Lithium LTS
Latest
Osmium LTS
Neon LTS
Mercury LTS
Lithium LTS
Krypton LTS
Iodine LTS
Helium LTS
Gallium LTS
Fermium LTS
Europium LTS
Standalone Applications
BioEddie
BioEddie Developer's Guide
BioEddie User's Guide
BioEddie Interface Overview
Toolbar of BioEddie
Monomer Library Panel
Dialogues
Working in the Editor
Import to BioEddie
Editing molecules in BioEddie
Selection of molecule parts
Create a bond
Deleting molecule parts
Add - Insert - Replace - Delete a monomer
Moving molecules on the canvas
Clean
Zooming
Editing domains
Annotations
Monomer Library
Load library
Grouping monomers
Library Manager
Saving a structure
Replace tool
BioEddie System Requirements
BioEddie Licensing
BioEddie Getting Help and Support
BioEddie History of Changes
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
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 - cHemTS
Login in Compliance Checker
Single Check
File check
Admin Guide - cHemTS
Install Guide - cHemTS
System Requirements - cHemTS
Installing - cHemTS
Configuring cHemTS
Administration GUI - cHemTS
Integration API
cHemTS Getting Help and Support
cHemTS History of Changes
cHemTS - Software
cHemTS - Knowledge Base
Compliance Checker
User Guide - Compliance Checker
Login in Compliance Checker
Single Check
File check
Admin Guide - Compliance Checker
Install Guide - Compliance Checker
System Requirements - Compliance Checker
Installing Compliance Checker
Configuring Compliance Checker
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
Integration API
Workflow tools
Compliance Checker Getting Help and Support
Compliance Checker History of Changes
Compliance Checker - Software
Compliance Checker - Knowledge Base
Try out!
Compound Registration
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
Compound Registration User's Guide
Overview
Compound Registration Abbreviations
Definitions of Terms
Compound Registration Introduction
Login
Dashboard page
Autoregistration
Registration page
Register a Virtual Compound
Bulk Upload
Upload compounds
Upload 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
Administration page
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
Message Queues
Deployment Guide
Compound Registration Installation requirements
Database setup
Deploying the application
Install through the wizard
Upgrade guide
Command Line Tools
Compound Registration FAQ
Compound Registration System Requirements
Compound Registration History of Changes
API documentation
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 a new project
Shared Projects
IJC Schemas
About IJC Schemas
Adding a New Schema
Connecting to an existing IJC schema
Logging in to an IJC schema
Editing Schema Connection Settings
Deleting a schema
Backing up and restoring schemas
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 5 framework
Scripting
Updating Instant JChem
About Updating Instant JChem
About Managing Plugins
Updating IJC
Managing IJC Update Centers
Installing Plugins Offline
Updating a Multi-User IJC Installation
Activating and Deactivating a Plugin
Plugin Manager - Downloaded
Plugins Manager - Available Plugins
Plugins Manager - Installed
Plugins Manager - Settings
Plugins Manager - Updates
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
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
Using Oracle Text in Instant JChem
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
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
New Features
New Features in IJC Q4 2020
New Features in IJC Q3 2020
New Features in IJC Q2 2020
New Features in IJC Q1 2020
New Features in IJC Q4 2019
New Features in IJC Q3 2019
New Features in IJC Q2 2019
New Features in IJC Q1 2019
New Features in IJC Q4 2018
New Features in IJC Q3 2018
New Features in IJC Q2 2018
New Features in IJC Q1 2018
New Features in IJC Q4 2017
New Features in IJC Q3 2017
New Features in IJC Q2 2017
New Features in IJC Q1 2017
New Features in IJC Q4 2016
New Features in IJC Q3 2016
New Features in IJC Q2 2016
New Features in IJC Q1 2016
New Features in IJC Q4 2015
New Features in IJC Q3 2015
New Features in IJC Q2 2015
New Features in IJC Q1 2015
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
Design Hub
History of changes
Install guide
Configuration guide
Plugin Catalogue
Developer guide - REST API
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 - company support plugins
Developer guide - registry plugins
Developer guide - theme customization
Install guide - Kubernetes
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
Draw 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 List and NOT List
Atom Properties
Generic Query Atom
Homology Group
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
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
MarvinSketch Application Options
Java VM Options in MarvinSketch
Running the Applications
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
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
Application Options
Options
Java VM Options
Property Colors
Marvin Desktop Suite Installation and Upgrade
Marvin Desktop Suite History of Changes
Marvin Desktop Suite Licensing
Molconvert
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 - Jupyter Example of usage
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 - About Chemaxon Licensing
Plexus Connect - End User License Agreement (EULA)
Plexus Connect - Installing Licenses
Plexus Connect - Merging License Files
Plexus Connect - Frequently Asked Questions about Licensing
Plexus Connect - License Report
Plexus Connect - Getting Help and Support
Plexus Connect - Troubleshooting for Plexus Connect
Plexus Connect - FAQ
Plexus Connect - Privacy Policy
Plexus Connect - Terms of Use for the Demo Site
Plexus Connect - History of Changes
Plexus Connect - Schema Refresh Without Restart
Zosimos
Zosimos User's Guide
Technical Information
LMS Integration Guides
Chemistry exercise types
Quick Start Guide for Teachers
Quick Start Example Content Library for Teachers
Quick Start Guide for Teachers with an LMS
Quick Start Guide for Students
Content Developer Guide
Videos
Frequently Asked Questions
Getting Help and Support
What's New
Trainer Engine
Introduction
Installation
User Guide
Configuration
History of Changes
Known Issues
Getting help & support
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
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 CP
Repeating units
Position variation bonds
Homology Groups CP
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
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
Biomolecule Toolkit
Biomolecule Toolkit Administrator's Guide
Biomolecule Toolkit Deployment Guide
Biomolecule Toolkit Docker Setup
Running the Biomolecule Toolkit Container
Biomolecule Toolkit WAR Deployment
Download Package
System Environment Setup
License Files
Tomcat Deployment
Biomolecule Toolkit System Requirements
Database Setup for Biomolecule Toolkit
Schema Initialization
Biomolecule Toolkit User's Guide
Biomolecule Toolkit Library Manager
Biomolecule Toolkit Query Guide
Sequence Search Types
Query Features BMT
Sequence Search Options
Additional Data Handling
Biomolecule Toolkit API documentation
Biomolecule Toolkit History of Changes
Chemaxon Synergy
Chemaxon Synergy User Guide
Chemaxon Synergy User Guide for Team Members
Accessing Applicatons
Groups
Logging in to Chemaxon Synergy
Logging out of Synergy
Guide for Team Administrators
Inviting Other Users to the Team
Inactivating Users of the Team
Adding Another Team Administrator to the Team
Managing Groups
Managing Projects
Centrify configuration
Chemaxon Synergy Developer Guide
Application and Service Discovery
Application authentication
Application authorization
Chemaxon Synergy integration workshop
Synergy Features Catalogue
SF-001 Application info
SF-002 Healthcheck
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
Chemaxon Synergy Administrator Guide
Guide for System Administrators
Creating a Team Space
Registering Applications
Removing an application instance from a team space when it is not needed anymore
Chemaxon Synergy History of Changes
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
JChem Base Administration
Installation Guide
Administration Guide - JChem Manager
Multiuser Support
Tomcat Configuration
Administration Guide for Composite DB
Preparing and Running Batch Files and Shell Scripts
JChem Base Developer's 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
JChem Base User's Guide
Query Guide
Search types
Similarity search
Query features JCB
Stereochemistry JCB
Special search types
R-group structures JCB
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 JCB
Hit display-coloring
Appendix JCB
Matching Query - Target Examples
jcsearch Command Line Tool
jcunique Command Line Tool
Homology Groups in Markush Structures
JChem Base FAQ
JCB FAQ
JChem Base and Cartridge Performance Information JCB
Environment Information of Performance Benchmark JCB
JChem Base History of Changes
JChem History of Changes from version 1.0.4 to 6.3.4
JChem Base Getting Help and Support
JChem Choral
Choral Installation and Administration
Choral Installation on Amazon Oracle RDS
Choral Installation on Amazon Oracle RDS and Fargate
Choral API Usage
Second Generation Search Engine
Choral FAQ and Known Issues
Comparison of JChem Choral and JChem Oracle Cartridge
JChem Choral History of Changes
JChem Oracle Cartridge
JChem Oracle Cartidge Administration
JChem Oracle Cartridge - Getting started guide
Installation and administration of JChem Cartridge for Oracle
JChem Oracle Cartridge Developer's Guide
JChem Cartridge for Oracle
Cartridge API
Cartridge API - Deferrred Error Handling
Description of parameters
External Java interfaces
Generic Molecular Descriptor Support
JChem Oracle Cartridge FAQ
JOC FAQ
JChem Cartridge Performance Information
JOC Environment Information of Performance Benchmark
JChem Oracle Cartridge History of Changes
JChem Oracle Cartridge Getting Help and Support
JChem Microservices
Calculations Web Services
DB Web Services
IO Web Services
Markush Web Services
Reactor Web Services
Structure Checker Web Services
Structure Manipulation
Second Generation Search Engine
JChem Microservices FAQ and Known Issues
JChem Microservices History of Changes
JChem PostgreSQL Cartridge
Getting Started JChem PostgreSQL Cartridge
JChem PostgreSQL Cartridge Manual
Installation and Administration
Install JPC on non standard PostgreSQL setup
JPC HA Installation Guide
Upgrade of PostgreSQL database together with JChem PostgreSQL Cartridge
API Usage
Deprecated API
Custom Structure Checker and Fixer in JPC
Citus Distibuted JChem PostgreSQL Cartridge
JDBC Caution
Second Generation Search Engine
JChem PostgreSQL Cartridge FAQ and Known Issues
JChem PostgreSQL Cartridge History of Changes
JChem PostgreSQL Cartridge Getting Help and Support
JChem PostgreSQL Cartridge Licensing
Comparison of JChem PostgreSQL Cartridge and JChem Oracle Cartridge
Migration Guide
JKlustor
What is JKlustor
Clustering methods
Hierarchical clustering
MCS search and LibMCS
Maximum Common Substructure (MCS) search
Library MCS (LibMCS) clustering
LibMCS GUI
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 Pro
Installation
How Do I?
Draw a Simple Molecule (Penicillin)
Draw a Simple Molecule (Phytol)
Draw a Synthesis Scheme
Use Basic Chemical Intelligence
Draw a Publication Image
References
Tools Overview
Shortcuts
Handling of Abbreviated Groups
Comparison of Marvin Pro and Marvin JS Feature Sets
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
Reactor in Plexus Suite
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
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 EULA
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 StrCh
Fixers
Structure Checking of Molecules
Working with Structure Checker
Checker List
Abbreviated Group StrCh
Absent Chiral Flag
Absolute Stereo Configuration
Alias
Aromaticity Error
Atom Map
Atom Query Property
Atom Value
Atropisomer
Attached Data StrCh
Bond Angle
Bond Length
Brackets
Chiral Flag
Chiral Flag Error
Circular R-group Reference
Coordination System Error
Covalent Counterion
Crossed Double Bond
Custom Checkers and Fixers
Double Bond Stereo Error
EZ Double Bond
Empty Structure
Explicit Hydrogen
Explicit Lone Pairs
Incorrect Tetrahedral Stereo
Isotope
Metallocene Error
Missing Atom Map
Missing R-group Reference
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
R-atom
Reacting Center Bond Mark
Reaction Map Error
Relative Stereo
R-group Attachment Error
R-group Bridge Error
R-group Reference Error
Ring Strain Error
Solvent
Star Atom
Stereo Care Box
Stereo Inversion Retention Mark
Straight Double Bond
Substructure
Three Dimension 3D
Unbalanced Reaction
Unused R-group Reference
Valence Error
Valence Property
Wedge Error
Wiggly Bond
Wiggly Double Bond
Creating a Configuration StrCh
Interfaces StrCh
MarvinSketch StrCh
Structure Checker Application
Structure Checker Editor
Structure Checker Command Line Application
JChem Cartridge StrCh
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 EULA
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
KNIME Nodes
Administration
Licensing
Getting Help and Support
History of Changes
Pipeline Pilot Components
Administration
Product Presentation
Getting Help and Support
Licensing
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
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 Molconverter
Molecule Formats
CML
CML Export Options
MDL MOL files
MDL MOLfiles, RGfiles, SDfiles, Rxnfiles, RDfiles formats
Chemaxon specific information in MDL MOL files
MOL file compression
MDL MOL Import and Export Options
Default valence of metal atoms
Daylight SMILES related formats
SMILES
SMARTS
SMILES and SMARTS import and export options
Chemaxon SMILES extensions
Chemaxon Extended SMILES and SMARTS - CXSMILES and CXSMARTS
CXSMILES and CXSMARTS import and export options
Chemaxon SMILES Abbreviated Group
IUPAC InChI, InChIKey, RInChI and RInChIKey
InChi and InChiKey export options
Name
Sequences - peptide, DNA, RNA
Peptide import and export options
FASTA file format
FASTA import options
Protein Data Bank (PDB) file format
Standard PDB residues
PDB import and export options
Tripos SYBYL MOL and MOL2 formats
Tripos Mol2 format
Tripos SYBYL MOL format
XYZ format
XYZ import and export options
Gaussian related file formats
Gaussian Cube format
Gaussian Cube import and export options
Gaussian input-output format
Markush DARC format - VMN
VMN peptide import option
CSV
Input and Output System
Supported formats
Input and Output System - Import
Input and Output System - Export
Image generation
Importing and Exporting molecule properties
Molecule converter
Integrating your own format
License Management
License Installation
Installing to Desktops
Installing to Servers
License Server Configuration
Licensing Applets
Licensing via Java Web Start
Setting environment variables
License Management FAQ
About Chemaxon Licensing
Licensing Prior Version 5.0
License Report
Merging Licenses
EULA
Long Term Supported Releases - LTS
LTS Release
LTS Release Versions
Documentation - LTS release
Notice about CAS Registry Numbers®
Public Repository
Scientific Background
Aromatization
Methods
Differences between the Basic and General aromatization methods
Aromatization of query structures
Dearomatization
Stereochemistry
Parity
Tetrahedral Stereo
Cis-trans stereo
Axial stereoisomerism - atropisomerism
Valence Calculations
Alkali metals and Hydrogen
Alkaline earth metals
Transition metals, Lanthanoids and Actinoids
Boron group
Carbon group
Nitrogen group
Oxygen group
Halogens
Noble gases
Aromatic systems
Special cases - abbreviations query properties
Structure Representation
Structure Representation - Class Representation
MolAtom
MolBond
Molecule Graph
R-group structures
Implementation
Representation of reactions
S-groups
Examples for Molecule representation
Aromaticity
Converting structure from Kekule form to aromatic form
Differences between the basic and general methods
Converting structure from aromatic form to Kekule form
Implicit, Explicit and Query Hydrogens
Converting explicit Hydrogens to implicit
Converting implicit Hydrogens to explicit
Query Hydrogens
Assigning stereochemistry descriptors
CIP Stereo chemistry
Stereoisomers around double bonds
Cis Trans stereoisomers in 0 Dimension
Cis Trans stereoisomers in 2 or 3 Dimensions
EZ stereoisomers
Parity information
Parity information in 0 Dimension
Parity information in 2 or 3 Dimensions
Chirality
Cleaning options
Deprecated and Removed Methods
All of the Deprecated and Removed Methods
Methods Deprecated or Removed in version 14.7.7.0
Methods Deprecated or Removed in version 6.3
Methods Deprecated or Removed in version 6.2
Methods Deprecated or Removed in version 6.1
Relative configuration of tetrahedral stereo centers
Iterator Factory
Atom and bond-set handling
Graphic object handling
Supported Java Versions
Legal
Legal Documents
Cookie Policy
End User License Agreement
End User Subscription Agreement - EUSA
Personal Data Management - General
Personal Data Management - Newsletter Subscriptions
Privacy Policy
Privacy Policy for Chemaxon Synergy
Terms of Use
Terms and Conditions for UX Research Program
Notice for Chemaxon Software User Experience (UX) Research
Recording Policy
White Papers
Chemicalize Security White Paper
Hosted Services Security White Paper
SaaS Security White Paper
Discontinued Products
Document to Database
Document to Database Administration Guide
Document to Database System Requirements
Document to Database Licensing
Document to Database Getting Help and Support
Document to Database History of Changes
Fragmenter
JChem Neo4j Cartridge
JChem Neo4j Cartridge History of Changes
Markush Overlap
MarvinSpace
MarvinSpace User's Guide
What is MarvinSpace
MarvinSpace GUI Overview
Canvas - MarvinSpace
Menu bar
File Menu
Edit Menu
Display Menu
Draw Type Submenu
Color Type Submenu
Quality Submenu
Depth Cue menu item
Anti-alias menu item
Options Menu
Visualizers Tab
Surface Tab
Secondary Structure Tab
Colors Tab
Controls Tab
Show Menu
Labels submenu
Surface submenu
Secondary Structure menu item
Animation Menu
Help Menu
Pop-up menu
Toolbar
Controls
Monitors
Pharmacophore models
Display tools
Selection Panel
How to use MarvinSpace features
MarvinSpace Operations
MarvinSpace Developer's Guide
MarvinSpace parameters
Scene parameters
Action parameters
Ligand parameters
Macromolecular parameters
Water parameters
Ion parameters
Pharmacophore parameters
Surface parameters
Secondary Structure parameters
Step-by-step example - displaying atom properties
Step-by-step code examples
Surface coloring in MarvinSpace
MarvinSpace History of Changes
Metabolizer
Plexus Suite
Quick Start Guide - Plexus Suite
Plexus Suite User Guide
Log in to Plexus Suite
The Plexus Suite Dashboard
Importing New Data
Exporting Your Data
Browsing in Your Data Set
Synchronized Database Views
Selecting Data
Searching in Your Database
Structure Search in Plexus Connect
Saved Queries
List Management
Sorting Data
Sharing Data with Other Users
Calculating Molecular Properties for Single Compounds
Adding calculated columns to tables
Scaffold Based Enumeration
Reaction Based Enumeration
Registering Molecules in the Corporate Database
Charts view
Plexus Suite Video Tutorials
Plexus Suite Administrator Guide
Plexus Suite Authentication
Sharing Schema Items Among Users
Business Flags
Row-level Security
Building blocks
Admin Tools
Messaging
Getting the Plexus Backend and Frontend Log Files
Adding JavaScript Files for Custom Functionality
Writing JavaScript Files for Custom Functionality
Integration with Chemaxon's Compound Registration System
Shared data sources in Plexus Connect
Configuration Files
Edit Views
Simple table
Installation and System Requirements of Plexus Suite
Plexus Suite Licensing
About Chemaxon Licensing - Plexus Suite
End User License Agreement (EULA) - Plexus Suite
Installing Licenses
Merging License Files
Frequently Asked Questions about Licensing - Plexus Suite
License Report - Plexus Suite
Getting Help and Support for Plexus Suite
Troubleshooting for Plexus Suite
Plexus Suite FAQ
Plexus Suite Privacy Policy
Terms of Use for the Plexus Suite Demo Site
Plexus Suite History of Changes
Schema Refresh Without Restart
JChem Web Services Classic
JChem Web Services Classic History of Changes
Trainer Engine
Welcome! You can find the documentation pages of ChemAxon's Trainer Engine below.
Introduction
Installation
User guide
Configuration
History of Changes
Known Issues
Getting help & support