CONFIGURATION GUIDE BIOVIA DRAW 2016

Transcription

1 CONFIGURATION GUIDE BIOVIA DRAW 2016

2 Copyright Notice 2016 Dassault Systèmes. All rights reserved. 3DEXPERIENCE, the Compass icon and the 3DS logo, CATIA, SOLIDWORKS, ENOVIA, DELMIA, SIMULIA, GEOVIA, EXALEAD, 3D VIA, BIOVIA and NETVIBES are commercial trademarks or registered trademarks of Dassault Systèmes or its subsidiaries in the U.S. and/or other countries. All other trademarks are owned by their respective owners. Use of any Dassault Systèmes or its subsidiaries trademarks is subject to their express written approval. Acknowledgments and References To print photographs or files of computational results (figures and/or data) obtained using BIOVIA software, acknowledge the source in an appropriate format. For example: "Computational results obtained using software programs from Dassault Systèmes BIOVIA. The ab initio calculations were performed with the DMol 3 program, and graphical displays generated with Draw." BIOVIA may grant permission to republish or reprint its copyrighted materials. Requests should be submitted to BIOVIA Support, either through electronic mail to BIOVIA.Support@3ds.com, or in writing to: BIOVIA Support 5005 Wateridge Vista Drive, San Diego, CA USA

3 Contents BIOVIA Draw Configuration iv Tasks iv Configuration Tasks iv Configuration Outside AccelrysDrawnet.xml v Editing the XML Configuration File v Specify XML Configuration Files vi Specify the Path to Custom XML Configuration Files vii Before: include= Points to Compiled Class Resources vii After: include= Points to Custom XML Configuration File vii Setting a Startup Structure vii Biopolymers viii Biopolymers: Sequence Tools viii Case-sensitive Sequence Residues viii Disabling the Feature viii Customize Draw for Biopolymer Searches and Registration ix Providing Standard Biopolymer Templates to Users ix Customizing the Standard Abbreviation Definitions File x Customizing BIOVIA Draw for Users xi Customizing BIOVIA Draw for Administrators xiii Creating Additional Abbreviations xiv Standard Abbreviation XML Reference xviii Enhanced Stereochemistry xx Disable the Stereochemistry Dialog xx Disable Stereochemistry Actions xx Expose the Purity Section xxi Hiding OR and AND Stereogroups xxii Customize Stereogroup Labels xxiii Enabling the Data Sgroup Tool to Control Sgroup Data xxiii Example for Data Sgroup Tool xxiv Customizing Draw for Attached Data xxv Attached Data in Biopolymer Representation xxv Other Attached Data xxv Data Validation, Registration, and the Attached Data Dialog xxvii Cleaning Data Sgroups xxvii Enabling or Disabling Rgroup Atom and Building Block Tools xxix Specify a Custom Ptable and Custom Weights xxix Templates xxx Adding Templates to the Toolbar Manager xxx Add a Directory to the Template Directory xxxi Template Security xxxii Removing Template Toolbars xxxii Specify Display of Templates Containing Abbreviated Structures xxxii Display Preference Settings xxxiii Specify Display Preferences xxxiii Example: AromaticRingCircles, AtomHighlightDotWidth xxxiii Synchronize Display Settings xxxv default.xml with Custom Settings for Display Preferences xxxv Removing a Feature xxxv Example: Removing the Data Sgroup Feature xxxvi Example: Removing from the Chemistry menu xxxvi Show Explicit Carbon Label xxxviii Disabling Arrow Toolbar Autohide xxxix Removing a Menu Item xxxix Removing the Insert Option from the File Menu xxxix Removing the Formatting Toolbar Item from the Window Menu xli ChemCheck Configuration xlii Migrating Custom Toolbars xliv Command-line Image File Conversion xlvi Online Help on the ImageGenerator xlvi Converting Single File Examples xlvi Convert a Batch of Files Example xlvii Creating a Custom Ptable xlviii Custom Ptable Example xlviii Custom Ptable Path xlviii Running the Example xlix Add-Ins l Cheshire Actions li Specify a Custom Ptable and Custom Weights li AccelrysDraw-net.xml liii About the Draw XML Configuration Files liii How to Edit XML Tags in the XML Configuration Files liii Sample Screens liii Main Screen liv Drop-down Menu lvi Dialog box lvi

4 Attached Data Dialog Attributes Parent Element Child Elements Example Hierarchy of Elements XML Configuration Elements Alphabetic List of Elements Description of Elements abbreviationtoolbar action button checkbox combobox dialog DisplayPreferences donetoolbar fieldname folder label listvalue menu menuitem menustrip module multitool operator palette palettebar panel popup radiobutton radiogroup separator shortcut shortcuts selection space templatedirectory templatetoolbar templatetoolbarmanager tool toolbar Trigger Table lvii lvii lvii lviii lviii lviii lix lxii lxiv lxiv lxv lxviii lxviii lxix lxxi lxxii lxxiii lxxiii lxxvi lxxvi lxxvii lxxviii lxxix lxxx lxxxi lxxxiii lxxxv lxxxv lxxxvi lxxxvii lxxxviii lxxxix xci xci xcii xcii xciii xciii xciv xcvi xcvi xcvii c ci

5 BIOVIA Draw Configuration XML tags define the menus, tools, toolbars, and other items that display indraw. The AccelrysDrawnet.xml file is the primary XML configuration file and specifies the secondary class resources or XML configuration files that affect Draw. The AccelrysDraw-net.xml file is located in the installation directory. The AccelrysDraw-net.xml file points to secondary XML configuration files located in: BIOVIA\BIOVIA Draw <version>\xmlconfig\ The menustrip.xml, a secondary configuration file, points to tertiary XML Configuration files that affect each menu on the menu bar. The following are a list of affected menus: menubar-file.xml menubar-edit.xml menubar-object.xml menubar-chemistry.xml menubar-window.xml menubar-help.xml The XML parser in Draw does not validate parent-child tag relationships. However, if a relationship is not valid, the object defined by the tags do not display. Tasks Biopolymers Standard Abbreviation XML Reference Enhanced Stereochemistry Enabling the Data Sgroup Tool to Control Sgroup Data Enabling or Disabling Rgroup Atom and Building Block Tools Templates Display Preference Settings ChemCheck Configuration Migrating Custom Toolbars Command-line Image File Conversion iv viii xviii xx xxiii xxix xxx xxxiii xlii xliv xlvi Tasks Configuration Tasks You can configure Draw without writing applications or using the Draw API by updating the AccelrysDraw-net.xml configuation file or setting a custom start-up structure. The XML configuration file affects the initial loading of BIOVIA Draw when a user opens the application. When a Draw application user changes one or more display settings, using Options > Settings, those local settings override the default or custom values defined in the configuration file, AccelrysDrawnet.xml. You must have administrator privileges to edit Draw, the AccelrysDraw-net.xml. BIOVIA Draw Configuration Page iv

6 Always back up the AccelrysDraw-net.xml before making any changes in the configuration file. The elements and attributes in the XML files are case-sensitive, for example, Dog, and not the same as dog in an XML file. You can update the Action, Tool, and ContextMenu elements in the AccelrysDraw-net.xml file. If you are editing the AccelrysDraw-net.xml configuration file to add the functionality of a third-party add-in, you should not make the add-in available from more than one location such as context menu, toolbar, or as a menu option in Draw. You can make the following edits: Change the default value for a setting Customize chemical drawing Enforce business rules for biopolymer representation Specify a custom Ptable Enable or disable the Data Sgroup tool (attached data) Hide enhanced stereochemistry Enable or disable the Rgroup Atom and building block tools Add more templates to the toolbar Edit display text or images Remove certain actions or tools Edit dialog boxes Migrate custom toolbars created in previous versions of Draw Configuration Outside AccelrysDraw-net.xml Most tasks described in the BIOVIA Draw Configuration Guide consist of edits inside the configuration file, AccelrysDraw-net.xml and the XML Configuration files to which it points. The exceptions are: Writing one or more batch files that cause BIOVIA Draw to start up in association with a particular XML configuration file. See Specifying XML Configuration Files. Safeguarding and administering the central set of templates at your site. See Templates: Customizing. Command-line conversion of structure files into image files. See Command-line Image File Conversion: ImageGenerator. Notes: BIOVIA Draw can be the structure editor for ISIS/Base (Options > Structure Editor). Editing the XML Configuration File To customize the BIOVIA Draw graphical user interface, edit the primary XML Configuration file and the XML Configuration files it points to. See Specify the Path to Your Custom XML Configuration Files. The default name of the primary XML Configuration file is AccelrysDraw-net.xml, which is installed in the root directory of the BIOVIA Draw installation, which this document refers to as <draw_home>. Page v BIOVIA Draw Configuration Guide

7 IMPORTANT! Keep a backup copy of the original versions of any XML Configuration files undergoing edits. It is very easy to break the XML and not always easy to fix, so it is good to be able to revert to a version that works. Do NOT change entries in the AccelrysDraw-net.xml file (or the XML Configuration files it points to) except according to the product documentation and the instructions included in the comments of the default AccelrysDraw-net.xml file and the XML Configuration files it points to. Any other changes might cause unexpected results. Only the BIOVIA Administrator should make changes on behalf of the end-users. End-users should not alter the XML files. For each configuration task, make the change in only one of the following areas of the XML: Action, Tool, or ContextMenu. Unexpected results might occur, for example, if you make an add-in available in more than one of the following ways: from the menu bar (action), from the vertical toolbar (tool), or from the right-click context menu. The entries in the XML files are case-sensitive. Be careful that the spelling of elements and attributes is exactly correct, including the case. Specify XML Configuration Files You can specify the XML configuration file using the following methods: At start up the BIOVIADraw.exe looks for the XML configuration file, AccelrysDraw-net.xml located in the installation directory. If Draw does not find AccelrysDraw-net.xml in the root directory of the installation, it loads an internal XML configuration file. If you launch Draw with a batch file, the batch file can specify the primary XML configuration file. The primary XML configuration file and the secondary XML configuration files it points to implement the graphical user interface, including which features are visible and enabled. You can use more than one XML configuration files, as follows: A file that points to palettebarstereochemistryenable.xml with stereochemistry enabled A file that points to palettebarstereochemistrydisable.xml with stereochemistry disabled. A batch file that specifies a structure file to load at start-up. Use the command line after launching Draw with from a command-line console prompt. You can specify the XML configuration file, the following as showing in the example: The simple path: C:\myFolder>BIOVIADraw.exe Alt_Config\MyConfig.xml A Path with spaces and quotation marks: \\"Program Files (x86)\biovia\biovia Draw<version number>\bioviadraw.exe" c:\myfolder\myaccelrysdraw-net.xml The UNC_path: \\Program Files (x86)\biovia\<version_number>\bioviadraw.exe \\myserver\sharedfolder\accelrysdraw-net.xml You can change the properties of the start menu shortcut to point to a custom target location for Draw. Use the Draw API to set the primary XML configuration file. Always backup the original versions of any XML configuration files that you plan to edit. BIOVIA Draw Configuration Page vi

8 Specify the Path to Custom XML Configuration Files Some of the XML Configuration files point by default to compiled class resources, but you can make them point to your custom XML Configuration files. To do so, give the full path after include=. For complete step-by-step examples, see Adding a set of templates to the Toolbar Manager and Removing a Menu Item. For an explanation of which XML Configuration files can specify other XML Configuration files, see About the BIOVIA Draw XML Configuration Files. Before: include= Points to Compiled Class Resources The primary XML Configuration file, AccelrysDraw-net.xml, points to compiled class resources that you cannot edit. <menustrip include="mdl.draw.editor.xmlconfig.menustrip.xml" /> <maintoolstrip include="mdl.draw.editor.xmlconfig.maintoolstrip.xml" /> <toolbar include="mdl.draw.editor.xmlconfig.templatetoolstrip.xml" /> <palettestrip include="mdl.draw.editor.xmlconfig.palettestrip.xml" /> After: include= Points to Custom XML Configuration File To specify the XML Configuration files that contain your custom configuration, change the include= assignment for the element to point to the full path of your new XML configuration file(s). In this example, we specify custom XML Configuration files with the full path for the mymenustrip.xml, my-maintoolstrip.xml, and my-templatetoolstrip.xml, but continue to use the compile class resource for the palettestrip.xml. <menustrip include="c:\program Files (x86)\biovia\biovia Draw 2016\XmlConfig\my-menustrip.xml" /> <maintoolstrip include="c:\program Files (x86)\biovia\biovia Draw 2016\XmlConfig\my-maintoolstrip.xml" /> <toolbar include="c:\program Files (x86)\biovia\biovia Draw 2016\XmlConfig\my-templatetoolstrip.xml" /> <palettestrip include="mdl.draw.editor.xmlconfig.palettestrip.xml" /> Setting a Startup Structure For testing purposes, you might want BIOVIA Draw to open with the display of a particular structure. The following example illustrates how to open a molfile when BIOVIA Draw starts up: 1. Close all open versions of BIOVIA Draw and navigate to the root directory of your BIOVIA Draw installation. 2. Make a copy of AccelrysDraw-net.xml and name it myxmlconfigfile.xml. IMPORTANT! BIOVIA recommends that you always keep a backup copy of the original XML configuration files. 3. Navigate to the Examples\C#\GettingStarted directory of your installation and copy test.mol to the root directory of your Draw installation. 4. Make a batch file called MyDraw.bat file in the root directory of your BIOVIA Draw installation that contains the following text: BIOVIADraw.exe myxmlconfigfile.xml test.mol 5. Run MyDraw.bat to start the BIOVIA Draw Editor with the specified structure already loaded and the file name in the title bar. Page vii BIOVIA Draw Configuration Guide

9 Biopolymers Biopolymers: Sequence Tools You can configure Draw and your company s databases to comply with the business rules for searching and registering biopolymers, by: Customizing the standard abbreviation definitions file, std_abbrev_defs.xml, to provide biopolymer templates for the Draw Sequence tools. The std_abbrev_defs.xml file is located in the installation directory. Customizing Draw to enforce your company s business rules biopolymer representation. Implementing subsequence searching in applications that access databases that contain biopolymers. For more information, see Biopolymer Representation in the BIOVIA Chemical Representation Guide located in the Draw installation directory's docs folder. The Draw Sequence tools use the templates that are specified in the version of std_abbrev_defs.xml that is located in the BIOVIA Draw installation directory. BIOVIA recommends that you do not allow users to modify the default Sequence tools. Case-sensitive Sequence Residues The default setting in BIOVIA Draw displays D- sequence residues with a single lower-case letter, and L- sequence residues with a single uppercase letter. For example, "a" creates D-alanine and "A" creates L-alanine. When this feature is enabled, the D- form also precedes the L- form for 3-letter residues. Disabling the Feature In the Settings, dialog, set Make sequence residue case sensitive to Off. BIOVIA Draw Configuration Page viii

10 Customize Draw for Biopolymer Searches and Registration To customize Draw so chemists can illustrate biopolymers to comply with business rules for biopolymer representation, do the following: Provide standard templates for biopolymer residues, protecting groups, and polyethylene glycol groups (PEG). Provide a read-only directory of templates on the company network. Configure the standard abbreviation definitions file to reference the templates in the read-only directory. Edit the Draw configuration file to include customizations for your enterprise. Distribute the customized version of Draw. When Draw users start the customized application, the toolbars for each Sequence tool displays the biopolymer templates in the write-protected directory. End-users cannot create their own residue templates. However, users can create templates for protecting groups in their personal template directories. Providing Standard Biopolymer Templates to Users BIOVIA Draw supports four different conventions for representation of biopolymers. To enforce your chosen structure convention, ensure that all chemists use the same set of write-protected templates for biopolymer residues, protecting groups, and PEG groups: 1. Provide a directory for the templates that is visible in the corporate network. End-users should have read-only privileges to this directory. Administrators should have write and delete privileges. 2. Install BIOVIA Draw on your workstation. 3. Copy the directory that contains the biopolymer templates from your local hard drive to the directory that you created in Step 1. Notes: Biopolymer templates are located in the following directory and its subdirectories in the BIOVIA Draw installation on your local hard drive: <draw_home>\stdabbreviations 4. Configure the standard abbreviation definitions file to reference the templates in the directory that you created in Step 1. See Customizing the standard abbreviation definitions file. 5. Copy the standard abbreviation definitions file that you edited in Step 3 to the directory that you created in Step Edit the BIOVIA Draw XML configuration file as needed. See Customizing BIOVIA Draw for end users. 7. Provide your end users with a customized BIOVIA Draw that uses the edited BIOVIA Draw configuration file that you created in Step 5. When your users start the customized version of BIOVIA Draw, the toolbars for each Sequence Tool will display the biopolymer templates in the write-protected directory. End-users will not be able to create Page ix BIOVIA Draw Configuration Guide

11 their own residue templates, but they can create templates for protecting groups in their personal template directories. Customizing the Standard Abbreviation Definitions File The standard abbreviation definitions file, std_abbrev_defs.xml, specifies the biopolymer templates that display on the toolbar for each sequence tool. Entries in the standard abbreviation definitions file specify the structure convention for each abbreviation (full, *atom, or pseudoatom), the full structure that the abbreviation represents, and other information. For more information see Standard Abbreviation XML Reference. BIOVIA Draw provides four example versions of the standard abbreviation definitions file, each corresponding to one of the conventions for representation of biopolymers. Each file contains the following abbreviations: Standard 1-letter abbreviations for 21 of the 22 naturally occurring amino acids, and for DNA and RNA nucleotides Abbreviations for widely used protecting groups for amino acids. Example abbreviations for PEG structures BIOVIA recommends that you use one of these files as the basis for creating your own standard abbreviation definitions file. You can customize this file to add your own abbreviations. Note: The version of std_abbrev_defs.xml that is located in the BIOVIA Draw installation directory is the same as std_abbrev_defs_fullctab.xml in the examples directory, except that the file in the BIOVIA Draw installation directory references the <draw_home>\stdabbreviations directory on your local hard drive. Therefore, BIOVIA recommends using std_abbrev_defs_fullctab.xml instead. To configure the standard abbreviation definitions file: 1. Use the following table to choose the example standard abbreviation definitions file that corresponds to the biopolymer structure convention that you want to use in your database. Structure Convention File Name Full *Atoms alone (condensed) Pseudoatoms alone (condensed) <draw_home>\examples\sequencetool\std_abbrev_defs_ful lctab.xml <draw_home>\examples\sequencetool\std_abbrev_defs_sta ratom.xml <draw_home>\examples\sequencetool\std_abbrev_defs_pse udoatom.xml *Atoms and pseudoatoms (condensed) <draw_home>\examples\sequencetool\std_abbrev_defs_ staratompluspseudoatom.xml 2. Copy the selected file to the location where the standard abbreviation templates are stored (see Step 1 in Providing standard biopolymer templates to users). 3. Rename the copied file std_abbrev_defs.xml. 4. Edit the directory specifications at the beginning of your std_abbrev_defs.xml to point to the location where the biopolymer template files are stored. BIOVIA Draw Configuration Page x

12 For example, if the biopolymer template files are on a network drive named x in the directory MyMolfiles/StdAbbrevs, change the text from the original: <!ENTITY ABBREVROOT "CompanyMolTemplates/StdAbbreviations/"> <!ENTITY AADir "&ABBREVROOT;Sequence-AA/"> <!ENTITY DNADir "&ABBREVROOT;Sequence-DNA/"> <!ENTITY RNADir "&ABBREVROOT;Sequence-RNA/"> <!ENTITY SAGDir "&ABBREVROOT;Sequence-SAG/"> To the following (changes are in bold): <!ENTITY ABBREVROOT "x:/mymolfiles/stdabbreviations/"> <!ENTITY AADir "&ABBREVROOT;Sequence-AA/"> <!ENTITY DNADir "&ABBREVROOT;Sequence-DNA/"> <!ENTITY RNADir "&ABBREVROOT;Sequence-RNA/"> <!ENTITY SAGDir "&ABBREVROOT;Sequence-SAG/"> where: ABBREVROOT defines the root directory that contains the biopolymer templates. AADir, DNADir, and RNADir specify the locations of the directories that contain residue templates for amino acid, DNA, and RNA sequences. SAGDir specifies the directory that contains templates for single-attachment groups such as protecting groups and PEG groups. If the template files are on a Web server called CompanyServer, you can specify ABBREVROOT as follows: <!ENTITY ABBREVROOT " 5. Customize the file as needed to provide additional abbreviation. See Creating additional abbreviations. Customizing BIOVIA Draw for Users To ensure that users create polymers that use the templates that you specify in your standard abbreviation definitions file, provide users with a customized version of BIOVIA Draw. To customize BIOVIA Draw, you must edit the BIOVIA Draw XML configuration files, and provide them to your users. To configure a custom toolbar: 1. Make a copy of AccelrysDraw-net.xml in your Draw installation folder. The version will appear as follows: <!-- This is an XML configuration file for the BIOVIA Draw Editor. It defines all the windows, menus, tools, and actions that will be displayed in the Editor&apos;s environment. By editing this file you can customize the Editor&apos;s User interface to the needs of the end users.--> <mdldraw width="950" height="700" name="biovia Draw 2016"> <module class="mdl.draw.modules.editor.editormodule"> <shortcuts> <shortcut char=" " method="swaptool"/> <!-- <shortcut char="." method="toggledebug" /> --> </shortcuts> <!-- If you edit any of the following files, keep a backup of the original, and change include= to point to the full path of your new file, Page xi BIOVIA Draw Configuration Guide

13 for example, include="c:\program Files\BIOVIA\BIOVIA Draw 2016\XmlConfig\mymenubar.xml" --> <!-- File edit etc menus--> <menustrip include="mdl.draw.editor.xmlconfig.menustrip.xml"/> <!-- new open etc buttons--> <maintoolstrip include="mdl.draw.editor.xmlconfig.maintoolstrip.xml"/> <!--template toolbar. --> <!--<toolbar include="mdl.draw.editor.xmlconfig.templatetoolstrip.xml"/> --> <!--vertical tool strip lasso, etc--> <palettestrip include="xmlconfig\palettestrip.xml"/> <atomtoolbar name="atoms" direction="horizontal"/> <bondtoolbar name="bonds" direction="horizontal"/> <arrowtoolbar name="arrows" direction="horizontal" autohide="true"/> </module> </mdldraw> It references palettestrip.xml in subfolder XmlConfig. 2. Make a copy of XmlConfig/palettstrip and place the following version in the Draw installation folder. It has 2 lines modified lines: Line 1190 was added: <abbreviationtoolbar name="modified Amino Acids" path="%mdldraw%std_ abbrev_defs.xml" sequence="true" toolbartype="modified"/> In line 1206 the toolbar type modified was added: <sequencetoolbutton name="amino Acid Sequences" image="seqtoolaa1.png" toolbartype="aa,daa,modified,sag,linker,asm"/> 3. Make a copy of std_abbrev_defs and place it in your Draw installation folder. The block with the modified residues and their location was added: <toolbartype name="modified" class="aa"> <abbreviation displayname="met_m" oneletterdisplayname="m*" fullname="lmethionine_modified" isqueryonly="no"> <molfile>%mdldraw%aadir;methionine1.mol</molfile> </abbreviation> <abbreviation displayname="phe-m" oneletterdisplayname="f*" fullname="lphenylalanine_modified" isqueryonly="no"> <molfile>%mdldraw%aadir;phehylalnine1.mol</molfile> </abbreviation> <abbreviation displayname="pro_m" oneletterdisplayname="p*" fullname="lproline_modified" isqueryonly="no"> <molfile>%mdldraw%aadir;proline1.mol</molfile> </abbreviation> </toolbartype> BIOVIA Draw Configuration Page xii

14 The 3.mol files were placed in the following folder: C:\Program Files \BIOVIA\BIOVIA Draw 4.2\StdAbbreviations\Sequence-AA You can define an alternate folder and create a path variable in std_abbrev_defs.xml. Customizing BIOVIA Draw for Administrators Administrators are responsible for creating and maintaining the biopolymer template files that the Sequence Tools use. To perform this task, administrators require access to the Enhanced Template Editor dialog, which allows you to edit attachment atoms on the structures of biopolymer residues. This dialog is hidden so that end users cannot accidentally alter the templates. Creating and editing biopolymer templates requires additional settings that differ from the BIOVIA Draw defaults: Display explicit hydrogen leaving groups on non-terminal attachment atoms in contracted amino acid residues. These groups are hidden by default. For information on why explicit hydrogen leaving groups are necessary, see BIOVIA Chemical Representation, Biopolymer Representation, Explicit hydrogen leaving groups on attachment atoms of reactive side chains. This document is installed as: <draw_home>\docs\draw\devguide\bioviachemicalrepresentation.pdf Use right-click, rather than double-click, to start the Template Editor. By default, clicking an abbreviation on a any template toolbar adds the corresponding structure to the drawing area, while double-clicking displays the Template Editor. Using right-click avoids avoid accidentally adding templates to the drawing area while you create and edit biopolymer template files. Use the following procedure to customize BIOVIA Draw for administrator users: 1. Create a settings file, biopolymer.xml, that contains the recommended settings for editing biopolymer templates. See To create the settings file. 2. Edit a copy of the BIOVIA Draw XML configuration files to provide access to the Advanced Template Editor and to the settings file that you created in the previous step. See To edit the BIOVIA Draw configuration files. 3. Distribute the edited copy of the XML configuration and the settings file biopolymer.xml to administrator users. Instruct each user to copy biopolymer.xml to the Preferences subdirectory on their local hard drive: C:\Users\<user_name>\AppData\Roaming\BIOVIA\BIOVIA Draw\Preferences\ Create the Settings File Two settings that administrator users require are available on the Settings dialog in BIOVIA Draw. The setting to display non-terminal leaving groups is hidden and therefore not available on the Settings dialog. To specify the value of a hidden setting, you must edit the settings file manually. Use the following procedure to create the settings file biopolymer.xml: 1. Start BIOVIA Draw using the customized version of the XML configuration that you created for end users. For more information, see Customizing BIOVIA Draw for end users. 2. Choose Options > Settings from the menu. The Settings dialog opens. 3. Change the General setting Invoke Template Editor with from Double Click to Right-Click. 4. (Optional) Change any other settings that administrator users require. 5. On the Settings dialog, click Save As. 6. Enter biopolymer.xml as the file name, click Save, and then click Cancel to exit the Settings dialog. 7. Exit BIOVIA Draw. Page xiii BIOVIA Draw Configuration Guide

15 8. Navigate to the directory on your hard drive that contains your personal settings: C:\Users\<user_name>\AppData\Roaming\BIOVIA\BIOVIA Draw\Preferences\ 9. Edit biopolymer.xml to add the hidden setting that enables display of internal leaving groups: <DisplayInternalLeavingGroup>true</DisplayInternalLeavingGroup> The following example shows a portion of biopolymer.xml, with the added setting in bold: <DisplayPreferences xmlns:xsd=" xmlns:xsi=" <TemplateEditorInvokingGesture>RightClick</TemplateEditorInvokingGesture> <DisplayInternalLeavingGroup>true</DisplayInternalLeavingGroup>... (additional settings)... </DisplayPreferences> 10. Save the edited biopolymer.xml file. Edit the Configuration Files Use the following procedure to enable the Advanced Template Editor and specify biopolymer.xml as the default settings file: 1. Create a copy of the version of the XML configurations that you customized for end users. For more information, see Customizing BIOVIA Draw for end users. Edit this copy as described in the steps that follow. 2. To enable the Enhanced Template Editor dialog, edit the value for MDL.Draw.Modules.Editor.EditorModule. The following example shows the default XML: <mdldraw width="950" height="640" name="mdl Draw"> <module class="mdl.draw.modules.splitter" orientation="horizontal" percentage="70"> <module class="mdl.draw.modules.editor.editormodule"> The following example shows the XML after editing (changes are in bold): <mdldraw width="950" height="640" name="mdl Draw"> <module class="mdl.draw.modules.splitter" orientation="horizontal" percentage="70"> <module class="mdl.draw.modules.editor.editormodule" enablemultipleattachmenttemplatemode="true"> 3. To specify biopolymer.xml as the default settings file, change the name of the default settings file, default.xml, to biopolymer.xml. For example: <DisplayPreferences file="biopolymer.xml" /> IMPORTANT! The settings file must be located in the user s personal settings directory, as shown in this example. You cannot use a different path for the file. 4. Save the edited copy of the XML configuration. Creating Additional Abbreviations You can provide your users with additional abbreviations for biopolymer residues, protecting groups, and PEG groups. For example, you can provide abbreviations for non-natural amino acids like 2- aminoisobutyric acid (Aib), or PEG groups of differing molecular weights. All of these procedures involve adding entries to the standard abbreviations file. When you add new entries to the standard abbreviation file, the templates display on the sequence toolbars as soon as you restart BIOVIA Draw. BIOVIA Draw Configuration Page xiv

16 The sections that follow give procedures for each category of biopolymer abbreviation: biopolymer residues, protecting groups, and PEG groups. Note: To understand how to create new entries in your standard abbreviation definitions file, BIOVIA recommends that you study the entries in the example standard abbreviation definitions files and the comments for the entries. Creating Abbreviations for Biopolymer Residues Creating abbreviations for additional biopolymer residues uses procedures necessary to ensure that end-users cannot alter the templates. For example: BIOVIA Draw prevents users from accessing the Enhanced Template Editor, which must be used to define attachment atoms and leaving groups on residue templates. If you want to add more residue abbreviations, you must edit your copy of the BIOVIA Draw XML configuration file to allow editing of biopolymer residues. See Customizing BIOVIA Draw for end users and Customizing BIOVIA Draw for administrators. A biopolymer template does not display on the top toolbar of any sequence tool until you add an entry for that template to the appropriate section of the standard abbreviation definitions file. Consequently, creating a biopolymer residue template involves not only creating and editing the structure in BIOVIA Draw, but also editing the standard abbreviation definitions file. The complete procedure for creating a residue template consists of the following steps: 1. Use BIOVIA Draw to create the underlying structure of the residue, contract the structure to an abbreviation, and save the structure to a molfile in the directory where other residue templates are located. For detailed instructions, see the following index entry in the BIOVIA Draw Online Help: biopolymer administration, creating residue templates. 2. Edit the standard abbreviation definitions file to add entries for each template that you created in Step 1. Add the entry to the section of the standard abbreviation file that corresponds to the abbreviation class of the residue: a. Use copy/paste to create a duplicate of an existing entry of the same abbreviation class. For example, to create an abbreviation for an amino acid residue, duplicate the entry for L-alanine. b. Change the displayname attribute of the duplicate entry to the symbol that you want to display on the toolbar. c. Change the molfile attribute in the duplicate entry so that it refers to the file that contains the structure of the new residue. d. Change the fullname attribute of the duplicate entry. e. Change any other attributes that are required for full structure, *atom, or pseudoatom representation. For information on which attributes to edit, see the examples of edited entries later in this section. f. Repeat Steps a through e for additional abbreviations. 3. Restart BIOVIA Draw and use the Enhanced Template Editor to define attachment atoms and leaving groups, as described in the following index entry in the BIOVIA Draw Online Help: biopolymer administration, creating residue templates. Full Structure Representation The following example shows duplicate entries for the full structure representation of L-alanine: <abbreviation displayname="ala" oneletterdisplayname="a" fullname="l-alanine" isqueryonly="no"> <molfile>&aadir;alanine.mol</molfile> Page xv BIOVIA Draw Configuration Guide

17 </abbreviation> <abbreviation displayname="ala" oneletterdisplayname="a" fullname="l-alanine" isqueryonly="no"> <molfile>&aadir;alanine.mol</molfile> </abbreviation> The following example shows how the second entry has been edited to refer to the non-natural amino acid 2-aminoisobutyric acid (Aib). The structure of the residue is in the molfile aib.mol, which is located in the same directory as the structures of other amino acids. Aib lacks a 1-letter abbreviation, so the displayname appears in both 1-letter and 3-letter mode (changes are in bold): <abbreviation displayname="ala" oneletterdisplayname="a" fullname="l-alanine" isqueryonly="no"> <molfile>&aadir;alanine.mol</molfile> </abbreviation> <abbreviation displayname="aib" fullname="2-aminoisobutyric acid (Aib)" isqueryonly="no"> <molfile>&aadir;aib.mol</molfile> </abbreviation> *Atom Representation The following example shows duplicate entries for the *atom representation of L-alanine: <abbreviation staratomname="aa-ala" displayname="ala" oneletterdisplayname="a" fullname="l-alanine" isqueryonly="no"> <molfile>&aadir;alanine.mol</molfile> </abbreviation> <abbreviation staratomname="aa-ala" displayname="ala" oneletterdisplayname="a" fullname="l-alanine" isqueryonly="no"> <molfile>&aadir;alanine.mol</molfile> </abbreviation> The following example shows how the second entry has been edited to refer to the non-natural amino acid 2-aminoisobutyric acid (Aib). The structure of the residue is in the molfile aib.mol, which is located in the same directory as the structures of other amino acids. Aib lacks a 1-letter abbreviation, so the displayname appears in both 1-letter and 3-letter mode (changes are in bold): <abbreviation staratomname="aa-ala" displayname="ala" oneletterdisplayname="a" fullname= L-alanine isqueryonly="no"> <molfile>&aadir;alanine.mol </molfile> </abbreviation> <abbreviation staratomname="aa-aib" displayname="aib" fullname="2-aminoisobutyric acid (Aib)" isqueryonly="no"> <molfile>&aadir;aib.mol</molfile> </abbreviation> Creating Abbreviations for Protecting Groups 1. Draw the abbreviated structures in BIOVIA Draw and add them to a personal toolbar on your local hard drive. For detailed instructions, see the following index entry in the BIOVIA Draw Online Help: biopolymer administration, creating protecting groups. BIOVIA Draw Configuration Page xvi

18 2. After creating the new template files, copy the files from your local hard drive to the directory where single-attachment groups are stored. 3. Edit the standard abbreviation definitions file to add entries for each template that you created in Step 1. Add the entry to the section of the standard abbreviation definitions file that contains protecting groups: a. Use copy/paste to create a duplicate of an existing entry. b. Change the displayname attribute of the duplicate entry. c. Change the molfile attribute in the duplicate entry so that it refers to the file that contains the structure of the new protecting group. d. Change the fullname attribute of the duplicate entry. e. Repeat Steps a through d for additional abbreviations. Creating Abbreviations for PEG Groups Templates for PEG groups contain solely a single *atom or pseudoatom. To create new PEG groups, you need to duplicate an existing template and then edit the template in BIOVIA Draw. Use the procedure that follows to create abbreviations for PEG groups: 1. Draw the abbreviated structures in BIOVIA Draw and add them to a personal toolbar on your local hard drive. For detailed instructions, see the following index entry in the BIOVIA Draw Online Help: "biopolymer administration, creating PEG groups". 2. After creating the new template files, copy the files from your local hard drive to the directory where single-attachment groups are stored. 3. Edit the standard abbreviation definitions file to add entries for each template that you created in Step 1. Add the entry to the section of the standard abbreviation definitions file that contains protecting groups: a. Use copy/paste to create a duplicate of an existing entry. b. Change the displayname attribute of the duplicate entry to the symbol that you want to display on the toolbar. c. Change the molfile attribute in the duplicate entry so that it refers to the file that contains the structure of the new PEG group. d. Change the fullname attribute of the duplicate entry. e. Change the formulaweight attribute of the duplicate entry to the desired average molecular weight. f. Repeat Steps a through e for additional PEG groups. The examples in the following sections show how to create an abbreviation for a PEG group with an average molecular weight of 5,000 in both the *atom and pseudoatom representations. *Atom Representation of PEG Groups The following example shows duplicate entries for PEG-20000: <abbreviation displayname="peg20000" fullname="polyethylene glycol, average molecular weight = 20,000" staratomname="mpeg-20000" formulaweight=" " isqueryonly="no"> <molfile>&sagdir;peg20000.mol</molfile> </abbreviation> <abbreviation displayname="peg20000" fullname="polyethylene glycol, average molecular weight = 20,000" Page xvii BIOVIA Draw Configuration Guide

19 staratomname="mpeg-20000" formulaweight=" " isqueryonly="no"> <molfile>&sagdir;peg20000.mol</molfile> </abbreviation> The following example shows how the second entry has been edited to represent PEG-5000 (changes are in bold): <abbreviation displayname="peg20000" fullname="polyethylene glycol, average molecular weight = 20,000" staratomname="mpeg-20000" formulaweight=" " isqueryonly="no"> <molfile>&sagdir;peg20000.mol</molfile> </abbreviation> <abbreviation displayname="peg5000" fullname="polyethylene glycol, average molecular weight = 5,000" staratomname="mpeg-5000" formulaweight=" " isqueryonly="no"> <molfile>&sagdir;peg5000.mol</molfile> </abbreviation> Pseudoatom Representation of PEG Groups The following example shows duplicate entries for PEG-20000: <abbreviation displayname="peg20000" pseudoatomname="pdb" fullname=" Polyethylene glycol, average molecular weight = 20,000 formulaweight=" " isqueryonly="no"> <molfile>&sagdir;pdb.mol</molfile> </abbreviation> <abbreviation displayname="peg20000" pseudoatomname="pdb" fullname=" Polyethylene glycol, average molecular weight = 20,000 formulaweight=" " isqueryonly="no"> <molfile>&sagdir;pdb.mol</molfile> </abbreviation> The following example shows how the second entry has been edited to represent PEG-5000, which is represented as the pseudoatom PXY in the Ptable (changes are in bold): <abbreviation displayname="peg20000" pseudoatomname="pdb" fullname=" Polyethylene glycol, average molecular weight = 20,000 formulaweight=" " isqueryonly="no"> <molfile>&sagdir;pdb.mol</molfile> </abbreviation> <abbreviation displayname="peg5000" pseudoatomname="pxy" fullname="polyethylene glycol, average molecular weight = 5,000 formulaweight=" " isqueryonly="no"> <molfile>&sagdir;pxy.mol</molfile> </abbreviation> Standard Abbreviation XML Reference The table describes the elements in the standard abbreviation definitions file, and specifies the following information for each abbreviation. BIOVIA Draw Configuration Page xviii

20 Element displayname oneletterdisplayname staratomname pseudoatomname formulaweight fullname isqueryonly comment molfile Description (Required) Residue symbol. For amino acid sequences, this is the 3-letter abbreviation that displays in 3-letter mode. For DNA and RNA residues, this is the 1-letter abbreviation that displays in the toolbars of the DNA and RNA Sequence Tools, respectively. (Optional) For structures that have both 1-letter and multi-letter symbols (for example, amino acid and nucleic acid residues), the 1-letter symbol. The 1- letter symbol displays when in amino acid 1-letter mode. One-letter symbols must be the standard symbols approved by International Union of Pure and Applied Chemistry and the International Union of Biochemistry and Molecular Biology,IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN). For more information, see the Nomenclature and Symbolism for Amino Acids and Peptides. (Optional) The Sgroup data that is attached to the *atom representation of the residue and that uniquely identifies each residue. Required for abbreviations that use the *atom representation. (Optional) If the residue is to be represented as a pseudoatom rather than a *atom, the pseudoatom name. (Optional) The formula weight of the residue or group. Use this for fragments whose molfiles lack the full connection tables, such as the *atom and pseudoatom representations of PEG groups. The Chemistry > Calculator command in Draw also uses this value in calculating molecular weight. (Optional, but recommended) Specifies the full name of the residue, for example L-glutamine. The fullname displays as the tooltip for the template on the top toolbar of the Sequence Tool. (Optional)Indicates whether the structure is usable only for queries. The valid values are as follows: Yes, use only for queries and do not register to a database. No, the structure is usable in queries, and can be registered to a database. (Optional) Comment (Required) Path to template molfile that contains the underlying structure of the abbreviation. This molfile contains the structure that displays when you right-click the structure and choose Expand. The Chemistry > Calculator command in BIOVIA Draw also uses this structure to calculate molecular weight and other values. The staratomname and pseudoatomname elements are optional. These three element names have the following precedence: pseudoatomname > staratomname > displayname Element name precedence: If an entry in std_abbrev_defs.xml does not contain a pseudoatomname or staratomname but has displayname, then the structure of the corresponding abbreviation is saved as a fully defined structure (full connection table or ctab) in a sequence. Page xix BIOVIA Draw Configuration Guide

21 If an entry in std_abbrev_defs.xml has both staratomname and displayname, but does not have a pseudoatomname, then the structure of the corresponding abbreviation is saved as a *atom in a sequence. If an entry in std_abbrev_defs.xml has both pseudoatomname and displayname, but does not have staratomname, then the structure of the corresponding abbreviation is saved as a pseudoatom in a sequence. If an entry in std_abbrev_defs.xml has all three names (pseudoatomname, staratomname, and displayname), then the structure of the corresponding abbreviation is saved as pseudoatom in a sequence because pseudoatomname has the highest priority. Enhanced Stereochemistry You can edit the XML Configuration for stereochemistry. For more information, see Specify the Path to Custom XML Configuration Files. The Stereochemistry dialog and actions in BIOVIA Draw enable users to create structures with stereochemistry features. The original (classic) stereochemical representation is a subset of the current (enhanced) stereochemical representation. For more information on stereochemical representation, see the following in BIOVIA Chemical Representation, which is installed as <draw_ home>\docs\draw\devguide\bioviachemicalrepresentation.pdf Your users can continue to register structures that use your existing business rules until you adapt your business rules to the enhanced representation. If you have not yet upgraded your business rules, you can customize BIOVIA Draw to hide the stereochemistry dialog and actions. End-users can also change their own Stereochemistry preferences. Select the Options > Settings > Stereochemistry > Label display at stereogenic centers > Classic instead of the default value of IUPAC Style. Disable the Stereochemistry Dialog To disable the Stereochemistry dialog: Use comment notation (<!-- and -->) to remove all the lines related to StereoChemTool in the BIOVIA\BIOVIA Draw <version>\xmlconfig\palettestrip.xml file. Some tools have multiple XML entries. The tool element looks similar to the following in the palettestrip.xml" <tool class="mdl.draw.modules.editor.tools.stereochemtool" With comment notation: <!-- begin comment <tool class="mdl.draw.modules.editor.tools.stereochemtool" </tool> end comment --> Disable Stereochemistry Actions To disable the stereochemistry actions: BIOVIA Draw Configuration Page xx

22 Use comment notation (<!-- and -->) to remove all the lines in the BIOVIA\BIOVIA Draw <version>\xmlconfig\\xmlconfig\palettestrip.xml file that are related to actions. For example use comment notation as follows: <!-- begin comment <menu command="stereo" text="set StereoChemistry"> <menuitem command="abs" text="absolute" /> <menuitem command="and" text="and Enantiomer" /> <menuitem command="or" text="or Enantiomer" /> </menu> end comment --> Expose the Purity Section In Draw, the Purity section for unspecified stereocenters is disabled by default. You can enable or disable sections to provide or hide functionality from end users. The following section of BIOVIA\BIOVIA Draw <version>\xmlconfig\\xmlconfig\palettestrip.xml file exposes the Purity section. <panel margin="3"> </panel> <label text="purity (optional):" style="bold" width="250" height="25" /> <radiogroup> <radiobutton text="unknown / unimportant" command="unknown" update="t" width="250" /> <radiobutton text="pure" command="pure" update="t" width="250" /> <radiobutton text="partially resolved" command="partial" layout="horizontal" listener="mdl.draw.gui.grayoutchildren" update="t" width="130"> <combobox command="puritycombo" editable="t" update="t" enabled="f" select="3" width="50"> <selection text="50%" /> <selection text="60%" /> <selection text="70%" /> <selection text="80%" /> <selection text="90%" /> <selection text="100%" /> </combobox> <label text=" ee" enabled="f" /> </radiobutton> </radiogroup> <!-- END OF stereogroup's Purity values section --> In the example above, the default value is the third selection as set by the value 3 in the select="3" attribute, making the default value 70%. Page xxi BIOVIA Draw Configuration Guide

23 Hiding OR and AND Stereogroups Both the OR stereogroups button and the AND stereogroups button are enabled in the [draw-home] \XmlConfig\palettestrip.xml file. To hide these buttons, look in the XML palettebar.xml for this comment: <!-- To remove OR stereogroup comment out the following section and assure that the features you want to hide are inside XML comments <! >. For example, the following example is of a section that is not commented out: <!-- To remove OR stereogroup, comment out the following section -->... Here, the same section that is commented out: <!-- To remove OR stereogroup, comment out the following section... --> In the following section, the OR stereogroups is not commented out: <!-- To remove OR stereogroup, comment out the following section--> <space height="10" /> <panel border="t" layout="horizontal"> <panel margin="4"> <panel> <radiobutton text="add to OR# group" command="or#" variable="t" update="t" width="162" /> </panel> <radiobutton text="create new OR group" command="createor#" width="162" /> </panel> <panel margin="3"> <label image="stereoor.png" /> </panel> </panel> The following AND stereogroups section has been commented out. <!-- To remove AND stereogroup, comment out the following section <space height="10" /> <panel border="t" layout="horizontal"> <panel margin="4" width="140"> <panel> <radiobutton text="add to AND# group" command="and#" variable="t" update="t" width="162" /> </panel> <radiobutton text="create new AND group" command="createand#"width="162" /> </panel> <panel margin="3"> <label image="stereoand.png" /> </panel> </panel> --> BIOVIA Draw Configuration Page xxii

24 Customize Stereogroup Labels You can customize the appearance of stereogroup labels such as for ABS, OR, or AND stereogroups by manually editing the default.xml. You can find the user preferences default.xml file in a location similar to the following: \\Users\<user_name>\AppData\Roaming\BIOVIA\BIOVIA Draw <version_ number>\preferences The following example of a default.xml file shows an user s custom settings for the display of stereochemistry preferences, which are set using Options > Settings, and setting the label options in the Stereochemistry group. <?xml version="1.0"?> <DisplayPreferences xmlns:xsd=" xmlns:xsi=" <DisplayChiralStereoLabels>Enhanced</DisplayChiralStereoLabels> <StereoAbsLabel>*</StereoAbsLabel> <StereoAndLabel>#</StereoAndLabel> <StereoGroupDisplay>LabelsAndBonds</StereoGroupDisplay> </DisplayPreferences> The resulting StereoAndLabel display uses the following pattern: #1, #2, #3. You cannot change &1 into # because the numeric part is appended automatically when used with StereoAndLabel or StereoOrLabel. Enabling the Data Sgroup Tool to Control Sgroup Data Organizations have different business rules for chemically-significant data (attached data or Sgroup data) that end-users attach to targets, such as atoms, bond, fragments, or entire structures. BIOVIA allows you to control the vocabulary for data Sgroups. By default, <draw_home>\xmlconfig\palettestrip.xml enables the SimpleDataSgroupTool that allows end-users to specify a database field, search operator, and data that might or might not be valid. However, if you enable the DataSgroupTool, you can "pre-populate" picklists to control the data Sgroup choices available to end-users. To specify the types of attached data and targets that your organization requires, edit the examples in the comments for DataSgroupTool in <draw_home>\xmlconfig\palettestrip.xml. Page xxiii BIOVIA Draw Configuration Guide

25 Notes: Keep a backup copy of the original versions of any XML Configuration files undergoing edits. It is very easy to break the XML and not always easy to fix, so it is good to be able to revert to a version that works. If your company s business rules require attached data, you need to customize BIOVIA Draw and create Sgroup fields in your databases. For complete information on the procedures that are required to implement business rules for attached data, see the "Attached Data" chapter in BIOVIA Chemical Representation, which is installed as <draw_home>\docs\draw\devguide\bioviachemicalrepresentation.pdf If you enable the DataSgroupTool, you should disable the SimpleDataSgroupTool. See also <!-- <tool class="mdl.draw.modules.editor.tools.simpledatasgrouptool"> <popup> <menuitem command="attachcol" text="attach Data..." /> </popup> </tool> --> Comments in <draw_home>\xmlconfig\palettebar.xml on DataSgroupTool, which provide: Procedures for disabling or enabling the DataSgroupTool XML code for examples of attached data for various targets, with explanatory comments. To specify the types of attached data and targets that your company s business rules require, edit these examples. fieldname in the XML reference Attached Data dialog (data Sgroups) in Sample Screens, which shows an example of a dialog box for end-users. Specify the Path to Custom XML Configuration Files. Example for Data Sgroup Tool There are many examples and many places to either comment out or uncomment. Before (commented out) - disabled <!-- Vocabulary of allowed values: R, S, P, M, E, Z, none. <fieldname readablename="non-tetrahedral chirality" name="chiral_ NONTETRAHEDRAL" target="sketch" type="text" unit="" value="list"> <listvalue value="(none)" /> <listvalue value="r" /> <listvalue value="s" /> <listvalue value="p" /> <listvalue value="m" /> <listvalue value="e" /> <listvalue value="z" /> </fieldname>... --> After (exposed) - enabled The following snippet is one of many places where the comments are removed. BIOVIA Draw Configuration Page xxiv

26 Vocabulary of allowed values: R, S, P, M, E, Z, none. --> <fieldname readablename="non-tetrahedral chirality" name="chiral_ NONTETRAHEDRAL" target="sketch" type="text" unit="" value="list"> <listvalue value="(none)" /> <listvalue value="r" /> <listvalue value="s" /> <listvalue value="p" /> <listvalue value="m" /> <listvalue value="e" /> <listvalue value="z" /> </fieldname>... Note: In this context, "sketch" means any structure drawn on the canvas, not the sketch file format with the.skc extension. Customizing Draw for Attached Data Users have access to the Data Sgroup Properties dialog that allows them to type in a Field Description, which might or might not be the correct database Field Name. However, you can: Hide the Data Sgroup Properties dialog by commenting out its appearances in the XML configuration file. Make available the Attached Data dialog, which can have a drop-down list for Field Name, so that end-users choose from a standard set of field names that you establish. Attached Data in Biopolymer Representation To enable your users to create biopolymers that contain the correct types of attached data, see Customizing BIOVIA Draw for Registration and Searching of Biopolymers. Note: The attached data required for biopolymer representation is invisible to end users. See BIOVIA Chemical Representation > Biopolymer Representation. This document is installed as: <draw_home>\docs\draw\devguide\bioviachemicalrepresentation.pdf Other Attached Data If you have incorporated additional categories of attached data into your business rules for chemical substance representation, enable the Attached Data dialog in BIOVIA Draw to allow your users to create and edit attached data. For information on enabling this dialog, see Data Validation, Registration, and the Attached Data dialog. The dialog is hidden in BIOVIA Draw. To make the dialog available, customize the BIOVIA Draw XML configuration. 1. Add the required Sgroup fields to your database. 2. Make a backup copy of the XML configuration files. 3. Use a text editor or XML editor to open and locate the section that contains examples of attached data. You can do this by searching for the text string "Examples of Attached Data". 4. Follow the instructions in the comments to adapt relevant examples to the categories of attached data that you have defined. Two elements are associated with the definition of attached data, operator and fieldname: Each occurrence of the element operator specifies a comparison operator that is available for searching numeric data. Page xxv BIOVIA Draw Configuration Guide

27 Each occurrence of the element fieldname in the XML configuration defines a type of attached data that the user can select in the Attached Data dialog box, and that is associated with a particular Sgroup field. For each category of attached data, you can optionally use the listvalue element to provide a set of allowed values (vocabulary) for user to choose from. IMPORTANT! BIOVIA Draw does not check the name, type, or other attributes against information in the database. If you enter incorrect values for these attributes, the attached data can be saved to a molfile but cannot be registered to the target database or used in a search. For example, if the Sgroup field name is incorrect, the data is not registered to the database. If a search operator that you specify is not available in the target database, queries that use that operator will be invalid. To ensure that these attributes are correct, you need to test the customized XML configuration as described in Step 7 below. 5. For each type of target for which you specified attached data in Step 4, remove the comments from the associated menu command. Each menu command has the following format: <menuitem command="<target>" text="attach data..."/> </popup> 6. Save the edited XML configuration. 7. Test the edited XML configuration: a. Start BIOVIA Draw and open a structure file. b. Select the Properties Tool [X] from the palettebar. c. Select the target that you specified in Step 4. d. Select Attach data from the popup menu. The dialog, as defined in the XML file, appears. e. Save the file with the structure and its attached data to a molfile. f. Register the structure to a test database. BIOVIA Draw Configuration Page xxvi

28 g. Use the structure as a query to retrieve the structure that you registered in the previous step. h. Conduct additional searches to ensure that the customized XML configuration is valid. For example, to ensure users can use search operators. 8. Distribute the customized version of the XML configuration to end-users. Data Validation, Registration, and the Attached Data Dialog BIOVIA Draw does not validate attached data. For example, BIOVIA Draw provides no mechanism for limiting the range of numeric data that end-users enter. Therefore, BIOVIA Draw cannot enforce that attached data that represents a percentage lie between 0 to 100. Your searching or registration application should therefore check the validity of attached data against your company s business rules. For text data, BIOVIA recommends that you provide a set of allowed values in the Attached Data dialog. If scientists want to find structures with more than one value for the attached data, they can run multiple queries and then apply list logic to merge the result sets. Use search operators in substructure-search queries. If you are customizing BIOVIA Draw for use in a registration application, you can prevent users from adding operators to attached data by commenting out the operator values in the XML configuration. For example: <!-- Hide numeric search operators <operator value="none"/> <operator value=">"/> <operator value=">="/> <operator value="<"/> <operator value="<="/> <operator value="<>"/> --> For information on using attached data in substructure search queries, see BIOVIA Chemical Representation, Substructure Search (SSS), Substructure Search of Attached Data. The document is installed as: <draw_home>\docs\draw\devguide\bioviachemicalrepresentation.pdf For examples of customizing BIOVIA Draw for attached data, see the <draw_ home>\xmlconfig\palettestrip.xml file. For reference information on the XML elements in the examples, see the AccelrysDraw-net.xml chapter. Cleaning Data Sgroups The end-user can click Chemistry > Clean to improve the appearance of one or more selected structures by giving them uniform bond lengths and angles. In so doing, Clean changes the x- and y-coordinates of the atoms, bonds, and attached data (Sgroup data). Relative Coordinates An Sgroup basis is the atoms and bonds with which the attached data is associated. BIOVIA Draw uses the version of the internal Cheshire Clean script that ensures that each Sgroup datum is located in the same position relative to its Sgroup basis. Page xxvii BIOVIA Draw Configuration Guide

29 Absolute Coordinates You might want Clean to lock the attached data position at the original location in the drawing area (absolute coordinates), regardless of the location of the associated atom or bond. For example, your organization might have a business rule that requires all attached data to be in the lower right corner. ISIS/Draw creates data Sgroups with absolute coordinates, and BIOVIA Draw creates data Sgroups with relative coordinates. One structure can have both kinds of attached data if the structure was created in ISIS/Draw (absolute coordinates), and gets a second data Sgroup in BIOVIA Draw (relative coordinates). BIOVIA Draw s Clean operation converts the absolute coordinates of data Sgroups into relative coordinates. You can configure BIOVIA Draw to preserve the absolute coordinates of attached data created in ISIS/Draw. This change does not affect the rule that BIOVIA Draw creates data Sgroups with relative coordinates. IMPORTANT! Preserving absolute coordinates for attached data means that the Clean operation might relocate the atoms and bonds of the Sgroup basis at coordinates that are distant from their attached data. To configure BIOVIA Draw to use the version of Clean that preserves the absolute coordinates of attached data, perform the following two steps in <draw_home>\xmlconfig\menubarchemistry.xml. 1. Comment out the default Clean that positions attached data relative to the structure (relative coordinates): <action name="cl&ean" class="mdl.draw.modules.editor.actions.calcs.relativecleanaction"/> 2. Uncomment the Clean that preserves the original coordinates of the attached data (absolute coordinates). <action name="c&lean" class="mdl.draw.modules.editor.actions.calcs.cleanaction"/> BIOVIA Draw Configuration Page xxviii

30 Enabling or Disabling Rgroup Atom and Building Block Tools The Rgroup Atom and Building Block tools are enabled so that users of BIOVIA Draw can create Markush structures for registration into library and/or building blocks database. Notes: Although superficially similar to Markush queries, Markush structures differ in important ways. To avoid confusion between the different types of Rgroup structures, BIOVIA Draw supplies a separate palette of tools for drawing generic structures and building blocks. The default setting for the Rgroup Query tool is enabled. See also Specify the Path to Your Custom XML Configuration Files Rgroup Atom Tool and Building Block Tool in <draw_home>xmlconfig\palettestrip.xml Specifying the Custom Ptable and Custom Weights Markush structure in the BIOVIA Draw Online Help For more information about generic databases and building-blocks database, see the documentation for Relational-Chemical Database Administration, such as the Relational-Chemical Database Administration Command Reference, which gives the syntax for the CREATE DATABASE command. Specify a Custom Ptable and Custom Weights Before specifying a custom periodic table, review the information in Custom Ptable Example and Custom Ptable Path. If Draw is using a custom Ptable with custom weights, the BIOVIA Cheshire scripts must also use the custom Ptable with custom weights. You can edit the Ptable and weights file to match any custom elements and weights for your organization. Although the Ptable contains a weight for each element, the custom weights file determines the weight for calculations within Draw. Other BIOVIA products, such as BIOVIA Direct, might interpret the format of the atomic weight as Fortran format F10 more strictly leading to different results.if your business rules require Ptable customization, you must customize Draw and set the chemical environment at your site for all products that interact with Draw to use the same Ptable. Note: The bold format indicates updates you make to the configuration file. To specify a custom Ptable and custom Weights: 1. Close Draw. 2. Navigate to the BIOVIA\BIOVIA Draw <version>\examples\cheshireaction directory. 3. Make a backup copy of CheshireActionExample.xml. 4. Edit the following line in the CheshireActionExample.xml file to specify the custom Ptable for Draw. <module class="mdl.draw.modules.editor.editormodule" ptable="biovia\biovia Draw <version>\examples\ptable\myptable.txt"> 5. Modify the line to look similar to the following: <module class="mdl.draw.modules.editor.editormodule" ptable="<draw_ home>\examples\ptable\myptable.txt"> The BIOVIA\BIOVIA Draw <version> represents the absolute path to the root directory of your Page xxix BIOVIA Draw Configuration Guide

31 BIOVIA Draw installation. 6. Edit the following line in the CheshireActionExample.xml file to make the calculations available as options on the Draw Chemistry menu use the custom weights associated with the custom Ptable. <menustripitem text="&chemistry"> <action name="&calculator..." class="mdl.draw.modules.editor.actions.calcs.molvaluesaction"> 7. Modify the line to look similar to the following: <menustripitem text="&chemistry"> <action name="&calculator..." class="mdl.draw.modules.editor.actions.calcs.molvaluesaction" weights="custom" weightsscript="..\ptable\myweights.cct"> To verify the implementation of the custom Ptable and weights: 1. Run the batch file, CheshireActionExample.bat. 2. Open the CheshireAction.mol file. 3. In Draw, select Chemistry > Cheshire Scripts > Rotate Molecule. The Cheshire script rotates and cleans the molecule. 4. Right-click an atom and select Atom Symbol. The three custom elements (PC1, PC2, PC3) of the custom Ptable are available. 5. Click PC1. 6. Select Chemistry > Calculator. The custom weight displays. 7. Paste the calculated values onto the canvas. Templates You can customize the structure templates by editing the XML configuration file. End-users cannot create or edit biopolymer sequence templates. See also Biopolymers: Sequence Tools Specify the Path to Your Custom XML Configuration Files Adding Templates to the Toolbar Manager In this example, we add two directories that contain structure files. mynitrogens is the default template directory (selected="true"), and has the display name of mynitrogens MySugarTemplates is specified with an absolute directory, and has the display name of mysugars 1. Copy <draw_home>\xmlconfig\templatetoolstrip.xml and rename it to <draw_ home>\xmlconfig\mytemplatetoolstrip.xml. BIOVIA Draw Configuration Page xxx

32 2. In <draw_home>\xmlconfig\mytemplatetoolstrip.xml add entries: <templatetoolbarmanager class="mdl.draw.modules.editor.tools.configtemplatetool"...>... <templatetoolbar name="rings" path="%mdldraw%templates\template Sets\Rings\"/> <templatetoolbar name="mynitrogens" path="%mdldraw%mynitrogens\" selected="true"/> <!--Adding a shared template folder with absolute path --> <templatetoolbar name="mysugars" path="c:\mysugartemplates\" readonly="true" /> </templatetoolbarmanager> 3. Copy <draw_home>\accelrysdraw-net.xml and rename it to <draw_ home>\mytemplatetoolbarprimary.xml. 4. In <draw_home>\mytemplatetoolbarprimary.xml, change the reference to the new XML Configuration file for the toolbar. Before, with a reference to a compiled class resource. <toolbar include="mdl.draw.editor.xmlconfig.toolbar.xml"/> After, with an absolute path to an XML file. <toolbar include="c:\program Files (x86)\biovia\biovia Draw 2016\XmlConfig\myToolbar.xml"/> 5. To test, create a batch file that uses the new XML Configuration. BIOVIADraw.exe MyTemplateToolbarPrimary.xml 6. Start the batch file. 7. Open the templatetoolbar dropdown list. For XML reference details, see templatetoolbarmanager. Add a Directory to the Template Directory To display a particular folder under the Imported Templates directory in the Template Directory window, add a corresponding folder element under the templatedirectory element in the XML configuration file, in<draw_home>\xmlconfig\toolbar.xml: <templatedirectory...> <!-- Add folders here to add them into the Template Directory --> <folder name="mynewtemplatedirectory" path="d:\test\mytest\" readonly="true" /> </templatedirectory> Page xxxi BIOVIA Draw Configuration Guide

33 For XML reference details, see templatedirectory and folder in the XML Reference. See also Template Security Template Security BIOVIA recommends that you set the user permissions to the directories with your corporate templates files to be read-only. This precaution is to safeguard the templates from being overwritten. Be aware that blocking write permissions on corporate templates does not prevent end-users from changing files on their local machines. Removing Template Toolbars When a new version of BIOVIA Draw is installed, the user s access to any custom template toolbars is preserved. To remove access to any custom template toolbars, follow these steps: 1. Use Add/Remove Programs on the Windows Control Panel to uninstall the current version of BIOVIA Draw. 2. Delete the following directories and all the files within them: C:\Users\<user_name>\AppData\Roaming\BIOVIA\BIOVIA Draw <draw_home> where C: represents the drive on which BIOVIA Draw is installed, <user_name> represents the subdirectory with the name of the computer user, and <draw_home> represents the directory in which BIOVIA Draw is installed, such as C:\Program Files (x86)\biovia\biovia Draw 2016\ Specify Display of Templates Containing Abbreviated Structures The abbreviation display file, displayabbreviations.xml, enables you to control the display of the text label (abbreviation name) of individual abbreviated structures. You can use this file to: Apply formatting such as Greek letters, italics, subscripts, superscripts, and large or small fonts, to abbreviated structures that you save as templates. When you create an abbreviated structure to save as a template, you cannot apply special formats to the abbreviation name, because the abbreviation name is identical with the template filename. The formatting instructions (markup) specify characters that cannot be used in filenames. Override formula recognition for specific cases where formula recognition is not appropriate. BIOVIA Draw automatically applies appropriate formatting to any abbreviation name that can be interpreted as a formula, and displays these formulas appropriately when you reorient the structure. For example, if you enter the text string "C2H5" as the abbreviation for an ethyl group, Draw text recognizes the text "C2H5" as a formula and subscripts the numbers. Draw also recognizes "C" as the BIOVIA Draw Configuration Page xxxii

34 character that should attach to other structures (attachment character), so that the abbreviation name flips when you re-orient the structure. Automatic formula recognition is not appropriate for all templates, however. For example, the template for N-bromosuccinimide is named NBS. BIOVIA Draw displays the abbreviation as either "NBS" or "SBN", depending on whether the abbreviation is on the left or right side of the structure. You can override formula recognition by specifying "N" as the attachment character, so that the abbreviation name always displays as "NBS". Each user of BIOVIA Draw has an abbreviation display file at the following location on the local hard drive: C:\Users\<user_name>\AppData\Roaming\BIOVIA\BIOVIA Draw\DrawdisplayAbbreviations.xml This file contains any necessary markup for all templates that are supplied with BIOVIA Draw. If you have customized BIOVIA Draw to provide additional template directories and/or template toolbars, use the following procedure to provide a customized version of the abbreviation display file to your users: 1. Edit the XML configuration file using the instructions in the section, Adding a set of templates to the Toolbar Manager and/or To add a directory to the Template Directory. 2. Use an XML or text editor to edit the copy of displayabbreviations.xml on your local hard drive to add formatting instructions for all custom templates that need it. For a detailed instructions on creating entries in the abbreviation display file, see the following index entry in the BIOVIA Draw Online help: "abbreviation display file". 3. Distribute the edited displayabbreviations.xml to your users. Instruct each user to replace the default abbreviation display file with the one that you provide. Display Preference Settings Specify Display Preferences You can set values for display preferences (display settings) in <draw_home>\xmlconfig\menubaroptions.xml. For XML reference details, see Display Preferences. These values can also be set programmatically. See the API Reference for MDL.Draw.Renderer.Preferences.DisplayPreferences. IMPORTANT! Preferences set by the end-user in the GUI (Options > Settings) override the values specified in DisplayPreferences. See also Specify the Path to Custom XML Configuration Files Synchronizing Display Settings with default.xml Example: AromaticRingCircles, AtomHighlightDotWidth AccelrysDraw-net.xml points to menubar-options.xml, which resides in <draw_ home>\xmlconfig. Before you edit menubar-options.xml to add preference settings: <separator /> <action name="&settings..." class="mdl.draw.modules.editor.actions.preferencesaction"> <DisplayPreferences file="default.xml" /> Page xxxiii BIOVIA Draw Configuration Guide

35 Example rendering with default display settings: After you edit menubar-options.xml to add preference settings: <separator /> <action name="&settings..." class="mdl.draw.modules.editor.actions.preferencesaction"> <DisplayPreferences file="default.xml" > <AromaticRingCircles>true</AromaticRingCircles> <BackColor>yellow</BackColor> <AtomHighlightDotWidth>0.1</AtomHighlightDotWidth> <HighlightColor>Red</HighlightColor> <ForceV3000>true</ForceV3000> </DisplayPreferences> Example rendering with changed display settings: Note: Preferences can also be set using the API, for example, MDL.Draw.Renderer.Preferences.AtomHighlightDotWidth. Preferences set by the end-user in the GUI override the values specified in DisplayPreferences. See also Synchronizing Display Settings with default.xml BIOVIA Draw Configuration Page xxxiv

36 Synchronize Display Settings If your company has corporate standards for display settings, you can define the standard in the XML Configuration files. End-users can always locally set their own display settings for their copy of Draw by clicking Options > Settings to open the Settings dialog. The local preference setting are stored in a file called default.xml located in \\Users\<user_ name>\appdata\roaming\biovia\biovia Draw \Preferences directory. Software developers can synchronize the display settings of multiple renditors programmatically. For more informaiton, see Draw Developer's Guide, DemoRenditorMulti Example. The XML file for local preference settings that correspond to ISIS/Draw and earlier versions of BIOVIA Draw is IsisDraw.xml file. The IsisDraw.xml file is located in the same directory as default.xml file. See also Specify Display Preference Value default.xml with Custom Settings for Display Preferences The following is sample content of default.xml indicating that aromatic rings are displayed as circles. <?xml version="1.0"?> <DisplayPreferences xmlns:xsi=" xmlns:xsd=" <molprefs> <PiBondWriting>0</PiBondWriting> </molprefs> <LabelHeight>0.45</LabelHeight> <AromaticRingCircles>true</AromaticRingCircles> <AppsNeedingAuxThreading>iexplore.exe</AppsNeedingAuxThreading> <AndStereoLabelText>custom text 1</AndStereoLabelText> <OrStereoLabelText>custom text 2</OrStereoLabelText> <DefaultAngleRangeVal>10</DefaultAngleRangeVal> <PreferencesPath>C:\Users\<user_name>\AppData\Roaming\BIOVIA\BIOVIA Draw\Preferences\ </PreferencesPath> </DisplayPreferences> where smith is the <user>. To synchronize Display Settings, default.xml must be removed from every local machine. Alternatively, you can distribute your organization s standard version of default.xml to each local machine as C:\Users\<user_name>\AppData\Roaming\BIOVIA\BIOVIA Draw\Preferences\default.xml Some changes to default.xml cannot be made through the Settings dialog. For an example, see Custom Display of Stereogroup Labels such as abs, or, and. Removing a Feature To remove a feature by editing the XML configuration file, comment out each and every occurrence of the feature in the appropriate XML Configuration file. Page xxxv BIOVIA Draw Configuration Guide

37 See also Specify the Path to Custom XML Configuration Files Example: Removing the Data Sgroup Feature To disable a data Sgroup feature, comment out all the references in <draw_ home>\xmlconfig\palettestrip.xml to DataSgroupTool. Items that are commented out are within the open and close comments: <!-- commented out--> Enabled: <!-- To disable the DataSgroupTool for attaching data to an entire structure, comment out the popup menu command for the DataSgroup Tool below. --> <popup> <menuitem command="attachmol" text="attach Data..." /> </popup> <!-- End comment to hide DataSgroupTool for attaching data to an entire stucture--> </tool> --> Disabled: <!-- To disable the DataSgroupTool for attaching data to an entire structure, comment out the popup menu command for the DataSgroup Tool below. <popup> <menuitem command="attachmol" text="attach Data..." /> </popup> End comment to hide DataSgroupTool for attaching data to an entire stucture--> </tool> --> Similarly, to re-enable a feature you have commented, remove the comments of each of the references. Note: For developers, it is possible to remove the Chem Check feature that occurs when a user clicks the Transfer button in an application that uses a Renditor. See the Developer s Guide, Disabling Chem Check from Transfer back to Renditor. Example: Removing from the Chemistry menu To hide part of the Chemistry menu, such as the section for Generate Text from Structure and Generate Structure from Text (highlighted in yellow), complete the following steps. BIOVIA Draw Configuration Page xxxvi

38 Three XML Configuration files must be modified: <draw_home>\accelrysdraw-net.xml points to xmlconfig\menustrip.xml, which points to XmlConfig\menubar-chemistry.xml. 1. Make a copy of <draw_home>\xmlconfig\menubar-chemistry.xml and name the copy mymenubar-chemistry.xml 2. Locate the item (or section) that you want to remove in <draw_home>\xmlconfig\mymenubarchemistry.xml Page xxxvii BIOVIA Draw Configuration Guide

39 In the example above, a complete section was commented out, but you can comment out a single action. When you comment out a section, remove any nested comments. 3. Save mymenubar-chemistry.xml 4. Make a copy of <draw_home>\xmlconfig\menustrip.xml and name the copy mymenustrip.xml 5. Edit mymenustrip.xml to point to mymenubar-chemistry.xml Replace with include="mdl.draw.editor.xmlconfig.menubar-chemistry.xml"/> include="<draw_home>\xmlconfig\mymenubar-chemistry.xml"/> where <draw_home> represents the installation directory, such as C:\Program Files(x86) \BIOVIA\Draw Make a copy of <draw_home>\accelrysdraw-net.xml and name the copy MyAccelrysDraw-net.xml 7. Edit MyAccelrysDraw-net.xml to give the path and name of the edited file. <!-- <menustrip include="mdl.draw.editor.xmlconfig.menustrip.xml"/> commented out --> <menustrip include="<draw_home>\xmlconfig\mymenustrip.xml"/> where <draw_home> represents the installation directory, such as C:\Program Files(x86) \BIOVIA\BIOVIA Draw Write a batch file that points to your custom primary XML Configuration file. BIOVIADraw.exe MyAccelrysDraw-net.xml 9. To view the customized Chemistry menu, start Draw by launching the batch file. Show Explicit Carbon Label An example of a Display Preference you can configure is the context menu item, Show explicit Carbon label, which is governed by the XMLConfig\palettestrip.xml file. <tool class="mdl.draw.modules.editor.tools.cexplicittool"> <popup> <menu command="cshow" text="show explicit Carbon label"/> <menu command="chide" text="hide explicit Carbon label"/> </popup> </tool> BIOVIA Draw Configuration Page xxxviii

40 Disabling Arrow Toolbar Autohide The Arrow toolbar displays itself only when you are using the Arrow tool. To force the Arrow toolbar to display at all times, edit AccelrysDraw-net.xml as follows. Before After <arrowtoolbar name="arrows" direction="horizontal" autohide="true"/> <arrowtoolbar name="arrows" direction="horizontal" autohide="false"/> Removing a Menu Item Removing the Insert Option from the File Menu Complete the following steps to remove the Insert option from the File menu of the Draw Editor and modify the title bar. 1. Close any open versions of Draw. 2. Make a copy of <draw_home>\xmlconfig\menubar-file.xml, and rename it <draw_ home>\xmlconfig\mymenubar-file.xml 3. Edit the mymenubar-file.xml file. Find the Insert action by searching for "&Insert" and comment out the entire section: 4. Make a copy of <draw_home>\accelrysdraw-net.xml and rename it <draw_ home>\noinsert-accelrysdraw-net.xml 5. In NoInsert-AccelrysDraw-net.xml, change the name attribute of the MDLDraw element (on line 6) so that it reads as follows: <mdldraw width="950" height="700" name="my Draw - No Insert"> 6. Edit NoInsert-AccelrysDraw-net.xml to point to a custom mymenustrip.xml that you will create. <!-- <menustrip include="mdl.draw.editor.xmlconfig.menustrip.xml"/> --> <menustrip include="<draw_home>\xmlconfig\mymenustrip.xml"/> Page xxxix BIOVIA Draw Configuration Guide

41 where <draw_home> represents the installation directory, such as C:\Program Files(x86) \BIOVIA\Draw Make a copy of <draw_home>\xmlconfig\menustrip.xml and name the copy mymenustrip.xml 8. In mymenustrip.xml, assure that include= gives the full path to the custom XML configuration file. <!-- <menu text="&file" include="mdl.draw.editor.xmlconfig.menubar-file.xml"/> --> <menu text="&file" include="<draw_home>\xmlconfig\mymenubarfile.xml"/> where <draw_home> represents the installation directory, such as C:\Program Files (x86) \BIOVIA\BIOVIA Draw Create a batch file called NoInsert-Draw.bat that starts Draw by pointing to <draw_ home>\noinsertaccelrysdraw-net.xml. The content of the batch file is: BIOVIADraw.exe NoInsert-AccelrysDraw-net.xml 10. Verify the result. Before, with the Insert menu item under the Open menu item: After, with no Insert menu item: The title bar now says "My Draw - No Insert" and there is no longer an "Insert" action under the Open menu item. See also Specify the Path to Your Custom XML Configuration Files BIOVIA Draw Configuration Page xl

42 Removing the Formatting Toolbar Item from the Window Menu 1. Disable the Formatting Toolbar. a. Open the Windows Registry Editor. b. Navigate to HKEY_CURRENT_USER\Software\BIOVIA\BIOVIADraw\Client\2016 c. Set the value for Persistency.ShowFormattingToolbar to False. d. Exit the Windows Registry Editor. If you do not want the user to be able to enable the Formatting Toolbar from the Window menu, you must also hide the menu item. 2. Hide the menu item. a. Edit <draw-home>\xmlconfig\menubar-window.xml by adding the <!-- before and the - -> after: <!-- <menu text = "&Formatting Toolbar"> <action name="&enable Toolbar" class="mdl.draw.modules.editor.actions.formattingtoolbaronoffact ion" /> <action name="allow &Fading" class="mdl.draw.modules.editor.actions.formattingtoolbarfadeonof faction" /> <action name="&dynamic Position" class="mdl.draw.modules.editor.actions.formattingtoolbardynamicp ositionaction" /> </menu> <separator /> --> b. Edit <draw-home>\xmlconfig\menustrip.xml to point to the file the you edited in the previous step. BEFORE AFTER <menu text="&window" include="mdl.draw.editor.xmlconfig.menubar-window.xml"/> <!-- <menu text="&window" include="mdl.draw.editor.xmlconfig.menubar-window.xml"/> --> <menu text="&window" include="c:\program Files (x86) \BIOVIA\BIOVIADraw 2016\XmlConfig\menubar-window.xml"/> where C:\Program Files (x86)\biovia\biovia Draw 20162\XmlConfig\ represents the absolute path to your Draw home directory. c. Edit <draw-home>\accelrysdraw-net.xml to point to the file you edited in the previous step. BEFORE AFTER <menustrip include="mdl.draw.editor.xmlconfig.menustrip.xml"/> <!-- <menustrip include="mdl.draw.editor.xmlconfig.menustrip.xml"/> --> <menustrip include="c:\program Files (x86)\biovia\biovia Draw 2016\XmlConfig\menustrip.xml"/> Page xli BIOVIA Draw Configuration Guide

43 where C:\Program Files (x86)\biovia\biovia Draw 2016\XmlConfig\ represents the absolute path to your Draw home directory. 3. Test the result. ChemCheck Configuration You can configure the Chemistry > Run ChemCheck dialog for your end-users. After (customized XML): Copy menubar-chemistry.xml in the <draw_home>\xmlconfig folder, rename the copy mymenubar-chemistry.xml, and edit it to set add to true for options you want visible. Before: class="mdl.draw.modules.editor.actions.calcs.configurablecheminspector Action"> <checktypes> <checktype text="for query (SSSQUERY/RSSQUERY)" type="sssquery" add="true"/> <checktype text="for registration (RCG_SPECIFIC/RXNCARTRIDGE)" type="rcg_specific" add="true"/> <checktype text="for transform (TRANSFORM)" type="transform" add="false"/> <checktype text="for registration to Direct (DIRECT_SPECIFIC_2D)" type="direct_specific_2d" add="false"/> <checktype text="for registration to Direct (DIRECT_SPECIFIC_3D)" type="direct_specific_3d" add="false"/> <checktype text="for registration to Direct (DIRECT_REACTION)" type="direct_reaction" add="false"/> </checktypes> <checks> BIOVIA Draw Configuration Page xlii

44 <check text="reaction has Rgroup definition" command="rxnwithrgroup" add="true"/> <check text="valence Check" command="valence Check" add="true"/> <check text="atoms are overlapped" command="atom Overlap" add="true"/> <check text="bonds are overlapped" command="bond Overlap" add="true"/> <check text="structure needs V3000 molfile format" command="v3000check" add="false"/> </checks> </action> After (with changes in bold): class="mdl.draw.modules.editor.actions.calcs.configurablecheminspector Action"> <checktypes> <checktype text="for query (SSSQUERY/RSSQUERY)" type="sssquery" add="true"/> <checktype text="for registration (RCG_SPECIFIC/RXNCARTRIDGE)" type="rcg_specific" add="true"/> <checktype text="for transform (TRANSFORM)" type="transform" add="true"/> <checktype text="for registration to Direct (DIRECT_SPECIFIC_2D)" type="direct_specific_2d" add="true"/> <checktype text="for registration to Direct (DIRECT_SPECIFIC_3D)" type="direct_specific_3d" add="false"/> <checktype text="for registration to Direct (DIRECT_REACTION)" type="direct_reaction" add="false"/> </checktypes> <checks> <check text="reaction has Rgroup definition" command="rxnwithrgroup" add="false"/> <check text="valence Check" command="valence Check" add="true"/> <check text="atoms are overlapped" command="atom Overlap" add="true"/> <check text="bonds are overlapped" command="bond Overlap" add="true"/> <--! <check text="structure needs V3000 molfile format" command="v3000check" add="false"/> --> </checks> </action> 1. In the <draw_home>\xmlconfig\mymenustrip.xml file, specify the path to mymenubarchemistry.xml: <!-- <menu text="&chemistry" include="mdl.draw.editor.xmlconfig.menubarchemistry.xml"/>--> <menu text="&chemistry" include="<draw_home>\xmlconfig\mymenubar-chemistry.xml"/> where <draw_home> represents the installation directory, such as C:\Program Files(x86) \BIOVIA\Draw In the <draw_home> directory, copy AccelrysDraw-net.xml as myaccelrysdraw-net.xml, and edit it to specify the path to mymenustrip.xml <menustrip include="<draw_home>\xmlconfig\mymenustrip.xml"/> Page xliii BIOVIA Draw Configuration Guide

45 where <draw_home> represents the installation directory, such as C:\Program Files(x86) \BIOVIA\Draw Write a batch file: "<draw_home>\bioviadraw.exe" "<draw_home>\myaccelrysdraw-net.xml" where <draw_home> represents the installation directory, such as C:\Program Files(x86) \BIOVIA\Draw Run the batch file to verify your changes. Migrating Custom Toolbars To migrate custom toolbars from an earlier version, such as 3.3, to the current version, be aware of the following differences. Installation directory 4.0 or AccelrysDraw-net.xml for 4.1 and SymyxDraw-net.xml for 4.0 <arrowtoolbar name="arrows" direction="horizontal" autohide="true"/> <arrowtoolbar name="arrows" direction="horizontal"/> XmlConfig file 4.0 or atomtoolstri p.xml maintoolstri p.xml menubarchemistry.x ml menubaredit.xml menubarfile.xml menubarhelp.xml menubarobject.xml Note: this file is not in 4.0 or 4.1 <control type="sandbarbutton" command="new" image="mtb_new.png" tooltip="new"/> filefilter="all structure files (*.skc;*.mol;*.rxn;*.smi;*.cdx;*.xml) *.skc;*.mol;*.rx n;*.smi;*.cdx;*.xml sketch files (*.skc) *.skc molfiles (*.mol) *.mol rxnfiles (*.rxn) *.rxn SMILES files (*.smi) *.smi ChemDraw files (*.cdx) *.cdx Uniprot xml files (*.xml) *.xml"/> <atomtoolbar name="atoms" direction="horizontal" /> <control type="toolstripbutton" command="new" image="mtb_ new.png" tooltip="new"/> filefilter="all structure files (*.skc;*.mol;*.rxn;*.smi;*.cdx) *.skc;*.mol;*.rx n;*.smi;*.cdx sketch files (*.skc) *.skc molfiles (*.mol) *.mol rxnfiles (*.rxn) *.rxn SMILES files (*.smi) *.smi ChemDraw files (*.cdx) *.cdx"/> BIOVIA Draw Configuration Page xliv

46 XmlConfig file 4.0 or menubaroptions.xml menubarwindow.xml menustrip.x ml <action name="&small Buttons (16)" class="mdl.draw.modules.editor.actions.butto ns izeaction" size="16" /> <action name="&medium Buttons (24)" class="mdl.draw.modules.editor.actions.butto ns izeaction" size="24" /> <action name="&large Buttons (32)" class="mdl.draw.modules.editor.actions.butto ns izeaction" size="32" /> <action name="&custom Buttons" class="mdl.draw.modules.editor.actions.butt onsizeaction" size="custom" /> [Note: support for tabbed windows] <action name="windows" class="mdl.draw.modules.editor.actions. TabMen uaction" /> <action name="&small buttons" class="mdl.draw.modules.editor.ac tions.buttonsizeaction" size="16" /> <action name="&medium buttons" class="mdl.draw.modules.editor.ac tions.buttonsizeaction" size="24" /> <action name="&large buttons" class="mdl.draw.modules.editor.ac tions.buttonsizeaction" size="32" /> <action name="&translucent Tool Windows" class="mdl.draw.modules.editor.ac tions.tr ansluscentwindowsaction"/> <action name="&arrange" class="mdl.draw.modules.editor.ac tions.til ewindowmenuaction"/> <action name="tile &Vertical" class="mdl.draw.modules.editor.ac tions.til ewindowmenuaction" orientation="vertical"/> <action name="tile &Horizontal" class="mdl.draw.modules.editor.ac tions.til ewindowmenuaction" orientation="horizontal" /> <action name="windows" class="mdl.draw.modules.editor.ac tions.wi ndowmenuaction" /> Page xlv BIOVIA Draw Configuration Guide

47 XmlConfig file palettestrip. xml 4.0 or <tool class="mdl.draw.modules.editor.tools.cexplicit Tool"> <popup> <menu command="cshow" text="show explicit Carbon label"/> <menu command="chide" text="hide explicit Carbon label"/> </popup> </tool> templatetoo lstrip.xml Command-line Image File Conversion BIOVIA Draw includes the ImageGenerator command-line utility, which outputs image files that correspond to structure files.the input formats are molfile (mol), reaction files (rxn), sketch (skc), SMILES (smi), and ChemDraw Exchange (cdx). The output formats are: bmp (default), gif, png, and tif, true color when possible, otherwise black structure on white backaground. The ImageGenerator executable resides in the Tools subdirectory of your BIOVIA Draw installation. The API provides programmatic access to convert to image files formats bmp, gif, png, tif or wmf with MDL.Draw.Renderer.HeadlessRenderer.SaveMoleculeAsImage. When you "convert" structure files to imagine files, the original files remain unaltered. For conversion of MolfileString, SketchData, Smiles, StructureHandle, or Metafile, see the API Reference on MDL.Draw.StructureConversion.StructureConverter. Online Help on the ImageGenerator Invoke the ImageGenerator executable, which resides in the Tools subdirectory of your BIOVIA Draw installation. ImageGenerator Usage information is printed to the screen. Converting Single File Examples To interactively convert the specified molfile to a bmp, the default format, use the following: 1. Run the ImageGenerator.exe located in the Tools subdirectory of your BIOVIA\BIOVIA Draw <version>. 2. ImageGenerator -i test001.mol To interactively convert the specified molfile to a specified format, use the following: BIOVIA\BIOVIA Draw <version>\tools\imagegenerator -i test001.mol -f png where BIOVIA\BIOVIA Draw <version> represents the installation directory that is similar to the following: \\Program Files (x86)\biovia\biovia Draw 2016> The output file is put in the same directory as the input file, if you use the following: BIOVIA Draw Configuration Page xlvi

48 BIOVIA\BIOVIA Draw <version>\tools>imagegenerator -i "C:\myDir\objects.cdx" - f tif The utility displays the following message: C:\myDir\objects.cdx converted to C:\myDir\objects.tif To interactively convert the image using a specified width and height in pixels, use the following: ImageGenerator -i test001.mol -w 300 -h 350 Convert a Batch of Files Example To interactively convert a batch of files, use the following: 1. Create a list of the files in the directory using a DOC command such as dir/b > list.txt 2. Run the ImageGenerator.exe located in the Tools subdirectory of your BIOVIA\BIOVIA Draw <version>. 3. Use the following command to generate a batch of gif images from the list of files: ImageGenerator -l list.txt -f gif 4. (Optional) Specify additional options such as foreground and background color using the following command: ImageGenerator -l list.txt -f gif -fg purple -bg gold Page xlvii BIOVIA Draw Configuration Guide

49 Creating a Custom Ptable Custom Ptable Example To specify a custom periodic table (Ptable), do one of the following: Use PtableDemo.xml to understand Draw XML configuration for the module element. The ptable attribute specifies the path and name of the Ptable. Before: module class="mdl.draw.modules.editor.editormodule" After: module class="mdl.draw.modules.editor.editormodule" ptable="myptable.txt" For an overview of the Ptable, see the "Customizing the BIOVIA Ptable" in BIOVIA Chemical Representation Guide. You can find a copy at: \\docs\draw\devguide\bioviachemicalrepresentation.pdf. If you are developing a Java application and want to use a custom Ptable, see the Draw Developers Guide, custom Ptable for a JMolRendererCom Java application. Custom Ptable Path The custom Ptable, MyPtable.txt includes three elements that are not in the standard periodic table: PC1, PC2, and PC3. The Ptable example includes batch file that specifies that Draw loads a specific XML configuration file that identifies the custom Ptable and provides its location. You can specify relative, absolute, or a URL path to the Ptable. The following examples show the different path: Relative <module class="mdl.draw.modules.editor.editormodule" ptable="myptable.txt"> Absolute <module class="mdl.draw.modules.editor.editormodule" ptable="<biovia Draw installation directory>\examples\ptable\myptable.txt"> where <BIOVIA Draw installation directory> represents the absolute path to the root directory of your BIOVIA Draw installation. URL <module class="mdl.draw.modules.editor.editormodule" ptable=" To run the Ptable example: 1. Close Draw. 2. Double-click the batch file in the Examples\Ptable directory in BIOVIA\BIOVIA Draw <version>. 3. In the canvas, type the name of a custom element in the Ptable. The custom elements in this Ptable are PC1, PC2, and PC3. The keyboard sprouting feature places the custom element on the Draw canvas.the custom elements also appear in the list of available elements if the Show Extended Table check box is enabled. Creating a Custom Ptable Page xlviii

50 Running the Example Follow these steps to run the example: 1. Close any open versions of BIOVIA Draw. 2. Start BIOVIA Draw by double-clicking the batch file in the Examples\Ptable directory of your BIOVIA Draw installation. 3. In the canvas, type the name of a custom element in the Ptable. The custom elements in this Ptable are PC1, PC2, and PC3. 4. The keyboard sprouting feature places the custom element on the BIOVIA Draw canvas. The custom elements also appear in the list of available elements if the Show Extended Table checkbox is enabled. Setting a Custom Ptable Page xlix BIOVIA Draw Configuration Guide

51 Notes: See also Specifying the Custom Ptable and Custom Weights. PC1 is a pseudoatom, which is different from an abbreviated structure (abbreviation Sgroup), such as COOH. Abbreviated structures can be expanded to reveal the underlying structure. Pseudatoms cannot be expanded and do not have underlying structure. Add-Ins Software add-ins such as add-ins for ACD/Labs, Bioavailability (Rule of 5), and Isotopomer Distribution place options on menus indraw. After installing the add-ins and configuring Draw, you can access the added functionality from within Draw. Access these functions by selecting the new menu item from the Chemistry menu. To make Add-ins available to all users, load Add-ins to <Draw_Home>/AddIns. To load Add-ins to the user's personal profile: Create the folder AddIns: C:\users\<user_name>\AppData\Roaming\BIOVIA\BIOVIA Draw 2016\ For example: 1. Go to <DRAW_HOME>/Examples/C#/AddInActionExample 2. Create folder AddIns under C:\users\<user_name>\AppData\Roaming\BIOVIA\BIOVIA Draw 2016\ 3. Copy XML Document (DisplaySmilesString) and bin/release/mdl.draw.addin.displaysmilesstring.dll file to AddIns Folder 4. Launch BIOVIA Draw. 5. Draw any structure on the canvas. 6. Select Chemistry > Display SMILES String. Creating a Custom Ptable Page l

52 Cheshire Actions BIOVIA Draw contains the functionality of Accelrys Cheshire in an embedded version to support features such as such Clean and Uniprot file conversion. See also Specify a Custom Ptable and Custom Weights Specify a Custom Ptable and Custom Weights Before specifying a custom periodic table, review the information in Custom Ptable Example and Custom Ptable Path. If Draw is using a custom Ptable with custom weights, the BIOVIA Cheshire scripts must also use the custom Ptable with custom weights. You can edit the Ptable and weights file to match any custom elements and weights for your organization. Although the Ptable contains a weight for each element, the custom weights file determines the weight for calculations within Draw. Other BIOVIA products, such as BIOVIA Direct, might interpret the format of the atomic weight as Fortran format F10 more strictly leading to different results.if your business rules require Ptable customization, you must customize Draw and set the chemical environment at your site for all products that interact with Draw to use the same Ptable. Note: The bold format indicates updates you make to the configuration file. To specify a custom Ptable and custom Weights: 1. Close Draw. 2. Navigate to the BIOVIA\BIOVIA Draw <version>\examples\cheshireaction directory. 3. Make a backup copy of CheshireActionExample.xml. 4. Edit the following line in the CheshireActionExample.xml file to specify the custom Ptable for Draw. <module class="mdl.draw.modules.editor.editormodule" ptable="biovia\biovia Draw <version>\examples\ptable\myptable.txt"> 5. Modify the line to look similar to the following: <module class="mdl.draw.modules.editor.editormodule" ptable="<draw_ home>\examples\ptable\myptable.txt"> The BIOVIA\BIOVIA Draw <version> represents the absolute path to the root directory of your BIOVIA Draw installation. 6. Edit the following line in the CheshireActionExample.xml file to make the calculations available as options on the Draw Chemistry menu use the custom weights associated with the custom Ptable. <menustripitem text="&chemistry"> <action name="&calculator..." class="mdl.draw.modules.editor.actions.calcs.molvaluesaction"> 7. Modify the line to look similar to the following: <menustripitem text="&chemistry"> <action name="&calculator..." class="mdl.draw.modules.editor.actions.calcs.molvaluesaction" weights="custom" weightsscript="..\ptable\myweights.cct"> To verify the implementation of the custom Ptable and weights: 1. Run the batch file, CheshireActionExample.bat. 2. Open the CheshireAction.mol file. Page li BIOVIA Draw Configuration Guide

53 3. In Draw, select Chemistry > Cheshire Scripts > Rotate Molecule. The Cheshire script rotates and cleans the molecule. 4. Right-click an atom and select Atom Symbol. The three custom elements (PC1, PC2, PC3) of the custom Ptable are available. 5. Click PC1. 6. Select Chemistry > Calculator. The custom weight displays. 7. Paste the calculated values onto the canvas. Cheshire Actions Page lii

54 AccelrysDraw-net.xml About the Draw XML Configuration Files How to Edit XML Tags in the XML Configuration Files Hierarchy of Elements XML Configuration Elements Alphabetic List of Elements Description of Elements Trigger Table liii liii lviii lix lxii lxiv ci About the Draw XML Configuration Files XML tags define the menus, tools, toolbars, and other items that display in the Draw interface. The AccelrysDraw-net.xml file: Is the primary XML Configuration file Specifies the secondary class resources or XML Configuration files that affect the BIOVIA Draw Editor Is located in the installation directory, <draw_home> The secondary XML Configuration files that AccelrysDraw-net.xml points to are in <draw_ home>\xmlconfig\ One of the secondary XML Configuration files, menustrip.xml, points to tertiary XML Configuration files that affect each menu on the menubar: menubar-file.xml, menubar-edit.xml, menubarobject.xml, menubar-options.xml, menubar-chemistry.xml, menubar-window.xml, and menubarhelp.xml The Draw XML parser does not verify that parent-child tag relationships are valid. However, if a relationship is not valid, the object defined by the tags will not display. The valid parent-child tag hierarchies are documented in the Descriptions of Elements section. See also BIOVIA Draw Configuration Tasks Specifying XML Configuration Files Specify the Path to Your Custom XML Configuration Files. How to Edit XML Tags in the XML Configuration Files You can customize the BIOVIA Draw Editor user interface for your end-users by editing the AccelrysDraw-net.xml file and the files to which it points. For a list of typical tasks and associated XML tags, see Configuration Tasks. Sample Screens See also Hierarchy of Elements Alphabetic List of Elements. Page liii BIOVIA Draw Configuration Guide

55 Main Screen The following shows a splitter, which divides the screen into two spaces. One possibler use of a splitter is to display a module that contains buttons. AccelrysDraw-net.xml Page liv

56 Page lv BIOVIA Draw Configuration Guide

57 Drop-down Menu Note: Whereas a tool persists for reuse, an action is a one-time event, such as Save, Open, or Print. The items on a menu are actions. Dialog box To view the smolecular Value dialog box, open or draw a molecule and select Calculator in the Chemistry menu. AccelrysDraw-net.xml Page lvi

58 Attached Data Dialog When the user right-clicks an atom and selects Attach Data, the Data Sgroup Properties dialog displays. Attributes The data type of all attributes is CDATA. Attribute Required Description name No Specifies the name displayed in the title. height No Specifies the height of the dialog in pixels. width No Specifies the width of the dialog in pixels. Parent Element None Page lvii BIOVIA Draw Configuration Guide