Standalone Applications

• Chemaxon Assay
  • User guide for Assay
    • Processed data upload
    • Template File Usage
  • Administration guide for Assay
  • Assay Release Notes
    • Manual for Migration from Procedure to Protocol
• ChemCurator
  • ChemCurator Getting Help and Support
  • ChemCurator History of Changes
  • ChemCurator Installation and System Requirements
  • ChemCurator Licensing
  • ChemCurator User's Guide
  • Command-Line Mode
  • Integration Server Administrator Guide
• Chemicalize
  • Introduction to Chemicalize
  • Getting started with Chemicalize
  • Chemicalize User's Guide
  • Subscription management
  • Technical issues & Troubleshooting
  • Chemicalize Frequently Asked Questions
  • Getting Help & Support
• ChemLocator
  • ChemLocator Installation
    • Hardware Requirements
    • Software requirements
    • Prerequisites: Docker
    • Prerequisites: Azure AD
    • Installation Guide
    • Uninstallation
  • ChemLocator Configuration
    • First-time configuration
    • Indexing
  • ChemLocator Upgrade
  • ChemLocator Overview
    • File Formats
  • ChemLocator Search
    • Supported Browsers
  • ChemLocator Migration
  • How To
  • Troubleshoot
  • Changelog
• cHemTS
  • User Guide
    • Login in Compliance Checker
    • Single Check
    • File check
  • Administration Guide
    • Install Guide
    • System Requirements
    • Configuring
    • Administration GUI
  • Developer Guide
    • API integration
    • Workflow tools
  • Getting Help and Support
  • History of Changes
    • Software
    • Knowledge Base
• Compliance Checker
  • User Guide
    • Login in Compliance Checker
    • Single Check
    • File check
  • Administration Guide
    • Installation Guide
    • System Requirements
    • Configuring
    • Advanced settings
    • Administration GUI
      • Login as Administrator
      • Update the regulations
      • System monitor
      • Category group editor
      • User-defined category editor
      • History
        • Database update history
        • File check history
        • Single check history
      • Report template editor
  • Developer Guide
    • API integration
    • Workflow tools
  • Getting Help and Support
  • History of Changes
    • Software
    • Knowledge Base
  • Try out!
• Compound Registration
  • Administration Guide
    • Installation Guide
      • Database setup
      • Deploying the application
      • Install through the wizard
      • Command Line Tools
      • Configuration Guide
    • Upgrade Guide
    • System Requirements
  • User guide
    • Overview
    • Compound Registration Introduction
    • Compound Registration Abbreviations
    • Definitions of Terms
    • Quick Start Guide
      • Register a new compound
      • Register a new lot
      • Register a new compound reviewing matches
      • Dealing with failed submissions
      • Register compounds without structures
    • Login
    • Dashboard page
    • Autoregistration
      • Registration page
      • Register a Virtual Compound
    • Bulk Upload
      • Upload compounds
        • Upload summary page
      • Update compounds
        • Update summary page
      • Upload salts and solvates
    • Advanced Registration
      • Register from the Registration page
      • Registering from the Submission page
        • Registering new structures
        • Registering matching structures
        • Possible status messages - how to register
      • Staging area
        • Actions in the Staging area
        • Workspace
        • Status message
        • Structure area
        • Data fields
        • Card
    • Search
      • Structure search option
        • Type of search
        • Match type
        • Search query
      • Bulk edit of additional data
      • Download
    • User Profile
    • Browse page
      • Browser
      • Browse-card
      • Parent level amendment
      • Version level amendment
      • Lot level amendment
    • Appendix A. Calculations
    • Appendix B. Markush Structures
    • Multi-Component compounds
    • Restricted compounds
  • Configuration guide
    • Access Control
      • Users and groups
      • Groups and roles
      • Project based access
      • Authentication Providers
    • Forms and Fields
      • Form Editor
      • Dictionary Manager
    • Chemistry
    • Chemical structures
    • General settings
    • Workflow
    • Integration
    • Tools
    • Notifications
    • Pages Configuration
    • Navigation
    • Authentication
    • Database Connections
    • E-mail Server and User Repository
  • Developer guide
    • API documentation
    • API authentication
    • Downstream
  • History of Changes
  • FAQ
• Design Hub
  • History of changes
  • Install guide
    • Configuration guide
    • Install guide - Kubernetes
    • Developer guide - company support plugins
  • Plugin Catalogue
  • Developer guide - REST API
  • Developer guide - Plugins
  • Developer guide - resolver plugins
  • Developer guide - real time plugins
  • Developer guide - real time plugin templates
  • Developer guide - export plugins
  • Developer guide - storage plugins
  • Developer guide - import plugins
  • Developer guide - registry plugins
  • Developer guide - theme customization
• Instant JChem
  • Instant Jchem User Guide
    • Getting Started
      • About Instant JChem
      • Additional Help Material
      • Instant JChem Terminology
      • How the Instant JChem items fit together
      • Windows Menus and Toolbars
      • Instant JChem Quick Start
      • User Settings
      • Licenses
      • Instant JChem Dictionary
    • IJC Projects
      • About Projects
      • Creating New Project
      • Shared Projects
    • IJC Schemas
      • About IJC Schemas
      • Adding New Schema
      • Connecting to Existing Schema
      • Logging into Schema
      • Editing Schema Connection Settings
      • Deleting Schema
      • Backing up and Restoring Schema
      • Validating Schema
    • Viewing and Managing Data
      • Viewing Data
        • Multiple Data Result Set
        • Viewing multi-entity data
      • Form View
        • Design Mode
        • Browse Mode
        • Query Mode
      • Grid View in Instant JChem
      • Grid View from Selection
      • Form Widgets
        • Standard Widgets
          • TextField Widget
          • TextArea Widget
          • Button Widget
          • Label Widget
          • CheckBox Widget
          • Date Widget
          • List Widget
          • Browser Widget
          • Table Widget
          • Multi Field Sheet Widget
          • MolPane Widget
          • Structure Matrix Widget
          • TreeTable Widget
          • Canvas Widget
        • Visualisation Widgets
          • Histogram Widget
          • Scatter Plot Widgets
          • Radar Chart Widget
          • Box Plot Widget
        • Container Widgets
          • Panel Widget
          • Tabbed Panel Widget
      • Conditional Formatting
        • Step by Step guide
        • Creating Templates
      • Copying views
      • Adding and Deleting Rows
        • Editing Multiple Values
      • Printing
      • Renderers
      • Pivoting in IJC
    • Lists and Queries
      • Running Queries
        • Query Overview
        • Query Builder
        • Building Queries
        • Executing Queries
        • Form Based Query
        • Federated Search
      • List and Query Management
      • Cherry Picking
    • Collaboration
      • Sharing Items
      • Instant JChem URLs
    • Import and Export
      • Using File Import
      • RDF File Import
      • Merging Data
      • Exporting Data
    • Editing Databases
      • About Primary Keys
      • Controlling Editability
      • Editing Schemas
        • Editing Data Trees
        • Editing Entities
        • Editing Existing Schemas
        • Editing Fields
          • Calculated Fields
          • Extension Fields
          • Pick list
          • URL Fields
          • Standard Fields
        • Editing Relationships
      • Schema Editor
      • Structure Views
      • Using Multiple Database Schemas
    • Relational Data
      • About Relationships
      • About Data Trees
      • Editing Child Data
    • Chemical Calculations and Predictions
      • About Chemical Calculations and Predictions
      • Adding Chemical Terms Fields
    • Chemistry Functions
      • Performing an Overlap Analysis
      • Standardizer - Standardizing Structure Files
      • Markush Enumeration in IJC
      • Reaction Enumeration
      • R-group analysis
    • Security
      • About Instant JChem Security
      • Changing Security Settings
      • Managing User Database
      • Managing Current Users
      • Security Templates
      • Row level security
      • Using database authentication
      • Oracle JDBC connection encryption
      • Upgrade to Spring Security 6 framework
    • Scripting
    • Updating Instant JChem
      • About Updating Instant JChem
      • About Managing Plugins
      • Updating a Multi-User IJC Installation
    • Tips and Tricks
      • Memory Usage
      • Performance Tips
      • Database Implementation Notes
      • Using the database explorer
      • Change standardizer configuration for JChem table
      • Setting up cartridge tables for use in IJC
      • Triggers and sequences
        • Triggers and sequences - Derby
        • Triggers and sequences - MySQL
        • Triggers and sequences - Oracle
    • Instant JChem Tutorials
      • Building a relational form from scratch
      • Building more complex relational data models
      • Defining a security policy
      • Filtering items using roles
      • Lists and Queries management
      • Query building tutorial
      • Reaction enumeration analysis and visualization
      • SD file import basic visualization and overlap analysis
      • Using Import map and merge
      • Using Standardizer to your advantage
      • Pivoting tutorial
      • Handling Remote Data with Web Service Entity
      • Exploring Canvas Widget in Instant JChem
  • Instant JChem Administrator Guide
    • Admin Tool
      • Admin Tool connection
      • Clone operation
      • Finish Wizard
      • Migrate operation
      • Delete operation
      • Schema security operation
      • Unlock operation
      • Change owner operation
      • Create JWS files operation
      • Short Descriptions
        • ChangeOwnerShort
        • CloneShort
        • CreateSharedShort
        • DeleteShort
        • MigrateShort
        • RenameShort
        • SecurityShort
        • UnlockShort
      • Create *.ijs file for schema(s)
    • IJC Deployment Guide
    • Supported databases
    • JChem Cartridge
    • Choral Cartridge
    • Using Oracle Text in Instant JChem
    • JChem Postgres Cartridge in IJC
    • Deployment via Java Web Start
    • Startup Options
    • Shared project configuration
    • Accessing data with URLs
    • Instant JChem Meta Data Tables
    • Test to Production Metadata Migrator
    • Filtering Items
    • Deploying the IJC OData extension into Spotfire
    • Reporting a Problem
      • Extracting Version Information
      • Obtaining Log Files
      • Problems with Performance
        • Obtaining Performance Log
      • SQL Logging
      • Clean IJC Re-installation
    • Manual Instant JChem schema admin functions
    • SQL Scripts for Manual Schema Upgrade
    • Database Row Level Security
    • JccWithIJC
  • Instant JChem Developer Guide
    • Working With IJC Architecture
    • IJC API
    • Groovy Scripting
      • Good Practices
      • Schema and DataTree Scripts
        • Simple SDF Exporter
        • Relational SDF Exporter
        • CDX File Importer
        • Data Merger or Inserter from an SDF file
        • Markush DCR Structures Exporter
        • Select Representative Member of Clusters
        • Table Standardizer
        • Populate a Table with Microspecies
        • Create a Diverse Subset
        • Pearson Linear Correlation Co-efficient Calculator
        • PDF Trawler
        • Simple Substructure Search
        • Intersecting Sets
        • Find Entries with Duplicated Field Value
        • Importing Multiple SDF Files
        • Calling External Tools
        • Create Relational Data Tree
      • Forms Model Scripts
        • Create New Form
        • Create New Grid
        • Create New Panel
        • Create New Tabbed Pane
        • Copy Existing Form
        • Canvas Widget Scripts
      • Button Scripts
        • Execute Permanent Query
        • Patent Fetcher Button
        • Batch Searching Button
        • Import or Export a Saved Query SDF Button
        • Back and Next Buttons
        • Add Annotations Button
        • Simple Structure Checker Button
        • Advanced Structure Checker Button
        • Calculate MolWeight and generate SMILES
        • Get Current User
        • Simple ChemicalTerms evaluator
        • Edit Molecule Button
        • TanimotoMultiple
        • Execute Permanent Query Based On Its Name
        • Open existing view in the same dataTree
        • Export selection to file
        • Generate random resultset from actual resultset
      • Form Scripts
        • Drop Down Input Dialog
        • Log user and date upon row addition
        • Scripting hooks
      • Groovy Scriptlets
        • Buttons vs Scripts
        • Creating New Entities
        • Creating New Fields
        • Reading Molecules From a File
        • Insert or Update a Row
        • Evaluator
        • Create or Find a Relationship
        • Adding an Edge to a Data Tree
        • Exporting Data to a File
        • Connect to an External Database
        • Create a New Chemical Terms Field
        • Create a New Dynamic URL Field
        • Create a New Static URL Field
    • Java Plugins
      • IJC Plugin Quick Start
      • IJC Hello World Plugin
      • IJC Plugin tutorial - MyAddField plugin
      • IJC Plugin tutorial - MyMathCalc plugin
      • IJC Plugin tutorial - Renderer Example
      • IJC Plugin tutorial - MySCServer webapp
      • IJC Plugin tutorial - MySCClient plugin
      • IJC Plugin tutorial - Canvas widget
      • Java Plugins and Java Web Start
  • Instant JChem FAQ
  • Instant JChem Installation and Upgrade
    • Installation on Windows
    • Installation on Mac OS X
    • Installation on Linux or Solaris
    • Installation on Other Platforms
    • Uninstall
    • Changing Java Version
  • Instant JChem Licensing
  • IJC Getting Help and Support
  • Instant JChem System Requirements
  • Instant JChem History of Changes
• Markush Editor
  • Markush Editor Help and Support
  • Markush Editor History of Changes
  • Markush Editor Installation and System Requirements
  • Markush Editor Licensing
  • Markush Editor User's Guide
• Marvin Desktop Suite
  • MarvinSketch
    • User Guide
      • Getting Started
      • Graphical User Interface
        • Canvas
        • Menus
          • File Menu
          • Edit Menu
          • View Menu
          • Insert Menu
          • Atom Menu
          • Bond Menu
          • Structure Menu
          • Calculations Menu
          • Services Menu
          • Help Menu
        • Toolbars
          • General Toolbar
          • Tools Toolbar
          • Atoms Toolbar
          • Simple Templates Toolbar
          • Advanced Templates Toolbar
          • Search Online Toolbar
          • Special Toolbars
        • Context Menus
        • The Status Bar
        • Dialogs
          • Multipage Settings
          • Document Style
          • Template Library Manager
          • Edit Source
          • Customize
          • Where Are the Settings Stored
          • Format Dialog
          • Periodic Table
          • Preferences
          • Create Group Dialog
          • Attach Data
          • Edit Properties
          • About
        • Shortcuts
        • Customizing the GUI
        • Configurations
        • Services Module
          • Set Services
          • Settings of the Different Service Types
            • Local
            • HTTP Service
            • SOAP Service
      • Working in MarvinSketch
        • Structure Display Options
          • Customizing Structure Drawing Styles
            • Drawing Settings
            • Drawing Styles
          • Structure Display
          • Color Schemes
          • Display Options for Implicit and Explicit Hydrogens
          • Displaying the Label of Carbon Atoms
          • Error Highlighting
          • Saving Display Options
        • Basic Editing
          • Selecting a Structure
          • Copy-Paste and DragandDrop
          • Geometric Transformation of Structures and Objects
            • Moving and Rotating
            • Scaling
            • Flipping
            • Mirroring
            • Inverting
          • Cleaning
          • Deleting a Structure
          • Editing the Source
        • Drawing Simple Structures
          • Draw Atoms
          • Draw Bonds
          • Draw Chains
          • Sprouting
          • Merge Structures
          • Templates
          • Draw Stereocenters
          • Draw Coordination Compounds
          • Insert-Edit New Structure or Fragment
          • Atom Label Editor
        • Drawing More Complex Structures
          • Substructure Groups
            • Abbreviated (Superatom) Groups
            • Polymers
              • Draw Polymers
              • Structure-based Representation of Polymers
                • Structural Repeating Unit (SRU) Polymers
                • Repeating Units with Repetition Ranges - Frequency Variation
                • Copolymers
              • Source-based Representation of Polymers
            • Unordered Mixtures and Ordered Mixtures
            • Charge of the Group
          • Markush Structures
            • R-groups
            • Atom Lists and NOT Lists
            • Position Variation
            • Homology Groups
            • Frequency Variation
              • Repeating Units with Repetition Range
              • Link Nodes
          • Biomolecules
          • Atom, Bond, and Molecule Properties
        • Drawing Reactions
          • Creating Reactions
          • Mapping Reactions
          • Electron Flow Arrows
        • Using Integrated Calculations
        • Graphical Objects
          • Adding, Editing and Formatting Text
          • Drawing Shapes
        • Import and Export Options
          • Opening a Molecule File
          • Saving a Molecule File
          • Exporting to Image
        • Multipage Documents
          • Creating a Multipage Document
          • Navigating in Multipage Documents
        • Printing
      • Chemical Features
        • Valence Check
        • Structure Checker
        • Charges, Isotopes, Radicals
          • Charges
          • Isotopes
            • Isotope List Editing
          • Radicals
        • Stereochemistry
        • Reaction Schemes
        • Abbreviated Groups - Superatom Group
        • Query Features
          • R-groups
          • Link Nodes
          • Atom Lists and NOT Lists
          • Atom Properties
          • Generic Query Atoms
          • Homology Groups
        • Attached Data
        • Calculations
          • Analysis Box
          • Calculator Plugins in MarvinSketch
      • Marvin OLE User Guide
        • Install and Uninstall
        • How to Use
        • Customizing Marvin OLE Editing Mode
        • Redirecting Other Vendors' OLE Objects to Marvin OLE
        • Logging
        • Troubleshooting and Administration
        • Known Issues
      • Appendix
        • Customizing
        • Trademarks
      • Tutorials
      • Application Options
        • Java VM Options in MarvinSketch
        • Running the Applications
    • Developer Guide
      • Customizing the GUI - Server Side
        • Customizing the GUI
        • Customizing the GUI - Assign New Action
        • Clipboard Formats Configuration
        • Configure the Attach Data Dialog
      • Parameters and Events
        • Parameters
          • JavaBeans parameters
            • Display Parameters
              • Structure Templates
              • Query Properties in Molecule File Formats
            • Structure Display Parameters
            • Structure Parameters
            • Other Parameters
        • Events Fired by JavaBean
          • Action Events
          • Property Change Events
      • Marvin Beans for Java
        • Marvin Beans API Documentation
        • Marvin Beans Examples
          • Examples
            • Simple Bean
            • Images
            • Structure Display Parameters
            • Structure Templates
            • Text Box Example
              • JFileChooser Example
          • Examples
            • Simple Bean Example
            • JTable Example
            • Table View Example
            • Table View Example with Parameters
            • JFileChooser Example
            • Image Generation Using Marvin Beans
            • Excel Sheet Generation Using Marvin Beans
            • Installation Guide to jnlp Examples
        • Marvin Beans Frequently Asked Questions
      • Marvin Services
        • Manage Marvin Services
        • Service Implementations
          • Local Services
          • WSDL SOAP RPC Services
          • XML-RPC
          • JSON-RPC
          • HTTP
          • cxcalc integration
          • Chemical Terms Integration
          • Instant JChem Integration
          • JChem For Excel Integration
        • Configuration of Services
        • Calling Services
        • Viewing the Results
      • Java Web Start
  • MarvinView
    • User Guide
      • Getting started
      • How to Use MarvinView Features
        • Importing and Exporting Molecules
        • Editing Molecules
        • Structure Display Options
        • Manipulating the Molecule
        • How to Work with Multipage Molecular Documents
      • Graphical User Interface
        • Dialogs
          • Preferences Dialog
            • Display
            • Bonds
            • Structure Tab
            • Checkers Tab
            • Services Tab
            • Save-Load Tab
          • Edit Source Dialog
          • Table Options
          • About
        • Menus
          • File Menu
          • Edit Menu
          • View Menu
          • Table Menu
          • Structure Menu
          • Tools Menu
          • Pages
          • Help Menu
      • Application Options
        • Options
          • Java VM Options
          • Property Colors
    • Developer's Guide
      • JavaBeans Parameters
        • Display Parameters
        • Structure Display Parameters
        • Structure Parameters
        • 3D and Animation
          • RasMol Scripts
        • Molecule Tables
          • The layout Parameter
          • The param Parameter
          • The celli and celli_j parameters
          • Table View
        • Other Parameters
      • Events Fired by the JavaBean
      • Troubleshooting - MView and JMView Tables
  • Administration guide
    • Installation
    • System requirements
    • Licensing
    • Marvin bundles
  • Marvin Desktop Suite - History of Changes
• Plexus Connect
  • Plexus Connect - Quick Start Guide
  • Plexus Connect - User Guide
    • Plexus Connect - Log in
    • Plexus Connect - Dashboard
    • Plexus Connect - Exporting Your Data
    • Plexus Connect - Export Templates
    • Plexus Connect - Browsing in Your Data Set
    • Plexus Connect - Selecting Data
    • Plexus Connect - Searching in Your Database
      • Plexus Connect - Structure Search
    • Plexus Connect - Saved Queries
    • Plexus Connect - List Management
    • Plexus Connect - Sorting Data
    • Plexus Connect - Sharing Data with Other Users
    • Plexus Connect - Charts View
    • Plexus Connect - R-group Decomposition
  • Plexus Connect - Administrator Guide
    • Plexus Connect - Authentication
    • Plexus Connect - Sharing Schema Items Among Users
    • Plexus Connect - Business Flags
    • Plexus Connect - Row-level Security
    • Plexus Connect - Shared data sources
    • Plexus Connect - Plexus storage
    • Plexus Connect - Configuration Files
    • Plexus Connect - Simple table
    • Plexus Connect - Getting the Plexus Backend and Frontend Log Files
    • Plexus Connect - Form Editor
    • Plexus Connect - Scripting
      • Plexus Connect - Python Scripting
        • Plexus Connect - Supports Jupyter Notebook
        • Plexus Connect - Jupyter Notebook Advanced Example
        • Plexus Connect - In-View Python Scripting Console
      • Plexus Connect - JavaScript Scripting
    • Plexus Connect - API keys
    • Plexus Connect - Deploying Spotfire Middle Tier solution
  • Plexus Connect - Installation and System Requirements
  • Plexus Connect - Licensing
  • Plexus Connect - Getting Help and Support
    • Plexus Connect - Troubleshooting for Plexus Connect
  • Plexus Connect - FAQ
  • Plexus Connect - Privacy Policy
  • Plexus Connect - Demo Site
  • Plexus Connect - History of Changes
  • Plexus Connect - Schema Refresh Without Restart
  • Plexus Connect - Video Tutorials

Toolkits and Components

• AutoMapper
  • AutoMapper User's Guide
• Calculator Plugins
  • Introduction to Calculator Plugins
  • Calculator Plugins User's Guide
    • Physico-chemical plugins
      • pKa Plugin
      • Major Microspecies Plugin
      • Isoelectric Point Plugin
      • logP Plugin
      • logD Plugin
      • HLB Predictor
      • Solubility Predictor
      • NMR Predictor
      • Tautomer Generation Plugin
      • Stereoisomer Generator Plugin
      • Stereo Analysis - calculating stereo descriptors
      • CNS MPO Score Predictor
      • BBB Score Predictor
      • hERG Predictor
    • Molecular modeling plugins
      • Charge Plugin
      • Orbital Electronegativity Plugin
      • Polarizability Plugin
      • Dipole Moment Calculation Plugin
      • Conformer Plugin
      • 3D Alignment Plugin
      • Molecular Dynamics Plugin
    • Structural property plugins
      • Elemental Analysis Plugin
      • Topological Analysis Plugin
      • Geometrical Descriptors Plugin
      • Polar Surface Area Plugin 2D
      • Molecular Surface Area Plugin 3D
      • Structural Frameworks Plugin
      • Hydrogen Bond Donor Acceptor Plugin
      • Huckel Analysis Plugin
      • Refractivity Plugin
      • Resonance Plugin
    • Markush Enumerator Plugin
      • Markush features
        • R-groups
        • Atom lists
        • Bond lists
        • Link nodes
        • Repeating units
        • Position variation bonds
        • Homology Groups
      • Markush functionalities
        • Sequential enumeration
        • Selected part enumeration
        • Calculate library size
        • Random enumeration
        • Valence filter
        • Homology group enumeration
        • Scaffold alignment and coloring
        • Markush code generation
    • Training the Calculator Plugins
      • cxtrain command line tool
      • Training the logD Plugin
      • Training the logP Plugin
      • Training the pKa Plugin
    • cxcalc command line tool
      • cxcalc calculator functions
  • Calculator Plugins Developer's Guide
    • Calculator Plugins Web Services
    • Concurrent plugin API usage
    • Custom Calculator Plugin implementation
    • Integration of third-party calculations into Marvin and JChem
    • Introduction to developers
    • Plugin API usage examples
    • Using Calculator Plugins via API
  • Calculators in Playground
  • Background materials
    • Calculation of partial charge distribution
    • Generate3D
    • Isoelectric point (pI) calculation
    • LogP and logD calculations
    • NMR model prediction
    • pKa calculation
    • Red and blue representation of pKa values
    • Tautomerization and tautomers
    • Validation results
    • Tautomerization and tautomer models of Chemaxon
    • Theory of aqueous solubility prediction
    • The tautomerization models behind the JChem tautomer search
    • Calculators performance reports
  • Calculator Plugins Licensing
  • Calculator Plugins FAQ
  • Calculator Plugins Getting Help and Support
  • Calculator Plugins History of Changes
  • Calculator Plugins System Requirements
• Chemaxon .NET API
• Chemaxon Python API
  • Installation
  • Getting Started
  • Limitations
  • History of Changes
  • API Reference
• Chemaxon Cloud
  • User Guide
    • Guide for Team Members
      • Login
      • Logout
      • Accessing Applications
      • Groups
      • Projects
    • Guide for Team Administrators
      • Managing Team Members
      • Managing Groups
        • Adding Another Team Administrator to the Team
      • Managing Projects
    • Guide for System Administrators
      • Managing a Team Space
      • Managing Applications
      • Identity Federation Guide
        • Login flow diagram
        • Using external Okta as identity provider
          • Using external Okta as identity provider - Customer side
          • Using external Okta as identity provider - Chemaxon side
        • Using Azure AD as identity provider
  • Developer Guide
    • Basic Application Integration
    • Application authentication
    • Application authorization
    • Application and Service Discovery
    • Custom Claims in Okta tokens
    • Chemaxon Cloud Features Catalogue
      • SF-001 Application info
      • SF-002 Health check
      • SF-003 Application icon
      • SF-004 Web endpoints
      • SF-005 Logout
      • SF-006 Deep links
      • SF-007 Form
      • SF-008 Forms of type
      • SF-009 Form types
      • SF-010 Notification Event Types
      • SF-011 Login
  • Glossary
• Document to Structure
  • Document to Structure User Guide
    • Configuring OSR tools for Document to Structure
  • Document to Structure Developer Guide
  • Document to Structure Format Options
  • Document to Structure Licensing
  • Document to Structure Getting Help and Support
  • Document to Structure History of Changes
    • Document to Structure Migration Guide
• JChem Base
  • Administration Guide
    • Installation Guide
    • Upgrade Guide
    • System Requirements
    • Multiuser Support
    • Tomcat Configuration
    • Preparing and Running Batch Files and Shell Scripts
  • Developer Guide
    • Introduction for Java applications
    • JChem Chemical Database Concepts
    • File Import Export Tools
    • Modifying Structure Tables
    • R-group Decomposition Developer's Guide
    • Structure Searching
    • Utilities
    • JChem Base API documentation
  • User Guide
    • Query Guide
      • Search types
      • Similarity search
      • Query features
      • Stereochemistry
      • Special search types
        • R-group structures
        • R-group Decomposition User's Guide
        • Searching in Markush targets tables
        • Reaction search
        • Polymer search
        • Sophisticated chemical formula search
      • Search options
        • Atomproperty specific search options
        • Attached data specific search options
        • Bond specific search options
        • Chemical Terms specific search options
        • Database specific search options
        • General search options
        • Hitdisplay specific search options
        • Markush structure specific search options
        • Performance specific search options
        • Polymer specific search options
        • Query feature specific search options
        • Reaction specific search options
        • Resultset specific search options
        • Similarity specific search options
        • Stereo specific search options
        • Tautomer specific search options
        • Tautomer search - Vague bond search - sp-Hybridization
      • Standardization
      • Hit display-coloring
      • Appendix
      • Matching Query - Target Examples
    • jcsearch Command Line Tool
    • jcunique Command Line Tool
    • Homology Groups in Markush Structures
    • Maximum Common Substructure (MCS) search
  • FAQ
    • JCB FAQ
    • JChem Base and Cartridge Performance Information
      • Environment Information of Performance Benchmark
  • History of Changes
    • JChem History of Changes from version 1.0.4 to 6.3.4
  • Getting Help and Support
• JChem Choral
  • Administration Guide
    • Installation Guide
    • Upgrade Guide
    • System Requirements
    • Choral Installation on Amazon Oracle RDS
    • Choral Installation on AWS Oracle RDS and Fargate
    • Choral Upgrade without Downtime
  • Developer Guide
    • API Usage
  • Second Generation Search Engine
  • FAQ and Known Issues
  • Comparison of JChem Choral and JChem Oracle Cartridge
  • Migration guide to Choral from JOC
  • History of Changes
• JChem Microservices
  • Introduction
  • Administration Guide
    • Installation Guide
    • Upgrade Guide
    • System requirements
    • Licenses
    • Logging and monitoring
    • Architecture
    • Common modules
  • Developer Guide
  • Calculations Web Services
  • DB Web Services
    • DB Web Services before 25.3.0
  • IO Web Services
  • Markush Web Services
  • Reactor Web Services
  • Structure Checker Web Services
  • Structure Manipulation
  • Task Manager
  • Second Generation Search Engine
  • JChem Microservices FAQ and Known Issues
  • JChem Microservices History of Changes
• JChem Oracle Cartridge
  • Administration Guide
    • Installation Guide
    • Upgrade Guide
    • System Requirements
    • Getting Started Guide
    • Migration of JChem Oracle Cartidge
  • Developer Guide
    • JChem Cartridge for Oracle
    • Cartridge API
    • Cartridge API - Deferrred Error Handling
    • Description of parameters
    • External Java interfaces
    • Generic Molecular Descriptor Support
  • FAQ
    • JOC FAQ
    • JChem Cartridge Performance Information
      • JOC Environment Information of Performance Benchmark
  • History of Changes
  • Getting Help and Support
• JChem PostgreSQL Cartridge
  • Administration Guide
    • Installation Guide
    • Upgrade Guide
    • System Requirements
    • Getting Started
    • Install JPC on non standard PostgreSQL setup
    • JPC HA Installation Guide
    • Upgrade of PostgreSQL database together with JChem PostgreSQL Cartridge
    • Backup and Restore
  • Developer Guide
    • API Usage
    • JPC perf_out parameters
    • Deprecated API
    • Custom Structure Checker and Fixer in JPC
    • Citus Distibuted JChem PostgreSQL Cartridge
    • JDBC Caution
  • Second Generation Search Engine
  • FAQ and Known Issues
  • History of Changes
  • Getting Help and Support
  • Comparison of JChem PostgreSQL Cartridge and JChem Oracle Cartridge
  • Migration Guide
    • Migration guide to JPC from JOC
• JKlustor
  • What is JKlustor
  • Clustering methods
    • Hierarchical clustering
      • Library MCS
        • Library MCS (LibMCS) clustering
        • Library MCS licensing
      • Ward clustering
    • Non-hierarchical clustering
      • Bemis-Murcko clustering
      • Diverse Set Selection
      • Jarvis-Patrick clustering
      • K-means clustering
      • Sphere Exclusion clustering
      • Comparing libraries with Compr
  • CreateView
  • JKlustor History of Changes
  • JKlustor licensing
• Markush Tools
  • Markush Composer
  • Markush Enumeration
• Marvin JS
  • User Guide
    • Getting Started
    • Editor Overview
      • Editor Canvas
      • Dialogs
        • Abbreviated Groups Dialog
          • Default Abbreviated Group List
        • Atom Properties Dialog
        • Atom Query Properties Dialog
        • Attached Data Dialog
        • Bond Properties Dialog
        • Export Dialog
        • Import Dialog
        • Periodic Table Dialog
        • Pseudo Atom Dialog
        • R-group Dialog
        • R-logic Dialog
        • Set Box Color Dialog
        • S-group Dialog
        • Text Dialog
        • View Settings Dialog
      • Toolbars
        • Atom Toolbar - Right Toolbar
        • General Toolbar - Top Toolbar
        • Template Toolbar - Bottom Toolbar
        • Tools Toolbar - Left Toolbar
      • Context Menus
        • Abbreviated Group Context Menu
        • Atom Context Menu
        • Bond Context Menu
        • Empty Space Context Menu
        • Graphical Objects Context Menu
        • R-group Label Context Menu
        • Selection Context Menu
        • S-group Context Menu
    • Drawing and Editing Options
      • Abbreviations
      • Atom
      • Atom Mapping
      • Bond
      • Chains
      • Copy Structures
      • Graphical Objects
      • Groups
      • Radicals and Lone Pairs
      • Reaction
      • Reaction Mechanism
      • R-group Representation and Editing Options
      • Rotating in 2D
      • Snapped Objects
      • Structure Templates
      • Peptides
      • Text Editing
    • Feature Overview Pages
      • Markush Structures
      • Query Structures
      • Stereochemistry
      • Reactions and Mechanisms
      • Representation of JChem Base Query Functions
    • Keyboard Shortcuts
  • Developer Resources
    • Marvin JS Installation and System Requirements
    • Embedding Marvin JS
    • Extending Functionalities with Web Services
    • Troubleshooting
    • Third Party Licenses
    • Marvin JS Web Services
  • History of Changes
  • Frequently Asked Questions
  • Video Tutorials
  • Comparison of Marvin JS and MarvinSketch Feature Sets
• Marvin
  • Comparison with Marvin JS and Marvin Sketch
  • Shortcuts and tricks
  • Marvin with CLI
• Molconvert
  • User guide
• Name to Structure
  • Name to Structure User Guide
    • Custom Dictionary in Name Import
    • Custom Webservice in Name Import
  • Name to Structure Developer Guide
  • Name to Structure Format Options
  • Name to Structure Getting Help and Support
  • Name to Structure History of Changes
  • Name to Structure Licensing
• Reactor
  • Reactor User's Guide
    • Introduction to Reactor
      • Reactor Features
    • Reactor Getting Started
      • Reactor in Step-by-Step
    • Reactor Concepts
      • Virtual Library Design
      • Smart reactions
        • Stereoselectivity
        • Regioselectivity
    • Reactor Examples
      • Simple examples
      • Multiple reactants
      • Reactivity rules
      • Reactor usage examples
      • Selectivity rules
    • Working with Reactor
      • Specifying Reactions
        • Drawing a Reaction Scheme
          • Introducing the Reaction Scheme
          • Advanced Reaction Scheme Drawing
        • Reaction Library
      • Specifying Reactants
      • Reaction Mapping
        • Orphan atoms
        • Other reaction mapping styles
      • Reaction Rules
        • Exclude Rule
        • Reactivity Rule
        • Selectivity Rule
      • Reactant Combinations
      • Running Reactor
      • Reactor Interfaces
        • Reactor Application
          • Add reaction file
          • Specify reactants
          • Set runtime options for reaction processing
            • General options
            • Advanced options
            • Synthesis code options
            • Property Copy
          • Run the reaction and generate products in batch mode
        • Reactor Command-line Application
          • Using the react command-line interface
          • Options - react CLI
            • Reaction file - React CLI
            • Input (Reactants) - React CLI
            • Reactant processing modes - React CLI
            • Output - React CLI
            • Reaction rules - React CLI
            • Product related options
            • Reporting options
            • Mapping related options
            • Special options
            • Ratio - React CLI
            • Reverse reaction - React CLI
        • Reactor in Instant JChem
        • Reactor in JChem for Excel
          • JCReactProductStructure function
            • Prerequisites of JCReactProductStructure function
            • Insert JCReactProductStructure function
            • Populate cells with JCReactProductStructure results
            • Example on multiple product as result
          • JCReactReactionStructure function
            • Prerequisites - JCReactReactionStructure
            • Insert JCReactReactionStructure function
            • Populate cells with JCReactReactionStructure result
          • Reactor Examples inJChemforExcelUsage Reactor
        • Reactor in KNIME
          • Quick help
        • Reactor in Pipeline Pilot
        • API, Web Services
        • Glossary
          • Isotopes
          • Manual selection
          • Output file format
          • Product list
          • Ratio
          • Reaction File - Reaction Equation
          • Reaction stereo
          • Reversed reaction
          • Standardization in Reactor
          • Standard Properties in the Chemaxon Reaction Library
  • Reactor FAQ
  • Reactor Licensing
  • Reactor Getting Help and Support
  • Reactor History of Changes
  • Reactor Configuration Files
• Screen
  • Introduction to Virtual Screening
  • ScreenMD
  • Screen3D
  • Screen Developer Guide
  • Screen History of Changes
  • Screen licensing
• Standardizer
  • Standardizer User's Guide
    • Standardizer Introduction
      • Standardizer in a Nutshell
      • Why Use Standardizer
    • Standardizer Getting Started
      • Standardization in Step-by-Step
      • Quick Help on Configuration Design
    • Standardizer Concepts
      • Action
      • Standardizer Configuration
      • Standardizing Molecules
      • Typical Workflows
    • Working with Standardizer
      • Standardizer Actions
        • Add Explicit Hydrogens
        • Alias to Atom
        • Alias to Group
        • Aromatize
        • Clean 2D
        • Clean 3D
        • Clear Isotopes
        • Clear Stereo
        • Contract S-groups
        • Convert Double Bonds
        • Convert Pi-metal Bonds
        • Convert to Enhanced Stereo
        • Create Group
        • Dearomatize
        • Disconnect Metal Atoms
        • Expand S-groups
        • Expand Stoichiometry
        • Map
        • Map Reaction
        • Mesomerize
        • Neutralize
        • Rearrange Reaction
        • Remove Absolute Stereo
        • Remove Atom Values
        • Remove Attached Data
        • Remove Explicit Hydrogens
        • Remove Fragment
        • Remove R-group Definitions
        • Remove Stereo-Care Box
        • Replace Atoms
        • Set Absolute Stereo
        • Set Hydrogen Isotope Symbol
        • Strip Salts
        • Tautomerize
        • Transform
        • Ungroup S-groups
        • Unmap
        • Wedge Clean
        • Remove
        • Standardizer Transform
        • Custom Standardizer Actions
        • Remove Solvents
      • Creating a Configuration Standardizer
      • Interfaces Standardizer
        • Standardizer Application
          • Setting up Profiles
        • Standardizer Editor
        • Standardizer Command-line Application
        • Standardizer JChem Base
        • Standardizer JChem for Excel
        • Standardizer Instant JChem
        • Standardizer JChem Cartridge
        • Standardizer KNIME
        • Standardizer Pipeline Pilot
      • Standardizer File Formats
  • Standardizer Developer's Guide
  • Standardizer Installation and System Requirements
  • Standardizer Licensing
  • Standardizer Getting Help and Support
  • Standardizer History of Changes
• Structure Checker
  • Structure Checker User's Guide
    • Introduction
      • Structure Checker in a Nutshell
    • Structure Checker Getting Started
    • Structure Checker Concepts
      • Checkers
      • Fixers
      • Structure Checking of Molecules
    • Working with Structure Checker
      • Checker List
        • Abbreviated Group
        • Absent Chiral Flag
        • Absolute Stereo Configuration
        • Alias
        • Aromaticity Error
        • Atom Map
        • Atom Query Property
        • Atom Value
        • Atropisomer (deprecated)
        • Attached Data
        • Bond Angle
        • Bond Length
        • Bond Topology
        • Brackets
        • Chiral Flag
        • Chiral Flag Error
        • Circular R-group Reference
        • Coordination System Error
        • Covalent Counterion
        • Crossed Double Bond
        • Double Bond Stereo Error
        • Empty Structure
        • Explicit Hydrogen
        • Explicit Lone Pairs
        • EZ Double Bond
        • Incorrect Tetrahedral Stereo
        • Isotope
        • Metallocene Error
        • Missing Atom Map
        • Missing R-group
        • Molecule Charge
        • Multicenter
        • Multicomponent
        • Multiple Stereocenter
        • Non-standard Wedge Scheme
        • Non-stereo Wedge Bond
        • OCR Error
        • Overlapping Atoms
        • Overlapping Bonds
        • Pseudo Atom
        • Query Atom
        • Query Bond
        • Racemate
        • Radical
        • Rare Element
        • Reacting Center Bond Mark
        • Reaction Map Error
        • Relative Stereo
        • Ring Strain Error
        • R-atom
        • R-group Attachment Error
        • R-group Bridge Error
        • Solvent
        • Star Atom
        • Stereo-Care Box
        • Stereo Inversion Retention Mark
        • Straight Double Bond
        • Substructure
        • Three Dimension 3D
        • Unbalanced Reaction
        • Unused R-group
        • Valence Error
        • Valence Property
        • Wiggly Bond
        • Wiggly Double Bond
        • R-group Reference Error (discontinued)
        • Wedge Error (discontinued)
      • Creating a Configuration
      • Custom Checkers and Fixers
      • Interfaces of Structure Checker
        • Structure Checker in MarvinSketch
        • Structure Checker Application
        • Structure Checker Editor
        • Structure Checker Command Line Application
        • JChem Cartridge and Structure Checker
  • Structure Checker Developer's Guide
    • Introduction to Structure Checker API
    • Classes, interfaces and configuration
    • Implementing a new Structure Checker
    • Create Graphical User Interface for Checker Options
    • Implementing Fixers
  • Structure Checker Installation and System Requirements
  • Structure Checker Licensing
  • Structure Checker Getting Help and Support
  • Structure Checker History of Changes
• Structure to Name
  • Structure to Name User Guide
  • Structure to Name Developer Guide
  • Structure to Name Format Options
  • Structure to Name Licensing
  • Structure to Name Getting Help and Support
  • Structure to Name History of Changes

Third-Party Integration

• JChem for Office
  • Administration Guide
    • Installation Guide
      • Before Using
      • Installation
        • How to Check the Bit-version of MS Office
          • Microsoft Office 2013, 2016 and 2019
        • Silent Installation
      • Licensing of JChem for Office
      • Logging in JChem for Office
    • Upgrade and Uninstall Guide
    • System Requirements
  • User Guide
    • JChem for Excel User's Guide
      • JChem for Excel Ribbon
        • Standard Menu
        • Advanced Menu
      • Working with Structures in Excel
        • Add a Structure to a Cell
        • Edit a Structure in a Cell
        • Edit Structures in the Task Pane
        • Resize Structures
        • Structures in Merged Cells
        • Show and Hide Structures
        • Show and Hide Structures and Structure IDs
        • Insert Single Structures
        • Open Structure Files
        • Delete Structures from a Selected Range
        • Save Single Structure to a File
        • Print Structures
        • Copy and Paste with JChem for Excel
          • Inside Excel
            • Copy Structures with or without Data
            • Exclude Hidden Rows
          • To External Applications from JChem for Excel
            • Copy and Paste with IDs
            • To External Structure Editors
            • Copy and Paste Single Structures with Keyboard Shortcuts in JChem for Excel
          • From External Applications to JChem for Excel
            • From External Structure Editors to JChem for Excel
            • From Instant JChem to JChem for Excel
        • Convert from Structures
          • Convert Structures to Images
          • Convert Structures to Text
        • Convert to Structures
          • Convert Images to Structures
          • Convert Text to Structures
        • Convert ISIS, ChemDraw, Accord, and Insight for Excel Files to JChem for Excel Files
          • JChem for Excel File Converter Action
          • JChem for Excel File Converter Context Menu Item
          • JChem for Excel File Converter Tool
        • Calculations with Third-Party Services
        • Specify External Image and Name Services
      • Importing from Databases in JChem for Excel
        • Manage Connections
          • Add an Oracle Connection in JChem for Excel
          • Add a MySQL Connection in JChem for Excel
          • Add an MSSQL Connection in JChem for Excel
          • Add a PostgreSQL Connection in JChem for Excel
          • Add a JChem Web Services Connection in JChem for Excel
          • Favorite Entities in JChem for Excel
          • Edit and Delete Connections in JChem for Excel
        • Import from Database in JChem for Excel
          • Import from Database-Database Tab
          • Import from Database-Query Tab
          • Import from Database-Columns Tab
          • Import from Database-Rows Tab
          • Import from Database-Progress Tab
        • Import from IJC Database in JChem for Excel
          • Import from IJC Database-Source Tab
          • Import from IJC Database-Columns Tab
          • Import from IJC Database-Progress Tab
        • Import from Database by IDs
      • Resolve ID
        • Resolve IDs into Structures
        • Resolve CompReg IDs into Structures
      • Import from File
        • Import File
          • Import File-File Tab
          • Import File-Columns Tab
          • Import File-Progress Tab
        • Import from File by IDs
        • Import with Document to Structure in JChem for Excel
      • Export to File
      • Share Excel Files
        • Co-authoring
        • Save to Share
      • R-group Decomposition in JChem for Excel
        • R-group Decomposition-Select Query and Target Tab
        • R-group Decomposition-Options Tab
        • R-group Decomposition-Run Tab
      • SAR Table Generation
      • Structure Filter
        • Filtering Options
        • Work with Filter Results
        • Clone Results to a New Sheet
      • Options in JChem for Excel
        • General Options in JChem for Excel
        • Database Connection Options
        • Formatting Options
        • Licensing Options in JChem for Excel
        • File Import Options in JChem for Excel
        • IJC Import Options in JChem for Excel
        • File Export Options in JChem for Excel
        • Printing Options in JChem for Excel
        • Structure Sheet Options
        • Image Conversion Options
        • Structure Display Options in JChem for Excel
        • Structure Editor Options in JChem for Excel
        • Event Handling Options in JChem for Excel
        • Actions
        • Functions in JChem for Excel
        • Setting ACS 1996 style in JChem for Excel
      • Custom Chemical Functions in JChem for Excel
        • Use Custom Chemical Functions
        • Functions Reference
          • Normal
            • Charge in JChem for Excel
            • Chemical Terms in JChem for Excel
            • Dissimilarity
            • Drug Discovery Filtering in JChem for Excel
            • Elemental Analysis in JChem for Excel
            • Geometry in JChem for Excel
            • Hydrogen Bond Donor-Acceptor in JChem for Excel
            • Isomers in JChem for Excel
            • Naming
            • Protonation and Partitioning in JChem for Excel
            • Solubility
            • Tautomers in JChem for Excel
            • Topology Analysis in JChem for Excel
              • Ring-Based
              • Path-Based
              • Distance-Based
              • Refractivity
          • Structure in JChem for Excel
            • R-group Decomposition Functions
            • Reactor as JChem for Excel Functions
            • Markush Enumeration in JChem for Excel
            • Reactions in JChem for Excel
            • 2D and 3D Clean
            • MCS Structure
            • Structural Framework
            • Structure Checker in JChem for Excel
            • Standardizer in JChem for Excel
            • JCStructure
            • JCIDSYSStructure
          • Image
      • User Interface Customization in JChem for Excel
        • Customizing the Ribbon
        • Customizing the Context Menu
        • Actions Reference
          • Conversions
          • Copy-Paste
          • File Format Conversion
          • File Import and Export
          • Structure Transformation
      • Checking DirectX Information
    • JChem for Office User's Guide
      • JChem Ribbon
        • Customizing the Ribbon of JChem for Office
      • Working with Structures
        • Add a Structure
        • Edit a Structure
        • Redirecting Other Vendors' OLE Objects
        • Open Structure Files in JChem for Office
        • Copy and Paste
          • Inside MS Office Applications
            • Copy from JChem for Excel
              • Copy and Paste Single Structures with Keyboard Shortcuts
              • Copy and Paste Tables from Excel
          • To External Applications
            • Copy and Paste Single Structures
          • From External Applications
            • From Instant JChem to JChem for Office
            • From External Structure Editors
              • Convert to SMILES from Structure
              • Convert from SMILES to Structure
              • Convert from Text to Structure
      • Importing from Databases in JChem for Office
        • Manage Connections in JChem for Office
          • Add an Oracle Connection in JChem for Office
          • Add a MySQL Connection in JChem for Office
          • Add an MSSQL Connection in JChem for Office
          • Add a PostgreSQL Connection in JChem for Office
          • Add a JChem Web Services Connection in JChem for Office
          • Favorite Entities in JChem for Office
          • Edit and Delete Connections in JChem for Office
        • Import from Database in JChem for Office
          • Import from Database in JChem for Office-Database Tab
          • Import from Database in JChem for Office-Query Tab
          • Import from Database in JChem for Office-Columns Tab
          • Import from Database in JChem for Office-Rows Tab
          • Import from Database in JChem for Office-Progress Tab
        • Import from IJC Database
          • Import from IJC Database in JChem for Office-Source Tab
          • Import from IJC Database in JChem for Office-Columns Tab
          • Import from IJC Datebase in JChem for Office-Rows Tab
          • Import from IJC Database in Jchem for Office-Progress Tab
      • Import from File in Jchem for Office
        • Import File in JChem for Office
          • Import File in JChem for Office-File Tab
          • Import File in Jchem for Office-Columns Tab
          • Import File in Jchem for Office-Rows Tab
          • Import File in JChem for Office-Progress Tab
        • Import with Document to Structure
      • Options in JChem for Office
        • General Options in JChem for Office
        • Image Formatting
        • Structure Display in JChem for Office
        • Structure Editor in JChem for Office
        • Calculations in JChem for Office
        • File Import in JChem for Office
        • IJC Import
        • Database Import Options
        • Data Mapping Limitations Options
        • Event Handling
      • Properties in JChem for Office
        • Add Properties to a Document
        • Reference
          • Charge in JChem for Office
          • Drug Discovery Filtering
          • Elemental Analysis
          • Geometry in JChem for Office
          • Hydrogen Bond Donor-Acceptor
          • Isomers in JChem for Office
          • IUPAC Naming
          • Markush Enumeration in JChem for Office
          • Protonation and Partitioning
          • Structure
          • Tautomers in JChem for Office
          • Topology Analysis
      • Switching JChem for Office to Lite Mode
      • User Interface Customization in JChem for Office
    • JChem for Office Lite User's Guide
      • Copying, Pasting, and Editing Structures in JChem for Office Lite
      • Context Menu in JChem for Office Lite
        • Structure Renderer Options in JChem for Office Lite
        • Structure Editor Options in JChem for Office Lite
      • Use Marvin with JChem for Office Lite
    • JChem for Office Known Issues
      • Issues Detailed
    • Troubleshooting
      • Manually Enabling JChemExcel Functions
      • Disable and Re-enable JChem for Office Add-Ins
      • No Help Available for JChem for Excel Functions
    • Troubleshooting - JChem for Office
      • Structures are not displayed in Excel cell
      • JChem for Office Tutorial Videos
      • Enable JChemExcel.Functions add-in after it gets disabled
      • Structure rendering issues when moving the Excel window between different screens
      • How to collect event logs
      • Information to be sent for bug investigation
      • Logfiles to be sent for bug investigation
  • History of Changes
• KNIME Nodes
  • Administration
  • Licensing
  • Getting Help and Support
  • History of Changes

Cross-Product Documentation

• Chemaxon Configuration Folder
• Chemical Fingerprints
  • Extended Connectivity Fingerprint (ECFP)
  • Chemical Hashed Fingerprint
  • Pharmacophore Fingerprint
  • Reaction Fingerprint
  • MACCS-166 Fingerprint
  • Fingerprint and descriptor generation - GenerateMD
  • Pharmacophore perception - PMapper
  • Chemical Fingerprints licensing
• Chemical Terms
  • Available Functions
    • Functions by Categories
    • Functions in Alphabetic Order
    • Chemical Terms functions in alphabetic order
    • Notes on Chemical Terms functions
  • Chemical Terms Getting Help and Support
  • Chemical Terms Getting Started
  • Chemical Terms Introduction
  • Products using Chemical Terms
    • Chemical Terms Evaluator
      • Evaluator Examples
    • Chemical Terms - Instant JChem
    • Chemical Terms - JChem Base
    • Chemical Terms - JChem Cartridge
    • Chemical Terms - JChem for Excel
    • Chemical Terms - Reactor
    • Chemical Terms - KNIME
    • Chemical Terms - Pipeline Pilot
  • The Chemical Terms Language
    • Language Elements
    • Expression Syntax
    • Predefined Functional Groups and Named Molecule Groups
    • Initial Scripts
    • Input Contexts
    • Chemical Terms Configuration
    • Examples
      • Evaluator and JChem Cartridge Examples
      • Reactor Examples
      • Search Filter Examples
  • Chemical Terms Usage Examples
    • Basic Calculations
    • Search Filters
    • Reaction Processing
    • Markush Enumeration
• File Formats
  • Basic export options
  • Compression and Encoding
    • Base64
    • GZIP
  • Document formats
    • Marvin Documents - MRV
      • MRV Export Options
      • Schema and Validation
    • Marvin Documents - CXON
    • ISISDraw sketch file - SKC
      • Features imported from SKC files
      • Features exported to SKC format
    • ChemDraw sketch file - CDX, CDXML
      • Features imported from CDX and CDXML files
      • Features exported to CDX
      • Features exported to CDXML
  • Graphics Formats
    • Image Export in Marvin
      • JPEG
      • BMP
      • PNG
      • EMF
      • PDF
      • SVG
      • TIFF
      • EPS
    • Export to POV-Ray
    • Image Import in Marvin
  • Molecule file conversion with Molconvert
  • Molecule Formats
    • CML
      • CML Export Options
    • MDL MOL files
      • MDL MOLfiles, RGfiles, SDfiles, Rxnfiles, RDfiles formats
      • Chemaxon specific information in MDL MOL files
      • MOL file compression
      • MDL MOL Import and Export Options
      • Default valence of metal atoms
    • Daylight SMILES related formats
      • SMILES
      • SMARTS
      • SMILES and SMARTS import and export options
    • Chemaxon SMILES extensions
      • Chemaxon Extended SMILES and SMARTS - CXSMILES and CXSMARTS
      • CXSMILES and CXSMARTS import and export options
      • Chemaxon SMILES Abbreviated Group
    • IUPAC InChI, InChIKey, RInChI and RInChIKey
      • InChi and InChiKey export options
    • Name
    • Sequences - peptide, DNA, RNA
      • Peptide import and export options
    • FASTA file format
      • FASTA import options
    • Protein Data Bank (PDB) file format
      • Standard PDB residues
      • PDB import and export options
    • Tripos SYBYL MOL and MOL2 formats
      • Tripos Mol2 format
      • Tripos SYBYL MOL format
    • XYZ format
      • XYZ import and export options
    • Gaussian related file formats
      • Gaussian Cube format
      • Gaussian Cube import and export options
      • Gaussian input-output format
    • Markush DARC format - VMN
      • VMN peptide import option
    • CSV
• Input and Output System
  • Supported formats
  • Input and Output System - Import
  • Input and Output System - Export
  • Image generation
  • Importing and Exporting molecule properties
  • Molecule converter
  • Integrating your own format
• License Management
  • License Installation
    • Installing to Desktops
    • Installing to Servers
    • License Server Configuration
    • Licensing Applets
    • Licensing via Java Web Start
    • Setting environment variables
  • License Management FAQ
  • About Chemaxon Licensing
  • Licensing Prior Version 5.0
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• Long-Term Support (LTS)
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• Notice about CAS Registry Numbers®
• Public Repository
• Scientific Background
  • Aromatization
    • Methods
    • Differences between the Basic and General aromatization methods
    • Aromatization of query structures
    • Dearomatization
  • Stereochemistry
    • Parity
    • Tetrahedral Stereo
    • Cis-trans stereo
    • Axial stereoisomerism - atropisomerism
  • Valence Calculations
    • Alkali metals and Hydrogen
    • Alkaline earth metals
    • Transition metals, Lanthanoids and Actinoids
    • Boron group
    • Carbon group
    • Nitrogen group
    • Oxygen group
    • Halogens
    • Noble gases
    • Aromatic systems
    • Special cases - abbreviations query properties
  • Atom-by-Atom Search
• Structure Representation
  • Structure Representation - Class Representation
    • MolAtom
    • MolBond
    • Molecule Graph
    • R-group structures
      • Implementation
    • Representation of reactions
    • S-groups
    • Examples for Molecule representation
  • Aromaticity
    • Converting structure from Kekule form to aromatic form
    • Differences between the basic and general methods
    • Converting structure from aromatic form to Kekule form
  • Implicit, Explicit and Query Hydrogens
    • Converting explicit Hydrogens to implicit
    • Converting implicit Hydrogens to explicit
    • Query Hydrogens
  • Assigning stereochemistry descriptors
    • CIP Stereo chemistry
    • Stereoisomers around double bonds
      • Cis Trans stereoisomers in 0 Dimension
      • Cis Trans stereoisomers in 2 or 3 Dimensions
      • EZ stereoisomers
    • Parity information
      • Parity information in 0 Dimension
      • Parity information in 2 or 3 Dimensions
    • Chirality
  • Cleaning options
  • Deprecated and Removed Methods
    • All of the Deprecated and Removed Methods
    • Methods Deprecated or Removed in version 14.7.7.0
    • Methods Deprecated or Removed in version 6.3
    • Methods Deprecated or Removed in version 6.2
    • Methods Deprecated or Removed in version 6.1
  • Relative configuration of tetrahedral stereo centers
  • Iterator Factory
  • Atom and bond-set handling
  • Graphic object handling
• Supported Java Versions
• Used Libraries

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Discontinued Products

• BioEddie
  • BioEddie Developer's Guide
  • BioEddie User's Guide
    • BioEddie Interface Overview
      • Toolbar of BioEddie
      • Monomer Library Panel
      • Dialogues
    • Working in the Editor
      • Import to BioEddie
      • Editing molecules in BioEddie
        • Selection of molecule parts
        • Create a bond
        • Deleting molecule parts
        • Add - Insert - Replace - Delete a monomer
        • Moving molecules on the canvas
        • Clean
        • Zooming
        • Editing domains
      • Annotations
      • Monomer Library
        • Load library
        • Grouping monomers
        • Library Manager
    • Saving a structure
    • Replace tool
  • BioEddie System Requirements
  • BioEddie Licensing
  • BioEddie Getting Help and Support
  • BioEddie History of Changes
• Biomolecule Toolkit
  • Biomolecule Toolkit Administrator's Guide
    • Biomolecule Toolkit Deployment Guide
      • Biomolecule Toolkit Docker Setup
        • Running the Biomolecule Toolkit Container
      • Biomolecule Toolkit WAR Deployment
        • Download Package
        • System Environment Setup
        • License Files
        • Tomcat Deployment
      • Biomolecule Toolkit System Requirements
      • Database Setup for Biomolecule Toolkit
      • Schema Initialization
  • Biomolecule Toolkit User's Guide
    • Biomolecule Toolkit Library Manager
    • Biomolecule Toolkit Query Guide
      • Sequence Search Types
      • Query Features BMT
      • Sequence Search Options
      • Additional Data Handling
  • Biomolecule Toolkit API documentation
  • Biomolecule Toolkit History of Changes
• Document to Database
  • Document to Database Administration Guide
  • Document to Database System Requirements
  • Document to Database Licensing
  • Document to Database Getting Help and Support
  • Document to Database History of Changes
• Fragmenter
• JChem Neo4j Cartridge
  • JChem Neo4j Cartridge History of Changes
• JChem Web Services Classic
  • JChem Web Services Classic History of Changes
• Markush Overlap
• MarvinSpace
  • MarvinSpace User's Guide
    • What is MarvinSpace
    • MarvinSpace GUI Overview
      • Canvas - MarvinSpace
      • Menu bar
        • File Menu
        • Edit Menu
        • Display Menu
          • Draw Type Submenu
          • Color Type Submenu
          • Quality Submenu
          • Depth Cue menu item
          • Anti-alias menu item
          • Options Menu
            • Visualizers Tab
            • Surface Tab
            • Secondary Structure Tab
            • Colors Tab
            • Controls Tab
        • Show Menu
          • Labels submenu
          • Surface submenu
          • Secondary Structure menu item
        • Animation Menu
        • Help Menu
      • Pop-up menu
      • Toolbar
        • Controls
        • Monitors
        • Pharmacophore models
        • Display tools
      • Selection Panel
    • How to use MarvinSpace features
    • MarvinSpace Operations
  • MarvinSpace Developer's Guide
    • MarvinSpace parameters
      • Scene parameters
      • Action parameters
      • Ligand parameters
      • Macromolecular parameters
      • Water parameters
      • Ion parameters
      • Pharmacophore parameters
      • Surface parameters
      • Secondary Structure parameters
    • Step-by-step example - displaying atom properties
    • Step-by-step code examples
    • Surface coloring in MarvinSpace
  • MarvinSpace History of Changes
• Metabolizer
• Pipeline Pilot Components
  • Administration
  • Product Presentation
  • Getting Help and Support
  • Licensing
  • History of Changes
• Trainer Engine
  • Introduction
  • Installation
  • User Guide
  • Configuration
  • History of Changes
  • Known Issues
  • Getting help & support