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Standalone Applications
Chemaxon Assay
User guide for Assay
Processed data upload
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ChemCurator
ChemCurator Getting Help and Support
ChemCurator History of Changes
ChemCurator Installation and System Requirements
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Command-Line Mode
Integration Server Administrator Guide
Chemicalize
Introduction to Chemicalize
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Chemicalize User's Guide
Subscription management
Technical issues & Troubleshooting
Chemicalize Frequently Asked Questions
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ChemLocator
ChemLocator Installation
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Prerequisites: Docker
Prerequisites: Azure AD
Installation Guide
Uninstallation
ChemLocator Configuration
First-time configuration
Indexing
ChemLocator Upgrade
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File Formats
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Supported Browsers
ChemLocator Migration
How To
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Developer Guide
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Knowledge Base
Compliance Checker
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Login in Compliance Checker
Single Check
File check
Administration Guide
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Configuring
Administration GUI
Login as Administrator
Update the regulations
System monitor
Category group editor
User-defined category editor
History
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Report template editor
Developer Guide
API integration
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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
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User guide
Overview
Compound Registration Introduction
Compound Registration Abbreviations
Definitions of Terms
Quick Start Guide
Register a new compound
Register a new lot
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Dealing with failed submissions
Register compounds without structures
Login
Dashboard page
Autoregistration
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Register a Virtual Compound
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Upload compounds
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Upload salts and solvates
Advanced Registration
Register from the Registration page
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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
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Appendix A. Calculations
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Multi-Component compounds
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Configuration guide
Access Control
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Downstream
History of Changes
FAQ
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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
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IJC Schemas
About IJC Schemas
Adding New Schema
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Viewing and Managing Data
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Multiple Data Result Set
Viewing multi-entity data
Form View
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Grid View in Instant JChem
Grid View from Selection
Form Widgets
Standard Widgets
TextField Widget
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TreeTable Widget
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Visualisation Widgets
Histogram Widget
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Conditional Formatting
Step by Step guide
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Renderers
Pivoting in IJC
Lists and Queries
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Query Overview
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Instant JChem URLs
Import and Export
Using File Import
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About Primary Keys
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Calculated Fields
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Pick list
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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
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Security Templates
Row level security
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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
Molconvert
User guide
Administration guide
Installation
System requirements
Licensing
About Chemaxon Licensing
License Installation
Setting up proxy for licensing
License Report
Marvin bundles
Licensing Prior Version 5.0
Merging Licenses
EULA
License Management FAQ
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
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
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 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
Synergy 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
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
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
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
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
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
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
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 Structure Checker
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
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Before Using
Installation
How to Check the Bit-version of MS Office
Microsoft Office 2013, 2016 and 2019
Silent Installation
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User Guide
JChem for Excel User's Guide
JChem for Excel Ribbon
Standard Menu
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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
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Show and Hide Structures and Structure IDs
Insert Single Structures
Open Structure Files
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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
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Import from IJC Database in JChem for Excel
Import from IJC Database-Source Tab
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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
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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
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IJC Import Options in JChem for Excel
File Export Options in JChem for Excel
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Structure Sheet Options
Image Conversion Options
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Structure Editor Options in JChem for Excel
Event Handling Options in JChem for Excel
Actions
Functions 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
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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
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IJC Import
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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
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Structure
Tautomers in JChem for Office
Topology Analysis
Switching JChem for Office to Lite Mode
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JChem for Office Lite User's Guide
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JChem for Office Tutorial Videos
Enable JChemExcel.Functions add-in after it gets disabled
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CAS conversion and license key do not work
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KNIME Nodes
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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
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Chemical Fingerprints licensing
Chemical Terms
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Evaluator Examples
Instant JChem CT
JChem Base CT
Chemical Terms - JChem Cartridge
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The Chemical Terms Language
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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
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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
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Setting environment variables
License Management FAQ
About Chemaxon Licensing
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License Report
Merging Licenses
Long-Term Support (LTS)
LTS Releases
LTS Release Versions
LTS Release Documentation
Notice about CAS Registry Numbers®
Public Repository
Scientific Background
Aromatization
Methods
Differences between the Basic and General aromatization methods
Aromatization of query structures
Dearomatization
Stereochemistry
Parity
Tetrahedral Stereo
Cis-trans stereo
Axial stereoisomerism - atropisomerism
Valence Calculations
Alkali metals and Hydrogen
Alkaline earth metals
Transition metals, Lanthanoids and Actinoids
Boron group
Carbon group
Nitrogen group
Oxygen group
Halogens
Noble gases
Aromatic systems
Special cases - abbreviations query properties
Atom-by-Atom Search
Structure Representation
Structure Representation - Class Representation
MolAtom
MolBond
Molecule Graph
R-group structures
Implementation
Representation of reactions
S-groups
Examples for Molecule representation
Aromaticity
Converting structure from Kekule form to aromatic form
Differences between the basic and general methods
Converting structure from aromatic form to Kekule form
Implicit, Explicit and Query Hydrogens
Converting explicit Hydrogens to implicit
Converting implicit Hydrogens to explicit
Query Hydrogens
Assigning stereochemistry descriptors
CIP Stereo chemistry
Stereoisomers around double bonds
Cis Trans stereoisomers in 0 Dimension
Cis Trans stereoisomers in 2 or 3 Dimensions
EZ stereoisomers
Parity information
Parity information in 0 Dimension
Parity information in 2 or 3 Dimensions
Chirality
Cleaning options
Deprecated and Removed Methods
All of the Deprecated and Removed Methods
Methods Deprecated or Removed in version 14.7.7.0
Methods Deprecated or Removed in version 6.3
Methods Deprecated or Removed in version 6.2
Methods Deprecated or Removed in version 6.1
Relative configuration of tetrahedral stereo centers
Iterator Factory
Atom and bond-set handling
Graphic object handling
Supported Java Versions
Legal
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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
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Add - Insert - Replace - Delete a monomer
Moving molecules on the canvas
Clean
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Annotations
Monomer Library
Load library
Grouping monomers
Library Manager
Saving a structure
Replace tool
BioEddie System Requirements
BioEddie Licensing
BioEddie Getting Help and Support
BioEddie History of Changes
Biomolecule Toolkit
Biomolecule Toolkit Administrator's Guide
Biomolecule Toolkit Deployment Guide
Biomolecule Toolkit Docker Setup
Running the Biomolecule Toolkit Container
Biomolecule Toolkit WAR Deployment
Download Package
System Environment Setup
License Files
Tomcat Deployment
Biomolecule Toolkit System Requirements
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Schema Initialization
Biomolecule Toolkit User's Guide
Biomolecule Toolkit Library Manager
Biomolecule Toolkit Query Guide
Sequence Search Types
Query Features BMT
Sequence Search Options
Additional Data Handling
Biomolecule Toolkit API documentation
Biomolecule Toolkit History of Changes
Document to Database
Document to Database Administration Guide
Document to Database System Requirements
Document to Database Licensing
Document to Database Getting Help and Support
Document to Database History of Changes
Fragmenter
JChem Neo4j Cartridge
JChem Neo4j Cartridge History of Changes
JChem Web Services Classic
JChem Web Services Classic History of Changes
Markush Overlap
MarvinSpace
MarvinSpace User's Guide
What is MarvinSpace
MarvinSpace GUI Overview
Canvas - MarvinSpace
Menu bar
File Menu
Edit Menu
Display Menu
Draw Type Submenu
Color Type Submenu
Quality Submenu
Depth Cue menu item
Anti-alias menu item
Options Menu
Visualizers Tab
Surface Tab
Secondary Structure Tab
Colors Tab
Controls Tab
Show Menu
Labels submenu
Surface submenu
Secondary Structure menu item
Animation Menu
Help Menu
Pop-up menu
Toolbar
Controls
Monitors
Pharmacophore models
Display tools
Selection Panel
How to use MarvinSpace features
MarvinSpace Operations
MarvinSpace Developer's Guide
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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
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