- Standalone Applications
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- Appendix A. Calculations
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- Instant JChem
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- Pivoting tutorial
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- Table Standardizer
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- Calculate MolWeight and generate SMILES
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- Simple ChemicalTerms evaluator
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- 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
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- Creating New Entities
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- Evaluator
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- Adding an Edge to a Data Tree
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- 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
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- Instant JChem Licensing
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- Instant JChem System Requirements
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- Instant Jchem User Guide
- Markush Editor
- Marvin Desktop Suite
- MarvinSketch
- User Guide
- Getting Started
- Graphical User Interface
- Working in MarvinSketch
- Structure Display Options
- Basic Editing
- Drawing Simple Structures
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- Using Integrated Calculations
- Graphical Objects
- Import and Export Options
- Multipage Documents
- Printing
- Chemical Features
- Marvin OLE User Guide
- Appendix
- Tutorials
- Application Options
- Developer Guide
- User Guide
- MarvinView
- Molconvert
- Administration guide
- Marvin Desktop Suite - History of Changes
- MarvinSketch
- 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 - Saved Queries
- Plexus Connect - List Management
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- Plexus Connect - Charts View
- Plexus Connect - R-group Decomposition
- Plexus Connect - Administrator Guide
- Plexus Connect - Authentication
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- Plexus Connect - Business Flags
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- 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 - 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 - 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
- Toolkits and Components
- AutoMapper
- Biomolecule Toolkit
- Calculator Plugins
- Introduction to Calculator Plugins
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- Calculators on AWS Marketplace
- 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
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- Chemaxon .NET API
- Chemaxon Cloud
- Chemaxon Synergy
- Chemaxon Synergy User Guide
- Chemaxon Synergy Developer Guide
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- Document to Structure
- JChem Base
- Administration Guide
- Developer Guide
- User Guide
- Query Guide
- Search types
- Similarity search
- Query features
- Stereochemistry
- Special search types
- Search options
- Atomproperty specific search options
- Attached data specific search options
- Bond specific search options
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- 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
- 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
- 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
- JChem PostgreSQL Cartridge
- JKlustor
- Markush Tools
- Marvin JS
- User Guide
- Getting Started
- Editor Overview
- Editor Canvas
- Dialogs
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- Feature Overview Pages
- Keyboard Shortcuts
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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
- Reactant Combinations
- Running Reactor
- Reactor Interfaces
- Reactor Application
- Reactor Command-line Application
- Reactor in Instant JChem
- Reactor in JChem for Excel
- Reactor in KNIME
- Reactor in Pipeline Pilot
- API, Web Services
- Glossary
- Reactor FAQ
- Reactor Licensing
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- Reactor History of Changes
- Reactor Configuration Files
- Reactor User's Guide
- 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
- Structure Checker Getting Help and Support
- Structure Checker History of Changes
- 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
- 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 IJC Database in JChem for Excel
- Import from Database by IDs
- Manage Connections
- Resolve ID
- Import from File
- Export to File
- Share Excel Files
- R-group Decomposition in JChem for Excel
- SAR Table Generation
- Structure Filter
- Options in JChem for Excel
- General Options in JChem for Excel
- Database Connection Options
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- File Import Options in JChem for Excel
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- File Export Options in JChem for Excel
- Printing Options in JChem for Excel
- Structure Sheet Options
- Image Conversion Options
- Structure Display Options in JChem for Excel
- 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
- Structure in JChem for Excel
- Image
- Normal
- User Interface Customization in JChem for Excel
- Checking DirectX Information
- JChem for Office User's Guide
- JChem Ribbon
- Working with Structures
- 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
Star Atom
-
Checker searches for star atoms, inserted as Special node from the Advanced tab of the Periodic Table.
-
Fixer offers:
-
converting star atom to carbon atom (
converttocarbon); -
removing the star atom (
removeatom).
Example :
Star Atom Checker ( staratom)Warning: Fix Convert to Carbon ( converttocarbon)Delete Atom ( removeatom)Find Star Atom 
ex_staratom_ch
ex_staratom_f
ex_staratom_f -