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
      • 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
          • MCS search and LibMCS
            • Maximum Common Substructure (MCS) search
            • Library MCS (LibMCS) clustering
            • LibMCS 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: 6

Search | Chemaxon Docs

https://docs.chemaxon.com/display/docs/s?q=cleanoptions

The following clean options can be specified. Search | Chemaxon Docs · https://docs.chemaxon.com/display/docs/s?q=cleanoptions. Cleaning options · Command line ...

Search | Chemaxon Docs

https://docs.chemaxon.com/display/docs/s?q=parameters.cleanDim

https://docs.chemaxon.com/display/docs/s?q=cleanoptions. Options for 2D or 3D cleaning. cleanOpts accepts the same parameter values as clean2dOpts or ...

Clean 2D | Chemaxon Docs

https://docs.chemaxon.com/display/docs/standardizer_clean-2d.md

Clean 2D Action performs automatic two-dimensional atom coordinate calculation. The following clean options can be specified.

Cleaning options | Chemaxon Docs

https://docs.chemaxon.com/display/.../representation_cleaning-options.md

Cleaning options. One can use cleaning options in various cases, for example: Command line parameter in the MolConverter application.

Web Services | Chemaxon Docs

https://docs.chemaxon.com/display/docs/marvin-js_web-services-dev.md

... clean options> } }. Copy. Parameters. Option, Type, Description. dim, integer, clean dimensions; 2 or 3. opts, string, further clean options (optional) ...

Chemical Terms Evaluator | Chemaxon Docs

https://docs.chemaxon.com/display/docs/chemical-terms_evaluator.md

... cleanoptions.md) -f, --format <format> output format if result is molecule (default: smiles or smarts) (ignores the output options below) -x, --extract ...

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