Latest

  • 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
        • 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 ChemTerm 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 on AWS Marketplace
        • Getting started
        • Pricing
        • Developer's guide
      • 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
          • CAS conversion and license key do not work
        • Diagnostic Tool
      • 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 PF
      • Reaction Fingerprint RF
      • 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
        • Instant JChem CT
        • JChem Base CT
        • 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 CT
          • Search Filter Examples
      • Usage examples CT
        • Basic Calculations
        • Search Filters
        • Reaction Processing
        • Markush Enumeration CT
    • 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
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Total results: 50

RasMol Scripts | Chemaxon Docs

https://docs.chemaxon.com/display/docs/marvin_rasmol-scripts.md

RasMol Scripts. MarvinView can execute scripts containing 3D viewing commands delimited by semicolons or newlines. Comment lines start with #. Currently ...

In-View Python Scripting Console in Plexus Connect | Chemaxon ...

https://docs.chemaxon.com/.../plexus-connect_in-view-python-scripting-co...

Example 4: Adding Interactive 3D Chart. The following Python script is designed for visualizing the relationship between two variables and an outcome in ...

MarvinView 3D and Animation | Chemaxon Docs

https://docs.chemaxon.com/.../marvin_marvinview_3d-and-animation.md

... script. Note: To load the script from a file, use the script command: <param name="script" value="script myscript.spt">, N/A. spin spin0 spin1 spin2 ...

Search | Chemaxon Docs

https://docs.chemaxon.com/display/docs/s?q=3d.rendering

RasMol Scripts. MarvinView can execute scripts containing 3D viewing commands delimited by semicolons or newlines. ... Sticks rendering style.This command is ..

Preparing and Running Batch Files and Shell Scripts | Chemaxon ...

https://docs.chemaxon.com/.../preparing-and-running-batch-files-and-shell-...

High performance 3D visualization. mview, MarvinView, Displaying structure files. nneib, NNeib, Nearest neighbor search for creating input for Jarp ...

MarvinView Developer's Guide | Chemaxon Docs

https://docs.chemaxon.com/.../marvin_marvinview_developer-guide.md

MarvinView 3D and Animation · RasMol Scripts · Molecule Tables · The layout Parameter · The param Parameter · The celli and celli_j parameters · MarvinView ...

Standardizer Command-line Application | Chemaxon Docs

https://docs.chemaxon.com/.../standardizer-command-line-application.md

Prepare the usage of the standardize script or batch file as described here. ... 3D structures :<template file> perform template based clean in 2D clean3d ...

Standardizer File Formats | Chemaxon Docs

https://docs.chemaxon.com/display/docs/standardizer_file-formats.md

SQL Scripts for Manual Schema Upgrade · Database Row Level Security ... 3D Alignment Plugin · Molecular Dynamics Plugin · Structural property plugins.

Working with Data in the Grid View | Chemaxon Docs

https://docs.chemaxon.com/display/docs/grid-view-in-instant-jchem.md

Displaying 3D structures as 2D (3D coordinates are preserved). Displaying of ... This script should be applied through the schema disconnect/connect script window ...

jcsearch Command Line Tool | Chemaxon Docs

https://docs.chemaxon.com/.../jchem-base_jcsearch-command-line-tool.md

Note that the R-group decomposition functionality has been moved to a different script ... 3D molecules, specify color of non-hit atoms and bonds examples: "red ...

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