the color either by using the General Settings dialog or by using the context menu See also chapter 5 6 2 e Font type size and style for atoms and text You can change the font settings by using the General Settings dialog window e Bond thickness You can change the bond thickness either by using the General Settings dia
22. higher Please note JavaScript must be enabled Please note IC RENDIT is only supported for Windows based systems Chapter 1 Introduction ICEDIT Manual 10 2 2 1 ICEDIT Setup Windows application only Run Setup exe if the setup does not start automatically If there is no Java Runtime Environment JRE installed on your system the setup launches the Java Installer IMPORTANT We strongly recommend to use Add Remove Programs to uninstall IC EDIT Please note For automap and standardization functionalities a license file is required Please copy the icedit lic file into the installation path of IC EDIT Please contact us for further licensing information iceditsupport infochem de Using ICEDIT in Reaxys The installation of ICED T supports the integration in Elsevier s Reaxys as additional structure editor if Reaxys is installed Before using ICEDIT within Reaxys you have to download and install the Reaxys Structure Editor Plugins from the Reaxys homepage http www info reaxys com support downloads After having installed the Reaxys Structure Editor Plugins the IC EDIT for Reaxys component will be installed automatically with every new setup Please note If ICEDIT is already installed on your computer we recommend to uninstall and re install the application to get the ICED T for Reaxys component To set ICEDIT as default drawing tool in Reaxys under My Settings plea
23. ion and atom valence P Table Opens a dialog containing the Periodic Table of the Elements to select any element Furthermore this dialog contains additional buttons for non standard and query atoms A Draws an A query atom any atom excluding H Q Draws a Q query atom any atom excluding H and C X Draws an X atom atom type used for halogens no valid query feature R Draws an R atom no valid query feature Query atom The following query features are implemented and can be adjusted e Substitution count s0 s6 s e Ring bond count r0 r4 r e Reaction Stereo retention inversion e Reaction center not center R center will be supported in future e List opens a dialog with the Periodic Table of the Elements where you can create an atom list for a query e NOT List opens a dialog with the Periodic Table of the Elements where you can create a NOT atom list for a query In addition the following query settings can be adjusted e No Implicit Hydrogens HO e Unsaturated atom u e Exact change ext e Exact valence ev will be supported in future e Aromatic atom aa will be supported in future Please read the ICFSE_Tutorial odf from the download area of the InfoChem homepage http www infochem de for further information on the input and use of query features fe Draw carbon atoms Draws a carbon atom or converts an existing atom into a carbon atom After selection click in the drawing area
24. l text fields during one IC EDIT session can be adjusted in the General settings select Options Settings from the main menu see chapter 5 6 1 You can add particular symbols via the Symbols dialog window Click the Symbols button to open the Symbols dialog window The following symbols are supported E e 41414403 49944909 49994449 EEEEEEHI ESR e v s a Fig 22 The Symbols dialog window Chapter 6 Text ICEDIT Manual 44 7 1 1 Superatoms Preface The input and recognition of superatoms is supported by the IC EDIT application The superatom can either consist of i a standard abbreviation Me li a sequence of elements COOH or iii a mixture of both OMe If a superatom is recognized the label is shown in default font format plain style Please note If the label is shown in italic style it is not recognized as superatom Every valid recognized superatom can be expanded l e the label of the superatom can be replaced with the corresponding structure of the superatom The expanded structure of the superatom is highlighted in gray The expanded structure parts can be contracted again e Expand a single superatom To expand a single superatom select the specific label and use the right mouse button to open the context menu Choose Expand Superatom e Contract a single superatom To contract a single superatom select any atom of the s
25. lected by using the Color dialog window You can open the Color dialog window by choosing More colors form the color drop down box Swatches mm ee eee eee EME PEE Fr DPV _ EE k Eaa S Sees SS 1 _ _ Sees 1 1 a a ETA A See EMESS UUs E A 11111 ee M2 11711 MAMAS 111111114817 7 Preview O j Sample Text Sample Text A M Sample Text Sample Text Fig 20 The Color dialog window Chapter 5 Drawings IC EDIT Manual 6 42 Text Please use the text button from the ICEDI T application to enter a text string To edit any text please select the select button and double click the text label or right click the text label to open the Edit Text context menu and choose Edit Text to open the Edit Text dialog window ID Infochem Chemistry Editor Fie Edit Object Chemistry Templates Options 7 Ole lo gt EjQl9 gt 1 x e ATIC AMATO 1G 10 Delete Text Copy Edit Text ES Edit Text Edit Style Align Font Color TE Default color CH Clgj 20 C 3h Fig 21 The Edit Text dialog window Chapter 6 Text ICEDIT Manual 43 You can adjust the font the size the style the style effects and the color For this purpose please select any text fragment select the desired property and click OK Please note General text settings like font size style and color that are applied to al
26. log window or by using the Edit Bonds dialog window chapter 5 4 5 6 1 General Settings General Settings General tab The general tab of the General Settings dialog allows to change the color of all objects The changed settings will be used for all new objects including atom bond and text objects You can activate the chosen settings by clicking OK General Settings General Atoms Bonds Text Color W Draw antialiased Draw antiallased text Cyan Dark Gray Gray Green Light Gray Magenta Fig 11 The General Settings dialog window Chapter 5 Drawings ICEDIT Manual 35 Please note Since version 3 0 atoms and bonds are drawn with antialiasing by default To get the previous behavior please uncheck the Draw antialiased option Please note If you are changing any settings from the General settings dialog window you will be asked if you would like to use the changed settings also for already existing objects If you click Yes all already drawn objects will be adjusted as well If you click No the already existing objects will remain as drawn Ic Info Do you want to apply changes to the existing objects too ves no Fig 12 The General Settings dialog window Chapter 5 Drawings ICEDIT Manual 36 General Settings Atoms tab The atom tab of the General Settings dialog window opens the opportunity to adjus
27. lows rendering as well as editing functionalities of chemical structures and reactions in any HTML document Windows application The ICEDIT application offers full editing functionalities chemical as well as display functionalities IC EDIT is a registered OLE Server and therefore it allows the integration in MS Office Word Excel Access and PowerPoint and in any other OLE Client HTML5 based JavaScript editor Due to increasing difficulties with Java in general with the newest generation of most of the common browsers InfoChem has additionally developed an HTML5 based JavaScript version of the editor Of course the ICED T JavaScript version supports also all features needed by a chemical query editor for structures and reactions Java applet The ICED T Java applet is an Internet browser based query editor for the input of chemical structures and reactions It is downloaded on the fly and therefore it does not have to be installed on the user s computer Enhanced Java applet The ICEDIT enhanced applet is a Java applet with extended functionalities like full superatom support which can be used as front end in web applications managed by a servlet container like Apache Tomcat ICRENDIT The trusted applet IC RENDIT is an Internet browser based combination of rendering and or editing chemical structures and reactions For edit functionalities an IC EDIT application installation is required Therefore IC RENDIT does only work o
28. n Windows based systems Chapter 1 Introduction IC EDIT Manual 1 1 1 2 Overview Support of Drawing of structures reactions and fragments Atom query features Bond query features Reaction query features R group query features Integration in web applications Superatoms Calculation of molecule values InChls InChlKeys and SMILES Display features OLE functionalities MS Office integration Automap function Standardization of molecules reactions IC EDIT application ICEDIT JavaScript ICEDIT applet Enhanced ICEDIT applet ICRENDIT offers the opportunity to integrate the ICEDIT application in web applications Availability of the automap and the standardization functionality is dependent on the license file declaration Please contact us for further licensing information iceditsupport infochem de Chapter 1 Introduction ICEDIT Manual 3 1 2 ICEDIT Windows Application 1 2 1 Functionality 3 Infochem Chemistry Editor po Ex Fie Edit Object Chemistry Templates Options 7 Ola lo o IS xr Px ies ZATIAN Edit and template button bars D Drawing area IC Description of the current button IC 1D 3 4 Benzene Fig 1 The ICEDIT Windows application Chapter 1 Introduction ICEDIT Manual The Windows application of IC EDIT provides the following drawing features Drawing of chemical structures reactions and fragments Full su
29. n general ii for atoms iii for bonds and iv for text objects Please refer to chapter 5 6 1 for further details about the General Settings dialog General Settings General Atoms Bonds Text Font Size Style Arial talic E Plain ne Color show hydrogen labels Default color e OFF Fig 8 The General Settings dialog window Drawing Area Properties The maximum size of the drawing area width and height can be adjusted here Chapter 3 General Information ICEDIT Manual 20 3 1 7 Menu Help Opens a documentation file in PDF format About Returns information about ICEDIT the used components and their version numbers Chapter 3 General Information ICEDIT Manual 21 3 2 Context Menus Context menus are available by right clicking i on the drawing surface ii on specific bonds iii on specific atoms or iv on selected objects The following features are available within the context menu Edit Opens the Edit Bond or Edit Atom dialog window The currently selected atom s or bond s can now be edited Copy Object s Copies the selected object s into an internal buffer Paste Object s Pastes the selected object s from an internal buffer Duplicate Object s Duplicates the selected object s Copy Copies the selected object s into the Windows clipboard Keyboard shortcut CTRL Paste Pastes the object s
30. o not change their order Examples Left side superatom label Right side superatom label MeO OMe MeHN NHMe HOOC COOH TMS TMS H3C H2C s5 CH2 5CH3 The label of the superatom is changed automatically according to the direction of the connection to the target molecule in order to represent the connecting atom of the superatom group correctly E g the superatom label input on the left side of a molecule can be COOH and the output changes automatically to HOOC Please note Please refer to Chemistry Superatoms Show all from the main menu of the ICEDIT application to find a full list of supported superatoms and superatom labels Chapter 7 Superatoms ICEDIT Manual 46 pr Self defined Superatoms Select the desired part of a molecule and choose Create Superatom from the context menu to create a self defined superatom Enter the desired superatom label into the dialog window and click OK to create the superatom Example UN Infochem Chemistry Editor File Edit Object Chemistry Templates Options 7 DR R Hab 1 a alolololalojajalolelole Edit Bonds Edit Atoms Copy Object s Dacta MRacti oc Paste Objectis Duplicate Object s e o f fo JIER Po INES T gt Ungroup Enter the superatom label o canes Chapter 7 Superatoms ICEDIT Manual 47 File Edit Object Chemistry Templates Options DELLE eens ae to CeO COOIPr Stele fete Wel NINN Please note
31. on Edit brackets Bracket type Generic Bracket style Display square Fig 25 The Edit brackets dialog window Enter a Bracket Display You can enter any additional display information in the Display field The entered display information is shown on the upper right hand side of the right bracket pair Edit brackets Bracket type Repeat count Multiple group 12 Bracket style Display square la Fig 26 The Edit brackets dialog window Sth ZA Delete Brackets To delete a bracket please choose Delete Brackets from the Brackets context menu to remove the whole pair of brackets Chapter 9 Brackets ICEDIT Manual 54 10 No Structure Definition No Structures are used to enter non structural components into structure or reaction databases Some molecules cannot be represented by a drawn structure but do play significant roles in reactions like baker s yeast In these cases No Structure labels can be used to insert the molecules into the database This means the molecule is represented by a No Structure label recognized as valid database input and not by a structure Create a No Structure Please use either the context menu item Create No Structure or the main menu item Chemistry Create No Structure to open the Create No Structure dialog window Please enter a desired caption or use the default caption No Structure for yo
32. or reaction from MDL Sketch file format Please note Complex schemes and drawing elements are not yet supported Import SMILES Imports a structure from the SMILES format and generates coordinates Import Cdxfile Imports a structure or reaction from the Cambridge Soft CDX file format Please note Complex schemes and drawing elements are not yet supported Recent Files Includes a list of recently opened or imported files Print Prints the structures or reactions drawn in the drawing area Exit Closes the current application Chapter 3 General Information ICEDIT Manual 13 3 1 2 Edit Menu Undo Undoes the last operation Keyboard shortcut CTRL Z Redo Redoes the last undone operation Keyboard shortcut CTRL Y Copy Copies the current objects into the Windows clipboard Transfer to Microsoft Office products ISIS Draw MDLDraw and ChemDraw is supported Keyboard shortcut CTRL C Paste Pastes objects from the clipboard Transfer from Microsoft Office products ISIS Draw MDLDraw and ChemDraw is supported Keyboard shortcut CTRL V Please note Complex schemes and drawing elements are not yet supported Delete Deletes the selected objects Keyboard shortcut DEL Select all selects all objects Keyboard shortcut CTRL A Duplicate Duplicates the current selected objects Keyboard shortcut CTRL D Chapter 3 General Information ICEDIT Manual 14 3 1 3 Obj
33. pecific expanded structure and use the right mouse button to open the context menu Choose Contract Superatom e Expand all superatoms To expand all superatoms use the context menu Chemistry Superatoms Expand all e Contract all superatoms To contract all superatoms use the context menu Chemistry Superatoms Contract all Example os O COOH NN a ZA O gt COOH O Contracted form Expanded form Input of superatoms The input of superatoms is case sensitive e All atom symbols from superatoms have to be drawn as represented in the Periodic Table of the Elements e g COOH OMe SiMe3 Chapter 7 Superatoms ICEDIT Manual 45 e Abbreviations are case sensitive as well They are supported in the most common notation e g Me is supported me or ME is not supported The standard typing of abbreviations is as follows e Bn Boc Bt Bu Bz e Cbz Cy e EE Et e Fmoc e Me MEM Mes MOM MPM Ms e Naph NPhih e Ph Piv PMB PNB Pr e SEM Su e TBDMS TBDPS TBS TES Tf THP TIPS TMS Tol Tr Ts Display of superatom labels The display of superatom labels is sensitive regarding the direction of the connection of the superatom to the target molecule Example OMe OMe On the top the bottom and the right side of the target molecule the input of the superatom occurs in a standard way The output of the superatom on the left side however is in reversed order Please note Abbreviations d
34. pport of standard query features input and interpretation Drawing and support of complex R group query specifications Additional chemical features like full superatom support the calculation of molecule values and the input and interpretation of brackets Standardization of structures and reactions add in button functionality Automap function automatically mapping of reactions add in button functionality The Windows application of IC EDIT provides the following display features Color Bond thickness Atom font type size and style Text font type size and style The Windows application of IC EDIT provides the following additional features Integration in MS Office Word Excel PowerPoint and Access and any other OLE Client Application Programming Interface API for Java VB 6 VBA and NET 1 2 2 System Requirements Supported Platforms Windows 8 Windows 7 Windows Vista and Windows XP Chapter 1 Introduction ICEDIT Manual 5 1 3 ICEDIT JavaScript Editor LASA RARE oS A D AOD 9 a oo Fig 2 The JavaScript version of IC EDIT Since the HTML5 based JavaScript Editor is completely Java free this version of IC EDIT is the perfect query editor for modern web applications An installation on the client computer is not necessary and the editor can be used in all modern web browsers supporting HTML5 For a detailed description of the ICED T JavaScript Editor please see the separate documentation
35. remove mappings or reaction center information from multiple atoms bonds R Define Rgroups Draw a core structure and several Rgroups First click on the position of the core structure where you want to have the Rgroup attached Then click on the connection position of the Rgroups Chapter 4 Description of Standard Edit Buttons ICEDIT Manual 25 Example R Query resolved single Queries eS J Ri i s f Oo my r We oo co a r1 Please note To specify two different attachments in one Rgroup first define the attachment referring to the blue bond in the core structure then define the attachment referring to the red bond in the core structure Example R Query resolved single Queries H A a a N C C a y io N N N A cc C a Dar To change the Rgroup numbering please click at the object you want to edit and enter the new number with your keyboard To do this the Define Rgroups button must be selected Remove Rgroup Info from atom Click single atoms or draw a rectangle to remove the Rgroup information O Show info dialog Shows information about ICEDI T the used components and their version numbers Back Transfer structure back to calling application Transfers the current structure s or reaction back to the calling application and closes IC EDIT only visible if IC EDIT is called from another application Chapter 4 Description of Standard Edit Buttons ICEDIT Manual 26
36. ry e g My Templates in the Templates folder of the ICEDIT installation path To group the templates choose an existing subdirectory or create a new subdirectory multiple levels of subdirectories are supported Chapter 11 User defined Templates ICEDIT Manual 57 12 OLE Server Functionalities Windows application only 12 1 Integration in MS Office ICEDIT objects can be used in Microsoft Office Word Excel PowerPoint and Access 1 To start ICEDIT in MS Word MS Excel etc choose the item ICED T Document from menu Insert Object Draw an object Click the button Back to transfer the object from ICEDIT back to MS Office Double clicking the image starts IC EDIT again 2 Draw an object in IC EDIT Choose Copy from ICEDIT menu Edit to copy the object in the Windows clipboard Choose Paste to insert the object in MS Office Double clicking the image starts IC EDIT again The structure display format in MS Word Excel PowerPoint and Access is Windows Metafile which provides a high resolution for print out Chapter 12 OLE Server Functionalities ICEDIT Manual 58 13 Technical Documentation In addition to this IC DIT user manual a detailed technical documentation is available Please find the document ICEdit_ Technical Documentation pdf in the Documentation folder in the IC EDIT installation path In this technical documentation you will find detailed descriptions on
37. s Show The menu item is now enabled To disable automatic atom number select Atom Numbers Show again The menu item is now disabled Chapter 3 General Information ICEDIT Manual 17 Create No Structure Opens the Create No Structure dialog to create a No Structure label Please refer to chapter 10 for further details on No Structures Chapter 3 General Information ICEDIT Manual 18 3 1 5 Templates Menu Open Opens the Templates dialog window Insert templates To transfer a template into the drawing area click at a template in the dialog window The selected template will be highlighted Then click into the drawing area It is possible to choose the docking point atom or bond from the template This selected atom or bond is highlighted in red in the template dialog The template will be connected by clicking at an attachment point in a structure within the drawing area 3 Templates Templates See Crown Ethers i Cydoalkanes p Functional Groups Fused Rings Heterocycles i MyTemplates Nudeobases N Rings Steroids m i Sugars Terpenes Benzofuran Benzoic Acid Acenaphthwene Anthracene Benzene DAS Bipherylene Fig 7 The Templates dialog window Chapter 3 General Information ICEDIT Manual 19 3 1 6 Options Menu Settings Opens the General Settings dialog window and allows the adjustment of settings i i
38. se 1 Open Modify Application Settings 2 Select IC EDIT and click Save 3 Restart the browser Chapter 2 ICEDIT Setup ICEDIT Manual 11 3 3 1 3 1 1 General Information Description of the Menu Bar Windows application only File Menu Transfer to client Transfers the current structure reaction back to the calling application and closes IC EDIT only visible if IC EDIT is called from another application Keyboard shortcut CTRL B New Creates a new empty document Keyboard shortcut CTRL N Open Opens a structure or reaction from a file in icf format Keyboard shortcut CTRL O Save Saves a structure or reaction to a file in icf format Keyboard shortcut CTRL S Save As Saves a structure or reaction to a file in icf format with a different file name Export Mol Rxnfile Exports a structure to MDL MOL or a reaction to MDL RXN file format Export Skcfile Exports a structure or reaction to MDL Sketch file format Please note Complex schemes and drawing elements are not yet supported Export SMILES Exports a structure to SMILES file format Export Canonical SMILES Exports a structure to canonical SMILES file format Chapter 3 General Information ICEDIT Manual 12 Import Molfile Imports a structure from MDL MOL file format Import Rxnfile Imports a reaction from MDL RXN file format Import Skcfile Imports a structure
39. t i the atom font ii the atom font size iii the atom font style as well as iv the color of atoms In addition you can adjust the display of implicit hydrogen labels You may switch the display to e Off No implicit hydrogen label will be displayed e On Hetero Implicit hydrogen labels will be displayed on heteroatoms e On Hetero or Terminal Implicit hydrogen labels will be displayed on heteroatoms and on terminal carbon atoms e On All Implicit hydrogen labels will be displayed on all atoms General Settings General Atoms Bonds Text Font Size style Arial talic Bold Plain iw Color Show hydrogen labels TER Default color On Al Off On Hetero On Hetero or Terminal On All Fig 13 The General Settings dialog window Please note If you are changing any settings from the General settings dialog window you will be asked if you would like to use the changed settings also for already existing objects If you click Yes all already drawn objects will be adjusted as well If you click No the already existing objects will remain as drawn Chapter 5 Drawings ICEDIT Manual 37 Fig 14 The General Settings dialog window Chapter 5 Drawings ICEDIT Manual 38 General Settings Bonds tab The bond tab of the General Settings dialog window opens the opportunity to adjust i
40. the thickness of the bonds ii the length of the bonds as well as ili the color of the bonds General Settings General Atoms Bonds Text Color MO Default color Length ENS pizel Fig 15 The General Settings dialog window Please note If you are changing any settings from the General settings dialog window you will be asked if you would like to use the changed settings also for already existing objects If you click Yes all already drawn objects will be adjusted as well If you click No the already existing objects will remain as drawn 1c Info Do you want to apply changes to the existing objects too ves No Fig 16 The General Settings dialog window Chapter 5 Drawings ICEDIT Manual 39 General Settings Text tab The text tab of the General Settings dialog window opens the opportunity to adjust i the text font ii the text font size ili the text font style as well as iv the color of the text Please use the Edit Text functionality as described in chapter 6 for individual adjustments to text objects General Settings General Atoms Bonds Text Font Arial Color MO Default color Fig 17 The General Settings dialog window Please note If you are changing any settings from the General settings dialog window you will be asked if you would like to use the changed settings also for already e
41. tom or double click a specific atom For details of the Edit Atom dialog window please see chapter 4 2 3 Chapter 5 Drawings ICEDIT Manual 32 5 4 Edit Bonds Select one or several bond s and click on the right mouse button Select Edit Bond s from the context menu to open the Edit bond dialog window or double click a specific bond It is possible to change the bond type and to add reaction query features like reacting centers or the topology of the selected bond s In addition the thickness of the selected bond s is adjustable ina range of 1 to 10 pixels Edit Bond Bond Type a Double Triple Coordinative re P Reacting Center Either ETE Double Fither Topology Thickness Fig 10 Edit Bond dialog window The following bond types are supported Single Double Either Double Aromatic Triple TT dll m Single Double Single Aromatic ttl Down Double Aromatic N Either The following reaction query features are supported Reacting Center a Not Center i Make Break A Make 8 Change 4 Center us Change Topology Teh Chain Ring Chapter 5 Drawings ICEDIT Manual 33 9 0 9 9 1 Edit Objects Group or Ungroup Chemical Objects Group To group multiple chemical objects please select the desired objects and use either the context menu item Group the keyboard shortcut Ctrl G or the option Object Group from the main menu T
42. ur No Structure The No Structure label will be added to the drawing area by clicking OK Create No Structure Label No Structure Fig 27 The Create No Structure dialog window Edit a No Structure You can edit delete or color a No Structure by using the No Structure context menu To open the No Structure context menu please move the mouse cursor above the No Structure until a red frame appears You can now open the No Structure context menu by right clicking Chapter 10 No Structure ICEDIT Manual 55 Example 5 Infochem Chemistry Editor co see File Edit Object Chemistry Templates Options 7 Ola lo gt El P lt r Px ies AMADIOIOAVIILIC C OlO NOS z af a Mo Structure Edit NWo Structure Delete No Structure Copy Color E o N gl s Please note A reaction or molecule containing a self defined No Structure can be copied saved or exported like any other usual molecule However the No Structure together with its self defined No Structure label can only be exported into the ICF format The label and the position of the self defined No Structure cannot be transported by any other format and will be lost Chapter 10 No Structure ICEDIT Manual 11 96 User defined Templates Windows application only Draw the structure you want to use as template in ICEDIT and save it to the subdirectory Templates of your IC EDIT installation directo
43. xisting objects If you click Yes all already drawn objects will be adjusted as well If you click No the already existing objects will remain as drawn 3 Info Do you want to apply changes to the existing objects too ves ne Fig 18 The General Settings dialog window Chapter 5 Drawings IC EDIT Manual 5 6 2 Color 40 It is possible to change the color of selected objects Besides whole molecules and reactions also single bonds and atoms can be colored The color of text objects can be adjusted too You can change the color of object s either by using the context menu or by changing the color from the General Settings dialog window 3 Infochem Chemistry Editor File Edit Object Chemistry Templates Options 7 La ef ERG gt Xx e Px i ZATARAIN N Edit Bonds Edit Atoms Copy Object s Paste Object s Duplicate Object s JTE K i Ue ato m AERES Color Fig 19 Color context menu Create Chiral F Black Rea Blue Green Yellow Magenta Cyan Default color More colors Chapter 5 Drawings IC EDIT Manual 41 Please note The default color dyes all atoms and bonds black However expanded superatoms will be highlighted in dark gray see also chapter 7 Whereas the color black dyes everything black bonds atoms and expanded superatoms Beside the predefined standard colors any desired color can be se

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