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    Documentation
    • AutoMapper Home
      • AutoMapper
    • 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
      • Calculator Plugins licensing
      • Calculator Plugins FAQ
      • Calculator Plugins Getting Help and Support
      • History of Changes - Calculator Plugins
    • Chemical Terms Home
      • Chemical Terms Introduction
      • Chemical Terms Getting Started
      • 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
      • Available Functions
        • Functions by Categories
        • Functions in Alphabetic Order
      • Usage examples CT
        • Basic Calculations
        • Search Filters
        • Reaction Processing
        • Markush Enumeration CT
      • 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
      • Chemical Terms Getting Help and Support
    • Compliance Checker
      • Compliance Checker User's Guide
      • Admin Guide - Compliance Checker
        • Compliance Checker Installation Guide
          • System Requirements 1
          • Installing on Linux
          • Installing on Windows
        • Advanced LDAP settings
        • Administration GUI
      • Compliance Checker Getting Help and Support
      • Compliance Checker History of Changes
        • Compliance Checker - Software
        • Compliance Checker - Knowledge Base
    • Chemical Fingerprints - Home
      • Extended Connectivity Fingerprint ECFP
      • Chemical Hashed Fingerprint
      • Pharmacophore Fingerprint PF
      • Reaction fingerprint RF
      • Fingerprint and descriptor generation - GenerateMD
      • Pharmacophore perception - PMapper
    • Compound Registration
      • Quick Start Guide
        • Register a new compound
        • Register a new lot
        • Register a new compound reviewing matches
        • Dealing with failed submissions
      • Compound Registration User's Guide v161121
        • Overview
        • Compound Registration Abbreviations
        • Definitions of Terms
        • Compound Registration Introduction
        • Login
        • Dashboard page
        • Autoregistration
          • Registration page
          • Validation
          • Standardizing
          • Structure Checking and Fixing
          • Registering a new structure
          • Registering a match
        • Bulk Load
        • Manual Registration
          • Staging area
            • Tabs in Staging
          • Submission correction page
            • Workspace
            • Action bar
            • Status message
            • Structure area
            • Data fields
            • Submission details
            • Stereo Analyzer
            • Checkers
            • Switchers
          • Registering from the Submission page
            • Registering new structures 2
            • Registering matching structures 2
            • Possible status messages - how to register
        • Search
          • Search option
            • Type of search
            • Match type
            • Search query
        • Administration 1
        • Access Control
        • User Profile
        • Data export
        • Appendix A. Calculations
        • Appendix B. Markush Structures
        • Details page
          • Browser
          • Action bar 2
          • Data fields 2
          • Structure area 2
          • compound details 2
          • Stereo Analyzer 2
          • Checkers 2
          • Parent level amendment
          • Version level amendment
          • Lot level amendment
          • Amending compounds
      • Compound Registration Configuration Guide v161121
        • Forms and Fields page
        • Configuration page
        • Authentication
        • Database Connections
        • E-mail Server and User Repository
        • Message Queues
      • Compound Registration Deployment Guide
      • Compound Registration FAQ
      • Compound Registration Release Notes
      • Compound Registration System Requirements
      • Compound Registration History of Changes
    • ChemCurator Home
      • ChemCurator User's Guide
      • ChemCurator Installation and System Requirements
      • Integration Server Administrator Guide
      • Command-Line Mode
      • ChemCurator Licensing
      • ChemCurator Help and Support
      • ChemCurator History of Changes
    • Document to Database
      • Administration Guide
      • System Requirements
      • Document to Database Licensing
      • Document to Database Getting Help and Support
      • Document to Database History of Changes
    • Document to Structure Home
      • Document to Structure User's Guide
        • Configuring OSR tools for Document to Structure
      • Document to Structure Developer's 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
    • File Formats Home
      • Molecule File Conversion with MolConverter
      • 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
      • 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 and InChIKey
          • InChi and InChiKey export options
        • Name
          • Name import and export options
        • 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
      • Graphics Formats
        • Image Export in Marvin
          • JPEG
          • BMP
          • PNG
          • EMF
          • PDF
          • SVG
          • TIFF
          • EPS
        • Export to POV-Ray
        • Image Import in Marvin
      • Compression and Encoding
        • Base64
        • GZIP
      • Basic export options
    • General Documentation
    • Input and Output System Home
      • Supported formats
      • Import IO
      • Export IO
      • Image generation
      • Importing and Exporting molecule properties
      • Molecule converter
      • Integrating your own format
    • InstantJChem
      • 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
          • Export to Analysis
        • 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
        • IJC Deployment Guide
        • Supported databases
        • JChem Cartridge
        • Using Oracle Text in Instant JChem
        • Deployment via Java Web Start
        • Startup Options
        • Shared project configuration
        • Accessing data with URLs
        • Instant JChem Meta Data Tables
        • Test to Production Metadata Migrator
        • Filtering Items
        • Deploying the IJC OData extension into Spotfire
        • Reporting a Problem
        • Manual Instant JChem schema admin functions
        • SQL Scripts for Manual Schema Upgrade
        • Database Row Level Security
        • JccWithIJC
      • Instant JChem Developer Guide
        • Working With IJC Architecture
        • IJC API
          • API Changes
        • 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
          • 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
      • Release Notes
      • New Features
        • 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
      • Instant JChem Licensing
      • IJC Getting Help and Support
      • Instant JChem System Requirements
        • Chart Testing
      • Instant JChem History of Changes
    • JChem Base Home
      • 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
      • Developer's Guide JCB
        • 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's Guide JCB
        • Query Guide
          • Search types
          • Similarity search
          • Query features JCB
          • Stereochemistry jchembase
          • Special search types
            • R-group structures jchembase
            • 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
      • FAQ JCB
        • JChem Base FAQ
        • JChem Base and Cartridge Performance Information JCB