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href="compound-registration_install-through-the-wizard.md">Install through the wizard</a></li> <li><a href="compound-registration_command-line-tools.md">Command Line Tools</a></li> <li><a href="compound-registration_configuration-guide.md">Configuration Guide</a></li> </ul></li> <li><a href="compound-registration_upgrade-guide.md">Upgrade Guide</a></li> <li><a href="compound-registration_system-requirements.md">System Requirements</a></li> </ul></li> <li><a href="compound-registration_user-guide.md">User guide</a> <ul> <li><a href="compound-registration_overview.md">Overview</a></li> <li><a href="compound-registration_introduction.md">Compound Registration Introduction</a></li> <li><a href="compound-registration_abbreviations.md">Compound Registration Abbreviations</a></li> <li><a href="compound-registration_definitions-of-terms.md">Definitions of Terms</a></li> <li><a href="compound-registration_quick-start-guide.md">Quick Start Guide</a> <ul> <li><a href="compound-registration_register-a-new-compound.md">Register a new compound</a></li> <li><a href="compound-registration_register-a-new-lot.md">Register a new lot</a></li> <li><a href="compound-registration_register-a-new-compound-reviewing-matches.md">Register a new compound reviewing matches</a></li> <li><a href="compound-registration_dealing-with-failed-submissions.md">Dealing with failed submissions</a></li> <li><a href="compound-registration_register-compounds-without-structures.md">Register compounds without structures</a></li> </ul></li> <li><a href="compound-registration_login.md">Login</a></li> <li><a href="compound-registration_dashboard-page.md">Dashboard page</a></li> <li><a href="compound-registration_autoregistration.md">Autoregistration</a> <ul> <li><a href="compound-registration_registration-page.md">Registration page</a></li> <li><a href="compound-registration_register-a-virtual-compound.md">Register a Virtual Compound</a></li> </ul></li> <li><a href="compound-registration_bulk-upload.md">Bulk Upload</a> <ul> <li><a href="compound-registration_upload-compounds.md">Upload compounds</a> <ul> <li><a href="compound-registration_upload-summary-page.md">Upload summary page</a></li> </ul></li> <li><a href="compound-registration_update-compounds.md">Update compounds</a> <ul> <li><a href="compound-registration_update-summary-page.md">Update summary page</a></li> </ul></li> <li><a href="compound-registration_upload-salts-and-solvates.md">Upload salts and solvates</a></li> </ul></li> <li><a href="compound-registration_advanced-registration.md">Advanced Registration</a> <ul> <li><a href="compound-registration_register-from-the-registration-page.md">Register from the Registration page</a></li> <li><a href="compound-registration_registering-from-the-submission-page.md">Registering from the Submission page</a> <ul> <li><a href="compound-registration_registering-new-structures.md">Registering new structures</a></li> <li><a href="compound-registration_registering-matching-structures.md">Registering matching structures</a></li> <li><a href="compound-registration_possible-status-messages-how-to-register.md">Possible status messages - how to register</a></li> </ul></li> <li><a href="compound-registration_staging-area.md">Staging area</a> <ul> <li><a href="compound-registration_actions-in-the-staging-area.md">Actions in the Staging area</a></li> <li><a href="compound-registration_workspace.md">Workspace</a></li> <li><a href="compound-registration_status-message.md">Status message</a></li> <li><a href="compound-registration_structure-area.md">Structure area</a></li> <li><a href="compound-registration_data-fields.md">Data fields</a></li> <li><a href="compound-registration_card.md">Card</a></li> </ul></li> </ul></li> <li><a href="compound-registration_search2.md">Search</a> <ul> <li><a href="compound-registration_search-option.md">Structure search option</a> <ul> <li><a href="compound-registration_type-of-search.md">Type of search</a></li> <li><a href="compound-registration_match-type.md">Match type</a></li> <li><a href="compound-registration_search-query.md">Search query</a></li> </ul></li> <li><a href="compound-registration_bulk-edit-additional-data-search.md">Bulk edit of additional data</a></li> <li><a href="compound-registration_download.md">Download</a></li> </ul></li> <li><a href="compound-registration_user-profile.md">User Profile</a></li> <li><a href="compound-registration_browse-page.md">Browse page</a> <ul> <li><a href="compound-registration_browser.md">Browser</a></li> <li><a href="compound-registration_browse-card.md">Browse-card</a></li> <li><a href="compound-registration_parent-level-amendment.md">Parent level amendment</a></li> <li><a href="compound-registration_version-level-amendment.md">Version level amendment</a></li> <li><a href="compound-registration_lot-level-amendment.md">Lot level amendment</a></li> </ul></li> <li><a href="compound-registration_appendix-a-calculations.md">Appendix A. Calculations</a></li> <li><a href="compound-registration_appendix-b-markush-structures.md">Appendix B. Markush Structures</a></li> <li><a href="compound-registration_multi-component-compounds.md">Multi-Component compounds</a></li> <li><a href="compound-registration_restricted-compounds.md">Restricted compounds</a></li> </ul></li> <li><a href="compound-registration_administration-page.md">Configuration guide</a> <ul> <li><a href="compound-registration_access-control.md">Access Control</a> <ul> <li><a href="compound-registration_users-and-groups.md">Users and groups</a></li> <li><a href="compound-registration_groups-and-roles.md">Groups and roles</a></li> <li><a href="compound-registration_project-based-access.md">Project based access</a></li> <li><a href="compound-registration_authentication-providers.md">Authentication Providers</a></li> </ul></li> <li><a href="compound-registration_forms-and-fields.md">Forms and Fields</a> <ul> <li><a href="compound-registration_form-editor.md">Form Editor</a></li> <li><a href="compound-registration_dictionary-manager.md">Dictionary Manager</a></li> </ul></li> <li><a href="compound-registration_chemistry.md">Chemistry</a></li> <li><a href="compound-registration_chemical-structures.md">Chemical structures</a></li> <li><a href="compound-registration_general-settings.md">General settings</a></li> <li><a href="compound-registration_workflow.md">Workflow</a></li> <li><a href="compound-registration_integration.md">Integration</a></li> <li><a href="compound-registration_tools.md">Tools</a></li> <li><a href="compound-registration_notifications.md">Notifications</a></li> <li><a href="compound-registration_pages-configuration.md">Pages Configuration</a></li> <li><a href="compound-registration_navigation.md">Navigation</a></li> <li><a href="compound-registration_authentication.md">Authentication</a></li> <li><a href="compound-registration_database-connections.md">Database Connections</a></li> <li><a href="compound-registration_e-mail-server-and-user-repository.md">E-mail Server and User Repository</a></li> </ul></li> <li><a href="compound-registration_developer_guide.md">Developer guide</a> <ul> <li><a href="compound-registration_api-documentation.md">API documentation</a></li> <li><a href="compound-registration_downstream.md">Downstream</a></li> </ul></li> <li><a href="compound-registration_history-of-changes.md">History of Changes</a></li> <li><a href="compound-registration_faq.md">FAQ</a></li> </ul></li> <li><a href="design-hub_index.md">Design Hub</a> <ul> <li><a href="design-hub_history-of-changes.md">History of changes</a></li> <li><a href="design-hub_install-guide.md">Install guide</a> <ul> <li><a href="design-hub_configuration-guide.md">Configuration guide</a></li> <li><a href="design-hub_install-guide-kubernetes.md">Install guide - Kubernetes</a></li> <li><a href="design-hub_developer-guide-company-plugins.md">Developer guide - company support plugins</a></li> </ul></li> <li><a href="design-hub_plugin-catalogue.md">Plugin Catalogue</a></li> <li><a href="design-hub_developer-guide-rest-api.md">Developer guide - REST API</a></li> <li><a href="design-hub_developer-guide-plugins.md">Developer guide - Plugins</a></li> <li><a href="design-hub_developer-guide-resolver-plugins.md">Developer guide - resolver plugins</a></li> <li><a href="design-hub_developer-guide-real-time-plugins.md">Developer guide - real time plugins</a></li> <li><a href="design-hub_developer-guide-real-time-plugin-templates.md">Developer guide - real time plugin templates</a></li> <li><a href="design-hub_developer-guide-export-plugins.md">Developer guide - export plugins</a></li> <li><a href="design-hub_developer-guide-storage-plugins.md">Developer guide - storage plugins</a></li> <li><a href="design-hub_developer-guide-import-plugins.md">Developer guide - import plugins</a></li> <li><a href="design-hub_developer-guide-registry-plugins.md">Developer guide - registry plugins</a></li> <li><a href="design-hub_developer-guide-theme-customization.md">Developer guide - theme customization</a></li> </ul></li> <li><a href="instant-jchem_index.md">Instant JChem</a> <ul> <li><a href="instant-jchem_user-guide.md">Instant Jchem User Guide</a> <ul> <li><a href="instant-jchem_getting-started.md">Getting Started</a> <ul> <li><a href="instant-jchem_about-instant-jchem.md">About Instant JChem</a></li> <li><a href="instant-jchem_additional-help-material.md">Additional Help Material</a></li> <li><a href="instant-jchem_terminology.md">Instant JChem Terminology</a></li> <li><a href="instant-jchem_how-the-instant-jchem-items-fit-together.md">How the Instant JChem items fit together</a></li> <li><a href="instant-jchem_windows-menus-and-toolbars.md">Windows Menus and Toolbars</a></li> <li><a href="instant-jchem_quick-start.md">Instant JChem Quick Start</a></li> <li><a href="instant-jchem_user-settings.md">User Settings</a></li> <li><a href="instant-jchem_licenses.md">Licenses</a></li> <li><a href="instant-jchem_dictionary.md">Instant JChem Dictionary</a></li> </ul></li> <li><a href="instant-jchem_ijc-projects.md">IJC Projects</a> <ul> <li><a href="instant-jchem_about-projects.md">About Projects</a></li> <li><a href="instant-jchem_creating-a-new-project.md">Creating New Project</a></li> <li><a href="instant-jchem_shared-projects.md">Shared Projects</a></li> </ul></li> <li><a href="instant-jchem_ijc-schemas.md">IJC Schemas</a> <ul> <li><a href="instant-jchem_about-ijc-schemas.md">About IJC Schemas</a></li> <li><a href="instant-jchem_adding-a-new-schema.md">Adding New Schema</a></li> <li><a href="instant-jchem_connecting-to-an-existing-ijc-schema.md">Connecting to Existing Schema</a></li> <li><a href="instant-jchem_logging-in-to-an-ijc-schema.md">Logging into Schema</a></li> <li><a href="instant-jchem_editing-schema-connection-settings.md">Editing Schema Connection Settings</a></li> <li><a href="instant-jchem_deleting-a-schema.md">Deleting Schema</a></li> <li><a href="instant-jchem_backing-up-and-restoring-schemas.md">Backing up and Restoring Schema</a></li> <li><a href="instant-jchem_schema-validator.md">Validating Schema</a></li> </ul></li> <li><a href="instant-jchem_viewing-and-managing-data.md">Viewing and Managing Data</a> <ul> <li><a href="instant-jchem_viewing-data.md">Viewing Data</a> <ul> <li><a href="instant-jchem_multiple-data-result-set.md">Multiple Data Result Set</a></li> <li><a href="instant-jchem_viewing-multi-entity-data.md">Viewing multi-entity data</a></li> </ul></li> <li><a href="instant-jchem_form-view.md">Form View</a> <ul> <li><a href="instant-jchem_design-mode.md">Design Mode</a></li> <li><a href="instant-jchem_browse-mode.md">Browse Mode</a></li> <li><a href="instant-jchem_query-mode.md">Query Mode</a></li> </ul></li> <li><a href="instant-jchem_grid-view-in-instant-jchem.md">Grid View in Instant JChem</a></li> <li><a href="instant-jchem_grid-view-from-selection.md">Grid View from Selection</a></li> <li><a href="instant-jchem_form-widgets.md">Form Widgets</a> <ul> <li><a href="instant-jchem_standard-widgets.md">Standard Widgets</a> <ul> <li><a href="instant-jchem_textfield-widget.md">TextField Widget</a></li> <li><a href="instant-jchem_textarea-widget.md">TextArea Widget</a></li> <li><a href="instant-jchem_button-widget.md">Button Widget</a></li> <li><a href="instant-jchem_label-widget.md">Label Widget</a></li> <li><a href="instant-jchem_checkbox-widget.md">CheckBox Widget</a></li> <li><a href="instant-jchem_date-widget.md">Date Widget</a></li> <li><a href="instant-jchem_list-widget.md">List Widget</a></li> <li><a href="instant-jchem_browser-widget.md">Browser Widget</a></li> <li><a href="instant-jchem_table-widget.md">Table Widget</a></li> <li><a href="instant-jchem_multi-field-sheet-widget.md">Multi Field Sheet Widget</a></li> <li><a href="instant-jchem_molpane-widget.md">MolPane Widget</a></li> <li><a href="instant-jchem_structure-matrix-widget.md">Structure Matrix Widget</a></li> <li><a href="instant-jchem_treetable-widget.md">TreeTable Widget</a></li> <li><a href="instant-jchem_canvas-widget.md">Canvas Widget</a></li> </ul></li> <li><a href="instant-jchem_visualisation-widgets.md">Visualisation Widgets</a> <ul> <li><a href="instant-jchem_histogram-widget.md">Histogram Widget</a></li> <li><a href="instant-jchem_scatter-plot-widgets.md">Scatter Plot Widgets</a></li> <li><a href="instant-jchem_radar-chart-widget.md">Radar Chart Widget</a></li> <li><a href="instant-jchem_box-plot-widget.md">Box Plot Widget</a></li> </ul></li> <li><a href="instant-jchem_container-widgets.md">Container Widgets</a> <ul> <li><a href="instant-jchem_panel-widget.md">Panel Widget</a></li> <li><a href="instant-jchem_tabbed-panel-widget.md">Tabbed Panel Widget</a></li> </ul></li> </ul></li> <li><a href="instant-jchem_conditional-formatting.md">Conditional Formatting</a> <ul> <li><a href="instant-jchem_step-by-step-guide.md">Step by Step guide</a></li> <li><a href="instant-jchem_creating-templates.md">Creating Templates</a></li> </ul></li> <li><a href="instant-jchem_copying-views.md">Copying views</a></li> <li><a href="instant-jchem_adding-and-deleting-rows.md">Adding and Deleting Rows</a> <ul> <li><a href="instant-jchem_editing-multiple-values.md">Editing Multiple Values</a></li> </ul></li> <li><a href="instant-jchem_printing.md">Printing</a></li> <li><a href="instant-jchem_renderers.md">Renderers</a></li> <li><a href="instant-jchem_pivoting.md">Pivoting in IJC</a></li> </ul></li> <li><a href="instant-jchem_lists-and-queries.md">Lists and Queries</a> <ul> <li><a href="instant-jchem_running-queries.md">Running Queries</a> <ul> <li><a href="instant-jchem_query-overview.md">Query Overview</a></li> <li><a href="instant-jchem_query-builder.md">Query Builder</a></li> <li><a href="instant-jchem_building-queries.md">Building Queries</a></li> <li><a href="instant-jchem_executing-queries.md">Executing Queries</a></li> <li><a href="instant-jchem_form-based-query.md">Form Based Query</a></li> <li><a href="instant-jchem_federated-search.md">Federated Search</a></li> </ul></li> <li><a href="instant-jchem_list-and-query-management.md">List and Query Management</a></li> <li><a href="instant-jchem_cherry-picking.md">Cherry Picking</a></li> </ul></li> <li><a href="instant-jchem_collaboration.md">Collaboration</a> <ul> <li><a href="instant-jchem_sharing-items.md">Sharing Items</a></li> <li><a href="instant-jchem_urls.md">Instant JChem URLs</a></li> </ul></li> <li><a href="instant-jchem_import-and-export.md">Import and Export</a> <ul> <li><a href="instant-jchem_using-file-import.md">Using File Import</a></li> <li><a href="instant-jchem_rdf-file-import.md">RDF File Import</a></li> <li><a href="instant-jchem_merging-data.md">Merging Data</a></li> <li><a href="instant-jchem_exporting-data.md">Exporting Data</a></li> </ul></li> <li><a href="instant-jchem_editing-databases.md">Editing Databases</a> <ul> <li><a href="instant-jchem_about-primary-keys.md">About Primary Keys</a></li> <li><a href="instant-jchem_controlling-editability.md">Controlling Editability</a></li> <li><a href="instant-jchem_editing-schemas.md">Editing Schemas</a> <ul> <li><a href="instant-jchem_editing-data-trees.md">Editing Data Trees</a></li> <li><a href="instant-jchem_editing-entities.md">Editing Entities</a></li> <li><a href="instant-jchem_editing-existing-schemas.md">Editing Existing Schemas</a></li> <li><a href="instant-jchem_editing-fields.md">Editing Fields</a> <ul> <li><a href="instant-jchem_calculated-fields.md">Calculated Fields</a></li> <li><a href="instant-jchem_extension-fields.md">Extension Fields</a></li> <li><a href="instant-jchem_pick-list.md">Pick list</a></li> <li><a href="instant-jchem_url-fields.md">URL Fields</a></li> <li><a href="instant-jchem_standard-fields.md">Standard Fields</a></li> </ul></li> <li><a href="instant-jchem_editing-relationships.md">Editing Relationships</a></li> </ul></li> <li><a href="instant-jchem_schema-editor.md">Schema Editor</a></li> <li><a href="instant-jchem_structure-views.md">Structure Views</a></li> <li><a href="instant-jchem_using-multiple-database-schemas.md">Using Multiple Database Schemas</a></li> </ul></li> <li><a href="instant-jchem_relational-data.md">Relational Data</a> <ul> <li><a href="instant-jchem_about-relationships.md">About Relationships</a></li> <li><a href="instant-jchem_about-data-trees.md">About Data Trees</a></li> <li><a href="instant-jchem_editing-child-data.md">Editing Child Data</a></li> </ul></li> <li><a href="instant-jchem_chemical-calculations-and-predictions.md">Chemical Calculations and Predictions</a> <ul> <li><a href="instant-jchem_about-chemical-calculations-and-predictions.md">About Chemical Calculations and Predictions</a></li> <li><a href="instant-jchem_adding-chemical-terms-fields.md">Adding Chemical Terms Fields</a></li> </ul></li> <li><a href="instant-jchem_chemistry-functions.md">Chemistry Functions</a> <ul> <li><a href="instant-jchem_performing-an-overlap-analysis.md">Performing an Overlap Analysis</a></li> <li><a href="instant-jchem_standardizer-standardizing-structure-files.md">Standardizer - Standardizing Structure Files</a></li> <li><a href="instant-jchem_markush-enumeration.md">Markush Enumeration in IJC</a></li> <li><a href="instant-jchem_reaction-enumeration.md">Reaction Enumeration</a></li> <li><a href="instant-jchem_r-group-analysis.md">R-group analysis</a></li> </ul></li> <li><a href="instant-jchem_security.md">Security</a> <ul> <li><a href="instant-jchem_about-instant-jchem-security.md">About Instant JChem Security</a></li> <li><a href="instant-jchem_changing-security-settings.md">Changing Security Settings</a></li> <li><a href="instant-jchem_managing-user-database.md">Managing User Database</a></li> <li><a href="instant-jchem_managing-current-users.md">Managing Current Users</a></li> <li><a href="instant-jchem_security-templates.md">Security Templates</a></li> <li><a href="instant-jchem_row-level-security.md">Row level security</a></li> <li><a href="instant-jchem_using-database-authentication.md">Using database authentication</a></li> <li><a href="instant-jchem_oracle-jdbc-connection-encryption.md">Oracle JDBC connection encryption</a></li> <li><a href="instant-jchem_upgrade-to-spring-security-6-framework.md">Upgrade to Spring Security 6 framework</a></li> </ul></li> <li><a href="instant-jchem_scripting.md">Scripting</a></li> <li><a href="instant-jchem_updating-instant-jchem.md">Updating Instant JChem</a> <ul> <li><a href="instant-jchem_about-updating-instant-jchem.md">About Updating Instant JChem</a></li> <li><a href="instant-jchem_about-managing-plugins.md">About Managing Plugins</a></li> <li><a href="instant-jchem_updating-a-multi-user-ijc-installation.md">Updating a Multi-User IJC Installation</a></li> </ul></li> <li><a href="instant-jchem_tips-and-tricks.md">Tips and Tricks</a> <ul> <li><a href="instant-jchem_memory-usage.md">Memory Usage</a></li> <li><a href="instant-jchem_performance-tips.md">Performance Tips</a></li> <li><a href="instant-jchem_database-implementation-notes.md">Database Implementation Notes</a></li> <li><a href="instant-jchem_using-the-database-explorer.md">Using the database explorer</a></li> <li><a href="instant-jchem_change-standardizer-configuration-for-jchem-table.md">Change standardizer configuration for JChem table</a></li> <li><a href="instant-jchem_setting-up-cartridge-tables.md">Setting up cartridge tables for use in IJC</a></li> <li><a href="instant-jchem_triggers-and-sequences.md">Triggers and sequences</a> <ul> <li><a href="instant-jchem_triggers-and-sequences-derby.md">Triggers and sequences - Derby</a></li> <li><a href="instant-jchem_triggers-and-sequences-mysql.md">Triggers and sequences - MySQL</a></li> <li><a href="instant-jchem_triggers-and-sequences-oracle.md">Triggers and sequences - Oracle</a></li> </ul></li> </ul></li> <li><a href="instant-jchem_tutorials.md">Instant JChem Tutorials</a> <ul> <li><a href="instant-jchem_building-a-relational-form-from-scratch.md">Building a relational form from scratch</a></li> <li><a href="instant-jchem_building-more-complex-relational-data-models.md">Building more complex relational data models</a></li> <li><a href="instant-jchem_defining-a-security-policy.md">Defining a security policy</a></li> <li><a href="instant-jchem_filtering-items-using-roles.md">Filtering items using roles</a></li> <li><a href="instant-jchem_lists-and-queries-management.md">Lists and Queries management</a></li> <li><a href="instant-jchem_query-building-tutorial.md">Query building tutorial</a></li> <li><a href="instant-jchem_reaction-enumeration-analysis-and-visualization.md">Reaction enumeration analysis and visualization</a></li> <li><a href="instant-jchem_sd-file-import-basic-visualization-and-overlap-analysis.md">SD file import basic visualization and overlap analysis</a></li> <li><a href="instant-jchem_using-import-map-and-merge.md">Using Import map and merge</a></li> <li><a href="instant-jchem_using-standardizer-to-your-advantage.md">Using Standardizer to your advantage</a></li> <li><a href="instant-jchem_pivoting-tutorial.md">Pivoting tutorial</a></li> <li><a href="instant-jchem_handling-remote-data-with-web-service-entity.md">Handling Remote Data with Web Service Entity</a></li> <li><a href="instant-jchem_exploring-canvas-widget.md">Exploring Canvas Widget in Instant JChem</a></li> </ul></li> </ul></li> <li><a href="instant-jchem_administrator-guide.md">Instant JChem Administrator Guide</a> <ul> <li><a href="instant-jchem_admin-tool.md">Admin Tool</a> <ul> <li><a href="instant-jchem_admin-tool-connection.md">Admin Tool connection</a></li> <li><a href="instant-jchem_clone-operation.md">Clone operation</a></li> <li><a href="instant-jchem_finish-wizard.md">Finish Wizard</a></li> <li><a href="instant-jchem_migrate-operation.md">Migrate operation</a></li> <li><a href="instant-jchem_delete-operation.md">Delete operation</a></li> <li><a href="instant-jchem_schema-security-operation.md">Schema security operation</a></li> <li><a href="instant-jchem_unlock-operation.md">Unlock operation</a></li> <li><a href="instant-jchem_change-owner-operation.md">Change owner operation</a></li> <li><a href="instant-jchem_create-jws-files-operation.md">Create JWS files operation</a></li> <li><a href="instant-jchem_short-descriptions.md">Short Descriptions</a> <ul> <li><a href="instant-jchem_changeownershort.md">ChangeOwnerShort</a></li> <li><a href="instant-jchem_cloneshort.md">CloneShort</a></li> <li><a href="instant-jchem_createsharedshort.md">CreateSharedShort</a></li> <li><a href="instant-jchem_deleteshort.md">DeleteShort</a></li> <li><a href="instant-jchem_migrateshort.md">MigrateShort</a></li> <li><a href="instant-jchem_renameshort.md">RenameShort</a></li> <li><a href="instant-jchem_securityshort.md">SecurityShort</a></li> <li><a href="instant-jchem_unlockshort.md">UnlockShort</a></li> </ul></li> <li><a href="instant-jchem_create-ijs-file-for-schema-s.md">Create *.ijs file for schema(s)</a></li> </ul></li> <li><a href="instant-jchem_ijc-deployment-guide.md">IJC Deployment Guide</a></li> <li><a href="instant-jchem_supported-databases.md">Supported databases</a></li> <li><a href="instant-jchem_jchem-cartridge.md">JChem Cartridge</a></li> <li><a href="instant-jchem_choral-cartridge.md">Choral Cartridge</a></li> <li><a href="instant-jchem_using-oracle-text-in-instant-jchem.md">Using Oracle Text in Instant JChem</a></li> <li><a href="instant-jchem_postgresql-cartridge.md">JChem Postgres Cartridge in IJC</a></li> <li><a href="instant-jchem_deployment-via-java-web-start.md">Deployment via Java Web Start</a></li> <li><a href="instant-jchem_startup-options.md">Startup Options</a></li> <li><a href="instant-jchem_shared-project-configuration.md">Shared project configuration</a></li> <li><a href="instant-jchem_accessing-data-with-urls.md">Accessing data with URLs</a></li> <li><a href="instant-jchem_meta-data-tables.md">Instant JChem Meta Data Tables</a></li> <li><a href="instant-jchem_test-to-production-metadata-migrator.md">Test to Production Metadata Migrator</a></li> <li><a href="instant-jchem_filtering-items.md">Filtering Items</a></li> <li><a href="instant-jchem_deploying-the-ijc-odata-extension-into-spotfire.md">Deploying the IJC OData extension into Spotfire</a></li> <li><a href="instant-jchem_reporting-a-problem.md">Reporting a Problem</a> <ul> <li><a href="instant-jchem_extracting_version_information.md">Extracting Version Information</a></li> <li><a href="instant-jchem_obtaining-IJC-log-files.md">Obtaining Log Files</a></li> <li><a href="instant-jchem_problem-with-performance.md">Problems with Performance</a> <ul> <li><a href="instant-jchem_obtaining-performance-log.md">Obtaining Performance Log</a></li> </ul></li> <li><a href="instant-jchem_sql-logging.md">SQL Logging</a></li> <li><a href="instant-jchem_reinstallation.md">Clean IJC Re-installation</a></li> </ul></li> <li><a href="instant-jchem_manual-instant-jchem-schema-admin-functions.md">Manual Instant JChem schema admin functions</a></li> <li><a href="instant-jchem_sql-scripts-for-manual-schema-upgrade.md">SQL Scripts for Manual Schema Upgrade</a></li> <li><a href="instant-jchem_database-row-level-security.md">Database Row Level Security</a></li> <li><a href="instant-jchem_jccwithijc.md">JccWithIJC</a></li> </ul></li> <li><a href="instant-jchem_developer-guide.md">Instant JChem Developer Guide</a> <ul> <li><a href="instant-jchem_working-with-ijc-architecture.md">Working With IJC Architecture</a></li> <li><a href="instant-jchem_ijc-api.md">IJC API</a></li> <li><a href="instant-jchem_groovy-scripting.md">Groovy Scripting</a> <ul> <li><a href="instant-jchem_good-practices.md">Good Practices</a></li> <li><a href="instant-jchem_schema-and-datatree-scripts.md">Schema and DataTree Scripts</a> <ul> <li><a href="instant-jchem_simple-sdf-exporter.md">Simple SDF Exporter</a></li> <li><a href="instant-jchem_relational-sdf-exporter.md">Relational SDF Exporter</a></li> <li><a href="instant-jchem_cdx-file-importer.md">CDX File Importer</a></li> <li><a href="instant-jchem_data-merger-or-inserter-from-an-sdf-file.md">Data Merger or Inserter from an SDF file</a></li> <li><a href="instant-jchem_markush-dcr-structures-exporter.md">Markush DCR Structures Exporter</a></li> <li><a href="instant-jchem_select-representative-member-of-clusters.md">Select Representative Member of Clusters</a></li> <li><a href="instant-jchem_table-standardizer.md">Table Standardizer</a></li> <li><a href="instant-jchem_populate-a-table-with-microspecies.md">Populate a Table with Microspecies</a></li> <li><a href="instant-jchem_create-a-diverse-subset.md">Create a Diverse Subset</a></li> <li><a href="instant-jchem_pearson-linear-correlation-co-efficient-calculator.md">Pearson Linear Correlation Co-efficient Calculator</a></li> <li><a href="instant-jchem_pdf-trawler.md">PDF Trawler</a></li> <li><a href="instant-jchem_simple-substructure-search.md">Simple Substructure Search</a></li> <li><a href="instant-jchem_intersecting-sets.md">Intersecting Sets</a></li> <li><a href="instant-jchem_find-entries-with-duplicated-field-value.md">Find Entries with Duplicated Field Value</a></li> <li><a href="instant-jchem_importing-multiple-sdf-files.md">Importing Multiple SDF Files</a></li> <li><a href="instant-jchem_calling-external-tools.md">Calling External Tools</a></li> <li><a href="instant-jchem_create-relational-data-tree.md">Create Relational Data Tree</a></li> </ul></li> <li><a href="instant-jchem_forms-model-scripts.md">Forms Model Scripts</a> <ul> <li><a href="instant-jchem_create-new-form.md">Create New Form</a></li> <li><a href="instant-jchem_create-new-grid.md">Create New Grid</a></li> <li><a href="instant-jchem_create-new-panel.md">Create New Panel</a></li> <li><a href="instant-jchem_create-new-tabbed-pane.md">Create New Tabbed Pane</a></li> <li><a href="instant-jchem_copy-existing-form.md">Copy Existing Form</a></li> <li><a href="instant-jchem_groovy-scripts-for-canvas-widget.md">Canvas Widget Scripts</a></li> </ul></li> <li><a href="instant-jchem_button-scripts.md">Button Scripts</a> <ul> <li><a href="instant-jchem_execute-permanent-query.md">Execute Permanent Query</a></li> <li><a href="instant-jchem_patent-fetcher-button.md">Patent Fetcher Button</a></li> <li><a href="instant-jchem_batch-searching-button.md">Batch Searching Button</a></li> <li><a href="instant-jchem_import-or-export-a-saved-query-sdf-button.md">Import or Export a Saved Query SDF Button</a></li> <li><a href="instant-jchem_back-and-next-buttons.md">Back and Next Buttons</a></li> <li><a href="instant-jchem_add-annotations-button.md">Add Annotations Button</a></li> <li><a href="instant-jchem_simple-structure-checker-button.md">Simple Structure Checker Button</a></li> <li><a href="instant-jchem_advanced-structure-checker-button.md">Advanced Structure Checker Button</a></li> <li><a href="instant-jchem_calculate-molweight-and-generate-smiles.md">Calculate MolWeight and generate SMILES</a></li> <li><a href="instant-jchem_get-current-user.md">Get Current User</a></li> <li><a href="instant-jchem_simple-chemicalterms-evaluator.md">Simple ChemicalTerms evaluator</a></li> <li><a href="instant-jchem_edit-molecule-button.md">Edit Molecule Button</a></li> <li><a href="instant-jchem_tanimotomultiple.md">TanimotoMultiple</a></li> <li><a href="instant-jchem_execute-permanent-query-based-on-its-name.md">Execute Permanent Query Based On Its Name</a></li> <li><a href="instant-jchem_open-existing-view-in-the-same-datatree.md">Open existing view in the same dataTree</a></li> <li><a href="instant-jchem_export-selection-to-file.md">Export selection to file</a></li> <li><a href="instant-jchem_generate-random-resultset-from-actual-resultset.md">Generate random resultset from actual resultset</a></li> </ul></li> <li><a href="instant-jchem_form-scripts.md">Form Scripts</a> <ul> <li><a href="instant-jchem_drop-down-input-dialog.md">Drop Down Input Dialog</a></li> <li><a href="instant-jchem_log-user-and-date-upon-row-addition.md">Log user and date upon row addition</a></li> <li><a href="instant-jchem_scripting-hooks.md">Scripting hooks</a></li> </ul></li> <li><a href="instant-jchem_groovy-scriptlets.md">Groovy Scriptlets</a> <ul> <li><a href="instant-jchem_buttons-vs-scripts.md">Buttons vs Scripts</a></li> <li><a href="instant-jchem_creating-new-entities.md">Creating New Entities</a></li> <li><a href="instant-jchem_creating-new-fields.md">Creating New Fields</a></li> <li><a href="instant-jchem_reading-molecules-from-a-file.md">Reading Molecules From a File</a></li> <li><a href="instant-jchem_insert-or-update-a-row.md">Insert or Update a Row</a></li> <li><a href="instant-jchem_evaluator.md">Evaluator</a></li> <li><a href="instant-jchem_create-or-find-a-relationship.md">Create or Find a Relationship</a></li> <li><a href="instant-jchem_adding-an-edge-to-a-data-tree.md">Adding an Edge to a Data Tree</a></li> <li><a href="instant-jchem_exporting-data-to-a-file.md">Exporting Data to a File</a></li> <li><a href="instant-jchem_connect-to-an-external-database.md">Connect to an External Database</a></li> <li><a href="instant-jchem_create-a-new-chemterm-field.md">Create a New ChemTerm Field</a></li> <li><a href="instant-jchem_create-a-new-dynamic-url-field.md">Create a New Dynamic URL Field</a></li> <li><a href="instant-jchem_create-a-new-static-url-field.md">Create a New Static URL Field</a></li> </ul></li> </ul></li> <li><a href="instant-jchem_java-plugins.md">Java Plugins</a> <ul> <li><a href="instant-jchem_ijc-plugin-quick-start.md">IJC Plugin Quick Start</a></li> <li><a href="instant-jchem_ijc-hello-world-plugin.md">IJC Hello World Plugin</a></li> <li><a href="instant-jchem_ijc-plugin-tutorial-myaddfield-plugin.md">IJC Plugin tutorial - MyAddField plugin</a></li> <li><a href="instant-jchem_ijc-plugin-tutorial-mymathcalc-plugin.md">IJC Plugin tutorial - MyMathCalc plugin</a></li> <li><a href="instant-jchem_ijc-plugin-tutorial-renderer-example.md">IJC Plugin tutorial - Renderer Example</a></li> <li><a href="instant-jchem_ijc-plugin-tutorial-myscserver-webapp.md">IJC Plugin tutorial - MySCServer webapp</a></li> <li><a href="instant-jchem_ijc-plugin-tutorial-myscclient-plugin.md">IJC Plugin tutorial - MySCClient plugin</a></li> <li><a href="instant-jchem_ijc-plugin-for-canvas-widget.md">IJC Plugin tutorial - Canvas widget</a></li> <li><a href="instant-jchem_java-plugins-and-java-web-start.md">Java Plugins and Java Web Start</a></li> </ul></li> </ul></li> <li><a href="instant-jchem_faq.md">Instant JChem FAQ</a></li> <li><a href="instant-jchem_installation-and-upgrade.md">Instant JChem Installation and Upgrade</a> <ul> <li><a href="instant-jchem_installation-on-windows.md">Installation on Windows</a></li> <li><a href="instant-jchem_installation-on-mac-os-x.md">Installation on Mac OS X</a></li> <li><a href="instant-jchem_installation-on-linux-or-solaris.md">Installation on Linux or Solaris</a></li> <li><a href="instant-jchem_installation-on-other-platforms.md">Installation on Other Platforms</a></li> <li><a href="instant-jchem_uninstall.md">Uninstall</a></li> <li><a href="instant-jchem_changing-java-version.md">Changing Java Version</a></li> </ul></li> <li><a href="instant-jchem_licensing.md">Instant JChem Licensing</a></li> <li><a href="instant-jchem_ijc-getting-help-and-support.md">IJC Getting Help and Support</a></li> <li><a href="instant-jchem_system-requirements.md">Instant JChem System Requirements</a></li> <li><a href="instant-jchem_history-of-changes.md">Instant JChem History of Changes</a></li> </ul></li> <li><a href="markush-editor_index.md">Markush Editor</a> <ul> <li><a href="markush-editor_help-and-support.md">Markush Editor Help and Support</a></li> <li><a href="markush-editor_history-of-changes.md">Markush Editor History of Changes</a></li> <li><a href="markush-editor_installation-and-system-requirements.md">Markush Editor Installation and System Requirements</a></li> <li><a href="markush-editor_licensing.md">Markush Editor Licensing</a></li> <li><a href="markush-editor_user-guide.md">Markush Editor User's Guide</a></li> </ul></li> <li><a href="marvin_marvin-desktop-suite.md">Marvin Desktop Suite</a> <ul> <li><a href="marvin_marvinsketch.md">MarvinSketch</a> <ul> <li><a href="marvin_marvinsketch_user-guide.md">User Guide</a> <ul> <li><a href="marvin_marvinsketch_getting-started.md">Getting Started</a></li> <li><a href="marvin_marvinsketch_graphical-user-interface.md">Graphical User Interface</a> <ul> <li><a href="marvin_canvas-in-marvinsketch.md">Canvas</a></li> <li><a href="marvin_menus-of-marvinsketch.md">Menus</a> <ul> <li><a href="marvin_marvinsketch_file-menu.md">File Menu</a></li> <li><a href="marvin_marvinsketch_edit-menu.md">Edit Menu</a></li> <li><a href="marvin_marvinsketch_view-menu.md">View Menu</a></li> <li><a href="marvin_insert-menu.md">Insert Menu</a></li> <li><a href="marvin_atom-menu.md">Atom Menu</a></li> <li><a href="marvin_bond-menu.md">Bond Menu</a></li> <li><a href="marvin_marvinsketch_structure-menu.md">Structure Menu</a></li> <li><a href="marvin_calculations-menu.md">Calculations Menu</a></li> <li><a href="marvin_services-menu.md">Services Menu</a></li> <li><a href="marvin_marvinsketch_help-menu.md">Help Menu</a></li> </ul></li> <li><a href="marvin_toolbars-of-marvinsketch.md">Toolbars</a> <ul> <li><a href="marvin_general-toolbar-in-marvinsketch.md">General Toolbar</a></li> <li><a href="marvin_tools-toolbar-in-marvinsketch.md">Tools Toolbar</a></li> <li><a href="marvin_atoms-toolbar.md">Atoms Toolbar</a></li> <li><a href="marvin_simple-templates-toolbar.md">Simple Templates Toolbar</a></li> <li><a href="marvin_advanced-templates-toolbar.md">Advanced Templates Toolbar</a></li> <li><a href="marvin_search-online-toolbar.md">Search Online Toolbar</a></li> <li><a href="marvin_special-toolbars.md">Special Toolbars</a></li> </ul></li> <li><a href="marvin_pop-up-menus-of-marvinsketch.md">Context Menus</a></li> <li><a href="marvin_the-status-bar-of-marvinsketch.md">The Status Bar</a></li> <li><a href="marvin_marvinsketch_dialogs.md">Dialogs</a> <ul> <li><a href="marvin_multipage-settings.md">Multipage Settings</a></li> <li><a href="marvin_document-style.md">Document Style</a></li> <li><a href="marvin_template-library-manager.md">Template Library Manager</a></li> <li><a href="marvin_edit-source.md">Edit Source</a></li> <li><a href="marvin_customize.md">Customize</a></li> <li><a href="marvin_where-are-the-settings-stored.md">Where Are the Settings Stored</a></li> <li><a href="marvin_format-dialog.md">Format Dialog</a></li> <li><a href="marvin_periodic-table-of-chemical-elements.md">Periodic Table</a></li> <li><a href="marvin_marvinsketch_preferences.md">Preferences</a></li> <li><a href="marvin_create-group-dialog.md">Create Group Dialog</a></li> <li><a href="marvin_attach-data.md">Attach Data</a></li> <li><a href="marvin_edit-properties.md">Edit Properties</a></li> <li><a href="marvin_marvinsketch_about.md">About</a></li> </ul></li> <li><a href="marvin_shortcuts-in-marvinsketch.md">Shortcuts</a></li> <li><a href="marvin_customizing-marvinsketch-gui.md">Customizing the GUI</a></li> <li><a href="marvin_marvinsketch_configurations.md">Configurations</a></li> <li><a href="marvin_services-module.md">Services Module</a> <ul> <li><a href="marvin_set-services.md">Set Services</a></li> <li><a href="marvin_settings-of-the-different-service-types.md">Settings of the Different Service Types</a> <ul> <li><a href="marvin_local.md">Local</a></li> <li><a href="marvin_http-service.md">HTTP Service</a></li> <li><a href="marvin_soap-service.md">SOAP Service</a></li> </ul></li> </ul></li> </ul></li> <li><a href="marvin_working-in-marvinsketch.md">Working in MarvinSketch</a> <ul> <li><a href="marvin_marvinsketch_structure-display-options.md">Structure Display Options</a> <ul> <li><a href="marvin_customizing-structure-drawing-styles.md">Customizing Structure Drawing Styles</a> <ul> <li><a href="marvin_drawing-settings.md">Drawing Settings</a></li> <li><a href="marvin_drawing-styles.md">Drawing Styles</a></li> </ul></li> <li><a href="marvin_structure-display.md">Structure Display</a></li> <li><a href="marvin_color-schemes.md">Color Schemes</a></li> <li><a href="marvin_display-options-for-implicit-and-explicit-hydrogens.md">Display Options for Implicit and Explicit Hydrogens</a></li> <li><a href="marvin_displaying-the-label-of-carbon-atoms.md">Displaying the Label of Carbon Atoms</a></li> <li><a href="marvin_error-highlighting-in-marvinsketch.md">Error Highlighting</a></li> <li><a href="marvin_saving-display-options.md">Saving Display Options</a></li> </ul></li> <li><a href="marvin_basic-editing.md">Basic Editing</a> <ul> <li><a href="marvin_selecting-a-structure.md">Selecting a Structure</a></li> <li><a href="marvin_copy-paste-and-draganddrop.md">Copy-Paste and DragandDrop</a></li> <li><a href="marvin_geometric-transformation-of-structures-and-objects.md">Geometric Transformation of Structures and Objects</a> <ul> <li><a href="marvin_moving-and-rotating.md">Moving and Rotating</a></li> <li><a href="marvin_scaling.md">Scaling</a></li> <li><a href="marvin_flipping.md">Flipping</a></li> <li><a href="marvin_mirroring.md">Mirroring</a></li> <li><a href="marvin_inverting.md">Inverting</a></li> </ul></li> <li><a href="marvin_cleaning.md">Cleaning</a></li> <li><a href="marvin_deleting-a-structure.md">Deleting a Structure</a></li> <li><a href="marvin_editing-the-source.md">Editing the Source</a></li> </ul></li> <li><a href="marvin_drawing-simple-structures.md">Drawing Simple Structures</a> <ul> <li><a href="marvin_draw-atoms.md">Draw Atoms</a></li> <li><a href="marvin_draw-bonds.md">Draw Bonds</a></li> <li><a href="marvin_draw-chains.md">Draw Chains</a></li> <li><a href="marvin_sprouting.md">Sprouting</a></li> <li><a href="marvin_merge-structures.md">Merge Structures</a></li> <li><a href="marvin_templates-in-marvinsketch.md">Templates</a></li> <li><a href="marvin_draw-stereocenters.md">Draw Stereocenters</a></li> <li><a href="marvin_draw-coordination-compounds.md">Draw Coordination Compounds</a></li> <li><a href="marvin_insert-edit-new-structure-or-fragment.md">Insert-Edit New Structure or Fragment</a></li> <li><a href="marvin_atom-label-editor.md">Atom Label Editor</a></li> </ul></li> <li><a href="marvin_drawing-more-complex-structures.md">Drawing More Complex Structures</a> <ul> <li><a href="marvin_substructure-groups-in-marvinsketch.md">Substructure Groups</a> <ul> <li><a href="marvin_abbreviated-superatom-groups.md">Abbreviated (Superatom) Groups</a></li> <li><a href="marvin_polymers.md">Polymers</a> <ul> <li><a href="marvin_draw-polymers.md">Draw Polymers</a></li> <li><a href="marvin_structure-based-representation-of-polymers.md">Structure-based Representation of Polymers</a> <ul> <li><a href="marvin_structural-repeating-unit-sru-polymers.md">Structural Repeating Unit (SRU) Polymers</a></li> <li><a href="marvin_repeating-units-frequency-variation.md">Repeating Units with Repetition Ranges - Frequency Variation</a></li> <li><a href="marvin_copolymers.md">Copolymers</a></li> </ul></li> <li><a href="marvin_source-based-representation-of-polymers.md">Source-based Representation of Polymers</a></li> </ul></li> <li><a href="marvin_unordered-mixtures-and-ordered-mixtures.md">Unordered Mixtures and Ordered Mixtures</a></li> <li><a href="marvin_charge-of-the-group.md">Charge of the Group</a></li> </ul></li> <li><a href="marvin_markush-structures-in-marvinsketch.md">Markush Structures</a> <ul> <li><a href="marvin_r-groups-in-marvinsketch.md">R-groups</a></li> <li><a href="marvin_atom-lists-and-not-lists-in-marvinsketch.md">Atom Lists and NOT Lists</a></li> <li><a href="marvin_position-variation-in-marvinsketch.md">Position Variation</a></li> <li><a href="marvin_homology-groups-in-marvinsketch.md">Homology Groups</a></li> <li><a href="marvin_frequency-variation.md">Frequency Variation</a> <ul> <li><a href="marvin_repeating-units-in-marvinsketch.md">Repeating Units with Repetition Range</a></li> <li><a href="marvin_link-nodes-in-marvinsketch.md">Link Nodes</a></li> </ul></li> </ul></li> <li><a href="marvin_biomolecules.md">Biomolecules</a></li> <li><a href="marvin_atom-bond-and-molecule-properties.md">Atom, Bond, and Molecule Properties</a></li> </ul></li> <li><a href="marvin_drawing-reactions.md">Drawing Reactions</a> <ul> <li><a href="marvin_creating-reactions.md">Creating Reactions</a></li> <li><a href="marvin_mapping-reactions.md">Mapping Reactions</a></li> <li><a href="marvin_electron-flow-arrows.md">Electron Flow Arrows</a></li> </ul></li> <li><a href="marvin_using-integrated-calculations.md">Using Integrated Calculations</a></li> <li><a href="marvin_graphical-objects.md">Graphical Objects</a> <ul> <li><a href="marvin_adding-editing-and-formatting-text.md">Adding, Editing and Formatting Text</a></li> <li><a href="marvin_drawing-shapes.md">Drawing Shapes</a></li> </ul></li> <li><a href="marvin_import-and-export-options.md">Import and Export Options</a> <ul> <li><a href="marvin_opening-a-molecule-file.md">Opening a Molecule File</a></li> <li><a href="marvin_saving-a-molecule-file.md">Saving a Molecule File</a></li> <li><a href="marvin_exporting-to-image.md">Exporting to Image</a></li> </ul></li> <li><a href="marvin_multipage-documents.md">Multipage Documents</a> <ul> <li><a href="marvin_creating-a-multipage-document.md">Creating a Multipage Document</a></li> <li><a href="marvin_navigating-in-multipage-documents.md">Navigating in Multipage Documents</a></li> </ul></li> <li><a href="marvin_printing-in-marvinsketch.md">Printing</a></li> </ul></li> <li><a href="marvin_chemical-features-in-marvinsketch.md">Chemical Features</a> <ul> <li><a href="marvin_valence-check.md">Valence Check</a></li> <li><a href="marvin_structure-checker-in-marvinsketch.md">Structure Checker</a></li> <li><a href="marvin_charges-isotopes-radicals.md">Charges, Isotopes, Radicals</a> <ul> <li><a href="marvin_charges.md">Charges</a></li> <li><a href="marvin_isotopes-in-marvinsketch.md">Isotopes</a> <ul> <li><a href="marvin_isotope-list-editing.md">Isotope List Editing</a></li> </ul></li> <li><a href="marvin_radicals.md">Radicals</a></li> </ul></li> <li><a href="marvin_stereochemistry-in-marvinsketch.md">Stereochemistry</a></li> <li><a href="marvin_reaction-schemes.md">Reaction Schemes</a></li> <li><a href="marvin_abbreviated-groups-superatom-group.md">Abbreviated Groups - Superatom Group</a></li> <li><a href="marvin_query-features.md">Query Features</a> <ul> <li><a href="marvin_r-groups.md">R-groups</a></li> <li><a href="marvin_link-nodes.md">Link Nodes</a></li> <li><a href="marvin_atom-lists-and-not-lists.md">Atom Lists and NOT Lists</a></li> <li><a href="marvin_atom-properties.md">Atom Properties</a></li> <li><a href="marvin_generic-query-atoms.md">Generic Query Atoms</a></li> <li><a href="marvin_homology-groups.md">Homology Groups</a></li> </ul></li> <li><a href="marvin_attached-data.md">Attached Data</a></li> <li><a href="marvin_calculations.md">Calculations</a> <ul> <li><a href="marvin_analysis-box.md">Analysis Box</a></li> <li><a href="marvin_calculations-plugins-in-marvinsketch.md">Calculator Plugins in MarvinSketch</a></li> </ul></li> </ul></li> <li><a href="marvin_ole-user-guide.md">Marvin OLE User Guide</a> <ul> <li><a href="marvin_install-and-uninstall.md">Install and Uninstall</a></li> <li><a href="marvin_how-to-use.md">How to Use</a></li> <li><a href="marvin_customizing-marvin-ole-editing-mode.md">Customizing Marvin OLE Editing Mode</a></li> <li><a href="marvin_redirecting-other-vendors-ole-objects-to-marvin-ole.md">Redirecting Other Vendors' OLE Objects to Marvin OLE</a></li> <li><a href="marvin_logging.md">Logging</a></li> <li><a href="marvin_troubleshooting-and-administration.md">Troubleshooting and Administration</a></li> <li><a href="marvin_known-issues.md">Known Issues</a></li> </ul></li> <li><a href="marvin_marvinsketch_appendix.md">Appendix</a> <ul> <li><a href="marvin_customizing-marvinsketch.md">Customizing</a></li> <li><a href="marvin_trademarks.md">Trademarks</a></li> </ul></li> <li><a href="marvin_tutorials.md">Tutorials</a></li> <li><a href="marvin_marvinsketch_application-options.md">Application Options</a> <ul> <li><a href="marvin_marvinsketch_java-vm-options.md">Java VM Options in MarvinSketch</a></li> <li><a href="marvin_running-the-applications.md">Running the Applications</a></li> </ul></li> </ul></li> <li><a href="marvin_marvinsketch_developer-guide.md">Developer Guide</a> <ul> <li><a href="marvin_customizing-marvinsketch-gui-server-side.md">Customizing the GUI - Server Side</a> <ul> <li><a href="marvin_customizing-marvin-gui.md">Customizing the GUI</a></li> <li><a href="marvin_customizing-marvinsketch-gui-assign-new-action.md">Customizing the GUI - Assign New Action</a></li> <li><a href="marvin_clipboard-formats-configuration.md">Clipboard Formats Configuration</a></li> <li><a href="marvin_configure-the-attach-data-dialog.md">Configure the Attach Data Dialog</a></li> </ul></li> <li><a href="marvin_marvinsketch_parameters-and-events.md">Parameters and Events</a> <ul> <li><a href="marvin_parameters.md">Parameters</a> <ul> <li><a href="marvin_javabeans-parameters.md">JavaBeans parameters</a> <ul> <li><a href="marvin_display-parameters.md">Display Parameters</a> <ul> <li><a href="marvin_structure-templates.md">Structure Templates</a></li> <li><a href="marvin_query-properties-in-molecule-file-formats.md">Query Properties in Molecule File Formats</a></li> </ul></li> <li><a href="marvin_structure-display-parameters.md">Structure Display Parameters</a></li> <li><a href="marvin_structure-parameters.md">Structure Parameters</a></li> <li><a href="marvin_other-parameters.md">Other Parameters</a></li> </ul></li> </ul></li> <li><a href="marvin_events-fired-by-javabean.md">Events Fired by JavaBean</a> <ul> <li><a href="marvin_action-events.md">Action Events</a></li> <li><a href="marvin_property-change-events.md">Property Change Events</a></li> </ul></li> </ul></li> <li><a href="marvin_marvin-beans-for-java.md">Marvin Beans for Java</a> <ul> <li><a href="marvin_marvin-beans-api-documentation.md">Marvin Beans API Documentation</a></li> <li><a href="marvin_marvin-beans-examples.md">Marvin Beans Examples</a> <ul> <li><a href="marvin_marvinsketch_examples.md">Examples</a> <ul> <li><a href="marvin_marvinsketch_simple-bean.md">Simple Bean</a></li> <li><a href="marvin_marvinsketch_images.md">Images</a></li> <li><a href="marvin_marvinsketch_structure-display-parameters.md">Structure Display Parameters</a></li> <li><a href="marvin_marvinsketch_structure-templates.md">Structure Templates</a></li> <li><a href="marvin_text-box-example.md">Text Box Example</a> <ul> <li><a href="marvin_jfilechooser-example.md">JFileChooser Example</a></li> </ul></li> </ul></li> <li><a href="marvin_marvinview_examples.md">Examples</a> <ul> <li><a href="marvin_marvinview_simple-bean-example.md">Simple Bean Example</a></li> <li><a href="marvin_marvinview_in-jtable-example.md">JTable Example</a></li> <li><a href="marvin_marvinview_table-view-example.md">Table View Example</a></li> <li><a href="marvin_marvinview_table-view-example-with-parameters.md">Table View Example with Parameters</a></li> <li><a href="marvin_marvinview_jfilechooser-example.md">JFileChooser Example</a></li> <li><a href="marvin_image-generation-using-marvin-beans.md">Image Generation Using Marvin Beans</a></li> <li><a href="marvin_excel-sheet-generation-using-marvin-beans.md">Excel Sheet Generation Using Marvin Beans</a></li> <li><a href="marvin_installation-guide-to-jnlp-examples.md">Installation Guide to jnlp Examples</a></li> </ul></li> </ul></li> <li><a href="marvin_marvin-beans-frequently-asked-questions.md">Marvin Beans Frequently Asked Questions</a></li> </ul></li> <li><a href="marvin_services.md">Marvin Services</a> <ul> <li><a href="marvin_manage-marvin-services.md">Manage Marvin Services</a></li> <li><a href="marvin_service-implementations.md">Service Implementations</a> <ul> <li><a href="marvin_local-services.md">Local Services</a></li> <li><a href="marvin_wsdl-soap-rpc-services.md">WSDL SOAP RPC Services</a></li> <li><a href="marvin_xml-rpc.md">XML-RPC</a></li> <li><a href="marvin_json-rpc.md">JSON-RPC</a></li> <li><a href="marvin_http.md">HTTP</a></li> <li><a href="marvin_cxcalc-integration.md">cxcalc integration</a></li> <li><a href="marvin_chemical-terms-integration.md">Chemical Terms Integration</a></li> <li><a href="marvin_instant-jchem-integration.md">Instant JChem Integration</a></li> <li><a href="marvin_jchem-for-excel-integration.md">JChem For Excel Integration</a></li> </ul></li> <li><a href="marvin_configuration-of-services.md">Configuration of Services</a></li> <li><a href="marvin_calling-services.md">Calling Services</a></li> <li><a href="marvin_viewing-the-results.md">Viewing the Results</a></li> </ul></li> <li><a href="marvin_java-web-start.md">Java Web Start</a></li> </ul></li> </ul></li> <li><a href="marvin_marvinview.md">MarvinView</a> <ul> <li><a href="marvin_marvinview_user-guide.md">User Guide</a> <ul> <li><a href="marvin_marvinview_getting-started.md">Getting started</a></li> <li><a href="marvin_how-to-use-marvinview-features.md">How to Use MarvinView Features</a> <ul> <li><a href="marvin_importing-and-exporting-molecules.md">Importing and Exporting Molecules</a></li> <li><a href="marvin_editing-molecules.md">Editing Molecules</a></li> <li><a href="marvin_marvinview_structure-display-options.md">Structure Display Options</a></li> <li><a href="marvin_manipulating-the-molecule.md">Manipulating the Molecule</a></li> <li><a href="marvin_how-to-work-with-multipage-molecular-documents.md">How to Work with Multipage Molecular Documents</a></li> </ul></li> <li><a href="marvin_marvinview_graphical-user-interface.md">Graphical User Interface</a> <ul> <li><a href="marvin_marvinview_dialogs.md">Dialogs</a> <ul> <li><a href="marvin_marvinview_preferences.md">Preferences Dialog</a> <ul> <li><a href="marvin_display.md">Display</a></li> <li><a href="marvin_bonds.md">Bonds</a></li> <li><a href="marvin_structure-tab-in-marvinview.md">Structure Tab</a></li> <li><a href="marvin_marvinview_checkers-tab.md">Checkers Tab</a></li> <li><a href="marvin_services-tab-in-marvinview.md">Services Tab</a></li> <li><a href="marvin_save-load-tab-in-marvinview.md">Save-Load Tab</a></li> </ul></li> <li><a href="marvin_edit-source-dialog.md">Edit Source Dialog</a></li> <li><a href="marvin_table-options.md">Table Options</a></li> <li><a href="marvin_marvinview_about.md">About</a></li> </ul></li> <li><a href="marvin_menus-of-marvinview.md">Menus</a> <ul> <li><a href="marvin_marvinview_file-menu.md">File Menu</a></li> <li><a href="marvin_marvinview_edit-menu.md">Edit Menu</a></li> <li><a href="marvin_marvinview_view-menu.md">View Menu</a></li> <li><a href="marvin_table-menu.md">Table Menu</a></li> <li><a href="marvin_marvinview_structure-menu.md">Structure Menu</a></li> <li><a href="marvin_tools-menu.md">Tools Menu</a></li> <li><a href="marvin_pages.md">Pages</a></li> <li><a href="marvin_marvinview_help-menu.md">Help Menu</a></li> </ul></li> </ul></li> <li><a href="marvin_marvinview_application-options.md">Application Options</a> <ul> <li><a href="marvin_options.md">Options</a> <ul> <li><a href="marvin_marvinview_java-vm-options.md">Java VM Options</a></li> <li><a href="marvin_property-colors-in-marvinview.md">Property Colors</a></li> </ul></li> </ul></li> </ul></li> <li><a href="marvin_marvinview_developer-guide.md">Developer's Guide</a> <ul> <li><a href="marvin_marvinview_javabeans-parameters.md">JavaBeans Parameters</a> <ul> <li><a href="marvin_marvinview_display-parameters.md">Display Parameters</a></li> <li><a href="marvin_marvinview_structure-display-parameters.md">Structure Display Parameters</a></li> <li><a href="marvin_marvinview_structure-parameters.md">Structure Parameters</a></li> <li><a href="marvin_marvinview_3d-and-animation.md">3D and Animation</a> <ul> <li><a href="marvin_rasmol-scripts.md">RasMol Scripts</a></li> </ul></li> <li><a href="marvin_molecule-tables.md">Molecule Tables</a> <ul> <li><a href="marvin_the-layout-parameter.md">The layout Parameter</a></li> <li><a href="marvin_the-param-parameter.md">The param Parameter</a></li> <li><a href="marvin_the-celli-and-celli-j-parameters.md">The celli and celli_j parameters</a></li> <li><a href="marvin_marvinview_table-view.md">Table View</a></li> </ul></li> <li><a href="marvin_marvinview_other-parameters.md">Other Parameters</a></li> </ul></li> <li><a href="marvin_events-fired-by-the-javabean.md">Events Fired by the JavaBean</a></li> <li><a href="marvin_troubleshooting-mview-and-jmview-tables.md">Troubleshooting - MView and JMView Tables</a></li> </ul></li> </ul></li> <li><a href="molconvert_molc.md">Molconvert</a> <ul> <li><a href="molconvert_index.md">User guide</a></li> </ul></li> <li><a href="marvin_administration.md">Administration guide</a> <ul> <li><a href="marvin_installation-and-upgrade.md">Installation</a></li> <li><a href="marvin_systemreq.md">System requirements</a></li> <li><a href="marvin_licensing.md">Licensing</a> <ul> <li><a href="licensing_license-installation.md">License Installation</a></li> <li><a href="licensing_license-management-faq.md">License Management FAQ</a></li> <li><a href="licensing_about-chemaxon-licensing.md">About Chemaxon Licensing</a></li> <li><a href="licensing_prior-version-5-0.md">Licensing Prior Version 5.0</a></li> <li><a href="licensing_license-report.md">License Report</a></li> <li><a href="licensing_merging-licenses.md">Merging Licenses</a></li> <li><a href="legal_end-user-license-agreement-eula.md">EULA</a></li> <li><a href="marvin_marvin-bundles.md">Marvin bundles</a></li> </ul></li> </ul></li> <li><a href="marvin_history-of-changes.md">Marvin Desktop Suite - History of Changes</a></li> </ul></li> <li><a href="plexus-connect_index.md">Plexus Connect</a> <ul> <li><a href="plexus-connect_quick-start-guide.md">Plexus Connect - Quick Start Guide</a></li> <li><a href="plexus-connect_user-guide.md">Plexus Connect - User Guide</a> <ul> <li><a href="plexus-connect_log-in.md">Plexus Connect - Log in</a></li> <li><a href="plexus-connect_dashboard.md">Plexus Connect - Dashboard</a></li> <li><a href="plexus-connect_exporting-your-data.md">Plexus Connect - Exporting Your Data</a></li> <li><a href="plexus-connect_exporting-export-template.md">Plexus Connect - Export Templates</a></li> <li><a href="plexus-connect_browsing-in-your-data-set.md">Plexus Connect - Browsing in Your Data Set</a></li> <li><a href="plexus-connect_selecting-data.md">Plexus Connect - Selecting Data</a></li> <li><a href="plexus-connect_searching-in-your-database.md">Plexus Connect - Searching in Your Database</a> <ul> <li><a href="plexus-connect_structure-search.md">Plexus Connect - Structure Search</a></li> </ul></li> <li><a href="plexus-connect_saved-queries.md">Plexus Connect - Saved Queries</a></li> <li><a href="plexus-connect_list-management.md">Plexus Connect - List Management</a></li> <li><a href="plexus-connect_sorting-data.md">Plexus Connect - Sorting Data</a></li> <li><a href="plexus-connect_sharing-data-with-other-users.md">Plexus Connect - Sharing Data with Other Users</a></li> <li><a href="plexus-connect_charts-view.md">Plexus Connect - Charts View</a></li> <li><a href="plexus-connect_r-group-decomposition.md">Plexus Connect - R-group Decomposition</a></li> </ul></li> <li><a href="plexus-connect_administrator-guide.md">Plexus Connect - Administrator Guide</a> <ul> <li><a href="plexus-connect_authentication.md">Plexus Connect - Authentication</a></li> <li><a href="plexus-connect_sharing-schema-items-among-users.md">Plexus Connect - Sharing Schema Items Among Users</a></li> <li><a href="plexus-connect_business-flags.md">Plexus Connect - Business Flags</a></li> <li><a href="plexus-connect_row-level-security.md">Plexus Connect - Row-level Security</a></li> <li><a href="plexus-connect_shared-data-sources.md">Plexus Connect - Shared data sources</a></li> <li><a href="plexus-connect_plexus-storage.md">Plexus Connect - Plexus storage</a></li> <li><a href="plexus-connect_configuration-files.md">Plexus Connect - Configuration Files</a></li> <li><a href="plexus-connect_simple-table.md">Plexus Connect - Simple table</a></li> <li><a href="plexus-connect_getting-the-plexus-backend-and-frontend-log-files.md">Plexus Connect - Getting the Plexus Backend and Frontend Log Files</a></li> <li><a href="plexus-connect_form-editor.md">Plexus Connect - Form Editor</a></li> <li><a href="plexus-connect_scripting.md">Plexus Connect - Scripting</a> <ul> <li><a href="plexus-connect_python-scripting.md">Plexus Connect - Python Scripting</a> <ul> <li><a href="plexus-connect_supports-jupyter-notebook.md">Plexus Connect - Supports Jupyter Notebook</a></li> <li><a href="plexus-connect_example-usage.md">Plexus Connect - Jupyter Notebook Advanced Example</a></li> <li><a href="plexus-connect_in-view-python-scripting-console.md">Plexus Connect - In-View Python Scripting Console</a></li> </ul></li> <li><a href="plexus-connect_javascript-scripting.md">Plexus Connect - JavaScript Scripting</a></li> </ul></li> <li><a href="plexus-connect_api-keys.md">Plexus Connect - API keys</a></li> <li><a href="plexus-connect_deploying-spotfire-middle-tier-solution.md">Plexus Connect - Deploying Spotfire Middle Tier solution</a></li> </ul></li> <li><a href="plexus-connect_installation-and-system-requirements.md">Plexus Connect - Installation and System Requirements</a></li> <li><a href="plexus-connect_licensing.md">Plexus Connect - Licensing</a></li> <li><a href="plexus-connect_getting-help-and-support.md">Plexus Connect - Getting Help and Support</a> <ul> <li><a href="plexus-connect_troubleshooting-for-plexus-connect.md">Plexus Connect - Troubleshooting for Plexus Connect</a></li> </ul></li> <li><a href="plexus-connect_faq.md">Plexus Connect - FAQ</a></li> <li><a href="plexus-connect_privacy-policy.md">Plexus Connect - Privacy Policy</a></li> <li><a href="plexus-connect_terms-of-use-for-the-demo-site.md">Plexus Connect - Demo Site</a></li> <li><a href="plexus-connect_history-of-changes.md">Plexus Connect - History of Changes</a></li> <li><a href="plexus-connect_schema-refresh-without-restart.md">Plexus Connect - Schema Refresh Without Restart</a></li> <li><a href="plexus-connect_video-tutorials.md">Plexus Connect - Video Tutorials</a></li> </ul></li> <li><a href="trainer-engine_index.md">Trainer Engine</a> <ul> <li><a href="trainer-engine_introduction.md">Introduction</a></li> <li><a href="trainer-engine_installation.md">Installation</a></li> <li><a href="trainer-engine_user-guide.md">User Guide</a></li> <li><a href="trainer-engine_configuration.md">Configuration</a></li> <li><a href="trainer-engine_hoc.md">History of Changes</a></li> <li><a href="trainer-engine_known-issues.md">Known Issues</a></li> <li><a href="trainer-engine_help-support.md">Getting help & support</a></li> </ul></li> </ul></li> <li><a href="menu_toolkits-and-components.md">Toolkits and Components</a> <ul> <li><a href="automapper_index.md">AutoMapper</a> <ul> <li><a href="automapper_user-guide.md">AutoMapper User's Guide</a></li> </ul></li> <li><a href="biomolecule-toolkit_index.md">Biomolecule Toolkit</a> <ul> <li><a href="biomolecule-toolkit_administrator-guide.md">Biomolecule Toolkit Administrator's Guide</a> <ul> <li><a href="biomolecule-toolkit_deployment-guide.md">Biomolecule Toolkit Deployment Guide</a> <ul> <li><a href="biomolecule-toolkit_docker-setup.md">Biomolecule Toolkit Docker Setup</a> <ul> <li><a href="biomolecule-toolkit_running-the-biomolecule-toolkit-container.md">Running the Biomolecule Toolkit Container</a></li> </ul></li> <li><a href="biomolecule-toolkit_war-deployment.md">Biomolecule Toolkit WAR Deployment</a> <ul> <li><a href="biomolecule-toolkit_download-package.md">Download Package</a></li> <li><a href="biomolecule-toolkit_system-environment-setup.md">System Environment Setup</a></li> <li><a href="biomolecule-toolkit_license-files.md">License Files</a></li> <li><a href="biomolecule-toolkit_tomcat-deployment.md">Tomcat Deployment</a></li> </ul></li> <li><a href="biomolecule-toolkit_system-requirements.md">Biomolecule Toolkit System Requirements</a></li> <li><a href="biomolecule-toolkit_database-setup-for-biomolecule-toolkit.md">Database Setup for Biomolecule Toolkit</a></li> <li><a href="biomolecule-toolkit_schema-initialization.md">Schema Initialization</a></li> </ul></li> </ul></li> <li><a href="biomolecule-toolkit_user-guide.md">Biomolecule Toolkit User's Guide</a> <ul> <li><a href="biomolecule-toolkit_library-manager.md">Biomolecule Toolkit Library Manager</a></li> <li><a href="biomolecule-toolkit_query-guide.md">Biomolecule Toolkit Query Guide</a> <ul> <li><a href="biomolecule-toolkit_sequence-search-types.md">Sequence Search Types</a></li> <li><a href="biomolecule-toolkit_query-features.md">Query Features BMT</a></li> <li><a href="biomolecule-toolkit_sequence-search-options.md">Sequence Search Options</a></li> <li><a href="biomolecule-toolkit_additional-data-handling.md">Additional Data Handling</a></li> </ul></li> </ul></li> <li><a href="biomolecule-toolkit_api-documentation.md">Biomolecule Toolkit API documentation</a></li> <li><a href="biomolecule-toolkit_history-of-changes.md">Biomolecule Toolkit History of Changes</a></li> </ul></li> <li><a href="calculators_index.md">Calculator Plugins</a> <ul> <li><a href="calculators_introduction-to-calculator-plugins.md">Introduction to Calculator Plugins</a></li> <li><a href="calculators_user-guide.md">Calculator Plugins User's Guide</a> <ul> <li><a href="calculators_physico-chemical-plugins.md">Physico-chemical plugins</a> <ul> <li><a href="calculators_pka-plugin.md">pKa Plugin</a></li> <li><a href="calculators_major-microspecies-plugin.md">Major Microspecies Plugin</a></li> <li><a href="calculators_isoelectric-point-plugin.md">Isoelectric Point Plugin</a></li> <li><a href="calculators_logp-plugin.md">logP Plugin</a></li> <li><a href="calculators_logd-plugin.md">logD Plugin</a></li> <li><a href="calculators_hlb-predictor.md">HLB Predictor</a></li> <li><a href="calculators_solubility-predictor.md">Solubility Predictor</a></li> <li><a href="calculators_nmr-predictor.md">NMR Predictor</a></li> <li><a href="calculators_tautomer-generation-plugin.md">Tautomer Generation Plugin</a></li> <li><a href="calculators_stereoisomer-generator-plugin.md">Stereoisomer Generator Plugin</a></li> <li><a href="calculators_stereo-analysis-calculating-stereo-descriptors.md">Stereo Analysis - calculating stereo descriptors</a></li> <li><a href="calculators_cns-mpo-score.md">CNS MPO Score Predictor</a></li> <li><a href="calculators_bbb-score.md">BBB Score Predictor</a></li> <li><a href="calculators_herg.md">hERG Predictor</a></li> </ul></li> <li><a href="calculators_molecular-modeling-plugins.md">Molecular modeling plugins</a> <ul> <li><a href="calculators_charge-plugin.md">Charge Plugin</a></li> <li><a href="calculators_orbital-electronegativity-plugin.md">Orbital Electronegativity Plugin</a></li> <li><a href="calculators_polarizability-plugin.md">Polarizability Plugin</a></li> <li><a href="calculators_dipole-moment-calculation-plugin.md">Dipole Moment Calculation Plugin</a></li> <li><a href="calculators_conformer-plugin.md">Conformer Plugin</a></li> <li><a href="calculators_3d-alignment-plugin.md">3D Alignment Plugin</a></li> <li><a href="calculators_molecular-dynamics-plugin.md">Molecular Dynamics Plugin</a></li> </ul></li> <li><a href="calculators_structural-property-plugins.md">Structural property plugins</a> <ul> <li><a href="calculators_elemental-analysis-plugin.md">Elemental Analysis Plugin</a></li> <li><a href="calculators_topological-analysis-plugin.md">Topological Analysis Plugin</a></li> <li><a href="calculators_geometrical-descriptors-plugin.md">Geometrical Descriptors Plugin</a></li> <li><a href="calculators_polar-surface-area-plugin-2d.md">Polar Surface Area Plugin 2D</a></li> <li><a href="calculators_molecular-surface-area-plugin-3d.md">Molecular Surface Area Plugin 3D</a></li> <li><a href="calculators_structural-frameworks-plugin.md">Structural Frameworks Plugin</a></li> <li><a href="calculators_hydrogen-bond-donor-acceptor-plugin.md">Hydrogen Bond Donor Acceptor Plugin</a></li> <li><a href="calculators_huckel-analysis-plugin.md">Huckel Analysis Plugin</a></li> <li><a href="calculators_refractivity-plugin.md">Refractivity Plugin</a></li> <li><a href="calculators_resonance-plugin.md">Resonance Plugin</a></li> </ul></li> <li><a href="calculators_markush-enumerator-plugin.md">Markush Enumerator Plugin</a> <ul> <li><a href="calculators_markush-features.md">Markush features</a> <ul> <li><a href="marvin_r-groups.md">R groups</a></li> <li><a href="calculators_atom-lists.md">Atom lists</a></li> <li><a href="calculators_bond-lists.md">Bond lists</a></li> <li><a href="calculators_link-nodes.md">Link nodes</a></li> <li><a href="calculators_repeating-units.md">Repeating units</a></li> <li><a href="calculators_position-variation-bonds.md">Position variation bonds</a></li> <li><a href="calculators_homology-groups.md">Homology Groups</a></li> </ul></li> <li><a href="calculators_markush-functionalities.md">Markush functionalities</a> <ul> <li><a href="calculators_sequential-enumeration.md">Sequential enumeration</a></li> <li><a href="calculators_selected-part-enumeration.md">Selected part enumeration</a></li> <li><a href="calculators_calculate-library-size.md">Calculate library size</a></li> <li><a href="calculators_random-enumeration.md">Random enumeration</a></li> <li><a href="calculators_valence-filter.md">Valence filter</a></li> <li><a href="calculators_homology-group-enumeration.md">Homology group enumeration</a></li> <li><a href="calculators_scaffold-alignment-and-coloring.md">Scaffold alignment and coloring</a></li> <li><a href="calculators_markush-code-generation.md">Markush code generation</a></li> </ul></li> </ul></li> <li><a href="calculators_training-the-calculator-plugins.md">Training the Calculator Plugins</a> <ul> <li><a href="calculators_cxtrain-command-line-tool.md">cxtrain command line tool</a></li> <li><a href="calculators_training-the-logd-plugin.md">Training the logD Plugin</a></li> <li><a href="calculators_training-the-logp-plugin.md">Training the logP Plugin</a></li> <li><a href="calculators_training-the-pka-plugin.md">Training the pKa Plugin</a></li> </ul></li> <li><a href="calculators_cxcalc-command-line-tool.md">cxcalc command line tool</a> <ul> <li><a href="calculators_cxcalc-calculator-functions.md">cxcalc calculator functions</a></li> </ul></li> </ul></li> <li><a href="calculators_developer-guide.md">Calculator Plugins Developer's Guide</a> <ul> <li><a href="calculators_web-services.md">Calculator Plugins Web Services</a></li> <li><a href="calculators_concurrent-plugin-api-usage.md">Concurrent plugin API usage</a></li> <li><a href="calculators_custom-calculator-plugin-implementation.md">Custom Calculator Plugin implementation</a></li> <li><a href="calculators_integration-of-third-party-calculations-into-marvin-and-jchem.md">Integration of third-party calculations into Marvin and JChem</a></li> <li><a href="calculators_introduction-to-developers.md">Introduction to developers</a></li> <li><a href="calculators_plugin-api-usage-examples.md">Plugin API usage examples</a></li> <li><a href="calculators_using-calculator-plugins-via-api.md">Using Calculator Plugins via API</a></li> </ul></li> <li><a href="calculators_aws-marketplace.md">Calculators on AWS Marketplace</a> <ul> <li><a href="calculators_aws-marketplace-getting-started.md">Getting started</a></li> <li><a href="calculators_aws-marketplace-pricing.md">Pricing</a></li> <li><a href="calculators_aws-marketplace-developer-guide.md">Developer's guide</a></li> </ul></li> <li><a href="calculators_playground.md">Calculators in Playground</a></li> <li><a href="calculators_background-materials.md">Background materials</a> <ul> <li><a href="calculators_calculation-of-partial-charge-distribution.md">Calculation of partial charge distribution</a></li> <li><a href="calculators_generate3d.md">Generate3D</a></li> <li><a href="calculators_isoelectric-point-pi-calculation.md">Isoelectric point (pI) calculation</a></li> <li><a href="calculators_logp-and-logd-calculations.md">LogP and logD calculations</a></li> <li><a href="calculators_nmr-model-prediction.md">NMR model prediction</a></li> <li><a href="calculators_pka-calculation.md">pKa calculation</a></li> <li><a href="calculators_red-and-blue-representation-of-pka-values.md">Red and blue representation of pKa values</a></li> <li><a href="calculators_tautomerization-and-tautomers.md">Tautomerization and tautomers</a></li> <li><a href="calculators_validation-results.md">Validation results</a></li> <li><a href="calculators_tautomerization-and-tautomer-models-of-chemaxon.md">Tautomerization and tautomer models of Chemaxon</a></li> <li><a href="calculators_theory-of-aqueous-solubility-prediction.md">Theory of aqueous solubility prediction</a></li> <li><a href="calculators_the-tautomerization-models-behind-the-jchem-tautomer-search.md">The tautomerization models behind the JChem tautomer search</a></li> <li><a href="calculators_performance-reports.md">Calculators performance reports</a></li> </ul></li> <li><a href="calculators_licensing.md">Calculator Plugins Licensing</a></li> <li><a href="calculators_faq.md">Calculator Plugins FAQ</a></li> <li><a href="calculators_getting-help-and-support.md">Calculator Plugins Getting Help and Support</a></li> <li><a href="calculators_history-of-changes.md">Calculator Plugins History of Changes</a></li> <li><a href="calculators_system-requirements.md">Calculator Plugins System Requirements</a></li> </ul></li> <li><a href="dotnet-api_chemaxon-dotnet-api.md">Chemaxon .NET API</a></li> <li><a href="chemaxon-cloud_index.md">Chemaxon Cloud</a> <ul> <li><a href="chemaxon-cloud_user-guide_index.md">User Guide</a> <ul> <li><a href="chemaxon-cloud_user-guide_team-member_index.md">Guide for Team Members</a> <ul> <li><a href="chemaxon-cloud_user-guide_team-member_login.md">Login</a></li> <li><a href="chemaxon-cloud_user-guide_team-member_logout.md">Logout</a></li> <li><a href="chemaxon-cloud_user-guide_team-member_accessing-applications.md">Accessing Applications</a></li> <li><a href="chemaxon-cloud_user-guide_team-member_groups.md">Groups</a></li> <li><a href="chemaxon-cloud_user-guide_team-member_projects.md">Projects</a></li> </ul></li> <li><a href="chemaxon-cloud_user-guide_team-admin_index.md">Guide for Team Administrators</a> <ul> <li><a href="chemaxon-cloud_user-guide_team-admin_managing-team-members.md">Managing Team Members</a></li> <li><a href="chemaxon-cloud_user-guide_team-admin_managing-groups.md">Managing Groups</a> <ul> <li><a href="chemaxon-cloud_user-guide_team-admin_managing-groups.md#adding-another-team-administrator-to-the-team">Adding Another Team Administrator to the Team</a></li> </ul></li> <li><a href="chemaxon-cloud_user-guide_team-admin_managing-projects.md">Managing Projects</a></li> </ul></li> <li><a href="chemaxon-cloud_user-guide_system-administrator_index.md">Guide for System Administrators</a> <ul> <li><a href="chemaxon-cloud_user-guide_system-administrator_managing-a-team-space.md">Managing a Team Space</a></li> <li><a href="chemaxon-cloud_user-guide_system-administrator_managing-applications.md">Managing Applications</a></li> <li><a href="chemaxon-cloud_user-guide_system-administrator_identity-federation_index.md">Identity Federation Guide</a> <ul> <li><a href="chemaxon-cloud_user-guide_system-administrator_identity-federation_login-flow.md">Login flow diagram</a></li> <li><a href="chemaxon-cloud_user-guide_system-administrator_identity-federation_using-okta.md">Using external Okta as identity provider</a> <ul> <li><a href="chemaxon-cloud_user-guide_system-administrator_identity-federation_using-okta_customer.md">Using external Okta as identity provider - Customer side</a></li> <li><a href="chemaxon-cloud_user-guide_system-administrator_identity-federation_using-okta_chemaxon.md">Using external Okta as identity provider - Chemaxon side</a></li> </ul></li> <li><a href="chemaxon-cloud_user-guide_system-administrator_identity-federation_using-azure.md">Using Azure AD as identity provider</a></li> </ul></li> </ul></li> </ul></li> <li><a href="chemaxon-cloud_developer-guide_index.md">Developer Guide</a> <ul> <li><a href="chemaxon-cloud_developer-guide_integration-basic.md">Basic Application Integration</a></li> <li><a href="chemaxon-cloud_developer-guide_application-authentication.md">Application authentication</a></li> <li><a href="chemaxon-cloud_developer-guide_application-authorization.md">Application authorization</a></li> <li><a href="chemaxon-cloud_developer-guide_application-and-service-discovery.md">Application and Service Discovery</a></li> <li><a href="chemaxon-cloud_developer-guide_custom-claims.md">Custom Claims in Okta tokens</a></li> <li><a href="chemaxon-cloud_developer-guide_features-catalogue_index.md">Synergy Features Catalogue</a> <ul> <li><a href="chemaxon-cloud_developer-guide_features-catalogue_sf-001-application-info.md">SF-001 Application info</a></li> <li><a href="chemaxon-cloud_developer-guide_features-catalogue_sf-002-healthcheck.md">SF-002 Health check</a></li> <li><a href="chemaxon-cloud_developer-guide_features-catalogue_sf-003-application-icon.md">SF-003 Application icon</a></li> <li><a href="chemaxon-cloud_developer-guide_features-catalogue_sf-004-web-endpoints.md">SF-004 Web endpoints</a></li> <li><a href="chemaxon-cloud_developer-guide_features-catalogue_sf-005-logout.md">SF-005 Logout</a></li> <li><a href="chemaxon-cloud_developer-guide_features-catalogue_sf-006-deep-links.md">SF-006 Deep links</a></li> <li><a href="chemaxon-cloud_developer-guide_features-catalogue_sf-007-form.md">SF-007 Form</a></li> <li><a href="chemaxon-cloud_developer-guide_features-catalogue_sf-008-forms-of-type.md">SF-008 Forms of type</a></li> <li><a href="chemaxon-cloud_developer-guide_features-catalogue_sf-009-form-types.md">SF-009 Form types</a></li> <li><a href="chemaxon-cloud_developer-guide_features-catalogue_sf-010-notification-event-types.md">SF-010 Notification Event Types</a></li> <li><a href="chemaxon-cloud_developer-guide_features-catalogue_sf-011-login">SF-011 Login</a></li> </ul></li> </ul></li> <li><a href="chemaxon-cloud_glossary.md">Glossary</a></li> </ul></li> <li><a href="synergy_index.md">Chemaxon Synergy</a> <ul> <li><a href="synergy_user-guide.md">Chemaxon Synergy User Guide</a> <ul> <li><a href="synergy_user-guide-for-team-members.md">Chemaxon Synergy User Guide for Team Members</a> <ul> <li><a href="synergy_accessing-applicatons.md">Accessing Applicatons</a></li> <li><a href="synergy_groups.md">Groups</a></li> <li><a href="synergy_logging-in-to-chemaxon-synergy.md">Logging in to Chemaxon Synergy</a></li> <li><a href="synergy_logging-out-of-synergy.md">Logging out of Synergy</a></li> </ul></li> <li><a href="synergy_guide-for-team-administrators.md">Guide for Team Administrators</a> <ul> <li><a href="synergy_inviting-other-users-to-the-team.md">Inviting Other Users to the Team</a></li> <li><a href="synergy_inactivating-users-of-the-team.md">Inactivating Users of the Team</a></li> <li><a href="synergy_adding-another-team-administrator-to-the-team.md">Adding Another Team Administrator to the Team</a></li> <li><a href="synergy_managing-groups.md">Managing Groups</a></li> <li><a href="synergy_managing-projects.md">Managing Projects</a></li> <li><a href="synergy_centrify-configuration.md">Centrify configuration</a></li> </ul></li> </ul></li> <li><a href="synergy_developer-guide.md">Chemaxon Synergy Developer Guide</a> <ul> <li><a href="synergy_application-and-service-discovery.md">Application and Service Discovery</a></li> <li><a href="synergy_application-authentication.md">Application authentication</a></li> <li><a href="synergy_application-authorization.md">Application authorization</a></li> <li><a href="synergy_integration-workshop.md">Chemaxon Synergy integration workshop</a></li> <li><a href="synergy_features-catalogue.md">Synergy Features Catalogue</a> <ul> <li><a href="synergy_sf-001-application-info.md">SF-001 Application info</a></li> <li><a href="synergy_sf-002-healthcheck.md">SF-002 Healthcheck</a></li> <li><a href="synergy_sf-003-application-icon.md">SF-003 Application icon</a></li> <li><a href="synergy_sf-004-web-endpoints.md">SF-004 Web endpoints</a></li> <li><a href="synergy_sf-005-logout.md">SF-005 Logout</a></li> <li><a href="synergy_sf-006-deep-links.md">SF-006 Deep links</a></li> <li><a href="synergy_sf-007-form.md">SF-007 Form</a></li> <li><a href="synergy_sf-008-forms-of-type.md">SF-008 Forms of type</a></li> <li><a href="synergy_sf-009-form-types.md">SF-009 Form types</a></li> <li><a href="synergy_sf-010-notification-event-types.md">SF-010 Notification Event Types</a></li> </ul></li> </ul></li> <li><a href="synergy_administrator-guide.md">Chemaxon Synergy Administrator Guide</a> <ul> <li><a href="synergy_guide-for-system-administrators.md">Guide for System Administrators</a> <ul> <li><a href="synergy_creating-a-team-space.md">Creating a Team Space</a></li> <li><a href="synergy_registering-applications.md">Registering Applications</a></li> <li><a href="synergy_removing-an-application-instance-from-a-team-space.md">Removing an application instance from a team space when it is not needed anymore</a></li> </ul></li> </ul></li> <li><a href="synergy_history-of-changes.md">Chemaxon Synergy History of Changes</a></li> </ul></li> <li><a href="document-to-structure_index.md">Document to Structure</a> <ul> <li><a href="document-to-structure_user-guide.md">Document to Structure User Guide</a> <ul> <li><a href="document-to-structure_configuring-osr-tools.md">Configuring OSR tools for Document to Structure</a></li> </ul></li> <li><a href="document-to-structure_developer-guide.md">Document to Structure Developer Guide</a></li> <li><a href="document-to-structure_format-options.md">Document to Structure Format Options</a></li> <li><a href="document-to-structure_licensing.md">Document to Structure Licensing</a></li> <li><a href="document-to-structure_getting-help-and-support.md">Document to Structure Getting Help and Support</a></li> <li><a href="document-to-structure_history-of-changes.md">Document to Structure History of Changes</a> <ul> <li><a href="document-to-structure_migration-guide.md">Document to Structure Migration Guide</a></li> </ul></li> </ul></li> <li><a href="jchem-base_index.md">JChem Base</a> <ul> <li><a href="jchem-base_administration-guide-jchem-manager.md">Administration Guide</a> <ul> <li><a href="jchem-base_installation-guide.md">Installation Guide</a></li> <li><a href="jchem-base_upgrade-guide.md">Upgrade Guide</a></li> <li><a href="jchem-base_system-requirements.md">System Requirements</a></li> <li><a href="jchem-base_multiuser-support.md">Multiuser Support</a></li> <li><a href="jchem-base_tomcat-configuration.md">Tomcat Configuration</a></li> <li><a href="jchem-base_preparing-and-running-batch-files-and-shell-scripts.md">Preparing and Running Batch Files and Shell Scripts</a></li> </ul></li> <li><a href="jchem-base_developer-guide.md">Developer Guide</a> <ul> <li><a href="jchem-base_introduction-for-java-applications.md">Introduction for Java applications</a></li> <li><a href="jchem-base_jchem-chemical-database-concepts.md">JChem Chemical Database Concepts</a></li> <li><a href="jchem-base_file-import-export-tools.md">File Import Export Tools</a></li> <li><a href="jchem-base_modifying-structure-tables.md">Modifying Structure Tables</a></li> <li><a href="jchem-base_r-group-decomposition-developer-guide.md">R-group Decomposition Developer's Guide</a></li> <li><a href="jchem-base_structure-searching.md">Structure Searching</a></li> <li><a href="jchem-base_utilities.md">Utilities</a></li> <li><a href="jchem-base_api-documentation.md">JChem Base API documentation</a></li> </ul></li> <li><a href="jchem-base_user-guide.md">User Guide</a> <ul> <li><a href="jchem-base_query-guide.md">Query Guide</a> <ul> <li><a href="jchem-base_search-types.md">Search types</a></li> <li><a href="jchem-base_similarity-search.md">Similarity search</a></li> <li><a href="jchem-base_query-features.md">Query features</a></li> <li><a href="jchem-base_stereochemistry.md">Stereochemistry</a></li> <li><a href="jchem-base_special-search-types.md">Special search types</a> <ul> <li><a href="jchem-base_r-group-structures.md">R-group structures</a></li> <li><a href="jchem-base_r-group-decomposition-user-guide.md">R-group Decomposition User's Guide</a></li> <li><a href="jchem-base_searching-in-markush-targets-tables.md">Searching in Markush targets tables</a></li> <li><a href="jchem-base_reaction-search.md">Reaction search</a></li> <li><a href="jchem-base_polymer-search.md">Polymer search</a></li> <li><a href="jchem-base_sophisticated-chemical-formula-search.md">Sophisticated chemical formula search</a></li> </ul></li> <li><a href="jchem-base_search-options.md">Search options</a> <ul> <li><a href="jchem-base_atomproperty-specific-search-options.md">Atomproperty specific search options</a></li> <li><a href="jchem-base_attached-data-specific-search-options.md">Attached data specific search options</a></li> <li><a href="jchem-base_bond-specific-search-options.md">Bond specific search options</a></li> <li><a href="jchem-base_chemical-terms-specific-search-options.md">Chemical terms specific search options</a></li> <li><a href="jchem-base_database-specific-search-options.md">Database specific search options</a></li> <li><a href="jchem-base_general-search-options.md">General search options</a></li> <li><a href="jchem-base_hitdisplay-specific-search-options.md">Hitdisplay specific search options</a></li> <li><a href="jchem-base_markush-structure-specific-search-options.md">Markush structure specific search options</a></li> <li><a href="jchem-base_performance-specific-search-options.md">Performance specific search options</a></li> <li><a href="jchem-base_polymer-specific-search-options.md">Polymer specific search options</a></li> <li><a href="jchem-base_query-feature-specific-search-options.md">Query feature specific search options</a></li> <li><a href="jchem-base_reaction-specific-search-options.md">Reaction specific search options</a></li> <li><a href="jchem-base_resultset-specific-search-options.md">Resultset specific search options</a></li> <li><a href="jchem-base_similarity-specific-search-options.md">Similarity specific search options</a></li> <li><a href="jchem-base_stereo-specific-search-options.md">Stereo specific search options</a></li> <li><a href="jchem-base_tautomer-specific-search-options.md">Tautomer specific search options</a></li> <li><a href="jchem-base_tautomer-search-vague-bond-search-sp-hybridization.md">Tautomer search - Vague bond search - sp-Hybridization</a></li> </ul></li> <li><a href="jchem-base_standardization.md">Standardization</a></li> <li><a href="jchem-base_hit-display-coloring.md">Hit display-coloring</a></li> <li><a href="jchem-base_appendix.md">Appendix</a></li> <li><a href="jchem-base_matching-query-target-examples.md">Matching Query - Target Examples</a></li> </ul></li> <li><a href="jchem-base_jcsearch-command-line-tool.md">jcsearch Command Line Tool</a></li> <li><a href="jchem-base_jcunique-command-line-tool.md">jcunique Command Line Tool</a></li> <li><a href="jchem-base_homology-groups.md">Homology Groups in Markush Structures</a></li> </ul></li> <li><a href="jchem-base_faq.md">FAQ</a> <ul> <li><a href="jchem-base_jcb-faq.md">JCB FAQ</a></li> <li><a href="jchem-base_and-cartridge-performance-information.md">JChem Base and Cartridge Performance Information</a> <ul> <li><a href="jchem-base_environment-information-of-performance-benchmark.md">Environment Information of Performance Benchmark</a></li> </ul></li> </ul></li> <li><a href="jchem-base_history-of-changes.md">History of Changes</a> <ul> <li><a href="jchem-base_jchem-history-of-changes-from-version-1-0-4-to-6-3-4.md">JChem History of Changes from version 1.0.4 to 6.3.4</a></li> </ul></li> <li><a href="jchem-base_getting-help-and-support.md">Getting Help and Support</a></li> </ul></li> <li><a href="jchem-choral_index.md">JChem Choral</a> <ul> <li><a href="jchem-choral_installation-and-administration.md">Administration Guide</a> <ul> <li><a href="jchem-choral_installation-guide.md">Installation Guide</a></li> <li><a href="jchem-choral_upgrade-guide.md">Upgrade Guide</a></li> <li><a href="jchem-choral_system-requirements.md">System Requirements</a> </li> <li><a href="jchem-choral_installation-on-amazon-oracle-rds.md">Choral Installation on Amazon Oracle RDS</a></li> <li><a href="jchem-choral_installation-on-aws-oracle-rds-and-fargate.md">Choral Installation on AWS Oracle RDS and Fargate</a></li> <li><a href="jchem-choral_upgrade-without-downtime.md">Choral Upgrade without Downtime</a></li> </ul></li> <li><a href="jchem-choral_developer-guide.md">Developer Guide</a> <ul> <li><a href="jchem-choral_api-usage.md">API Usage</a></li> </ul></li> <li><a href="general_second-generation-search-engine.md">Second Generation Search Engine</a></li> <li><a href="jchem-choral_faq-and-known-issues.md">FAQ and Known Issues</a></li> <li><a href="jchem-choral_comparison-of-jchem-choral-and-jchem-oracle-cartridge.md">Comparison of JChem Choral and JChem Oracle Cartridge</a></li> <li><a href="jchem-choral_migration-guide-from-jchem-oracle-cartridge.md">Migration guide to Choral from JOC</a></li> <li><a href="jchem-choral_history-of-changes.md">History of Changes</a></li> </ul></li> <li><a href="jchem-microservices_index.md">JChem Microservices</a> <ul> <li><a href="jchem-microservices_introduction.md">Introduction</a></li> <li><a href="jchem-microservices_administration-guide.md">Administration Guide</a> <ul> <li><a href="jchem-microservices_installation-guide.md">Installation Guide</a></li> <li><a href="jchem-microservices_upgrade-guide.md">Upgrade Guide</a></li> <li><a href="jchem-microservices_system-requirements.md">System requirements</a></li> <li><a href="jchem-microservices_licenses.md">Licenses</a></li> <li><a href="jchem-microservices_logging-and-monitoring.md">Logging and monitoring</a></li> <li><a href="jchem-microservices_architecture.md">Architecture</a></li> <li><a href="jchem-microservices_common-modules.md">Common modules</a></li> </ul></li> <li><a href="jchem-microservices_developer-guide.md">Developer Guide</a></li> <li><a href="jchem-microservices_calculations-web-services.md">Calculations Web Services</a></li> <li><a href="jchem-microservices_db-web-services.md">DB Web Services</a></li> <li><a href="jchem-microservices_io-web-services.md">IO Web Services</a></li> <li><a href="jchem-microservices_markush-web-services.md">Markush Web Services</a></li> <li><a href="jchem-microservices_reactor-web-services.md">Reactor Web Services</a></li> <li><a href="jchem-microservices_structure-checker-web-services.md">Structure Checker Web Services</a></li> <li><a href="jchem-microservices_structure-manipulation.md">Structure Manipulation</a></li> <li><a href="jchem-microservices_task-manager.md">Task Manager</a></li> <li><a href="general_second-generation-search-engine.md">Second Generation Search Engine</a></li> <li><a href="jchem-microservices_faq-and-known-issues.md">JChem Microservices FAQ and Known Issues</a></li> <li><a href="jchem-microservices_history-of-changes.md">JChem Microservices History of Changes</a></li> </ul></li> <li><a href="jchem-oracle-cartridge_index.md">JChem Oracle Cartridge</a> <ul> <li><a href="jchem-oracle-cartridge_installation-and-administration-of-jchem-cartridge-for-oracle.md">Administration Guide</a> <ul> <li><a href="jchem-oracle-cartridge_installation-guide.md">Installation Guide</a></li> <li><a href="jchem-oracle-cartridge_upgrade-guide.md">Upgrade Guide</a></li> <li><a href="jchem-oracle-cartridge_system-requirements.md">System Requirements</a></li> <li><a href="jchem-oracle-cartridge_getting-started-guide.md">Getting Started Guide</a></li> <li><a href="jchem-oracle-cartridge_migration-of-jchem-oracle-cartridge.md">Migration of JChem Oracle Cartidge</a></li> </ul></li> <li><a href="jchem-oracle-cartridge_developer-guide.md">Developer Guide</a> <ul> <li><a href="jchem-oracle-cartridge_jchem-cartridge-for-oracle.md">JChem Cartridge for Oracle</a></li> <li><a href="jchem-oracle-cartridge_cartridge-api.md">Cartridge API</a></li> <li><a href="jchem-oracle-cartridge_cartridge-api-deferrred-error-handling.md">Cartridge API - Deferrred Error Handling</a></li> <li><a href="jchem-oracle-cartridge_description-of-parameters.md">Description of parameters</a></li> <li><a href="jchem-oracle-cartridge_external-java-interfaces.md">External Java interfaces</a></li> <li><a href="jchem-oracle-cartridge_generic-molecular-descriptor-support.md">Generic Molecular Descriptor Support</a></li> </ul></li> <li><a href="jchem-oracle-cartridge_faq.md">FAQ</a> <ul> <li><a href="jchem-oracle-cartridge_joc-faq.md">JOC FAQ</a></li> <li><a href="jchem-oracle-cartridge_jchem-cartridge-performance-information.md">JChem Cartridge Performance Information</a> <ul> <li><a href="jchem-oracle-cartridge_joc-environment-information-of-performance-benchmark.md">JOC Environment Information of Performance Benchmark</a></li> </ul></li> </ul></li> <li><a href="jchem-oracle-cartridge_history-of-changes.md">History of Changes</a></li> <li><a href="jchem-oracle-cartridge_getting-help-and-support.md">Getting Help and Support</a></li> </ul></li> <li><a href="jchem-postgresql-cartridge_index.md">JChem PostgreSQL Cartridge</a> <ul> <li><a href="jchem-postgresql-cartridge_installation-and-administration.md">Administration Guide</a> <ul> <li><a href="jchem-postgresql-cartridge_installation-guide.md">Installation Guide</a></li> <li><a href="jchem-postgresql-cartridge_upgrade-guide.md">Upgrade Guide</a></li> <li><a href="jchem-postgresql-cartridge_system-requirements.md">System Requirements</a> </li> <li><a href="jchem-postgresql-cartridge_getting-started.md">Getting Started</a></li> <li><a href="jchem-postgresql-cartridge_install-jpc-on-non-standard-postgresql-setup.md">Install JPC on non standard PostgreSQL setup</a></li> <li><a href="jchem-postgresql-cartridge_jpc-ha-installation-guide.md">JPC HA Installation Guide</a></li> <li><a href="jchem-postgresql-cartridge_upgrade-of-postgresql-database-together-with-jchem-postgresql-cartridge.md">Upgrade of PostgreSQL database together with JChem PostgreSQL Cartridge</a></li> </ul></li> <li><a href="jchem-postgresql-cartridge_developer-guide.md">Developer Guide</a> <ul> <li><a href="jchem-postgresql-cartridge_api-usage.md">API Usage</a></li> <li><a href="jchem-postgresql-cartridge_perf-out-parameters.md">JPC perf_out parameters</a></li> <li><a href="jchem-postgresql-cartridge_deprecated-api.md">Deprecated API</a></li> <li><a href="jchem-postgresql-cartridge_custom-structure-checker-and-fixer.md">Custom Structure Checker and Fixer in JPC</a></li> <li><a href="jchem-postgresql-cartridge_citus-distibuted-jchem-postgresql-cartridge.md">Citus Distibuted JChem PostgreSQL Cartridge</a></li> <li><a href="jchem-postgresql-cartridge_jdbc-caution.md">JDBC Caution</a></li> </ul></li> <li><a href="general_second-generation-search-engine.md">Second Generation Search Engine</a></li> <li><a href="jchem-postgresql-cartridge_faq-and-known-issues.md">FAQ and Known Issues</a></li> <li><a href="jchem-postgresql-cartridge_history-of-changes.md">History of Changes</a></li> <li><a href="jchem-postgresql-cartridge_getting-help-and-support.md">Getting Help and Support</a></li> <li><a href="jchem-postgresql-cartridge_comparison-to-jchem-oracle-cartridge.md">Comparison of JChem PostgreSQL Cartridge and JChem Oracle Cartridge</a></li> <li><a href="jchem-postgresql-cartridge_migration-guide.md">Migration Guide</a> <ul> <li><a href="jchem-postgresql-cartridge_migration-guide-from-jchem-oracle-cartridge.md">Migration guide to JPC from JOC</a></li> </ul></li> </ul></li> <li><a href="jklustor_index.md">JKlustor</a> <ul> <li><a href="jklustor_what-is-jklustor.md">What is JKlustor</a></li> <li><a href="jklustor_clustering-methods.md">Clustering methods</a> <ul> <li><a href="jklustor_hierarchical-clustering.md">Hierarchical clustering</a> <ul> <li><a href="jklustor_mcs-search-and-libmcs.md">MCS search and LibMCS</a> <ul> <li><a href="jklustor_maximum-common-substructure-mcs-search.md">Maximum Common Substructure (MCS) search</a></li> <li><a href="jklustor_library-mcs-libmcs-clustering.md">Library MCS (LibMCS) clustering</a></li> <li><a href="jklustor_libmcs-licensing.md">LibMCS licensing</a></li> </ul></li> <li><a href="jklustor_ward-clustering.md">Ward clustering</a></li> </ul></li> <li><a href="jklustor_non-hierarchical-clustering.md">Non-hierarchical clustering</a> <ul> <li><a href="jklustor_bemis-murcko-clustering.md">Bemis-Murcko clustering</a></li> <li><a href="jklustor_diverse-set-selection.md">Diverse Set Selection</a></li> <li><a href="jklustor_jarvis-patrick-clustering.md">Jarvis-Patrick clustering</a></li> <li><a href="jklustor_k-means-clustering.md">K-means clustering</a></li> <li><a href="jklustor_sphere-exclusion-clustering.md">Sphere 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href="marvin-js_abbreviated-groups-dialog.md">Abbreviated Groups Dialog</a> <ul> <li><a href="marvin-js_default-abbreviated-group-list.md">Default Abbreviated Group List</a></li> </ul></li> <li><a href="marvin-js_atom-properties-dialog.md">Atom Properties Dialog</a></li> <li><a href="marvin-js_atom-query-properties-dialog.md">Atom Query Properties Dialog</a></li> <li><a href="marvin-js_attached-data-dialog.md">Attached Data Dialog</a></li> <li><a href="marvin-js_bond-properties-dialog.md">Bond Properties Dialog</a></li> <li><a href="marvin-js_export-dialog.md">Export Dialog</a></li> <li><a href="marvin-js_import-dialog.md">Import Dialog</a></li> <li><a href="marvin-js_periodic-table-dialog.md">Periodic Table Dialog</a></li> <li><a href="marvin-js_pseudo-atom-dialog.md">Pseudo Atom Dialog</a></li> <li><a href="marvin-js_r-group-dialog.md">R-group Dialog</a></li> <li><a href="marvin-js_r-logic-dialog.md">R-logic Dialog</a></li> <li><a href="marvin-js_set-box-color-dialog.md">Set Box Color Dialog</a></li> <li><a href="marvin-js_s-group-dialog.md">S-group Dialog</a></li> <li><a href="marvin-js_text-dialog.md">Text Dialog</a></li> <li><a href="marvin-js_view-settings-dialog.md">View Settings Dialog</a></li> </ul></li> <li><a href="marvin-js_toolbars.md">Toolbars</a> <ul> <li><a href="marvin-js_atom-toolbar-right-toolbar.md">Atom Toolbar - Right Toolbar</a></li> <li><a href="marvin-js_general-toolbar-top-toolbar.md">General Toolbar - Top Toolbar</a></li> <li><a href="marvin-js_template-toolbar-bottom-toolbar.md">Template Toolbar - Bottom Toolbar</a></li> <li><a href="marvin-js_tools-toolbar-left-toolbar.md">Tools Toolbar - Left Toolbar</a></li> </ul></li> <li><a href="marvin-js_context-menus.md">Context Menus</a> <ul> <li><a href="marvin-js_abbreviated-group-context-menu.md">Abbreviated Group Context Menu</a></li> <li><a href="marvin-js_atom-context-menu.md">Atom Context Menu</a></li> <li><a href="marvin-js_bond-context-menu.md">Bond Context Menu</a></li> <li><a href="marvin-js_empty-space-context-menu.md">Empty Space Context Menu</a></li> <li><a href="marvin-js_graphical-objects-context-menu.md">Graphical Objects Context Menu</a></li> <li><a href="marvin-js_r-group-label-context-menu.md">R-group Label Context Menu</a></li> <li><a href="marvin-js_selection-context-menu.md">Selection Context Menu</a></li> <li><a href="marvin-js_s-group-context-menu.md">S-group Context Menu</a></li> </ul></li> </ul></li> <li><a href="marvin-js_drawing-and-editing-options.md">Drawing and Editing Options</a> <ul> <li><a href="marvin-js_abbreviations.md">Abbreviations</a></li> <li><a href="marvin-js_atom.md">Atom</a></li> <li><a href="marvin-js_atom-mapping.md">Atom Mapping</a></li> <li><a href="marvin-js_bond.md">Bond</a></li> <li><a href="marvin-js_chains.md">Chains</a></li> <li><a href="marvin-js_copy-structures.md">Copy Structures</a></li> <li><a href="marvin-js_graphical-objects.md">Graphical Objects</a></li> <li><a href="marvin-js_groups.md">Groups</a></li> <li><a href="marvin-js_radicals-and-lone-pairs.md">Radicals and Lone Pairs</a></li> <li><a href="marvin-js_reaction.md">Reaction</a></li> <li><a href="marvin-js_reaction-mechanism.md">Reaction Mechanism</a></li> <li><a href="marvin-js_r-group-representation-and-editing-options.md">R-group Representation and Editing Options</a></li> <li><a href="marvin-js_rotating-in-2d.md">Rotating in 2D</a></li> <li><a href="marvin-js_snapped-objects.md">Snapped Objects</a></li> <li><a href="marvin-js_structural-templates.md">Structure Templates</a></li> <li><a href="marvin-js_peptides.md">Peptides</a></li> <li><a href="marvin-js_text-editing.md">Text Editing</a></li> </ul></li> <li><a href="marvin-js_feature-overview-pages.md">Feature Overview Pages</a> <ul> <li><a href="marvin-js_markush-structures.md">Markush Structures</a></li> <li><a href="marvin-js_query-structures.md">Query Structures</a></li> <li><a href="marvin-js_stereochemistry.md">Stereochemistry</a></li> <li><a href="marvin-js_reactions-and-mechanisms.md">Reactions and Mechanisms</a></li> <li><a href="marvin-js_representation-of-jchem-base-query-functions.md">Representation of JChem Base Query Functions</a></li> </ul></li> <li><a href="marvin-js_keyboard-shortcuts.md">Keyboard Shortcuts</a></li> </ul></li> <li><a href="marvin-js_developer-resources.md">Developer Resources</a> <ul> <li><a href="marvin-js_installation-and-upgrade.md">Marvin JS Installation and System Requirements</a></li> <li><a href="marvin-js_how-to-embed.md">Embedding Marvin JS</a></li> <li><a href="marvin-js_web-services-dev.md">Extending Functionalities with Web Services</a></li> <li><a href="marvin-js_troubleshooting.md">Troubleshooting</a></li> <li><a href="marvin-js_third-party-licenses.md">Third Party Licenses</a></li> <li><a href="marvin-js_web-services.md">Marvin JS Web Services</a></li> </ul></li> <li><a href="marvin-js_history-of-changes.md">History of Changes</a></li> <li><a href="marvin-js_faq.md">Frequently Asked Questions</a></li> <li><a href="marvin-js_video-tutorials.md">Video Tutorials</a></li> <li><a href="marvin-js_marvin-js-and-marvin-sketch.md">Comparison of Marvin JS and MarvinSketch Feature Sets</a></li> </ul></li> <li><a href="marvin_index.md">Marvin</a> <ul> <li><a href="marvin_sketch-js-comparison.md">Comparison with Marvin JS and Marvin Sketch</a></li> <li><a href="marvin_shortcuts-and-tricks.md">Shortcuts and tricks</a> </li> </ul></li> <li><a href="name-to-structure_index.md">Name to Structure</a> <ul> <li><a href="name-to-structure_user-guide.md">Name to Structure User Guide</a> <ul> <li><a href="name-to-structure_custom-dictionary.md">Custom Dictionary in Name Import</a></li> <li><a href="name-to-structure_custom-webservice.md">Custom Webservice in Name Import</a></li> </ul></li> <li><a href="name-to-structure_developer-guide.md">Name to Structure Developer Guide</a></li> <li><a href="name-to-structure_format-options.md">Name to Structure Format Options</a></li> <li><a href="name-to-structure_getting-help-and-support.md">Name to Structure Getting Help and Support</a></li> <li><a href="name-to-structure_history-of-changes.md">Name to Structure History of Changes</a></li> <li><a href="name-to-structure_licensing.md">Name to Structure Licensing</a></li> </ul></li> <li><a href="reactor_index.md">Reactor</a> <ul> <li><a href="reactor_user-guide.md">Reactor User's Guide</a> <ul> <li><a href="reactor_introduction-to-reactor.md">Introduction to Reactor</a> <ul> <li><a href="reactor_features.md">Reactor Features</a></li> </ul></li> <li><a href="reactor_getting-started.md">Reactor Getting Started</a> <ul> <li><a href="reactor_step-by-step.md">Reactor in Step-by-Step</a></li> </ul></li> <li><a href="reactor_concepts.md">Reactor Concepts</a> <ul> <li><a href="reactor_virtual-library-design.md">Virtual Library Design</a></li> <li><a href="reactor_smart-reactions.md">Smart reactions</a> <ul> <li><a href="reactor_stereoselectivity.md">Stereoselectivity</a></li> <li><a href="reactor_regioselectivity.md">Regioselectivity</a></li> </ul></li> </ul></li> <li><a href="reactor_examples.md">Reactor Examples</a> <ul> <li><a href="reactor_simple-examples.md">Simple examples</a></li> <li><a href="reactor_multiple-reactants.md">Multiple reactants</a></li> <li><a href="reactor_reactivity-rules.md">Reactivity rules</a></li> <li><a href="reactor_usage-examples.md">Reactor usage examples</a></li> <li><a href="reactor_selectivity-rules.md">Selectivity rules</a></li> </ul></li> <li><a href="reactor_working-with-reactor.md">Working with Reactor</a> <ul> <li><a href="reactor_specifying-reactions.md">Specifying Reactions</a> <ul> <li><a href="reactor_drawing-a-reaction-scheme.md">Drawing a Reaction Scheme</a> <ul> <li><a href="reactor_introducing-the-reaction-scheme.md">Introducing the Reaction Scheme</a></li> <li><a href="reactor_advanced-reaction-scheme-drawing.md">Advanced Reaction Scheme Drawing</a></li> </ul></li> <li><a href="reactor_reaction-library.md">Reaction Library</a></li> </ul></li> <li><a href="reactor_specifying-reactants.md">Specifying Reactants</a></li> <li><a href="reactor_reaction-mapping.md">Reaction Mapping</a> <ul> <li><a href="reactor_orphan-atoms.md">Orphan atoms</a></li> <li><a href="reactor_other-reaction-mapping-styles.md">Other reaction mapping styles</a></li> </ul></li> <li><a href="reactor_reaction-rules.md">Reaction Rules</a> <ul> <li><a href="reactor_exclude-rule.md">Exclude Rule</a></li> <li><a href="reactor_reactivity-rule.md">Reactivity Rule</a></li> <li><a href="reactor_selectivity-rule.md">Selectivity Rule</a></li> </ul></li> <li><a href="reactor_reactant-combinations.md">Reactant Combinations</a></li> <li><a href="reactor_running-reactor.md">Running Reactor</a></li> <li><a href="reactor_interfaces.md">Reactor Interfaces</a> <ul> <li><a href="reactor_application.md">Reactor Application</a> <ul> <li><a href="reactor_add-reaction-file.md">Add reaction file</a></li> <li><a href="reactor_specify-reactants.md">Specify reactants</a></li> <li><a href="reactor_set-runtime-options-for-reaction-processing.md">Set runtime options for reaction processing</a> <ul> <li><a href="reactor_general-options.md">General options</a></li> <li><a href="reactor_advanced-options.md">Advanced options</a></li> <li><a href="reactor_synthesis-code-options.md">Synthesis code options</a></li> <li><a href="reactor_property-copy.md">Property Copy</a></li> </ul></li> <li><a href="reactor_run-the-reaction-and-generate-products-in-batch-mode.md">Run the reaction and generate products in batch mode</a></li> </ul></li> <li><a href="reactor_command-line-application.md">Reactor Command-line Application</a> <ul> <li><a href="reactor_using-the-react-command-line-interface.md">Using the react command-line interface</a></li> <li><a href="reactor_options-react-cli.md">Options - react CLI</a> <ul> <li><a href="reactor_reaction-file-react-cli.md">Reaction file - React CLI</a></li> <li><a href="reactor_input-reactants-react-cli.md">Input (Reactants) - React CLI</a></li> <li><a href="reactor_reactant-processing-modes-react-cli.md">Reactant processing modes - React CLI</a></li> <li><a href="reactor_output-react-cli.md">Output - React CLI</a></li> <li><a href="reactor_reaction-rules-react-cli.md">Reaction rules - React CLI</a></li> <li><a href="reactor_product-related-options.md">Product related options</a></li> <li><a href="reactor_reporting-options.md">Reporting options</a></li> <li><a href="reactor_mapping-related-options.md">Mapping related options</a></li> <li><a href="reactor_special-options.md">Special options</a></li> <li><a href="reactor_ratio-react-cli.md">Ratio - React CLI</a></li> <li><a href="reactor_reverse-reaction-react-cli.md">Reverse reaction - React CLI</a></li> </ul></li> </ul></li> <li><a href="reactor_reactor-in-instant-jchem.md">Reactor in Instant JChem</a></li> <li><a href="reactor_reactor-in-jchem-for-excel.md">Reactor in JChem for Excel</a> <ul> <li><a href="reactor_jcreactproductstructure-function.md">JCReactProductStructure function</a> <ul> <li><a href="reactor_prerequisites-of-jcreactproductstructure-function.md">Prerequisites of JCReactProductStructure function</a></li> <li><a href="reactor_insert-jcreactproductstructure-function.md">Insert JCReactProductStructure function</a></li> <li><a href="reactor_populate-cells-with-jcreactproductstructure-results.md">Populate cells with JCReactProductStructure results</a></li> <li><a href="reactor_example-on-multiple-product-as-result.md">Example on multiple product as result</a></li> </ul></li> <li><a href="reactor_jcreactreactionstructure-function.md">JCReactReactionStructure function</a> <ul> <li><a href="reactor_prerequisites-jcreactreactionstructure.md">Prerequisites - JCReactReactionStructure</a></li> <li><a href="reactor_insert-jcreactreactionstructure-function.md">Insert JCReactReactionStructure function</a></li> <li><a href="reactor_populate-cells-with-jcreactreactionstructure-result.md">Populate cells with JCReactReactionStructure result</a></li> </ul></li> <li><a href="reactor_examples-injchemforexcelusage-reactor.md">Reactor Examples inJChemforExcelUsage Reactor</a></li> </ul></li> <li><a href="reactor_reactor-in-knime.md">Reactor in KNIME</a> <ul> <li><a href="reactor_quick-help.md">Quick help</a></li> </ul></li> <li><a href="reactor_reactor-in-pipeline-pilot.md">Reactor in Pipeline Pilot</a></li> <li><a href="reactor_api-web-services.md">API, Web Services</a></li> <li><a href="reactor_glossary.md">Glossary</a> <ul> <li><a href="reactor_isotopes.md">Isotopes</a></li> <li><a href="reactor_manual-selection.md">Manual selection</a></li> <li><a href="reactor_output-file-format.md">Output file format</a></li> <li><a href="reactor_product-list.md">Product list</a></li> <li><a href="reactor_ratio.md">Ratio</a></li> <li><a href="reactor_reaction-file-reaction-equation.md">Reaction File - Reaction Equation</a></li> <li><a href="reactor_reaction-stereo.md">Reaction stereo</a></li> <li><a href="reactor_reversed-reaction.md">Reversed reaction</a></li> <li><a href="reactor_standardization-in-reactor.md">Standardization in Reactor</a></li> <li><a href="reactor_standard-properties-in-the-chemaxon-reaction-library.md">Standard Properties in the Chemaxon Reaction Library</a></li> </ul></li> </ul></li> </ul></li> </ul></li> <li><a href="reactor_faq.md">Reactor FAQ</a></li> <li><a href="reactor_licensing.md">Reactor Licensing</a></li> <li><a href="reactor_getting-help-and-support.md">Reactor Getting Help and Support</a></li> <li><a href="reactor_history-of-changes.md">Reactor History of Changes</a></li> <li><a href="reactor_configuration-files.md">Reactor Configuration Files</a></li> </ul></li> <li><a href="screen_index.md">Screen</a> <ul> <li><a href="screen_introduction-to-virtual-screening.md">Introduction to Virtual Screening</a></li> <li><a href="screen_screenmd.md">ScreenMD</a></li> <li><a href="screen_screen3d.md">Screen3D</a></li> <li><a href="screen_developer-guide.md">Screen Developer Guide</a></li> <li><a href="screen_history-of-changes.md">Screen History of Changes</a></li> <li><a href="screen_licensing.md">Screen licensing</a></li> </ul></li> <li><a href="standardizer_index.md">Standardizer</a> <ul> <li><a href="standardizer_user-guide.md">Standardizer User's Guide</a> <ul> <li><a href="standardizer_introduction.md">Standardizer Introduction</a> <ul> <li><a href="standardizer_in-a-nutshell.md">Standardizer in a Nutshell</a></li> <li><a href="standardizer_why-use-standardizer.md">Why Use Standardizer</a></li> </ul></li> <li><a href="standardizer_getting-started.md">Standardizer Getting Started</a> <ul> <li><a href="standardizer_standardization-in-step-by-step.md">Standardization in Step-by-Step</a></li> <li><a href="standardizer_quick-help-on-configuration-design.md">Quick Help on Configuration Design</a></li> </ul></li> <li><a href="standardizer_concepts.md">Standardizer Concepts</a> <ul> <li><a href="standardizer_action.md">Action</a></li> <li><a href="standardizer_configuration.md">Standardizer Configuration</a></li> <li><a href="standardizer_standardizing-molecules.md">Standardizing Molecules</a></li> <li><a href="standardizer_typical-workflows.md">Typical Workflows</a></li> </ul></li> <li><a href="standardizer_working-with-standardizer.md">Working with Standardizer</a> <ul> <li><a href="standardizer_actions.md">Standardizer Actions</a> <ul> <li><a href="standardizer_add-explicit-hydrogens.md">Add Explicit Hydrogens</a></li> <li><a href="standardizer_alias-to-atom.md">Alias to Atom</a></li> <li><a href="standardizer_alias-to-group.md">Alias to Group</a></li> <li><a href="standardizer_aromatize.md">Aromatize</a></li> <li><a href="standardizer_clean-2d.md">Clean 2D</a></li> <li><a href="standardizer_clean-3d.md">Clean 3D</a></li> <li><a href="standardizer_clear-isotopes.md">Clear Isotopes</a></li> <li><a href="standardizer_clear-stereo.md">Clear Stereo</a></li> <li><a href="standardizer_contract-s-groups.md">Contract S-groups</a></li> <li><a href="standardizer_convert-double-bonds.md">Convert Double Bonds</a></li> <li><a href="standardizer_convert-pi-metal-bonds.md">Convert Pi-metal Bonds</a></li> <li><a href="standardizer_convert-to-enhanced-stereo.md">Convert to Enhanced Stereo</a></li> <li><a href="standardizer_create-group.md">Create Group</a></li> <li><a href="standardizer_dearomatize.md">Dearomatize</a></li> <li><a href="standardizer_disconnect-metal-atoms.md">Disconnect Metal Atoms</a></li> <li><a href="standardizer_expand-s-groups.md">Expand S-groups</a></li> <li><a href="standardizer_expand-stoichiometry.md">Expand Stoichiometry</a></li> <li><a href="standardizer_map.md">Map</a></li> <li><a href="standardizer_map-reaction.md">Map Reaction</a></li> <li><a href="standardizer_mesomerize.md">Mesomerize</a></li> <li><a href="standardizer_neutralize.md">Neutralize</a></li> <li><a href="standardizer_rearrange-reaction.md">Rearrange Reaction</a></li> <li><a href="standardizer_remove-absolute-stereo.md">Remove Absolute Stereo</a></li> <li><a href="standardizer_remove-atom-values.md">Remove Atom Values</a></li> <li><a href="standardizer_remove-attached-data.md">Remove Attached Data</a></li> <li><a href="standardizer_remove-explicit-hydrogens.md">Remove Explicit Hydrogens</a></li> <li><a href="standardizer_remove-fragment.md">Remove Fragment</a></li> <li><a href="standardizer_remove-r-group-definitions.md">Remove R-group Definitions</a></li> <li><a href="standardizer_remove-stereo-care-box.md">Remove Stereo Care Box</a></li> <li><a href="standardizer_replace-atoms.md">Replace Atoms</a></li> <li><a href="standardizer_set-absolute-stereo.md">Set Absolute Stereo</a></li> <li><a href="standardizer_set-hydrogen-isotope-symbol.md">Set Hydrogen Isotope Symbol</a></li> <li><a href="standardizer_strip-salts.md">Strip Salts</a></li> <li><a href="standardizer_tautomerize.md">Tautomerize</a></li> <li><a href="standardizer_transform.md">Transform</a></li> <li><a href="standardizer_ungroup-s-groups.md">Ungroup S-groups</a></li> <li><a href="standardizer_unmap.md">Unmap</a></li> <li><a href="standardizer_wedge-clean.md">Wedge Clean</a></li> <li><a href="standardizer_remove.md">Remove</a></li> <li><a href="standardizer_standardizer-transform.md">Standardizer Transform</a></li> <li><a href="standardizer_custom-standardizer-actions.md">Custom Standardizer Actions</a></li> <li><a href="standardizer_remove-solvents.md">Remove Solvents</a></li> </ul></li> <li><a href="standardizer_creating-a-configuration-standardizer.md">Creating a Configuration Standardizer</a></li> <li><a href="standardizer_interfaces-standardizer.md">Interfaces Standardizer</a> <ul> <li><a href="standardizer_application.md">Standardizer Application</a> <ul> <li><a href="standardizer_setting-up-profiles.md">Setting up Profiles</a></li> </ul></li> <li><a href="standardizer_editor.md">Standardizer Editor</a></li> <li><a href="standardizer_command-line-application.md">Standardizer Command-line Application</a></li> <li><a href="standardizer_jchem-base.md">Standardizer JChem Base</a></li> <li><a href="standardizer_jchem-for-excel.md">Standardizer JChem for Excel</a></li> <li><a href="standardizer_instant-jchem.md">Standardizer Instant JChem</a></li> <li><a href="standardizer_jchem-cartridge.md">Standardizer JChem Cartridge</a></li> <li><a href="standardizer_knime.md">Standardizer KNIME</a></li> <li><a href="standardizer_pipeline-pilot.md">Standardizer Pipeline Pilot</a></li> </ul></li> <li><a href="standardizer_file-formats.md">Standardizer File Formats</a></li> </ul></li> </ul></li> <li><a href="standardizer_developer-guide.md">Standardizer Developer's Guide</a></li> <li><a href="standardizer_installation-and-system-requirements.md">Standardizer Installation and System Requirements</a></li> <li><a href="standardizer_licensing.md">Standardizer Licensing</a></li> <li><a href="standardizer_getting-help-and-support.md">Standardizer Getting Help and Support</a></li> <li><a href="standardizer_history-of-changes.md">Standardizer History of Changes</a></li> </ul></li> <li><a href="structure-checker_index.md">Structure Checker</a> <ul> <li><a href="structure-checker_user-guide.md">Structure Checker User's Guide</a> <ul> <li><a href="structure-checker_introduction.md">Introduction</a> <ul> <li><a href="structure-checker_in-a-nutshell.md">Structure Checker in a Nutshell</a></li> </ul></li> <li><a href="structure-checker_getting-started.md">Structure Checker Getting Started</a></li> <li><a href="structure-checker_concepts.md">Structure Checker Concepts</a> <ul> <li><a href="structure-checker_checkers.md">Checkers</a></li> <li><a href="structure-checker_fixers.md">Fixers</a></li> <li><a href="structure-checker_structure-checking-of-molecules.md">Structure Checking of Molecules</a></li> </ul></li> <li><a href="structure-checker_working-with-structure-checker.md">Working with Structure Checker</a> <ul> <li><a href="structure-checker_checker-list.md">Checker List</a> <ul> <li><a href="structure-checker_abbreviated-group-strch.md">Abbreviated Group</a></li> <li><a href="structure-checker_absent-chiral-flag.md">Absent Chiral Flag</a></li> <li><a href="structure-checker_absolute-stereo-configuration.md">Absolute Stereo Configuration</a></li> <li><a href="structure-checker_alias.md">Alias</a></li> <li><a href="structure-checker_aromaticity-error.md">Aromaticity Error</a></li> <li><a href="structure-checker_atom-map.md">Atom Map</a></li> <li><a href="structure-checker_atom-query-property.md">Atom Query Property</a></li> <li><a href="structure-checker_atom-value.md">Atom Value</a></li> <li><a href="structure-checker_atropisomer.md">Atropisomer</a></li> <li><a href="structure-checker_attached-data-strch.md">Attached Data</a></li> <li><a href="structure-checker_bond-angle.md">Bond Angle</a></li> <li><a href="structure-checker_bond-length.md">Bond Length</a></li> <li><a href="structure-checker_bond-topology.md">Bond Topology</a></li> <li><a href="structure-checker_brackets.md">Brackets</a></li> <li><a href="structure-checker_chiral-flag.md">Chiral Flag</a></li> <li><a href="structure-checker_chiral-flag-error.md">Chiral Flag Error</a></li> <li><a href="structure-checker_circular-r-group-reference.md">Circular R-group Reference</a></li> <li><a href="structure-checker_coordination-system-error.md">Coordination System Error</a></li> <li><a href="structure-checker_covalent-counterion.md">Covalent Counterion</a></li> <li><a href="structure-checker_crossed-double-bond.md">Crossed Double Bond</a></li> <li><a href="structure-checker_custom-checkers-and-fixers.md">Custom Checkers and Fixers</a></li> <li><a href="structure-checker_double-bond-stereo-error.md">Double Bond Stereo Error</a></li> <li><a href="structure-checker_ez-double-bond.md">EZ Double Bond</a></li> <li><a href="structure-checker_empty-structure.md">Empty Structure</a></li> <li><a href="structure-checker_explicit-hydrogen.md">Explicit Hydrogen</a></li> <li><a href="structure-checker_explicit-lone-pairs.md">Explicit Lone Pairs</a></li> <li><a href="structure-checker_incorrect-tetrahedral-stereo.md">Incorrect Tetrahedral Stereo</a></li> <li><a href="structure-checker_isotope.md">Isotope</a></li> <li><a href="structure-checker_metallocene-error.md">Metallocene Error</a></li> <li><a href="structure-checker_missing-atom-map.md">Missing Atom Map</a></li> <li><a href="structure-checker_missing-r-group-reference.md">Missing R-group Reference</a></li> <li><a href="structure-checker_molecule-charge.md">Molecule Charge</a></li> <li><a href="structure-checker_multicenter.md">Multicenter</a></li> <li><a href="structure-checker_multicomponent.md">Multicomponent</a></li> <li><a href="structure-checker_multiple-stereocenter.md">Multiple Stereocenter</a></li> <li><a href="structure-checker_non-standard-wedge-scheme.md">Non-standard Wedge Scheme</a></li> <li><a href="structure-checker_non-stereo-wedge-bond.md">Non-stereo Wedge Bond</a></li> <li><a href="structure-checker_ocr-error.md">OCR Error</a></li> <li><a href="structure-checker_overlapping-atoms.md">Overlapping Atoms</a></li> <li><a href="structure-checker_overlapping-bonds.md">Overlapping Bonds</a></li> <li><a href="structure-checker_pseudo-atom.md">Pseudo Atom</a></li> <li><a href="structure-checker_query-atom.md">Query Atom</a></li> <li><a href="structure-checker_query-bond.md">Query Bond</a></li> <li><a href="structure-checker_racemate.md">Racemate</a></li> <li><a href="structure-checker_radical.md">Radical</a></li> <li><a href="structure-checker_rare-element.md">Rare Element</a></li> <li><a href="structure-checker_r-atom.md">R-atom</a></li> <li><a href="structure-checker_reacting-center-bond-mark.md">Reacting Center Bond Mark</a></li> <li><a href="structure-checker_reaction-map-error.md">Reaction Map Error</a></li> <li><a href="structure-checker_relative-stereo.md">Relative Stereo</a></li> <li><a href="structure-checker_r-group-attachment-error.md">R-group Attachment Error</a></li> <li><a href="structure-checker_r-group-bridge-error.md">R-group Bridge Error</a></li> <li><a href="structure-checker_r-group-reference-error.md">R-group Reference Error</a></li> <li><a href="structure-checker_ring-strain-error.md">Ring Strain Error</a></li> <li><a href="structure-checker_solvent.md">Solvent</a></li> <li><a href="structure-checker_star-atom.md">Star Atom</a></li> <li><a href="structure-checker_stereo-care-box.md">Stereo Care Box</a></li> <li><a href="structure-checker_stereo-inversion-retention-mark.md">Stereo Inversion Retention Mark</a></li> <li><a href="structure-checker_straight-double-bond.md">Straight Double Bond</a></li> <li><a href="structure-checker_substructure.md">Substructure</a></li> <li><a href="structure-checker_three-dimension-3d.md">Three Dimension 3D</a></li> <li><a href="structure-checker_unbalanced-reaction.md">Unbalanced Reaction</a></li> <li><a href="structure-checker_unused-r-group-reference.md">Unused R-group Reference</a></li> <li><a href="structure-checker_valence-error.md">Valence Error</a></li> <li><a href="structure-checker_valence-property.md">Valence Property</a></li> <li><a href="structure-checker_wedge-error.md">Wedge Error</a></li> <li><a href="structure-checker_wiggly-bond.md">Wiggly Bond</a></li> <li><a href="structure-checker_wiggly-double-bond.md">Wiggly Double Bond</a></li> </ul></li> <li><a href="structure-checker_creating-a-configuration-strch.md">Creating a Configuration Structure Checker</a></li> <li><a href="structure-checker_interfaces-strch.md">Interfaces of Structure Checker</a> <ul> <li><a href="structure-checker_marvinsketch-strch.md">Structure Checker in MarvinSketch</a></li> <li><a href="structure-checker_application.md">Structure Checker Application</a></li> <li><a href="structure-checker_editor.md">Structure Checker Editor</a></li> <li><a href="structure-checker_command-line-application.md">Structure Checker Command Line Application</a></li> <li><a href="structure-checker_jchem-cartridge-strch.md">JChem Cartridge and Structure Checker</a></li> </ul></li> </ul></li> </ul></li> <li><a href="structure-checker_developer-guide.md">Structure Checker Developer's Guide</a> <ul> <li><a href="structure-checker_introduction-to-structure-checker-api.md">Introduction to Structure Checker API</a></li> <li><a href="structure-checker_classes-interfaces-and-configuration.md">Classes, interfaces and configuration</a></li> <li><a href="structure-checker_implementing-a-new-structure-checker.md">Implementing a new Structure Checker</a></li> <li><a href="structure-checker_create-graphical-user-interface-for-checker-options.md">Create Graphical User Interface for Checker Options</a></li> <li><a href="structure-checker_implementing-fixers.md">Implementing Fixers</a></li> </ul></li> <li><a href="structure-checker_installation-and-system-requirements.md">Structure Checker Installation and System Requirements</a></li> <li><a href="structure-checker_licensing.md">Structure Checker Licensing</a></li> <li><a href="structure-checker_getting-help-and-support.md">Structure Checker Getting Help and Support</a></li> <li><a href="structure-checker_history-of-changes.md">Structure Checker History of Changes</a></li> </ul></li> <li><a href="structure-to-name_index.md">Structure to Name</a> <ul> <li><a href="structure-to-name_user-guide.md">Structure to Name User Guide</a></li> <li><a href="structure-to-name_developer-guide.md">Structure to Name Developer Guide</a></li> <li><a href="structure-to-name_format-options.md">Structure to Name Format Options</a></li> <li><a href="structure-to-name_licensing.md">Structure to Name Licensing</a></li> <li><a href="structure-to-name_getting-help-and-support.md">Structure to Name Getting Help and Support</a></li> <li><a href="structure-to-name_history-of-changes.md">Structure to Name History of Changes</a></li> </ul></li> </ul></li> <li><a href="menu_third-party-integration.md">Third-Party Integration</a> <ul> <li><a href="jchem-for-office_index.md">JChem for Office</a> <ul> <li><a href="jchem-for-office_administration.md">Administration Guide</a> <ul> <li><a href="jchem-for-office_installation-guide.md">Installation Guide</a> <ul> <li><a href="jchem-for-office_before-using.md">Before Using</a></li> <li><a href="jchem-for-office_installation.md">Installation</a> <ul> <li><a href="jchem-for-office_how-to-check-the-bit-version-of-ms-office.md">How to Check the Bit-version of MS Office</a> <ul> <li><a href="jchem-for-office_microsoft-office-bit-version.md">Microsoft Office 2013, 2016 and 2019</a></li> </ul></li> <li><a href="jchem-for-office_silent-installation.md">Silent Installation</a></li> </ul></li> <li><a href="jchem-for-office_licensing-of-jchem-for-office.md">Licensing of JChem for Office</a></li> <li><a href="jchem-for-office_logging-in-jchem-for-office.md">Logging in JChem for Office</a></li> </ul></li> <li><a href="jchem-for-office_uninstall-and-upgrade.md">Upgrade and Uninstall Guide</a></li> <li><a href="jchem-for-office_supported-versions.md">System Requirements</a></li> </ul></li> <li><a href="jchem-for-office_user-guide-general.md">User Guide</a> <ul> <li><a href="jchem-for-office_jchem-for-excel-user-guide.md">JChem for Excel User's Guide</a> <ul> <li><a href="jchem-for-office_jchem-for-excel-ribbon.md">JChem for Excel Ribbon</a> <ul> <li><a href="jchem-for-office_standard-menu.md">Standard Menu</a></li> <li><a href="jchem-for-office_advanced-menu.md">Advanced Menu</a></li> </ul></li> <li><a href="jchem-for-office_working-with-structures-in-excel.md">Working with Structures in Excel</a> <ul> <li><a href="jchem-for-office_add-a-structure-to-a-cell.md">Add a Structure to a Cell</a></li> <li><a href="jchem-for-office_edit-a-structure-in-a-cell.md">Edit a Structure in a Cell</a></li> <li><a href="jchem-for-office_edit-structures-in-the-task-pane.md">Edit Structures in the Task Pane</a></li> <li><a href="jchem-for-office_resize-structures.md">Resize Structures</a></li> <li><a href="jchem-for-office_structures-in-merged-cells.md">Structures in Merged Cells</a></li> <li><a href="jchem-for-office_show-and-hide-structures.md">Show and Hide Structures</a></li> <li><a href="jchem-for-office_show-and-hide-structures-and-structure-ids.md">Show and Hide Structures and Structure IDs</a></li> <li><a href="jchem-for-office_insert-single-structures.md">Insert Single Structures</a></li> <li><a href="jchem-for-office_open-structure-files.md">Open Structure Files</a></li> <li><a href="jchem-for-office_delete-structures-from-a-selected-range.md">Delete Structures from a Selected Range</a></li> <li><a href="jchem-for-office_save-single-structure-to-a-file.md">Save Single Structure to a File</a></li> <li><a href="jchem-for-office_print-structures.md">Print Structures</a></li> <li><a href="jchem-for-office_copy-and-paste-with-jchem-for-excel.md">Copy and Paste with JChem for Excel</a> <ul> <li><a href="jchem-for-office_inside-excel.md">Inside Excel</a> <ul> <li><a href="jchem-for-office_copy-structures-with-or-without-data.md">Copy Structures with or without Data</a></li> <li><a href="jchem-for-office_exclude-hidden-rows.md">Exclude Hidden Rows</a></li> </ul></li> <li><a href="jchem-for-office_to-external-applications-from-jchem-for-excel.md">To External Applications from JChem for Excel</a> <ul> <li><a href="jchem-for-office_copy-and-paste-with-ids.md">Copy and Paste with IDs</a></li> <li><a href="jchem-for-office_to-external-structure-editors.md">To External Structure Editors</a></li> <li><a href="jchem-for-office_copy-and-paste-single-structures-with-keyboard-shortcuts-in-jchem-for-excel.md">Copy and Paste Single Structures with Keyboard Shortcuts in JChem for Excel</a></li> </ul></li> <li><a href="jchem-for-office_from-external-applications-to-jchem-for-excel.md">From External Applications to JChem for Excel</a> <ul> <li><a href="jchem-for-office_from-external-structure-editors-to-jchem-for-excel.md">From External Structure Editors to JChem for Excel</a></li> <li><a href="jchem-for-office_from-instant-jchem-to-jchem-for-excel.md">From Instant JChem to JChem for Excel</a></li> </ul></li> </ul></li> <li><a href="jchem-for-office_convert-from-structures.md">Convert from Structures</a> <ul> <li><a href="jchem-for-office_convert-structures-to-images.md">Convert Structures to Images</a></li> <li><a href="jchem-for-office_convert-structures-to-text.md">Convert Structures to Text</a></li> </ul></li> <li><a href="jchem-for-office_convert-to-structures.md">Convert to Structures</a> <ul> <li><a href="jchem-for-office_convert-images-to-structures.md">Convert Images to Structures</a></li> <li><a href="jchem-for-office_convert-text-to-structures.md">Convert Text to Structures</a></li> </ul></li> <li><a href="jchem-for-office_convert-isis-chemdraw-accord-and-insight-for-excel-files-to-jchem-for-excel-files.md">Convert ISIS, ChemDraw, Accord, and Insight for Excel Files to JChem for Excel Files</a> <ul> <li><a href="jchem-for-office_jchem-for-excel-file-converter-action.md">JChem for Excel File Converter Action</a></li> <li><a href="jchem-for-office_jchem-for-excel-file-converter-context-menu-item.md">JChem for Excel File Converter Context Menu Item</a></li> <li><a href="jchem-for-office_jchem-for-excel-file-converter-tool.md">JChem for Excel File Converter Tool</a></li> </ul></li> <li><a href="jchem-for-office_calculations-with-third-party-services.md">Calculations with Third-Party Services</a></li> <li><a href="jchem-for-office_specify-external-image-and-name-services.md">Specify External Image and Name Services</a></li> </ul></li> <li><a href="jchem-for-office_importing-from-databases-in-jchem-for-excel.md">Importing from Databases in JChem for Excel</a> <ul> <li><a href="jchem-for-office_manage-connections.md">Manage Connections</a> <ul> <li><a href="jchem-for-office_add-an-oracle-connection-in-jchem-for-excel.md">Add an Oracle Connection in JChem for Excel</a></li> <li><a href="jchem-for-office_add-a-mysql-connection-in-jchem-for-excel.md">Add a MySQL Connection in JChem for Excel</a></li> <li><a href="jchem-for-office_add-an-mssql-connection-in-jchem-for-excel.md">Add an MSSQL Connection in JChem for Excel</a></li> <li><a href="jchem-for-office_add-a-postgresql-connection-in-jchem-for-excel.md">Add a PostgreSQL Connection in JChem for Excel</a></li> <li><a href="jchem-for-office_add-a-jchem-web-services-connection-in-jchem-for-excel.md">Add a JChem Web Services Connection in JChem for Excel</a></li> <li><a href="jchem-for-office_favorite-entities-in-jchem-for-excel.md">Favorite Entities in JChem for Excel</a></li> <li><a href="jchem-for-office_edit-and-delete-connections-in-jchem-for-excel.md">Edit and Delete Connections in JChem for Excel</a></li> </ul></li> <li><a href="jchem-for-office_import-from-database-in-jchem-for-excel.md">Import from Database in JChem for Excel</a> <ul> <li><a href="jchem-for-office_import-from-database-database-tab.md">Import from Database-Database Tab</a></li> <li><a href="jchem-for-office_import-from-database-query-tab.md">Import from Database-Query Tab</a></li> <li><a href="jchem-for-office_import-from-database-columns-tab.md">Import from Database-Columns Tab</a></li> <li><a href="jchem-for-office_import-from-database-rows-tab.md">Import from Database-Rows Tab</a></li> <li><a href="jchem-for-office_import-from-database-progress-tab.md">Import from Database-Progress Tab</a></li> </ul></li> <li><a href="jchem-for-office_import-from-ijc-database-in-jchem-for-excel.md">Import from IJC Database in JChem for Excel</a> <ul> <li><a href="jchem-for-office_import-from-ijc-database-source-tab.md">Import from IJC Database-Source Tab</a></li> <li><a href="jchem-for-office_import-from-ijc-database-columns-tab.md">Import from IJC Database-Columns Tab</a></li> <li><a href="jchem-for-office_import-from-ijc-database-progress-tab.md">Import from IJC Database-Progress Tab</a></li> </ul></li> <li><a href="jchem-for-office_import-from-database-by-ids.md">Import from Database by IDs</a></li> </ul></li> <li><a href="jchem-for-office_resolve-id.md">Resolve ID</a> <ul> <li><a href="jchem-for-office_resolve-ids-into-structures.md">Resolve IDs into Structures</a></li> <li><a href="jchem-for-office_resolve-compreg-ids-into-structures.md">Resolve CompReg IDs into Structures</a></li> </ul></li> <li><a href="jchem-for-office_import-from-file.md">Import from File</a> <ul> <li><a href="jchem-for-office_import-file.md">Import File</a> <ul> <li><a href="jchem-for-office_import-file-file-tab.md">Import File-File Tab</a></li> <li><a href="jchem-for-office_import-file-columns-tab.md">Import File-Columns Tab</a></li> <li><a href="jchem-for-office_import-file-progress-tab.md">Import File-Progress Tab</a></li> </ul></li> <li><a href="jchem-for-office_import-from-file-by-ids.md">Import from File by IDs</a></li> <li><a href="jchem-for-office_import-with-document-to-structure-in-jchem-for-excel.md">Import with Document to Structure in JChem for Excel</a></li> </ul></li> <li><a href="jchem-for-office_export-to-file.md">Export to File</a></li> <li><a href="jchem-for-office_share-excel-files.md">Share Excel Files</a> <ul> <li><a href="jchem-for-office_co-authoring.md">Co-authoring</a></li> <li><a href="jchem-for-office_save-to-share.md">Save to Share</a></li> </ul></li> <li><a href="jchem-for-office_r-group-decomposition-in-jchem-for-excel.md">R-group Decomposition in JChem for Excel</a> <ul> <li><a href="jchem-for-office_r-group-decomposition-select-query-and-target-tab.md">R-group Decomposition-Select Query and Target Tab</a></li> <li><a href="jchem-for-office_r-group-decomposition-options-tab.md">R-group Decomposition-Options Tab</a></li> <li><a href="jchem-for-office_r-group-decomposition-run-tab.md">R-group Decomposition-Run Tab</a></li> </ul></li> <li><a href="jchem-for-office_sar-table-generation.md">SAR Table Generation</a></li> <li><a href="jchem-for-office_structure-filter.md">Structure Filter</a> <ul> <li><a href="jchem-for-office_filtering-options.md">Filtering Options</a></li> <li><a href="jchem-for-office_work-with-filter-results.md">Work with Filter Results</a></li> <li><a href="jchem-for-office_clone-results-to-a-new-sheet.md">Clone Results to a New Sheet</a></li> </ul></li> <li><a href="jchem-for-office_options-in-jchem-for-excel.md">Options in JChem for Excel</a> <ul> <li><a href="jchem-for-office_general-options-in-jchem-for-excel.md">General Options in JChem for Excel</a></li> <li><a href="jchem-for-office_database-connection-options.md">Database Connection Options</a></li> <li><a href="jchem-for-office_formatting-options.md">Formatting Options</a></li> <li><a href="jchem-for-office_licensing-options-in-jchem-for-excel.md">Licensing Options in JChem for Excel</a></li> <li><a href="jchem-for-office_file-import-options-in-jchem-for-excel.md">File Import Options in JChem for Excel</a></li> <li><a href="jchem-for-office_ijc-import-options-in-jchem-for-excel.md">IJC Import Options in JChem for Excel</a></li> <li><a href="jchem-for-office_file-export-options-in-jchem-for-excel.md">File Export Options in JChem for Excel</a></li> <li><a href="jchem-for-office_printing-options-in-jchem-for-excel.md">Printing Options in JChem for Excel</a></li> <li><a href="jchem-for-office_structure-sheet-options.md">Structure Sheet Options</a></li> <li><a href="jchem-for-office_image-conversion-options.md">Image Conversion Options</a></li> <li><a href="jchem-for-office_structure-display-options-in-jchem-for-excel.md">Structure Display Options in JChem for Excel</a></li> <li><a href="jchem-for-office_structure-editor-options-in-jchem-for-excel.md">Structure Editor Options in JChem for Excel</a></li> <li><a href="jchem-for-office_event-handling-options-in-jchem-for-excel.md">Event Handling Options in JChem for Excel</a></li> <li><a href="jchem-for-office_actions.md">Actions</a></li> <li><a href="jchem-for-office_functions-in-jchem-for-excel.md">Functions in JChem for Excel</a></li> </ul></li> <li><a href="jchem-for-office_custom-chemical-functions-in-jchem-for-excel.md">Custom Chemical Functions in JChem for Excel</a> <ul> <li><a href="jchem-for-office_use-custom-chemical-functions.md">Use Custom Chemical Functions</a></li> <li><a href="jchem-for-office_functions-reference.md">Functions Reference</a> <ul> <li><a href="jchem-for-office_normal.md">Normal</a> <ul> <li><a href="jchem-for-office_charge-in-jchem-for-excel.md">Charge in JChem for Excel</a></li> <li><a href="jchem-for-office_chemical-terms-in-jchem-for-excel.md">Chemical Terms in JChem for Excel</a></li> <li><a href="jchem-for-office_dissimilarity.md">Dissimilarity</a></li> <li><a href="jchem-for-office_drug-discovery-filtering-in-jchem-for-excel.md">Drug Discovery Filtering in JChem for Excel</a></li> <li><a href="jchem-for-office_elemental-analysis-in-jchem-for-excel.md">Elemental Analysis in JChem for Excel</a></li> <li><a href="jchem-for-office_geometry-in-jchem-for-excel.md">Geometry in JChem for Excel</a></li> <li><a href="jchem-for-office_hydrogen-bond-donor-acceptor-in-jchem-for-excel.md">Hydrogen Bond Donor-Acceptor in JChem for Excel</a></li> <li><a href="jchem-for-office_isomers-in-jchem-for-excel.md">Isomers in JChem for Excel</a></li> <li><a href="jchem-for-office_naming.md">Naming</a></li> <li><a href="jchem-for-office_protonation-and-partitioning-in-jchem-for-excel.md">Protonation and Partitioning in JChem for Excel</a></li> <li><a href="jchem-for-office_solubility.md">Solubility</a></li> <li><a href="jchem-for-office_tautomers-in-jchem-for-excel.md">Tautomers in JChem for Excel</a></li> <li><a href="jchem-for-office_topology-analysis-in-jchem-for-excel.md">Topology Analysis in JChem for Excel</a> <ul> <li><a href="jchem-for-office_ring-based.md">Ring-Based</a></li> <li><a href="jchem-for-office_path-based.md">Path-Based</a></li> <li><a href="jchem-for-office_distance-based.md">Distance-Based</a></li> <li><a href="jchem-for-office_refractivity.md">Refractivity</a></li> </ul></li> </ul></li> <li><a href="jchem-for-office_structure-in-jchem-for-excel.md">Structure in JChem for Excel</a> <ul> <li><a href="jchem-for-office_r-group-decomposition-functions.md">R-group Decomposition Functions</a></li> <li><a href="jchem-for-office_reactor-as-jchem-for-excel-functions.md">Reactor as JChem for Excel Functions</a></li> <li><a href="jchem-for-office_markush-enumeration-in-jchem-for-excel.md">Markush Enumeration in JChem for Excel</a></li> <li><a href="jchem-for-office_reactions-in-jchem-for-excel.md">Reactions in JChem for Excel</a></li> <li><a href="jchem-for-office_2d-and-3d-clean.md">2D and 3D Clean</a></li> <li><a href="jchem-for-office_mcs-structure.md">MCS Structure</a></li> <li><a href="jchem-for-office_structural-framework.md">Structural Framework</a></li> <li><a href="jchem-for-office_structure-checker-in-jchem-for-excel.md">Structure Checker in JChem for Excel</a></li> <li><a href="jchem-for-office_standardizer-in-jchem-for-excel.md">Standardizer in JChem for Excel</a></li> <li><a href="jchem-for-office_jcstructure.md">JCStructure</a></li> <li><a href="jchem-for-office_jcidsysstructure.md">JCIDSYSStructure</a></li> </ul></li> <li><a href="jchem-for-office_image.md">Image</a></li> </ul></li> </ul></li> <li><a href="jchem-for-office_user-interface-customization-in-jchem-for-excel.md">User Interface Customization in JChem for Excel</a> <ul> <li><a href="jchem-for-office_customizing-the-ribbon.md">Customizing the Ribbon</a></li> <li><a href="jchem-for-office_customizing-the-context-menu.md">Customizing the Context Menu</a></li> <li><a href="jchem-for-office_actions-reference.md">Actions Reference</a> <ul> <li><a href="jchem-for-office_conversions.md">Conversions</a></li> <li><a href="jchem-for-office_copy-paste.md">Copy-Paste</a></li> <li><a href="jchem-for-office_file-format-conversion.md">File Format Conversion</a></li> <li><a href="jchem-for-office_file-import-and-export.md">File Import and Export</a></li> <li><a href="jchem-for-office_structure-transformation.md">Structure Transformation</a></li> </ul></li> </ul></li> <li><a href="jchem-for-office_checking-directx-information.md">Checking DirectX Information</a></li> </ul></li> <li><a href="jchem-for-office_user-guide.md">JChem for Office User's Guide</a> <ul> <li><a href="jchem-for-office_jchem-ribbon.md">JChem Ribbon</a> <ul> <li><a href="jchem-for-office_customizing-the-ribbon-of-jchem-for-office.md">Customizing the Ribbon of JChem for Office</a></li> </ul></li> <li><a href="jchem-for-office_working-with-structures.md">Working with Structures</a> <ul> <li><a href="jchem-for-office_add-a-structure.md">Add a Structure</a></li> <li><a href="jchem-for-office_edit-a-structure.md">Edit a Structure</a></li> <li><a href="jchem-for-office_redirecting-other-vendors-ole-objects.md">Redirecting Other Vendors' OLE Objects</a></li> <li><a href="jchem-for-office_open-structure-files-in-jchem-for-office.md">Open Structure Files in JChem for Office</a></li> <li><a href="jchem-for-office_copy-and-paste.md">Copy and Paste</a> <ul> <li><a href="jchem-for-office_inside-ms-office-applications.md">Inside MS Office Applications</a> <ul> <li><a href="jchem-for-office_copy-from-jchem-for-excel.md">Copy from JChem for Excel</a> <ul> <li><a href="jchem-for-office_copy-and-paste-single-structures-with-keyboard-shortcuts.md">Copy and Paste Single Structures with Keyboard Shortcuts</a></li> <li><a href="jchem-for-office_copy-and-paste-tables-from-excel.md">Copy and Paste Tables from Excel</a></li> </ul></li> </ul></li> <li><a href="jchem-for-office_to-external-applications.md">To External Applications</a> <ul> <li><a href="jchem-for-office_copy-and-paste-single-structures.md">Copy and Paste Single Structures</a></li> </ul></li> <li><a href="jchem-for-office_from-external-applications.md">From External Applications</a> <ul> <li><a href="jchem-for-office_from-instant-jchem-to-jchem-for-office.md">From Instant JChem to JChem for Office</a></li> <li><a href="jchem-for-office_from-external-structure-editors.md">From External Structure Editors</a> <ul> <li><a href="jchem-for-office_convert-to-smiles-from-structure.md">Convert to SMILES from Structure</a></li> <li><a href="jchem-for-office_convert-from-smiles-to-structure.md">Convert from SMILES to Structure</a></li> <li><a href="jchem-for-office_convert-from-text-to-structure.md">Convert from Text to Structure</a></li> </ul></li> </ul></li> </ul></li> </ul></li> <li><a href="jchem-for-office_importing-from-databases-in-jchem-for-office.md">Importing from Databases in JChem for Office</a> <ul> <li><a href="jchem-for-office_manage-connections-in-jchem-for-office.md">Manage Connections in JChem for Office</a> <ul> <li><a href="jchem-for-office_add-an-oracle-connection-in-jchem-for-office.md">Add an Oracle Connection in JChem for Office</a></li> <li><a href="jchem-for-office_add-a-mysql-connection-in-jchem-for-office.md">Add a MySQL Connection in JChem for Office</a></li> <li><a href="jchem-for-office_add-an-mssql-connection-in-jchem-for-office.md">Add an MSSQL Connection in JChem for Office</a></li> <li><a href="jchem-for-office_add-a-postgresql-connection-in-jchem-for-office.md">Add a PostgreSQL Connection in JChem for Office</a></li> <li><a href="jchem-for-office_add-a-jchem-web-services-connection-in-jchem-for-office.md">Add a JChem Web Services Connection in JChem for Office</a></li> <li><a href="jchem-for-office_favorite-entities-in-jchem-for-office.md">Favorite Entities in JChem for Office</a></li> <li><a href="jchem-for-office_edit-and-delete-connections-in-jchem-for-office.md">Edit and Delete Connections in JChem for Office</a></li> </ul></li> <li><a href="jchem-for-office_import-from-database-in-jchem-for-office.md">Import from Database in JChem for Office</a> <ul> <li><a href="jchem-for-office_import-from-database-in-jchem-for-office-database-tab.md">Import from Database in JChem for Office-Database Tab</a></li> <li><a href="jchem-for-office_import-from-database-in-jchem-for-office-query-tab.md">Import from Database in JChem for Office-Query Tab</a></li> <li><a href="jchem-for-office_import-from-database-in-jchem-for-office-columns-tab.md">Import from Database in JChem for Office-Columns Tab</a></li> <li><a href="jchem-for-office_import-from-database-in-jchem-for-office-rows-tab.md">Import from Database in JChem for Office-Rows Tab</a></li> <li><a href="jchem-for-office_import-from-database-in-jchem-for-office-progress-tab.md">Import from Database in JChem for Office-Progress Tab</a></li> </ul></li> <li><a href="jchem-for-office_import-from-ijc-database.md">Import from IJC Database</a> <ul> <li><a href="jchem-for-office_import-from-ijc-database-in-jchem-for-office-source-tab.md">Import from IJC Database in JChem for Office-Source Tab</a></li> <li><a href="jchem-for-office_import-from-ijc-database-in-jchem-for-office-columns-tab.md">Import from IJC Database in JChem for Office-Columns Tab</a></li> <li><a href="jchem-for-office_import-from-ijc-datebase-in-jchem-for-office-rows-tab.md">Import from IJC Datebase in JChem for Office-Rows Tab</a></li> <li><a href="jchem-for-office_import-from-ijc-database-in-jchem-for-office-progress-tab.md">Import from IJC Database in Jchem for Office-Progress Tab</a></li> </ul></li> </ul></li> <li><a href="jchem-for-office_import-from-file-in-jchem-for-office.md">Import from File in Jchem for Office</a> <ul> <li><a href="jchem-for-office_import-file-in-jchem-for-office.md">Import File in JChem for Office</a> <ul> <li><a href="jchem-for-office_import-file-in-jchem-for-office-file-tab.md">Import File in JChem for Office-File Tab</a></li> <li><a href="jchem-for-office_import-file-in-jchem-for-office-columns-tab.md">Import File in Jchem for Office-Columns Tab</a></li> <li><a href="jchem-for-office_import-file-in-jchem-for-office-rows-tab.md">Import File in Jchem for Office-Rows Tab</a></li> <li><a href="jchem-for-office_import-file-in-jchem-for-office-progress-tab.md">Import File in JChem for Office-Progress Tab</a></li> </ul></li> <li><a href="jchem-for-office_import-with-document-to-structure.md">Import with Document to Structure</a></li> </ul></li> <li><a href="jchem-for-office_options-in-jchem-for-office.md">Options in JChem for Office</a> <ul> <li><a href="jchem-for-office_general-options-in-jchem-for-office.md">General Options in JChem for Office</a></li> <li><a href="jchem-for-office_image-formatting.md">Image Formatting</a></li> <li><a href="jchem-for-office_structure-display-in-jchem-for-office.md">Structure Display in JChem for Office</a></li> <li><a href="jchem-for-office_structure-editor-in-jchem-for-office.md">Structure Editor in JChem for Office</a></li> <li><a href="jchem-for-office_calculations-in-jchem-for-office.md">Calculations in JChem for Office</a></li> <li><a href="jchem-for-office_file-import-in-jchem-for-office.md">File Import in JChem for Office</a></li> <li><a href="jchem-for-office_ijc-import.md">IJC Import</a></li> <li><a href="jchem-for-office_database-import-options.md">Database Import Options</a></li> <li><a href="jchem-for-office_data-mapping-limitations-options.md">Data Mapping Limitations Options</a></li> <li><a href="jchem-for-office_event-handling.md">Event Handling</a></li> </ul></li> <li><a href="jchem-for-office_properties-in-jchem-for-office.md">Properties in JChem for Office</a> <ul> <li><a href="jchem-for-office_add-properties-to-a-document.md">Add Properties to a Document</a></li> <li><a href="jchem-for-office_reference.md">Reference</a> <ul> <li><a href="jchem-for-office_charge-in-jchem-for-office.md">Charge in JChem for Office</a></li> <li><a href="jchem-for-office_drug-discovery-filtering.md">Drug Discovery Filtering</a></li> <li><a href="jchem-for-office_elemental-analysis.md">Elemental Analysis</a></li> <li><a href="jchem-for-office_geometry-in-jchem-for-office.md">Geometry in JChem for Office</a></li> <li><a href="jchem-for-office_hydrogen-bond-donor-acceptor.md">Hydrogen Bond Donor-Acceptor</a></li> <li><a href="jchem-for-office_isomers-in-jchem-for-office.md">Isomers in JChem for Office</a></li> <li><a href="jchem-for-office_iupac-naming.md">IUPAC Naming</a></li> <li><a href="jchem-for-office_markush-enumeration-in-jchem-for-office.md">Markush Enumeration in JChem for Office</a></li> <li><a href="jchem-for-office_protonation-and-partitioning.md">Protonation and Partitioning</a></li> <li><a href="jchem-for-office_structure.md">Structure</a></li> <li><a href="jchem-for-office_tautomers-in-jchem-for-office.md">Tautomers in JChem for Office</a></li> <li><a href="jchem-for-office_topology-analysis.md">Topology Analysis</a></li> </ul></li> </ul></li> <li><a href="jchem-for-office_switching-jchem-for-office-to-lite-mode.md">Switching JChem for Office to Lite Mode</a></li> <li><a href="jchem-for-office_user-interface-customization-in-jchem-for-office.md">User Interface Customization in JChem for Office</a></li> </ul></li> <li><a href="jchem-for-office_lite-user-guide.md">JChem for Office Lite User's Guide</a> <ul> <li><a href="jchem-for-office_copying-pasting-and-editing-structures-in-jchem-for-office-lite.md">Copying, Pasting, and Editing Structures in JChem 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href="formats_bmp.md">BMP</a></li> <li><a href="formats_png.md">PNG</a></li> <li><a href="formats_emf.md">EMF</a></li> <li><a href="formats_pdf.md">PDF</a></li> <li><a href="formats_svg.md">SVG</a></li> <li><a href="formats_tiff.md">TIFF</a></li> <li><a href="formats_eps.md">EPS</a></li> </ul></li> <li><a href="formats_export-to-pov-ray.md">Export to POV-Ray</a></li> <li><a href="formats_image-import-in-marvin.md">Image Import in Marvin</a></li> </ul></li> <li><a href="formats_molecule-file-conversion-with-molconverter.md">Molecule file conversion with Molconverter</a></li> <li><a href="formats_molecule-formats.md">Molecule Formats</a> <ul> <li><a href="formats_cml.md">CML</a> <ul> <li><a href="formats_cml-export-options.md">CML Export Options</a></li> </ul></li> <li><a href="formats_mdl-mol-files.md">MDL MOL files</a> <ul> <li><a href="formats_mdl-molfiles-rgfiles-sdfiles-rxnfiles-rdfiles-formats.md">MDL MOLfiles, RGfiles, SDfiles, Rxnfiles, RDfiles formats</a></li> <li><a href="formats_chemaxon-specific-information-in-mdl-mol-files.md">Chemaxon specific information in MDL MOL files</a></li> <li><a href="formats_mol-file-compression.md">MOL file compression</a></li> <li><a href="formats_mdl-mol-import-and-export-options.md">MDL MOL Import and Export Options</a></li> <li><a href="formats_default-valence-of-metal-atoms.md">Default valence of metal atoms</a></li> </ul></li> <li><a href="formats_daylight-smiles-related-formats.md">Daylight SMILES related formats</a> <ul> <li><a href="formats_smiles.md">SMILES</a></li> <li><a href="formats_smarts.md">SMARTS</a></li> <li><a href="formats_smiles-and-smarts-import-and-export-options.md">SMILES and SMARTS import and export options</a></li> </ul></li> <li><a href="formats_chemaxon-smiles-extensions.md">Chemaxon SMILES extensions</a> <ul> <li><a href="formats_chemaxon-extended-smiles-and-smarts-cxsmiles-and-cxsmarts.md">Chemaxon Extended SMILES and SMARTS - CXSMILES and CXSMARTS</a></li> <li><a href="formats_cxsmiles-and-cxsmarts-import-and-export-options.md">CXSMILES and CXSMARTS import and export options</a></li> <li><a href="formats_chemaxon-smiles-abbreviated-group.md">Chemaxon SMILES Abbreviated Group</a></li> </ul></li> <li><a href="formats_iupac-inchi-inchikey-rinchi-and-rinchikey.md">IUPAC InChI, InChIKey, RInChI and RInChIKey</a> <ul> <li><a href="formats_inchi-and-inchikey-export-options.md">InChi and InChiKey export options</a></li> </ul></li> <li><a href="formats_name.md">Name</a></li> <li><a href="formats_sequences-peptide-dna-rna.md">Sequences - peptide, DNA, RNA</a> <ul> <li><a href="formats_peptide-import-and-export-options.md">Peptide import and export options</a></li> </ul></li> <li><a href="formats_fasta-file-format.md">FASTA file format</a> <ul> <li><a href="formats_fasta-import-options.md">FASTA import options</a></li> </ul></li> <li><a href="formats_protein-data-bank-pdb-file-format.md">Protein Data Bank (PDB) file format</a> <ul> <li><a href="formats_standard-pdb-residues.md">Standard PDB residues</a></li> <li><a href="formats_pdb-import-and-export-options.md">PDB import and export options</a></li> </ul></li> <li><a href="formats_tripos-sybyl-mol-and-mol2-formats.md">Tripos SYBYL MOL and MOL2 formats</a> <ul> <li><a href="formats_tripos-mol2-format.md">Tripos Mol2 format</a></li> <li><a href="formats_tripos-sybyl-mol-format.md">Tripos SYBYL MOL format</a></li> </ul></li> <li><a href="formats_xyz-format.md">XYZ format</a> <ul> <li><a href="formats_xyz-import-and-export-options.md">XYZ import and export options</a></li> </ul></li> <li><a href="formats_gaussian-related-file-formats.md">Gaussian related file formats</a> <ul> <li><a href="formats_gaussian-cube-format.md">Gaussian Cube format</a></li> <li><a href="formats_gaussian-cube-import-and-export-options.md">Gaussian Cube import and export options</a></li> <li><a href="formats_gaussian-input-output-format.md">Gaussian input-output format</a></li> </ul></li> <li><a href="formats_markush-darc-format-vmn.md">Markush DARC format - VMN</a> <ul> <li><a href="formats_vmn-peptide-import-option.md">VMN peptide import option</a></li> </ul></li> <li><a href="formats_csv.md">CSV</a></li> </ul></li> </ul></li> <li><a href="io_input-and-output-system.md">Input and Output System</a> <ul> <li><a href="io_supported-formats.md">Supported formats</a></li> <li><a href="io_mport.md">Input and Output System - Import</a></li> <li><a href="io_export.md">Input and Output System - Export</a></li> <li><a href="io_image-generation.md">Image generation</a></li> <li><a href="io_importing-and-exporting-molecule-properties.md">Importing and Exporting molecule properties</a></li> <li><a href="io_molecule-converter.md">Molecule converter</a></li> <li><a href="io_integrating-your-own-format.md">Integrating your own format</a></li> </ul></li> <li><a href="licensing_index.md">License Management</a> <ul> <li><a href="licensing_license-installation.md">License Installation</a> <ul> <li><a href="licensing_installing-to-desktops.md">Installing to Desktops</a></li> <li><a href="licensing_installing-to-servers.md">Installing to Servers</a></li> <li><a href="licensing_license-server-configuration.md">License Server Configuration</a></li> <li><a href="licensing_applets.md">Licensing Applets</a></li> <li><a href="licensing_via-java-web-start.md">Licensing via Java Web Start</a></li> <li><a href="licensing_setting-environment-variables.md">Setting environment variables</a></li> </ul></li> <li><a href="licensing_license-management-faq.md">License Management FAQ</a></li> <li><a href="licensing_about-chemaxon-licensing.md">About Chemaxon Licensing</a></li> <li><a href="licensing_prior-version-5-0.md">Licensing Prior Version 5.0</a></li> <li><a href="licensing_license-report.md">License Report</a></li> <li><a href="licensing_merging-licenses.md">Merging Licenses</a></li> </ul></li> <li><a href="lts-releases_index.md">Long Term Supported Releases - LTS</a> <ul> <li><a href="lts-releases_lts-release.md">LTS Release</a></li> <li><a href="lts-releases_lts-release-versions.md">LTS Release Versions</a></li> <li><a href="lts-releases_documentation-lts-release.md">Documentation - LTS release</a></li> </ul></li> <li><a href="general_notice-about-cas-registry-numbers-r.md">Notice about CAS Registry Numbers庐</a></li> <li><a href="general_public-repository.md">Public Repository</a></li> <li><a href="background_index.md">Scientific Background</a> <ul> <li><a href="background_aromatization.md">Aromatization</a> <ul> <li><a href="background_methods.md">Methods</a></li> <li><a href="background_differences-between-the-basic-and-general-aromatization-methods.md">Differences between the Basic and General aromatization methods</a></li> <li><a href="background_aromatization-of-query-structures.md">Aromatization of query structures</a></li> <li><a href="background_dearomatization.md">Dearomatization</a></li> </ul></li> <li><a href="background_stereochemistry.md">Stereochemistry</a> <ul> <li><a href="background_parity.md">Parity</a></li> <li><a href="background_tetrahedral-stereo.md">Tetrahedral Stereo</a></li> <li><a href="background_cis-trans-stereo.md">Cis-trans stereo</a></li> <li><a href="background_axial-stereoisomerism-atropisomerism.md">Axial stereoisomerism - atropisomerism</a></li> </ul></li> <li><a href="background_valence-calculations.md">Valence Calculations</a> <ul> <li><a href="background_alkali-metals-and-hydrogen.md">Alkali metals and Hydrogen</a></li> <li><a href="background_alkaline-earth-metals.md">Alkaline earth metals</a></li> <li><a href="background_transition-metals-lanthanoids-and-actinoids.md">Transition metals, Lanthanoids and Actinoids</a></li> <li><a href="background_boron-group.md">Boron group</a></li> <li><a href="background_carbon-group.md">Carbon group</a></li> <li><a href="background_nitrogen-group.md">Nitrogen group</a></li> <li><a href="background_oxygen-group.md">Oxygen group</a></li> <li><a href="background_halogens.md">Halogens</a></li> <li><a href="background_noble-gases.md">Noble gases</a></li> <li><a href="background_aromatic-systems.md">Aromatic systems</a></li> <li><a href="background_special-cases-abbreviations-query-properties.md">Special cases - abbreviations query properties</a></li> </ul></li> <li><a href="background_graph-matching.md">Atom-by-Atom Search</a></li> </ul></li> <li><a href="representation_index.md">Structure Representation</a> <ul> <li><a href="representation_class-representation.md">Structure Representation - Class Representation</a> <ul> <li><a href="representation_molatom.md">MolAtom</a></li> <li><a href="representation_molbond.md">MolBond</a></li> <li><a href="representation_molecule-graph.md">Molecule Graph</a></li> <li><a href="representation_r-group-structures.md">R-group structures</a> <ul> <li><a href="representation_implementation.md">Implementation</a></li> </ul></li> <li><a href="representation_representation-of-reactions.md">Representation of reactions</a></li> <li><a href="representation_s-groups.md">S-groups</a></li> <li><a href="representation_examples-for-molecule-representation.md">Examples for Molecule representation</a></li> </ul></li> <li><a href="representation_aromaticity.md">Aromaticity</a> <ul> <li><a href="representation_converting-structure-from-kekule-form-to-aromatic-form.md">Converting structure from Kekule form to aromatic form</a></li> <li><a href="representation_differences-between-the-basic-and-general-methods.md">Differences between the basic and general methods</a></li> <li><a href="representation_converting-structure-from-aromatic-form-to-kekule-form.md">Converting structure from aromatic form to Kekule form</a></li> </ul></li> <li><a href="representation_implicit-explicit-and-query-hydrogens.md">Implicit, Explicit and Query Hydrogens</a> <ul> <li><a href="representation_converting-explicit-hydrogens-to-implicit.md">Converting explicit Hydrogens to implicit</a></li> <li><a href="representation_converting-implicit-hydrogens-to-explicit.md">Converting implicit Hydrogens to explicit</a></li> <li><a href="representation_query-hydrogens.md">Query Hydrogens</a></li> </ul></li> <li><a href="representation_assigning-stereochemistry-descriptors.md">Assigning stereochemistry descriptors</a> <ul> <li><a href="representation_cip-stereo-chemistry.md">CIP Stereo chemistry</a></li> <li><a href="representation_stereoisomers-around-double-bonds.md">Stereoisomers around double bonds</a> <ul> <li><a href="representation_cis-trans-stereoisomers-in-0-dimension.md">Cis Trans stereoisomers in 0 Dimension</a></li> <li><a href="representation_cis-trans-stereoisomers-in-2-or-3-dimensions.md">Cis Trans stereoisomers in 2 or 3 Dimensions</a></li> <li><a href="representation_ez-stereoisomers.md">EZ stereoisomers</a></li> </ul></li> <li><a href="representation_parity-information.md">Parity information</a> <ul> <li><a href="representation_parity-information-in-0-dimension.md">Parity information in 0 Dimension</a></li> <li><a href="representation_parity-information-in-2-or-3-dimensions.md">Parity information in 2 or 3 Dimensions</a></li> </ul></li> <li><a href="representation_chirality.md">Chirality</a></li> </ul></li> <li><a href="representation_cleaning-options.md">Cleaning options</a></li> <li><a href="representation_deprecated-and-removed-methods.md">Deprecated and Removed Methods</a> <ul> <li><a href="representation_all-of-the-deprecated-and-removed-methods.md">All of the Deprecated and Removed Methods</a></li> <li><a href="representation_methods-deprecated-or-removed-in-version-14-7-7-0.md">Methods Deprecated or Removed in version 14.7.7.0</a></li> <li><a href="representation_methods-deprecated-or-removed-in-version-6-3.md">Methods Deprecated or Removed in version 6.3</a></li> <li><a href="representation_methods-deprecated-or-removed-in-version-6-2.md">Methods Deprecated or Removed in version 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parameters</a></li> </ul></li> <li><a href="discontinued_marvinspace_step-by-step-example-displaying-atom-properties.md">Step-by-step example - displaying atom properties</a></li> <li><a href="discontinued_marvinspace_step-by-step-code-examples.md">Step-by-step code examples</a></li> <li><a href="discontinued_marvinspace_surface-coloring-in-marvinspace.md">Surface coloring in MarvinSpace</a></li> </ul></li> <li><a href="discontinued_marvinspace_history-of-changes.md">MarvinSpace History of Changes</a></li> </ul></li> <li><a href="discontinued_metabolizer.md">Metabolizer</a></li> </ul></li> </ul> </div> </div> <div class="documentation is-dark" :class="{'expanded': ! sidebar}"> <div class="container"> <ul></ul><h1>ScreenMD</h1> <p>This manual gives you a walk-through on how to use the ScreenMD command line tool:</p> <ul> <li> <p><a href="/display/docs/screen_screenmd.md#src-1806363-screenmd-introduction">Introduction</a></p> </li> <li> <p><a href="/display/docs/screen_screenmd.md#src-1806363-screenmd-metricsdissimilaritymetrics">Dissimilarity metrics</a></p> <ul> <li> <p><a href="/display/docs/screen_screenmd.md#src-1806363-screenmd-tanimototanimotodissimilaritymetrics">Tanimoto Dissimilarity metrics</a></p> </li> <li> <p><a href="/display/docs/screen_screenmd.md#src-1806363-screenmd-inttanimototanimotoforintegervalueddescriptors">Tanimoto for integer valued descriptors</a></p> </li> <li> <p><a href="/display/docs/screen_screenmd.md#src-1806363-screenmd-scaledtanimotoscaledtanimotometricforfingerprints">Scaled Tanimoto metric for fingerprints</a></p> </li> <li> <p><a href="/display/docs/screen_screenmd.md#src-1806363-screenmd-scaledinttanimotoscaledtanimotometricforintegerdescriptors">Scaled Tanimoto metric for integer descriptors</a></p> </li> <li> <p><a href="/display/docs/screen_screenmd.md#src-1806363-screenmd-asymmetricinttanimotoasymmetrictanimotometricforintegerdescriptors">Asymmetric Tanimoto metric for integer descriptors</a></p> </li> <li> <p><a href="/display/docs/screen_screenmd.md#src-1806363-screenmd-euclideaneuclideandistance">Euclidean distance</a></p> <ul> <li> <p><a href="/display/docs/screen_screenmd.md#src-1806363-screenmd-weightedeuclideanweightedeuclideanmetric">Weighted Euclidean metric</a></p> </li> <li> <p><a href="/display/docs/screen_screenmd.md#src-1806363-screenmd-asymmetriceuclideanasymmetriceuclideanmetric">Asymmetric Euclidean metric</a></p> </li> </ul> </li> <li> <p><a href="/display/docs/screen_screenmd.md#src-1806363-screenmd-mdsetmetricdissimilarityofmoleculardescriptorsets">Dissimilarity of Molecular Descriptor Sets</a></p> </li> </ul> </li> <li> <p><a href="/display/docs/screen_screenmd.md#src-1806363-screenmd-usageusage">Usage</a></p> </li> <li> <p><a href="/display/docs/screen_screenmd.md#src-1806363-screenmd-optionsoptions">Options</a></p> </li> <li> <p><a href="/display/docs/screen_screenmd.md#src-1806363-screenmd-dbcondatabaseconnections">Database Connections</a></p> </li> <li> <p><a href="/display/docs/screen_screenmd.md#src-1806363-screenmd-inputinput">Input</a></p> </li> <li> <p><a href="/display/docs/screen_screenmd.md#src-1806363-screenmd-outputoutput">Output</a></p> </li> <li> <p><a href="/display/docs/screen_screenmd.md#src-1806363-screenmd-commentscommentsonsomeparameters">Comments on Some Parameters</a></p> </li> <li> <p><a href="/display/docs/screen_screenmd.md#src-1806363-screenmd-configconfigurationfiles">Configuration Files</a></p> <ul> <li> <p><a href="/display/docs/screen_screenmd.md#src-1806363-screenmd-pfp2dconfig2dpharmacophorefingerprints">2D pharmacophore fingerprints</a></p> </li> <li> <p><a href="/display/docs/screen_screenmd.md#src-1806363-screenmd-cfpconfigchemicalfingerprints">Chemical fingerprints</a></p> </li> </ul> </li> <li> <p><a href="/display/docs/screen_screenmd.md#src-1806363-screenmd-examplesexamples">Examples</a> <a name="src-1806363-screenmd-introduction"></a></p> </li> </ul> <h1>Introduction</h1> <p>ScreenMD performs fast virtual screening of large compound libraries using molecular descriptor sets. Virtual screening aims to find compounds that exhibit required chemical, structural, pharmacological or other properties. Such properties are represented as molecular descriptor sets and these descriptor sets are compared against each other by calculating a <em>dissimilarity score</em> between them. Thus the goal of the screening procedure is often expressed as an allowed maximal dissimilarity score: structures with a dissimilarity score below such predefined <em>threshold</em> are accepted by the screening process, while others are rejected.</p> <p>Both file and database inputs are supported, and in either case molecular structures or molecular descriptor sets (generated by <a href="fingerprints_fingerprint-and-descriptor-generation-generatemd.md">GenerateMD</a>) are accepted on input.</p> <p>The output of the screening application is either a table of dissimilarity coefficients or an SDfile. The table contains the dissimilarity coefficients of the <em>hit set</em> , while SDfile output contains the hit molecules along with all original tags and new ones storing the dissimilarity coefficients.</p> <p>ScreenMD takes two input sources, <em>target structures</em> and <em>query structures</em> . These structures, or strictly speaking their corresponding descriptor sets are compared in a <em>pair-wise</em> manner. It is assumed that there are significantly more target structures/descriptors than queries, for instance a few million targets can easily be handled, while normally the number of queries should not exceed few times 10.</p> <p>Target structures/descriptors usually belong to a compound library with pharmacological or biological interest, while queries define the required properties the compound library is sought for. Queries are often referred to as <em>known actives</em> and the aim of the screening exercise is to find other structures in the target set that exhibit the same chemical, pharmacological or biological activity (e.g. they bind to the same receptor protein).</p> <p>It is reasonable to suppose that compounds with the same activity share <em>common patterns</em> in their corresponding descriptors. These common patterns can be represented by a <em>hypothesis</em> , which can be regarded as a model active structure (or the model of the active site of a receptor). The target library can be scanned for structures matching this hypothesis in contrast to individual query structures. The use of the hypothesis in the screening procedure not only increases the number of hits but also facilitates the more efficient scanning of the target library, since instead of several query descriptor sets (one corresponding to each known active compound) only one descriptor set has to be used.</p> <p>Descriptors offer a simple yet feasible way to create such models. A usual approach, adopted in ScreenMD too, is to calculate the intersection (common part) of query descriptors. This can be defined as the minimum of corresponding descriptor cells. ScreenMD provides further alternatives to create pharmacophore hypotheses, for instance the average of query fingerprints can also be used. Another possibility is to use the median hypothesis. In this case the median of non-zero values in the corresponding descriptor cells is taken, if the percentage of corresponding zero cells is lower, then a given threshold. If the percentage of zeros is higher, then the corresponding hypothesis cell is set to zero. <a name="src-1806363-screenmd-metricsdissimilaritymetrics"></a></p> <h1><a name="src-1806363-screenmd-metrics"></a>Dissimilarity metrics</h1> <p>The comparison of two descriptors involves the calculation of one or more <em>dissimilarity coefficients</em> using dissimilarity metrics. At present the following metrics are supported: Tanimoto and Euclidean.</p> <p>Values of these metrics are non-negative numbers. A zero dissimilarity value indicates that the two descriptors are identical, and the larger the value of the dissimilarity coefficient the bigger the difference between the the two structures is. <a name="src-1806363-screenmd-tanimototanimotodissimilaritymetrics"></a></p> <h2><a name="src-1806363-screenmd-tanimoto"></a>Tanimoto Dissimilarity metrics</h2> <p>In its original form, Tanimoto metrics can be applied to binary fingerprints and it is a similarity metric:</p> <img src="images/download/attachments/1806346/Tanimoto.png" alt="images/download/attachments/1806346/Tanimoto.png"/> <p>where a and b are two binary fingerprints, & denotes binary bit-wise and-operator, | denotes binary bit-wise or-operator and B( x ) is the number of 1 bits in any binary fingerprint x:</p> <img src="images/download/attachments/1806346/Brightness.png" alt="images/download/attachments/1806346/Brightness.png"/> <p>The larger the number of common bits in a and b are, the larger the value of T. Therefore larger values represent higher similarity between a and b, 1 is total similarity, when the two descriptors are the same, while 0 represents the absolute dissimilarity. From that it is straightforward to obtain a dissimilarity measure:</p> <img src="images/download/attachments/1806346/Dissimilarity.png" alt="images/download/attachments/1806346/Dissimilarity.png"/> <p>However, extending binary Tanimoto dissimilarity to Molecular Descriptors other than binary fingerprints is less obvious. <a name="src-1806363-screenmd-inttanimototanimotoforintegervalueddescriptors"></a></p> <h2><a name="src-1806363-screenmd-inttanimoto"></a>Tanimoto for integer valued descriptors</h2> <p>The idea is to represent an integer value as a unary number, that is, replace it by as many 1 bits as its value is. This can be extended to a binary fingerprint by adding leading zeros to the series of 1 so as to make the length of all series the same. This way a binary fingerprint is generated and the original Tanimoto metric can be applied to it. For example the series 13, 4, 7, 9 can be represented as unary numbers as follows:</p> <p>1111111111111, 1111, 1111111, 111111111</p> <p>The binary form is:</p> <p>1111111111111, 0000000001111, 0000001111111, 0000111111111</p> <p>which can simple be written as a binary fingerprint:</p> <p>1111111111111000000000111100000011111110000111111111</p> <p>for which applying Tanimoto is simple. With the above consideration in mind, Tanimoto can be rewritten for integer valued descriptor in the form below:</p> <img src="images/download/attachments/1806346/IntTanimoto.png" alt="images/download/attachments/1806346/IntTanimoto.png"/> <p><a name="src-1806363-screenmd-scaledtanimotoscaledtanimotometricforfingerprints"></a></p> <h2><a name="src-1806363-screenmd-scaledtanimoto"></a>Scaled Tanimoto metric for fingerprints</h2> <p>According to published results the selectivity of the binary Tanimoto dissimilarity metric can be improved by <em>scaling</em> . Scaling, however, is feasible only when several compounds exhibiting the same pharmacological activity are known. A consensus fingerprint is created from the descriptors of these known actives:</p> <img src="images/download/attachments/1806346/Consensus.png" alt="images/download/attachments/1806346/Consensus.png"/> <p>where a1,...,ana are the known actives. The consensus fingerprint is applied to accentuate both similarities and dissimilarities between a target compound and a query structure (which, apparently should not be involved in the construction of the hypothesis). Non-zero bits of the hypothesis scale the corresponding bits of the target and the query fingerprint:</p> <img src="images/download/attachments/1806346/ScaledTanimoto.png" alt="images/download/attachments/1806346/ScaledTanimoto.png"/> <p>The scale factor(s) is an arbitrary integer between 1 and 10 (larger values than 10 rarely improve the hits). <a name="src-1806363-screenmd-scaledinttanimotoscaledtanimotometricforintegerdescriptors"></a></p> <h2><a name="src-1806363-screenmd-scaledinttanimoto"></a>Scaled Tanimoto metric for integer descriptors</h2> <p>The extended Tanimoto formula for integer valued descriptors can be combined with the scaled Tanimoto metric in a natural way:</p> <img src="images/download/attachments/1806346/ScaledIntTanimoto.png" alt="images/download/attachments/1806346/ScaledIntTanimoto.png"/> <p><a name="src-1806363-screenmd-asymmetricinttanimotoasymmetrictanimotometricforintegerdescriptors"></a></p> <h2><a name="src-1806363-screenmd-asymmetricinttanimoto"></a>Asymmetric Tanimoto metric for integer descriptors</h2> <p>Pharmacophore hypotheses offer a sophisticated approach to improve the selectivity and efficiency of screening. Yet, they suffer from an apparent deficiency when used in ordinary Euclidean or Tanimoto or other dissimilarity calculation based on a symmetrical metric. Asymmetrical metrics are sometimes mentioned as directed metrics too.</p> <p>Imagine two descriptors, both at the same distance from a hypothesis, but on different "sides" of it. That is, one is 'smaller' while the other is 'larger' than the hypothesis, component-wise. In this case the dissimilarity values are exactly the same, however, the 'smaller' descriptor can be considered as one that does not satisfy requirements set by the hypothesis, while the other satisfies all these constraints. Apparently, two such descriptors should not be considered equally adequate, the smaller should be rejected while the greater should be accepted in a similarity search involving a</p> <img src="images/download/attachments/1806346/AsymmetricIntTanimoto.png" alt="images/download/attachments/1806346/AsymmetricIntTanimoto.png"/> <p>hypothesis. To tackle this problem asymmetrical metrics bias toward the hypothesis in the case of 'larger' descriptors with a predefined ratio 伪:</p> <img src="images/download/attachments/1806346/AsymmetricModIntTanimoto.png" alt="images/download/attachments/1806346/AsymmetricModIntTanimoto.png"/> <p>For simple technical reasons, an equivalent form is used in ScreenMD, since it is more natural to keep the asymmetry ratio between zero and one (and not two). The asymmetrical nature of this metric means that the role of a and h cannot be interchanged.The higher the value of the asymmetry ratio (伪) the more the 'smaller' descriptor is penalized.</p> <p>It is good practice to use asymmetric metrics when a compound library is sought for a hypothetical descriptor.</p> <p>Asymmetrical and scaled metrics can be combined into a scaled asymmetric metric that exploits the benefits of both scaling with and directing toward a hypothesis descriptor.</p> <p>All above extensions to integer descriptors work for real valued descriptors, too. <a name="src-1806363-screenmd-euclideaneuclideandistance"></a></p> <h2><a name="src-1806363-screenmd-euclidean"></a>Euclidean distance</h2> <p>The most widely used geometrical distance function, the Euclidean distance can be used to measure the distance (dissimilarity) between two non-spatial objects, in our case between two molecular descriptors. The formulation is very straightforward:</p> <img src="images/download/attachments/1806346/Euclidean.png" alt="images/download/attachments/1806346/Euclidean.png"/> <p>Note that this distance is a dissimilarity function in the sense, that 0 value represents total similarity. However, the Euclidean distance of two molecular descriptors is not upper-bounded: the larger the distance the higher the dissimilarity between the two descriptors. One could think that this characteristic of the Euclidean metric allows more accurate measurement of dissimilarity, but in practice this is seldom needed. Instead, the direct comparability of dissimilarity values is important. This is hard to achieve with the use of Euclidean distance since dissimilarity values obtained for a large compound library are scattered in a wide range and one should not necessarily have a priori ideas about suitable threshold for the dissimilarity value for acceptance/rejection. (In contrast to this, it is fairly simple to give such threshold value in the case of the above discussed Tanimoto metric, for instance 0.2 is a common choice and it can be interpreted as "at most 20% dissimilarity is still accepted", or "at least 80% similarity is required".)</p> <p>With these considerations in mind a natural requirement is to allow to use the Euclidean distance as a dissimilarity metrics, that is, one that computes dissimilarity ratios between 0 and 1, and not distance values between 0 and infinity. Such metric is called the Normalized Euclidean dissimilarity metric and can be defined as</p> <img src="images/download/attachments/1806346/NormalizedEuclidean.png" alt="images/download/attachments/1806346/NormalizedEuclidean.png"/> <p>Since values of dEN fall into the interval 0-1, it is a dissimilarity metric.</p> <p>Euclidean distance could be normalized various ways but the above form has one important advantage over many others, namely that it makes the absolute distances between the two descriptors' components relative, that is, proportional to the value of those components. To illustrate this idea image four descriptors consisting of three components (e.g. molecular weight, pKa and polar surface area). Let the values of the first components (the molecular weight) be 44, 135, 880, 919, respectively. The absolute distance between the first two is 91 while between the last two 99. Despite that 99 is greater than 91, the latter two should be considered more similar to each other than the first two. According to the above formula the relative difference between the first two is 91 / ( 44 + 135 ) = 0.5, while between the third and the fourth it is 99 / ( 880 + 919 ) = 0.05, which indicates a high degree of similarity between these two descriptors. <a name="src-1806363-screenmd-weightedeuclideanweightedeuclideanmetric"></a></p> <h3><a name="src-1806363-screenmd-weightedeuclidean"></a>Weighted Euclidean metric</h3> <p>In general, Euclidean is not any better than Tanimoto dissimilarity, just different. Their behavior on a certain target and query set, and molecular descriptor in question cannot be predicted, only tested. Therefore some software tools have been developed to assist the user in selecting the metric which suits the particular needs the best. However, as Tanimoto with the scaling principle, Euclidean can be improved significantly by weighting. In contrast to scaling, which is applied to the entire descriptor in a uniform way, weighting distinguishes between components of the descriptor: an independent weight factor is associated with each individual component of the descriptor. This allows the increase or decrease of the importance of each individual feature in the dissimilarity calculation:</p> <img src="images/download/attachments/1806346/WeightedEuclidean.png" alt="images/download/attachments/1806346/WeightedEuclidean.png"/> <p>Rich descriptors, for which n, the length of the descriptor is large, (e.g. a few hundreds) require a large number of weights. In order to achieve the best selectivity over a certain set of compounds these values need to be adjusted. Due to the large number of weights and also to their high dependency on each other, however, it is not feasible to adjust these weights manually. To alleviate the selection and tuning of weights (in a molecular descriptor specific manner) software tools are available in the molecular descriptors package. Applying such optimization techniques to set up the suitable weighting schema for a given pharmacological target can significantly improve the quality of hits found in a screening process. <a name="src-1806363-screenmd-asymmetriceuclideanasymmetriceuclideanmetric"></a></p> <h3><a name="src-1806363-screenmd-asymmetriceuclidean"></a>Asymmetric Euclidean metric</h3> <p>The Euclidean dissimilarity metric is symmetrical which, as explained above, can be a drawback when comparing descriptors to a hypothesis. To tackle this problem an asymmetrical version of the ordinary Euclidean metric can be defined. The idea is the same as in the case of asymmetric Tanimoto, though the formulation is different (since the base metric is different):</p> <img src="images/download/attachments/1806346/AsymmetricEuclidean.png" alt="images/download/attachments/1806346/AsymmetricEuclidean.png"/> <p>Note that the value of 伪 should not be larger than 0.5 since only the case when a<sub>i</sub> < h<sub>i</sub> has to be penalized. <a name="src-1806363-screenmd-mdsetmetricdissimilarityofmoleculardescriptorsets"></a></p> <h2><a name="src-1806363-screenmd-mdsetmetric"></a>Dissimilarity of Molecular Descriptor Sets</h2> <p>The distance (dissimilarity) of descriptor sets can be calculated as the weighted Euclidean distance of the corresponding components:</p> <img src="images/download/attachments/1806346/MDSetDissim.png" alt="images/download/attachments/1806346/MDSetDissim.png"/> <p>In the formula above, the component-wise dissimilarity function is an arbitrary dissimilarity metric and the index i indicates that the dissimilarity functions are independent (that is one can use Tanimoto for the first component while weighted Euclidean for the second etc.). <a name="src-1806363-screenmd-usageusage"></a></p> <h1><a name="src-1806363-screenmd-usage"></a>Usage</h1> <p>Virtual screening is available through the ScreenMD command. It has two different ways of usage:</p> <ol> <li> <p>Passing parameters in the command line:</p> <pre><code> screenmd [<target input file>] <query input file>[<[options |#options]>] </code></pre> </li> <li> <p>Passing parameters in an XML configuration file:</p> <pre><code> screenmd [<configuration file name> |#config] </code></pre> <p>These two modes are not strictly exclusive, they can be mixed various ways. Command line parameters can extend settings provided in the configuration file. File names can be specified in the command line even when parameters are defined in the configuration file, in this case the files defined in the command line are processed. However, this kind of usage is recommended only for expert users. Thus the exact specification of the command line syntax is as follows:</p> </li> </ol> <pre><code> screenmd [<configuration file name> |#config] [<target input file>] <query input file>[<[options |#options]>] </code></pre> <p>Note that when specified, the configuration file must be the first argument after the screenmd command in the command line. Similarly, file names are positional, if input is taken from file, filenames must follow either the command name or the name of the configuration file. Also note, that the order of the filenames is definite: first the target file is specified, followed by the name of the query file.</p> <p>Prepare the usage of the ScreenMD script or batch file as described in <a href="jchem-base_preparing-and-running-batch-files-and-shell-scripts.md">Preparing the Usage of JChem Batch Files and Shell Scripts</a>.</p> <p>The ScreenMD class can be invoked directly:</p> <ul> <li>Win32 / Java 2 (assuming that JChem is installed in c:\jchem):</li> </ul> <pre><code> java -cp &quot;c:\jchem\lib\jchem.jar;%CLASSPATH%&quot; \ *chemaxon.descriptors.ScreenMD* [<target input file>] <query input file> [<[options |#options]>] </code></pre> <ul> <li>Unix / Java 2 (assuming that JChem is installed in /usr/local/jchem):</li> </ul> <pre><code> java -cp &quot;/usr/local/jchem/lib/jchem.jar:$CLASSPATH&quot; \ *chemaxon.descriptors.ScreenMD* [<target input file>] <query input file> [<[options |#options]>] </code></pre> <p><a name="src-1806363-screenmd-optionsoptions"></a></p> <h1><a name="src-1806363-screenmd-options"></a>Options</h1> <p>Options and parameters can either be defined in the command line or be specified in an XML configuration file. The command line mode is more suitable for smaller experiments. In contrast to this, configuring ScreenMD from XML is convenient even for much larger virtual screening exercises, in which, for instance, numerous descriptors are combined with various parametrized metrics. Although an <a href="attachments/attachments_1828141_1_screenmd.xml">example configuration file</a> is available, users are not encouraged to write such configuration files manually. Instead, the use of an interactive XML configuration editor is highly recommended.</p> <pre><code>General options: -h, --help this help message -x, --expert-help advanced options for expert users -v, --verbose verbose -s --saveconf saves database settings Input/Output options: -a, --table-name <name> name of the structure table -q, --query <where> where clause of select statements to read targets -o, --output [ TABLE | SDF ] <filepath> output file type and name with full path Flag can be given more than once -g, --generate-id [<first>] generate unique structure identifiers an optional value for the first ID can be given -e, --precision <prec> number of decimal places after the decimal point Database options: -d, --driver <JDBC> JDBC driver -u, --dburl <url> URL of database -l, --login <login> login name -p, --password <pwd> password Descriptor options: -k, --descriptor <type> <descriptor options> create and use descriptors of the given type -k, --descriptor <name> use descriptors created and stored previously Descriptor options: -c, --config <configfile> path and name of the XML configuration file -t, --use-tag [<name>] use existing descriptor data -M, --metric \{<name>\} use the metric <name> as specified in the config file More than one metrics can be specified. Similarity options: -L, --threshold dissimilarity threshold -Q, --compare-queries compare against query descriptor sets -H, --compare-hypothesis [<name> [C]] generate hypothesis <name> and compare against it Valid names are: Minimum, Average, Median. Default hypothesis type is Minimum. 'C' indicates consensus fingerprint. This flag may occur more than once with different hypothesis types. Advanced options for expert users: SDfile options: -I, --id-tag <name> name of the tag storing unique molecule identifiers -N, --mol-name <name> name of the tag storing compound name Database options: -O, --proptable <table> name of the property table 2D pharmacophore fingerprint options: -P, --PMAP-tag [<name>] use existing PMAP data Similarity options: -C, --component-wise apply threshold for individual descriptors -r, --descriptors-and thresholds for all descriptors, default is any -m, --metrics-and thresholds for all metrics, default is any -Z, --zero-threshold percentage threshold for zero limit in median hypothesis </code></pre> <p>Merging short forms of command line options is not supported, that is, instead of <em>-rm</em> the form <em>-r -m</em> should be used.</p> <p>In the XML configuration file the same parameters can be defined. These options appear in the <em>config</em> configuration editor labeled with the above long forms of command line parameter names, with only small differences. In most of the cases only the first letters of words are capitalized. For example <em>--compare-queries</em> is displayed as CompareQueries. In other cases, especially when the option has parameters, instead of one edit field, a frame has to be filled in. For example, <em>--compare-hypothesis</em> is exchanged with a frame, where all the hypotheses can be specified with their type and a consensus can be selected. The use of the configuration editor is very straightforward and simple.</p> <blockquote> <p>{warning} To use ScreenMD a valid license key is needed. When no valid license key is found in the home directory, ScreenMD runs in demo mode, where the number of molecular descriptors to be processed is limited to 2000 (thus if several types of molecular descriptors are generated, then the number of structures may be limited to few hundreds).</p> </blockquote> <p><a name="src-1806363-screenmd-dbcondatabaseconnections"></a></p> <h1><a name="src-1806363-screenmd-dbcon"></a>Database Connections</h1> <p>For more information on setting connection parameters:</p> <ul> <li> <p>JDBC driver's class name ( <em>--driver</em> )</p> </li> <li> <p>JDBC URL of database ( <em>--dburl</em> )</p> </li> <li> <p>Login name ( <em>--login</em> )</p> </li> <li> <p>Password ( <em>--password</em> )</p> </li> </ul> <p>please visit the <a href="jchem-base_administration.md">Administration Guide of JChem</a> . <a name="src-1806363-screenmd-inputinput"></a></p> <h1><a name="src-1806363-screenmd-input"></a>Input</h1> <p>The target library to be screened can be retrieved either from a database or from a file, in both cases either structures or molecular descriptor sets can be processed. In contrast to this queries are always read from and SDfile. Target structures/descriptors can either be taken from a database or from a file, while query structures are specified in a molecular file. Targets can either be molecular structures or molecular descriptors (generated earlier with <a href="fingerprints_fingerprint-and-descriptor-generation-generatemd.md">GenerateMD</a>). Most molecular file formats are accepted.The type and the source of the target set is determined by the command line flags according to the rules below:</p> <ol> <li> <p>if <em>-a</em> is specified target come from a database</p> </li> <li> <p>if a descriptor type name is given after the <em>-k</em> flag then structures are retrieved, and descriptors are generated on-the-fly (in this case the <em>-c</em> flag is mandatory)</p> </li> <li> <p>otherwise, the name of a molecular descriptor generated and stored in the database earlier is given after <em>-k </em> (in this case the <em>-c </em> flag is not allowed)</p> </li> </ol> <p>otherwise target come from a text file</p> <ol> <li> <p>if a descriptor type name is given after the <em>-k</em> flag then structures are read from a molecular structure file, and descriptors are generated on-the-fly (in this case the <em>-c</em> flag is mandatory)</p> </li> <li> <p>otherwise, the name of a molecular descriptor file is given after <em>-k</em> (in this case the -c flag is not allowed)</p> </li> </ol> <p>If the target input file is an SDfile, it may already contain descriptors of molecules. This information can either be used or ignored in screening. The default behavior of ScreenMD is to ignore such information. This can be overridden with the <em>--use-tag</em> flag, in which case descriptors are not generated from the original molecular structures, but taken from the input file.</p> <p>The default SDfile tags for storing molecular descriptors and related data are:</p> <ol> <li> <p>CF, chemical fingerprint,</p> </li> <li> <p>PMAP, pharmacophore point type map,</p> </li> <li> <p>PF, 2D pharmacophore fingerprint.</p> </li> </ol> <p>Other than the default tag names can be specified with the <em>--use-tag</em> and <em>--PMAP-tag</em> options.</p> <p>SDfiles containing descriptors can be generated with <a href="fingerprints_fingerprint-and-descriptor-generation-generatemd.md">GenerateMD</a>. Existing descriptors are worth being reused as doing so can dramatically reduce running times (since descriptor generation is more time-consuming than the comparison of descriptors). Though SDfiles are capable of storing such data, the best practice is to store descriptors in database tables as it is more efficient, easier to share among users and easier to maintain their consistency.</p> <p>When screening through a structure table in a database all structures (or their descriptors, depending on the actual command-line) are processed. To restrict the scope of screening, the WHERE clause of an SQL SELECT statement can be specified. In this case only the logical expression should be written.</p> <p>Screening a structure file or structure table is typically much slower than using descriptors directly. Yet, screening structures can be important when descriptor parameters are tuned for the sake of optimal settings. For instance the minimal and maximal distances, pharmacophore point type definitions, the fuzzy smoothing factor and many other parameters have strong influence on the modeling power of the descriptor. It is a good practice to find a few promising settings in several coarse-grained screening experiments using on-the-fly descriptor generation and store only the best descriptors in the database. <a name="src-1806363-screenmd-outputoutput"></a></p> <h1><a name="src-1806363-screenmd-output"></a>Output</h1> <p>ScreenMD writes its results into a text file ( <em>--output</em> option). If no output is specified, results are written to standard output. <a name="src-1806363-screenmd-outputformat"></a>By default, results of the comparisons are printed in a table. Each row corresponds to one target structure (in their original order as read from the input source). The first column contains either the optional identifier of the target molecule as read from the input ( <em>--id-tag</em> ) or a positive integer value generated by the program. The number of further columns depends on</p> <ul> <li> <p>the number of query structures ( <em>nq</em> ),</p> </li> <li> <p>the use of a hypothesis,</p> </li> <li> <p>the number of dissimilarity metrics ( <em>nm</em> ).</p> </li> </ul> <p>If a hypothesis is constructed, then the next <em>nm</em> columns correspond to the similarity coefficients obtained from the comparison of the target structure to the hypothesis using the selected metrics. If the target structure was compared against individual queries too, further <em>nq路nm</em> columns follows, grouped by <em>nm</em> (that is each group contains <em>nm</em> dissimilarity coefficients): dq1m1, dq1m2, ?, dq1mnm, dq2m1, ?, dqnqmnm, where <em>dqimj</em> is the dissimilarity coefficient obtained from the comparison of query <em>qi</em> using metric <em>mj</em> .</p> <p>An alternative way to produce the output of a screening procedure is to write the hit-set (molecular structures accepted) along with dissimilarity values into an SDfile. This output format can be specified by <em>-o sdf foo.sdf</em> . Note, that the output modes are not exclusive both table and SDfile output can be printed simultaneously ( <em>-o sdf hits.sdf -o table hits.table</em> ). <a name="src-1806363-screenmd-commentscommentsonsomeparameters"></a></p> <h1><a name="src-1806363-screenmd-comments"></a>Comments on Some Parameters</h1> <p>Screening uses a wide varieties of dissimilarity metrics that are specified in the configuration XML file. By default, all available metrics are used. To select one or more of these, the <em>-M</em> flag can be used.</p> <p>Since several metrics and query structures can be used simultaneously, results (dissimilarity coefficients) of individual comparisons (i.e. one target against all queries and/or hypotheses) can be combined in filtering. The default behavior is less restrictive: if any of the coefficients calculated is under the corresponding threshold value the structure is accepted. However, if the flag <em>-m</em> ( <em>--metrics-and</em> ) is specified, dissimilarity coefficients obtained by each and every metrics must be under the threshold in the case of at least one query structure or hypothesis. Similarly, if <em>-r</em> ( <em>--descriptors-and</em> ) is set, the target is accepted only if all components of the descriptor is accepted. These two flags are independent, and they can be combined.</p> <p>The default behavior behavior of ScreenMD is to compare all individual structures in the query set against all structures in the target set. However, when comparing against a hypothesis (the <em>-H</em> flag is specified), individual queries do not take part in the comparison process, only the hypothesis is compared against each target descriptor. This behavior can be overridden by the <em>-Q</em> flag, thus when <em>-H -Q</em> is specified together, than both hypothesis and individual queries are compared to targets.</p> <p>The hypothesis <em>(-H</em> ) flag may take one or two optional parameters. The first of these is the name of the hypothesis, which by default is <em>Minimum</em> . Another available options are <em>Average</em> and <em>Median</em> . The second optional argument is the character <em>C</em> , which refers to consensus. When this is specified for a certain hypothesis, then that hypothesis is used as consensus descriptor for scaled metrics.</p> <p>The advanced flag <em>-Z</em> is used to set the zero threshold for median hypothesis. This threshold is a percentage value. For each cell of the molecular descriptor the hypothesis cell is set to zero, if the percentage of zeros in the corresponding cells of the hypothesis component descriptors (descriptors, from which the hypothesis is calculated) is higher than the given threshold. If the percentage of zeros is lower, then the median of non-zero values is taken.</p> <p>By default one dissimilarity value is obtained for each pair of compounds compared regardless the number of component of the descriptor sets (according to the formula defined above). However, it is also possible to get dissimilarity values for all components of the descriptor set by specifying the -C, <em>--component-wise</em> flag. Note, that in the case of one descriptor (one component in the descriptor set) component-wise dissimilarity is calculated. <a name="src-1806363-screenmd-configconfigurationfiles"></a></p> <h1><a name="src-1806363-screenmd-config"></a>Configuration Files</h1> <p>Besides the <a href="attachments/attachments_1828141_1_screenmd.xml">XML configuration file</a> that can be optionally used to specify parameter settings, the ScreenMD application takes mandatory configuration files, too. These files correspond to molecular descriptors used for screening, so there should be one file per descriptor.</p> <p>Different descriptor types require different parametrization. The actual parameter settings are defined in external text (XML) files. <a name="src-1806363-screenmd-pfp2dconfig2dpharmacophorefingerprints"></a></p> <h2><a name="src-1806363-screenmd-pfp2dconfig"></a>2D pharmacophore fingerprints</h2> <p>The pharmacophore configuration file has three main sections. One of these, the <em><ScreeningConfiguration></em> is directly related to screenmd. This section defines the metrics in <em><ParametrizedMetric></em> elements. Normally, the user of ScreenMD does not need to edit these definitions, since they are either provided as 'factory settings' or they are generated and written into the configuration file by other utilities. A brief explanation on all required and optional values (XML attributes) are given below.</p> <p><em>Name</em> is always required, this specifies the user defined name of the metric. This can be an arbitrary name which is printed in the outputs (hit sets), and this is the name to refer to a specific metric after the <em>-M</em> flag.</p> <p><em>ActiveFamily</em> distinguishes between different versions of the same base metric (e.g. Euclidean) applied to different therapeutic areas. Such distinction is needed because different areas need different settings for metric's parameters in order to produce optimal hits. The name of the active family helps the user to find the right metric for his or her particular needs.</p> <p><em>Metric</em> is the name of the base metric (dissimilarity metric). At present two base metrics are available: Tanimoto and Euclidean.</p> <p><em>Normalized</em> indicates that the metric is normalized or not.</p> <p><em>Threshold</em> sets the limit for dissimilarity ratios to be accepted.</p> <p><em>AsymmetryFactor</em> is used in asymmetrical metrics.</p> <p><em>ScaleFactor</em> is used in the scaled metrics. In the present implementation Tanimoto metric can be scaled.</p> <p><em>Weights</em> specify individual weight values for each fingerprint cell used by the metric. However, if the user requires to tweak the weights of the Euclidean metric, each weight value can be written as an individual element. In this case a weight values does not directly correspond to a fingerprint cell, but to a pharmacophore point type (e.g. donor, acceptor) or to a topological distance.</p> <img src="images/download/attachments/1806346/WeightedEuclidean2.png" alt="images/download/attachments/1806346/WeightedEuclidean2.png"/> <p>where <em>f1(i</em> ) and <em>f2(i</em> ) denote the two pharmacophore types associated with the i-th cell and <em>d</em> ( <em>i</em> ) is the corresponding topological distance.</p> <p>There are much less weights in this case than in the cell-wise weighting of the fingerprint: the number of pharmacophore point types + the number of topological distances considered. <a name="src-1806363-screenmd-cfpconfigchemicalfingerprints"></a></p> <h2><a name="src-1806363-screenmd-cfpconfig"></a>Chemical fingerprints</h2> <p>Chemical fingerprints take three parameters that can be defined in the <em><Parameters></em> section. These are <em>Length</em> which is the number of bits in the fingerprint. The default value is 512, values smaller than 128 result in poor descriptors. The number of bits should be multiple of 32. <em>BondCount</em> determines the longest path considered, and <em>BitCount</em> specifies the number of bits to be turned to 1 in the fingerprint for each feature identified.</p> <p>The other two sections, <em><StandardizerConfiguration></em> and <em><ScreeningConfiguration></em> are the same as in the case of any other molecular descriptor.</p> <p>It is important to know, that molecular descriptor specific configuration/parameter definition files are not always given in an explicit manner, only if both target and query sets are taken from molecular structure files. In all other cases configuration settings are stored either in a descriptor file or in the database when descriptors are generated with <a href="fingerprints_fingerprint-and-descriptor-generation-generatemd.md">GenerateMD</a>. <a name="src-1806363-screenmd-examplesexamples"></a></p> <h1><a name="src-1806363-screenmd-examples"></a>Examples</h1> <p>The following example reads the target and query molecular structures from files (targets.sdf and queries.smiles, respectively) and writes results to the standard output:</p> <pre><code>screenmd targets.sdf queries.smiles -g -k PF -c pharma-frag.xml</code></pre> <p>Target structures are defined in the SDfile named targets.sdf, and query molecules are read from queries.smiles. Pharmacophore fingerprint parameters are taken from the configuration file (specified after the <em>-c</em> flag). As no metrics are selected all available ones are used. The target structures are compared against each individual query structures, no pharmacophore hypothesis is constructed. The output file contains a table of the dissimilarity ratios, like the one shown below:</p> <pre><code>id q1_PF_Euclidean 2_PF_Euclidean 3_PF_Euclidean 4_PF_Euclidean 1 80.95 80.90 76.75 80.84 2 92.41 92.39 88.45 92.34 3 90.27 90.25 86.51 90.20 4 34.45 34.49 31.79 34.48 5 54.19 54.22 50.36 54.21 6 57.79 57.81 54.22 57.81 7 37.85 37.89 35.51 37.82 8 41.56 41.60 39.24 41.49 End of table</code></pre> <p>The above is the default format, where the precision of calculations and the display format is 2. 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