- Standalone Applications
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- 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
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- 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
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- IJC Plugin tutorial - Canvas widget
- Java Plugins and Java Web Start
- Instant JChem FAQ
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- Instant Jchem User Guide
- Markush Editor
- Marvin Desktop Suite
- MarvinSketch
- User Guide
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- Graphical User Interface
- Working in MarvinSketch
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- Marvin OLE User Guide
- Appendix
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- Developer Guide
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- Molconvert
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- Marvin Desktop Suite - History of Changes
- MarvinSketch
- Plexus Connect
- Plexus Connect - Quick Start Guide
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- Plexus Connect - Export Templates
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- Plexus Connect - Simple table
- Plexus Connect - Getting the Plexus Backend and Frontend Log Files
- Plexus Connect - Form Editor
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- Plexus Connect - Deploying Spotfire Middle Tier solution
- Plexus Connect - Installation and System Requirements
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- Trainer Engine
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- Background materials
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- 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
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- Chemaxon .NET API
- Chemaxon Cloud
- Chemaxon Synergy
- Chemaxon Synergy User Guide
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- Document to Structure
- JChem Base
- Administration Guide
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- User Guide
- Query Guide
- Search types
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- Stereochemistry
- Special search types
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- Atomproperty specific search options
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- General search options
- Hitdisplay specific search options
- Markush structure specific search options
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- 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
- Query Guide
- FAQ
- History of Changes
- Getting Help and Support
- JChem Choral
- JChem Microservices
- Introduction
- Administration Guide
- Developer Guide
- Calculations Web Services
- DB Web Services
- IO Web Services
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- JChem Oracle Cartridge
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- JKlustor
- Markush Tools
- Marvin JS
- User Guide
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- Editor Overview
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- User Guide
- Marvin
- Name to Structure
- Reactor
- Reactor User's Guide
- Introduction to Reactor
- Reactor Getting Started
- Reactor Concepts
- Reactor Examples
- Working with Reactor
- Specifying Reactions
- Specifying Reactants
- Reaction Mapping
- Reaction Rules
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- Reactor Interfaces
- Reactor Application
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- Reactor in Instant JChem
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- Reactor in KNIME
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- API, Web Services
- Glossary
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- Screen
- Standardizer
- Standardizer User's Guide
- Standardizer Introduction
- Standardizer Getting Started
- Standardizer Concepts
- 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 File Formats
- Standardizer Actions
- Standardizer Developer's Guide
- Standardizer Installation and System Requirements
- Standardizer Licensing
- Standardizer Getting Help and Support
- Standardizer History of Changes
- Standardizer User's Guide
- Structure Checker
- Structure Checker User's Guide
- Introduction
- Structure Checker Getting Started
- Structure Checker Concepts
- 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
- Checker List
- Structure Checker Developer's Guide
- Structure Checker Installation and System Requirements
- Structure Checker Licensing
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- Structure Checker User's Guide
- Structure to Name
- Third-Party Integration
- JChem for Office
- Before Using
- Supported Versions
- Installation
- Administration
- Diagnostic Tool
- JChem for Excel User's Guide
- JChem for Excel Ribbon
- 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
- Show and Hide Structures
- Show and Hide Structures and Structure IDs
- Insert Single Structures
- Open Structure Files
- Delete Structures from a Selected Range
- Save Single Structure to a File
- Print Structures
- Copy and Paste with JChem for Excel
- Convert from Structures
- Convert to Structures
- Convert ISIS, ChemDraw, Accord, and Insight for Excel Files to JChem for Excel Files
- Calculations with Third-Party Services
- Specify External Image and Name Services
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- Manage Connections
- Add an Oracle Connection in JChem for Excel
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- Favorite Entities in JChem for Excel
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- R-group Decomposition in JChem for Excel
- SAR Table Generation
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- Options in JChem for Excel
- General Options in JChem for Excel
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- Structure Sheet Options
- Image Conversion Options
- Structure Display Options in JChem for Excel
- Structure Editor Options in JChem for Excel
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- Actions
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- Custom Chemical Functions in JChem for Excel
- Use Custom Chemical Functions
- Functions Reference
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- Charge in JChem for Excel
- Chemical Terms in JChem for Excel
- Dissimilarity
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- 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
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- Structure in JChem for Excel
- Image
- Normal
- User Interface Customization in JChem for Excel
- Checking DirectX Information
- JChem for Office User's Guide
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- 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 IJC Database
- Manage Connections in JChem for Office
- Import from File in Jchem for Office
- Options in JChem for Office
- Properties in JChem for Office
- Switching JChem for Office to Lite Mode
- JChem for Office Lite User's Guide
- JChem for Office Known Issues
- JChem for Office History of Changes
- Troubleshooting - JChem for Office
- Structures are not displayed in Excel cell
- JChem for Office Tutorial Videos
- Enable JChemExcel.Functions add-in after it gets disabled
- Structure rendering issues when moving the Excel window between different screens
- How to collect event logs
- Information to be sent for bug investigation
- Logfiles to be sent for bug investigation
- KNIME Nodes
- Pipeline Pilot Components
- JChem for Office
- Cross-Product Documentation
- Chemaxon Configuration Folder
- Chemical Fingerprints
- Chemical Terms
- File Formats
- Basic export options
- Compression and Encoding
- Document formats
- Graphics Formats
- Molecule file conversion with Molconverter
- Molecule Formats
- CML
- MDL MOL files
- Daylight SMILES related formats
- Chemaxon SMILES extensions
- IUPAC InChI, InChIKey, RInChI and RInChIKey
- Name
- Sequences - peptide, DNA, RNA
- FASTA file format
- Protein Data Bank (PDB) file format
- Tripos SYBYL MOL and MOL2 formats
- XYZ format
- Gaussian related file formats
- Markush DARC format - VMN
- CSV
- Input and Output System
- License Management
- Long Term Supported Releases - LTS
- Notice about CAS Registry Numbers®
- Public Repository
- Scientific Background
- Structure Representation
- Structure Representation - Class Representation
- Aromaticity
- Implicit, Explicit and Query Hydrogens
- Assigning stereochemistry descriptors
- Cleaning options
- Deprecated and Removed Methods
- Relative configuration of tetrahedral stereo centers
- Iterator Factory
- Atom and bond-set handling
- Graphic object handling
- Supported Java Versions
- Legal
- Discontinued Products
- Document to Database
- Fragmenter
- JChem Neo4j Cartridge
- JChem Web Services Classic
- Markush Overlap
- MarvinSpace
- MarvinSpace User's Guide
- MarvinSpace Developer's Guide
- MarvinSpace History of Changes
- Metabolizer
JCStandardizeStructure
The figure below shows the available JCStandardizeStructure options.
Misc
Folder for Rule Set Files
Use this option to specify the folder which contains the XML file that describes the rules for the JCStandardizeStructure.