docs163140

    Documentation 16.3.14.0
    • 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
          • Hückel 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
            • 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
      • Background materials
        • Calculation of partial charge distribution
        • Generate3D
        • Isoelectric point (pI) calculation
        • LogP and logD calculations
        • NMR model prediction
        • pKa calculation
        • Red & blue representation of pKa values
        • Tautomerization and tautomers
        • Validation results
      • Calculator Plugins Licensing
      • Calculator Plugins FAQ
      • Calculator Plugins Getting Help and Support
      • Calculator Plugins History of Changes
    • Calculator Plugins History of Changes
    • ChemCurator
      • ChemCurator User's Guide
      • ChemCurator Installation
      • Integration Server Administrator Guide
      • Command-Line Mode
      • ChemCurator Licensing
      • ChemCurator Getting Help and Support
      • ChemCurator History of Changes
    • Chemical Fingerprints
      • Extended Connectivity Fingerprint (ECFP)
      • Chemical Hashed Fingerprint
      • Pharmacophore Fingerprint (PF)
      • Reaction fingerprint (RF)
      • Fingerprint and descriptor generation - GenerateMD
      • Pharmacophore perception - PMapper
    • Chemical Terms
      • Introduction to Chemical Terms
      • Chemical Terms Getting Started
      • The Chemical Terms Language
        • Language Elements
        • Expression Syntax
        • Predefined Functional Groups and Named Molecule Groups
        • Initial Scripts
        • Input Contexts
        • Configuration
        • Examples
          • Evaluator and JChem Cartridge Examples
          • Reactor Examples
          • Search Filter Examples
      • Available Functions
        • Functions by Categories
        • Functions in Alphabetic Order
      • Usage examples
        • Basic Calculations
        • Search Filters
        • Reaction Processing
        • Markush Enumeration
      • Products using Chemical Terms
        • Chemical Terms Evaluator
          • Evaluator Examples
        • Instant JChem CT
        • JChem Base CT
        • JChem Cartridge
        • JChem for Excel
        • Reactor
        • KNIME
        • Pipeline Pilot
      • Chemical Terms Getting Help and Support
    • Compliance Checker
    • Compound Registration
      • Compound Registration User's Guide
        • Overview
        • Abbreviations
        • Definitions of Terms
        • Introduction
        • Login
        • Dashboard page
        • Autoregistration
          • Registration page
          • Validation
          • Standardizing
          • Structure Checking and Fixing
          • Registering a new structure
          • Registering a match
        • Bulk Upload
        • Manual Registration
          • Staging area
            • Tabs and actions 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
            • Registering matching structures
            • Possible status messages - how to register
        • Compound Details
          • Browser
          • Action bar
          • Structure area
          • Data fields
          • Stereo Analyzer
          • Compound details
          • Checkers
          • Amending compounds
            • Parent level amendment
            • Version level amendment
            • Lot level amendment
        • Search
          • Search options
            • Search type
            • Match type
          • Search query
        • User Profile
        • Administration
        • Data export
        • Appendix A. Calculations
        • Appendix B. Markush Structures
      • Compound Registration Configuration Guide
        • Authentication
        • Business Workflow Settings and Web UI Customization
        • Database Connections
        • E-mail Server and User Repository
        • Message Queues
        • Validation Rules
      • Compound Registration Deployment Guide
      • Compound Registration FAQ
      • Compound Registration Release Notes
      • Compound Registration System Requirements
      • Compound Registration 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
    • Document to Structure
      • 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
      • Molecule file conversion with Molconverter
      • Document formats
        • Marvin Documents (MRV)
          • MRV Export Options
          • Schema and Validation
        • ISIS/Draw 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