Europium LTS
Latest
Osmium LTS
Neon LTS
Mercury LTS
Lithium LTS
Krypton LTS
Iodine LTS
Helium LTS
Gallium LTS
Fermium LTS
Europium LTS
Standalone Applications
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
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
Old Linux Installer
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 - Contents
Compliance Checker - Software
Compliance Checker Knowledge Base - Contents
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
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
Submission correction page
Workspace
Status message
Structure area
Data fields
Card
Search
Search option
Type of search
Match type
Search query
User Profile
Download
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
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
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
Sharing data with other applications
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
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
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
Deploying Spotfire Middle Tier solution
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
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
TanimotoSimilarityButton
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
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 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
New Features in IJC 14.7.7
New Features in IJC Q4 2019
Instant JChem Licensing
IJC Getting Help and Support
Instant JChem System Requirements
Chart Testing
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 Live
Marvin Live user guide
Marvin Live history of changes
Marvin Live install guide
Marvin Live - cloud deployment
Marvin Live developer guide - sending data
Marvin Live developer guide - resolver plugins
Marvin Live developer guide - real time plugins
Marvin Live developer guide - export plugins
Marvin Live developer guide - theme customization
Marvin Live migration guide
Marvin Live developer guide - storage plugins
Marvin Live developer guide - real time plugin templates
Marvin Live configuration guide
MarvinSketch
Introduction to MarvinSketch
MarvinSketch User's Guide
MarvinSketch Getting Started
Start to draw in MarvinSketch
Select
Deleting in MarvinSketch
Move Rotate Zoom Scale
Tricks and Tips
MarvinSketch Graphical User Interface
Canvas in MarvinSketch
Menus of MarvinSketch
File Menu in MarvinSketch
Edit Menu in MarvinSketch
View Menu in MarvinSketch
Insert Menu
Atom Menu
Bond Menu
Structure Menu in MarvinSketch
Calculations Menu
Services Menu
Help Menu in MarvinSketch
Toolbars of MarvinSketch
General Toolbar in MarvinSketch
Tools Toolbar in MarvinSketch
Atoms Toolbar
Simple Templates toolbar
Advanced Templates Toolbar
Special Toolbars
Chemical Toolbar
Markush Toolbar
3D Editing Toolbar
Pop-up Menus of MarvinSketch
Atom Pop-up Menu
Bond Pop-up Menu
Edit Pop-up Menu
Object Pop-up Menu
Status bar of MarvinSketch
Dialogs of MarvinSketch
Multipage Settings
Document Style
Template Library Manager
Edit Source
Customize
Where are the settings stored
Format Dialog
Atoms and Bonds
Graphics Objects
Periodic Table of Chemical Elements
Periodic Table tab
Advanced tab
Generic query atoms
Atom query properties
Periodic Table Groups
Special nodes and R-groups
Custom Properties
Preferences in MarvinSketch
Bonds tab
Structure tab
Text tab
Checkers tab
Services tab
Save-Load tab
3D Options tab
Analysis box tab
Create Group Dialog
Attach data
Edit properties
About MarvinSketch
Shortcuts in MarvinSketch
Customizing MarvinSketch GUI
Basic changes
Advanced Changes
Menus tab
Pop-ups tab
Toolbars tab
Keymap tab
Special commands
Changing the default Look and Feel
Configurations of MarvinSketch
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 in MarvinSketch
Saving Display Options
Basic Editing
Selecting a Structure
Copy-Paste and DragandDrop
Geometric transformation of structures and objects
Moving and Rotating
Scaling
Flip a molecule
Mirror a molecule
Central inversion of a molecule
Cleaning
Deleting a Structure
Editing the source
Drawing Simple Structures
How to Draw Atoms
How to Draw Bonds
How to Draw Chains
Sprouting
Merging Structures
Templates in MarvinSketch
Drawing stereocenters
How to draw coordination compounds
Insert-Edit new structure, fragment
Atom Label Editor
Drawing More Complex Structures
Substructure Groups in MarvinSketch
Abbreviated (superatom) groups
Polymers
Structure-based representation of polymers
Structural repeating unit (SRU) polymers
Repeating units with repetition ranges - Frequency variation
Copolymers
Source-based representation of polymers
How to draw polymers
Unordered Mixtures and Ordered Mixtures
Charge of the group
Draw R-groups in MarvinSketch
Draw link nodes
Homology Groups in MarvinSketch
Atom lists and NOT lists
Position variation in MarvinSketch
Markush structures in MarvinSketch
How to draw query structures
Biomolecules
Atom, bond and molecule properties
Drawing reactions
Create Reactions
Automatic Plus Signs in Single step Reactions
Manual Plus Signs
Mapping Reactions
Electron flow arrows
Use integrated calculations in Marvin
Graphical objects
How to add, edit and format text
How to draw shapes
Import and export options
Open a molecule file
Saving a molecule file
Export to image
Multipage documents
How to create a multipage document
How to navigate in multipage documents
Printing in MarvinSketch
Chemical Features in MarvinSketch
Valence Check
Structure Checker in MarvinSketch
Charges, Isotopes, Radicals
Charges
Isotopes in MarvinSketch
Isotope List Editing
Radicals
Stereochemistry in MarvinSketch
Reaction schemes
Abbreviated groups - Superatom group
Query Features
R-groups in MarvinSketch
Link Nodes
Atom List and NOT List
Atom Properties
Generic Query Atom
Homology group
Attached Data
Calculations
Analysis box
Calculations Plugins in MarvinSketch
Marvin OLE User's Guide
Install and Uninstall
How to Use
Customize Marvin OLE editing mode
Redirecting other Vendors' OLE objects to Marvin OLE
Logging
Troubleshooting and Administration
Known Issues
Appendix for MarvinSketch
Trademarks
Tutorials
Additional information
MarvinSketch Developer's Guide
Customizing MarvinSketch GUI - Server Side
Customizing Marvin GUI
Customizing MarvinSketch GUI - Assign new action
Clipboard formats configuration
Configure the Attach Data Dialog
MarvinSketch: Parameters and Events
Parameters
JavaBeans parameters
Display parameters
Structure Templates
Query properties in molecule file formats
Structure display parameters
The shapely color scheme in Marvin
Structure parameters
Other parameters
Events fired by JavaBean
Action events
Property change events
Marvin Beans for Java
Marvin Beans API documentation
Marvin Beans Examples
MarvinSketch Examples
Marvin Sketch Simple Bean
MarvinSketch Images
MarvinSketch Structure Display Parameters
MarvinSketch Structure Templates
Text Box Example
JFileChooser Example
MarvinView Examples
MarvinView Simple Bean Example
MarvinView In JTable Example
MarvinView Table View Example
MarvinView Table View Example with Parameters
MarvinView 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
Introduction to Java Web Start
Marvin Sketch Examples
Report a bug
MarvinSketch Application Options
Java VM options in MarvinSketch
Running the Applications
MarvinSketch Installation and Upgrade
System Requirements for Marvin
Installation of MarvinSketch
Version Number
MarvinSketch Licensing
MarvinSketch Getting Help and Support
MarvinSketch Downloads
MarvinSketch History of Changes
Current version of MarvinSketch
All changes in reversed chronological order
MarvinView
Introduction to MarvinView
MarvinView Developer's Guide
MarvinView Parameters and Events
MarvinView Parameters
MarvinView JavaBeans parameters
MarvinView Display parameters
MarvinView Structure display parameters
MarvinView Structure parameters
MarvinView 3D and animation
RasMol Scripts
Molecule tables
The layout parameter
The param parameter
The celli and celli_j parameters
MarvinView Table View
MarvinView Other parameters
MarvinView Applet only parameters
Events fired by the JavaBean
Troubleshooting - MView and JMView tables
MarvinView Application Options
Usage MV
Options
Java VM options
Property colors in MarvinView
Running MarvinView
MarvinView Installation and Upgrade
System Requirements for MarvinView
Installation of MarvinView
Version Numbering of MarvinView
MarvinView User's Guide
MarvinView Getting started
How to Use MarvinView Features
Importing and Exporting Molecules
Loading Molecules into MarvinView
Saving Molecules
Printing Molecules
Editing Molecules
Structure Display Options in MarvinView
Molecule Format
Color schemes in MarvinView
Display options for implicit and explicit hydrogens in MarvinView
Marking Atoms
Error Highlighting
Manipulating the Molecule
How to Work with Multipage Molecular Documents
MarvinView Graphical User Interface
Dialogs of MarvinView
Preferences dialog in MarvinView
Display
Bonds
Structure tab in MarvinView
Checkers tab in MarvinView
Services tab in MarvinView
Save-Load tab in MarvinView
OLEServer
Edit Source dialog
Table Options
About Marvin View
Menus of MarvinView
File Menu in MarvinView
Edit Menu in MarvinView
View Menu in MarvinView
Table Menu
Structure Menu in MarvinView
Tools Menu
Pages
Help Menu in MarvinView
MarvinView Licensing
About ChemAxon Licensing - MarvinView
End User License Agreement:EULA - MarvinView
Installing licenses in MarvinView
Installing licences to MarvinView desktops
Installing licences to servers
Licensing MarvinView via Java Web Start
Merging license files - MarvinView
License FAQ - MarvinView
Licensing prior version 5.0 - MarvinView
MarvinView Getting Help and Support
MarvinView Downloads
MarvinView History of changes
Current version
Earlier versions
Molconvert
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 plexus
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
ChemAxon Assay
User guide for Assay
Processed data upload
Processed data view
Administration guide for Assay
Assay Release Notes
Manual for Migration from Procedure to Protocol
Charts view
Plexus Suite Video Tutorials
Plexus Suite Administrator Guide
Plexus Connect 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
Zosimos
Zosimos User's Guide
Browser and device compatibility
Chemistry exercise types
Molecule representations
Getting Help and Support
Toolkits and Components
AutoMapper
AutoMapper User's Guide
Calculator Plugins
Introduction to Calculator Plugins
Calculator Plugins User's Guide
Physico-chemical plugins
HLB Predictor
Isoelectric Point Plugin
logD Plugin
logP Plugin
Major Microspecies Plugin
NMR Predictor
pKa Plugin
Solubility Predictor
Stereo Analysis - calculating stereo descriptors
Stereoisomer Generator Plugin
Tautomer Generation Plugin
Molecular modeling plugins
3D Alignment Plugin
Charge Plugin
Conformer Plugin
Dipole Moment Calculation Plugin
Molecular Dynamics Plugin
Orbital Electronegativity Plugin
Polarizability Plugin
Structural property plugins
Elemental Analysis Plugin
Geometrical Descriptors Plugin
Huckel Analysis Plugin
Hydrogen Bond Donor Acceptor Plugin
Molecular Surface Area Plugin 3D
Polar Surface Area Plugin 2D
Refractivity Plugin
Resonance Plugin
Structural Frameworks Plugin
Topological Analysis 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
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
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
Download Package
Biomolecule Toolkit System Requirements
System Environment Setup
Creating Environment Variables
Database Setup for Biomolecule Toolkit
Tomcat Deployment
License Files
Schema Initialization
Biomolecule Toolkit Docker Setup
Running the Biomolecule Toolkit Container
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
ChemAxon Synergy Administrator Guide
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
Code examples
Code
Document to Structure Licensing
Documents for Previous Releases
Document to Structure Developer's Guide - Document Extractor
Document to Structure Getting Help and Support
Document to Structure History of Changes
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
Tautomer search - Vague bond search - sp-Hybridization
Search Options Guide
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
Standardization JCB
Hit display-coloring
Appendix JCB
Matching Query - Target Examples
jcsearch Command Line Tool
jcunique Command Line Tool
Homology Groups and 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 Base Licensing
JChemBase EULA
JChem Base License Key
JChem Choral
Choral Installation and Administration
Choral API Usage
Choral FAQ and Known Issues
JChem Choral History of Changes
JChem Neo4j Cartridge
JChem Neo4j Cartridge 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 Oracle Cartridge Licensing
JChem Oracle Cartridge EULA
JChem Microservices
Calculations Web Services
DB Web Services
IO Web Services
Markush Web Services
Structure Manipulation
JChem Microservices History of Changes
Marvin JS Web Services
JChem PostgreSQL Cartridge
Getting Started JChem PostgreSQL Cartridge
JChem PostgreSQL Cartridge Manual
Installation and Administration
API Usage
Deprecated API
Citus Distibuted JChem PostgreSQL Cartridge
JDBC Caution
JChem PostgreSQL Cartridge History of Changes
JChem PostgreSQL Cartridge Getting Help and Support
JChem PostgreSQL Cartridge Licensing
JChem Web Services Classic
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
Markush Overlap
Marvin JS
Getting Started with Marvin JS
Create
Navigate on the canvas
Select-Move-Delete
Marvin JS Tips and Tricks
Marvin JS Installation and System Requirements
Browser compatibility
Marvin JS Developer's Guide
How to Embed it
Web services
Marvin JS User's Guide
Editor Overview
Editor Canvas
Dialogs
Abbreviated groups dialog
Default abbreviated group list in Marvin JS
Atom query properties dialog
Attached Data dialog
Bond properties dialog
Export dialog
Import dialog
Periodic table dialog
Atom properties dialog in Marvin JS
Pseudo atom dialog
Reaxys Group Generics dialog
Repeating group dialog
R-group dialog
R-logic dialog
Set box color dialog
Text dialog
View Settings dialog
Toolbars
Atom Toolbar - Right Toolbar
Frequently used atoms
Periodic table
Query Atoms
General Toolbar - Top Toolbar
Add-Remove explicit Hydrogen
Aromatize, dearomatize
Auto map
Calculate stereo
Clear
Cut-Copy-Paste
Export button
Import button
Rotate 3D
Structure Cleaning
Undo-Redo
View settings
Zoom
Template Toolbar - Bottom Toolar
Abbreviated group
Template
Tools Toolbar - Left Toolbar
Bond tools
Chain
Charge
Delete tool
Electron flow arrow
Graphical boxes
Radical and lone pair
Reaction tools
Repeating Group
R-group attachment
Selection MJS
Selection tools
Smart R-group
Text
Tools toolbar in Marvin JS
Slide toolbar buttons
Context menus
Atom Context menu
Bond Context menu
Empty Space Context menu
Graphical Objects Context menu
Abbreviated Group Context menu
R-group label Context Menu
Selection Context Menu
Repeating Group Context menu
Drawing and editing options
Atom
Atom mapping
Bond
Copy structures
Graphical Objects in Marvin JS
Radicals and Lone pairs
Reaction
Reaction Mechanism
R-group representation and editing options
Rotating in 2D
Snapped objects
Substructure elements-Templates, Abbreviations, Groups and Chains
Abbreviations
Chains
Groups-Link nodes
Groups-Repetition units
Structural Templates
Text editing
Feature overview pages
Markush Structures in Marvin JS
Query Structures in Marvin JS
Stereochemistry in Marvin JS
Reactions and mechanisms in Marvin JS
Keyboard Shortcuts in Marvin JS
Marvin JS API Reference
Online Examples
Marvin JS Licensing
Marvin JS EULA
Marvin JS History of Changes
Marvin JS FAQ
Marvin JS Getting Help and Support
Marvin JS Troubleshooting
Marvin JS Video Tutorials
Name to Structure
Name to Structure Developer's Guide
Name to Structure Format options
Name to Structure Getting Help and Support
Name to Structure History of Changes
Name to Structure Licensing
Name to Structure User's Guide
Custom Dictionary in Name Import
Custom Webservice in Name Import
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
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 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's 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 Documentation
KNIME Nodes
KNIME Nodes Administration
KNIME Nodes Licensing
KNIME Nodes Getting Help and Support
KNIME Nodes History of Changes
Pipeline Pilot Components
Pipeline Pilot Components Administration
Pipeline Pilot Components Product Presentation
Pipeline Pilot Components Getting Help and Support
Pipeline Pilot Components Licensing
Pipeline Pilot Components History of Changes
Pipeline Pilot Components History of Changes by Branches
Cross Product Documentation
ChemAxon Configuration Folder
Chemical Fingerprints
Extended Connectivity Fingerprint ECFP
Chemical Hashed Fingerprint
Pharmacophore Fingerprint PF
Reaction fingerprint RF
Fingerprint and descriptor generation - GenerateMD
Pharmacophore perception - PMapper
Chemical Fingerprints licensing
Chemical Terms
Available Functions
Functions by Categories
Functions in Alphabetic Order
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
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
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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®
Other versions
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
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Document to Database
Document to Database Administration Guide
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Document to Database Getting Help and Support
Document to Database History of Changes
Fragmenter
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
Compliance Checker Software - Contents