- Standalone Applications
- BioEddie
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- Appendix A. Calculations
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- API documentation
- Instant JChem
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- Instant JChem Administrator Guide
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- Working With IJC Architecture
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- Simple SDF Exporter
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- Markush DCR Structures Exporter
- Select Representative Member of Clusters
- Table Standardizer
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- Create a Diverse Subset
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- PDF Trawler
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- Importing Multiple SDF Files
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- Create Relational Data Tree
- Forms Model Scripts
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- Execute Permanent Query
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- Back and Next Buttons
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- 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
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- Creating New Entities
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- Evaluator
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- Connect to an External Database
- Create a New ChemTerm Field
- Create a New Dynamic URL Field
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- Java Plugins
- IJC Plugin Quick Start
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- 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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- Markush Editor
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- Install guide
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- Plugin Catalogue
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- Developer guide - export plugins
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- Developer guide - registry plugins
- Developer guide - theme customization
- Install guide - Kubernetes
- Marvin Desktop Suite
- MarvinSketch
- User Guide
- Getting Started
- 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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- MarvinView
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- Marvin Desktop Suite History of Changes
- Marvin Desktop Suite Licensing
- MarvinSketch
- Molconvert
- Plexus Connect
- Plexus Connect - Quick Start Guide
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- 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 - API keys
- Plexus Connect - Deploying Spotfire Middle Tier solution
- Plexus Connect - Installation and System Requirements
- Plexus Connect - Licensing
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- Plexus Connect - History of Changes
- Plexus Connect - Schema Refresh Without Restart
- Trainer Engine
- Toolkits and Components
- AutoMapper
- Calculator Plugins
- Introduction to Calculator Plugins
- Calculator Plugins User's Guide
- Calculator Plugins Developer's Guide
- 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
- Calculator Plugins FAQ
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- Calculator Plugins History of Changes
- Calculator Plugins System Requirements
- Biomolecule Toolkit
- Chemaxon .NET API
- Chemaxon Synergy
- Chemaxon Synergy User Guide
- Chemaxon Synergy Developer Guide
- Chemaxon Synergy Administrator Guide
- Chemaxon Synergy History of Changes
- Chemaxon Cloud
- Document to Structure
- JChem Base
- JChem Base Administration
- JChem Base Developer's Guide
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- Query Guide
- Search types
- Similarity search
- Query features JCB
- Stereochemistry JCB
- 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
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- Performance specific search options
- Polymer specific search options
- Query feature specific search options
- Reaction specific search options
- Resultset specific search options
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- Stereo specific search options
- Tautomer specific search options
- Tautomer search - Vague bond search - sp-Hybridization
- Standardization JCB
- Hit display-coloring
- Appendix JCB
- Matching Query - Target Examples
- jcsearch Command Line Tool
- jcunique Command Line Tool
- Homology Groups in Markush Structures
- Query Guide
- JChem Base FAQ
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- JChem Base Getting Help and Support
- JChem Choral
- JChem Oracle Cartridge
- JChem Microservices
- JChem PostgreSQL Cartridge
- Getting Started JChem PostgreSQL Cartridge
- JChem PostgreSQL Cartridge Manual
- Second Generation Search Engine
- JChem PostgreSQL Cartridge FAQ and Known Issues
- JChem PostgreSQL Cartridge History of Changes
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- JChem PostgreSQL Cartridge Licensing
- Comparison of JChem PostgreSQL Cartridge and JChem Oracle Cartridge
- Migration Guide
- JKlustor
- Markush Tools
- Marvin JS
- User Guide
- Getting Started
- Editor Overview
- Editor Canvas
- Dialogs
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- Feature Overview Pages
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- Developer Resources
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- Comparison of Marvin JS and MarvinSketch Feature Sets
- User Guide
- 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
- Reactor in Plexus Suite
- API, Web Services
- Glossary
- Reactor FAQ
- Reactor Licensing
- Reactor Getting Help and Support
- 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
- 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
- Formatting Options
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- File Import Options in JChem for Excel
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- 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
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- 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
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- Solubility
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- Topology Analysis in JChem for Excel
- Structure in JChem for Excel
- Image
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- User Interface Customization in JChem for Excel
- Checking DirectX Information
- JChem for Office User's Guide
- JChem Ribbon
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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
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- 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
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- JChem for Office History of Changes
- Troubleshooting - JChem for Office
- 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
- Markush Overlap
- MarvinSpace
- MarvinSpace User's Guide
- MarvinSpace Developer's Guide
- MarvinSpace History of Changes
- Metabolizer
- Plexus Suite
- Quick Start Guide - Plexus Suite
- Plexus Suite User Guide
- Log in to Plexus Suite
- The Plexus Suite Dashboard
- Importing New Data
- Exporting Your Data
- Browsing in Your Data Set
- Selecting Data
- Searching in Your Database
- Saved Queries
- List Management
- Sorting Data
- Sharing Data with Other Users
- Calculating Molecular Properties for Single Compounds
- Adding calculated columns to tables
- Scaffold Based Enumeration
- Reaction Based Enumeration
- Registering Molecules in the Corporate Database
- Charts view
- Plexus Suite Video Tutorials
- Plexus Suite Administrator Guide
- Plexus Suite Authentication
- Sharing Schema Items Among Users
- Business Flags
- Row-level Security
- Building blocks
- Admin Tools
- Adding JavaScript Files for Custom Functionality
- Writing JavaScript Files for Custom Functionality
- Integration with Chemaxon's Compound Registration System
- Shared data sources in Plexus Connect
- Configuration Files
- Edit Views
- Simple table
- Installation and System Requirements of Plexus Suite
- Plexus Suite Licensing
- Getting Help and Support for Plexus Suite
- Plexus Suite FAQ
- Plexus Suite Privacy Policy
- Terms of Use for the Plexus Suite Demo Site
- Plexus Suite History of Changes
- Schema Refresh Without Restart
- JChem Web Services Classic
Explicit Lone Pairs
-
Checker searches for explicitly drawn lone pairs (inserted as Special node from the Advanced tab of the Periodic Table).
-
Fixer offers removing the explicit lone pair (
removeatom).Example :
Explicit Lone Pairs checker ( explicitlp)Warning: Fix Delete Atom ( removeatom)Detect Explicit Lone Pair 
ex_expllp_ch
ex_expllp_f