• Toolkit Version 2025.2
    • 2025.2 Highlights
      • Release Highlights 2025.2
        • Shape: Features Extension
        • Saiph TK: New Toolkit for ETL
        • OEChem TK and Spruce TK: Improvements to CIF File Format Support
        • Supported Platforms
        • Related TK Versions
      • General Notices
    • Detailed Release Notes 2025.2
      • OEBioisostere TK 4.2.1
        • New Features
        • Minor Bug Fixes
      • OEChem TK 4.3.0
        • New Features
        • Major Bug Fixes
        • Minor Bug Fixes
      • OEBio TK 4.3.0
        • New Features
        • Major Bug Fixes
        • Minor Bug Fixes
      • OEGrid 4.3.0
        • New Features
      • OEDepict TK 2.6.0
      • OEDocking TK 4.3.4
        • Minor Bug Fixes
      • Eon TK 3.1.2
      • FastROCS TK 2.3.1
      • Grapheme TK 1.5.4
      • GraphSim TK 2.7.0
        • New Features
        • Minor Bug Fixes
      • Lexichem TK 2.9.4
        • Minor Bug Fixes
      • OEMedChem TK 1.2.5
      • MolProp TK 2.6.7
      • OEFF TK 2.9.1
      • Omega TK 6.1.1
        • Minor Bug Fixes
      • Quacpac TK 2.2.7
        • Minor Bug Fixes
      • Saiph TK 1.0.0
        • New Features
      • Shape TK 3.9.0
        • New Features
        • Minor Bug Fixes
      • Sitehopper TK 2.1.3
      • Spicoli TK 1.6.3
      • Spruce TK 1.8.0
        • New Features
        • Major Bug Fixes
        • Minor Bug Fixes
        • Documentation Changes
      • Szmap TK 1.7.3
      • Szybki TK 2.9.1
      • Zap TK 2.5.2
    • Recent Release History
      • OEToolkits 2025.1
        • OEToolkits 2025.1
      • OEToolkits 2024.2
        • OEToolkits 2024.2.1
        • OEToolkits 2024.2.0
      • OEToolkits 2024.1
        • OEToolkits 2024.1.3
        • OEToolkits 2024.1.0
      • OEToolkits 2023.2
        • OEToolkits 2023.2.0
        • General Notices
    • Previous Release History
      • OEToolkits 2023.1
        • OEToolkits 2023.1.1
        • OEToolkits 2023.1.0
        • General Notices
      • Release Highlights 2022.2
        • OEToolkits 2022.2.2
        • OEToolkits 2022.2.1
        • MCS based fix during OMEGA Conformer Generation
        • New ShapeFit Algorithm for Pose Prediction
        • Protein-ligand Optimization with ff14SB forcefield and PB solvent model
        • New BROOD Fragment Databases
      • Release Highlights 2022.1
        • Enhanced Stereo Information Support
        • Sheffield Solvation Model for Proteins
        • Spruce Filter and Design Unit Validation
        • Multistate Heuristic pKa Model
      • Release Highlights 2021.2
        • SiteHopper: New Toolkit for Protein Binding Site Comparison
        • SZYBKI: OpenFF-Sage force field support
        • OEChem: MMCIF and CIF writers
      • Release Highlights 2021.1
        • OEDocking TK: Receptors in Design Unit
        • OESiteHopper: Application Suite for Rapid Protein Binding Site Comparison
        • VIDA 5: Major Update and OEDesignUnit Support
        • Supported Platforms
        • Related TK Versions
        • General Notices
      • Release Highlights 2020.2
        • OEToolkits 2020.2.2
        • Omega TK: New fragment library
        • OEDocking TK: Improved receptors
        • Szybki TK: A new protein force field
        • Supported Platforms
        • Related TK Versions
        • General Notices
      • Release Highlights 2020.1
        • OEToolkits 2020.1.1
        • OEToolkits 2020.1
        • OEToolkits 2020.0
        • General Notices
      • OEToolkits 2019.Oct
        • Spruce TK: A new toolkit for biomolecular structure preparation
        • OEChem TK: Fast Substructure Search
        • OEFF TK: SMIRNOFF
        • General Notices
      • OEToolkits 2019.Apr
        • FastROCS TK: Color calculation on GPU
        • OEChem TK: OEZ compressed file format
        • OEGrapheme TK: Ramachandran plot
        • General Notices
      • OEToolkits 2018.Oct
        • Omega TK: Macrocycle
        • FastROCS TK: C++ and Java Support
        • Quacpac TK: Tautomers
        • General Notices
      • OEToolkits 2018.Feb
        • GraphSim TK: GPU-Accelerated Fast Fingerprint Similarity Searches
        • Grapheme TK : Unpaired Interaction Map
        • Conda Packages for Python
        • General Notices
      • OEToolkits 2017.Oct
        • Shape TK: Version 2.0.0
        • Omega TK: New Torsion Library
        • OEDepict TK and Grapheme TK: Interactive SVG Images
        • General Notices
      • OEToolkits 2017.Jun
        • Shape TK: Hermite
        • OEDepict TK and Grapheme TK: Interactive SVG images
        • GraphSim TK: Fast Fingerprint Similarity Search
        • General Notices
      • OEToolkits 2017.Feb
        • Alternative Starting Points for Shape Overlap Optimization in FastROCS TK
        • Charging Engine
        • New Maximum Common Substructure (MCS) Similarity Capability
        • Protein Preparation Update
        • General Notices
      • OEToolkits 2016.Oct
        • Protein Preparation
        • Protein-Ligand Interaction
        • FastROCS TK CUDA Implementation
        • General Notices
      • OEToolkits 2016.Jun
        • Single Build Distributions
        • Protein-Ligand Visualization
        • Tversky Similarity Scoring in FastROCS TK
        • General Notices
      • OEToolkits 2016.Feb
        • OpenEye Toolkit Security
        • FastROCS TK: Database Loading Performance Improvement
        • OEMedChem TK
        • General Notices
      • OEToolkits 2015.Oct
        • FastROCS TK
        • OEChem: Molecule Reading Performance Improvement
        • OEBio: Fragment Network
        • General Notices
      • OEToolkits 2015.Jun
        • PDB Splitting
        • PAINS Filter
        • Matched Molecular Pair Improvements
        • Custom Ring Template Dictionaries
        • Anaconda Support
        • One-Command Python Installation
        • General Notices
      • OEToolkits 2015.Feb
        • Protein-ligand Rendering
        • Documentation Refresh
        • Matched Pairs Transformations
        • Optimized Depiction Orientation
        • General Notices
      • OEToolkits 2014.Oct
        • Pictorial application for automatically writing OEDepict code
        • Major improvements to Quacpac’s protomer assignment algorithms
        • Major improvements to depiction of complex ring systems
        • Multi-precision conformer handling
        • New force field in Szybki
        • Matched Pairs analysis beta API added to OEMedChem TK
        • Major bug fixes
        • General notices
      • OEToolkits 2014.Jun
      • OEToolkits 2014.Feb
      • OEToolkits 2013.Oct
      • OEToolkits 2013.Jun
      • OEToolkits 2013.Feb
      • OEToolkits 2012.Oct
      • OEToolkits 2012.Jun
      • OEToolkits 2012.Feb
      • OEToolkits 2011.Oct
      • OEToolkits 2011.1
      • OEToolkits 1.7.4
      • OEToolkits 1.7.2
      • OEToolkits 1.7.1
      • OEToolkits 1.7.0
  • Introduction
    • Toolkit API
    • Release Cycle
  • Getting Started with OpenEye Java
    • License for OpenEye Toolkits
    • Introduction
    • Prerequisites
      • Platform Support
      • Java Versions
    • GPU Prerequisites
    • GPU-Related Requirements
      • Supported Platforms
      • Supported GPUs
      • NVIDIA Drivers
      • Performance Tuning
    • Download the OpenEye Java distribution
    • Installation
    • Using Apache Maven with OpenEye
      • Requirements
      • Creating a Maven Project
      • Using OpenEye Artifacts
      • Finding Available OpenEye Versions
      • Using OpenEye in HelloMaven
      • Using Maven to Compile and Run
      • Thoughts
      • Conclusion
    • How to Develop with the OpenEye Java Toolkit in Eclipse
      • Creating a New Project
      • Adding a Class to Our Project
      • Running Our Example inside Eclipse
      • Creating an Executable JAR
    • How to Develop with the OpenEye Java Toolkit in IntellJ IDEA
      • Creating a New Project
      • Create a Package and a Class
      • Running Our Example inside IDEA
      • Creating an Executable JAR
        • Create an Artifact Configuration
        • Create a Run Configuration
        • Run the Application with the Run Configuration
    • Creating an Example on the command line
    • Creating a custom oejava jar file
      • Examples of creating a special jar
    • How to import the toolkits
    • Legal Notices
      • Copyright and Trademarks
      • Sample Code
      • Citation
        • Orion®
        • Orion Floes
        • Toolkits and Applications
        • Publications for Bibliographies
        • OpenEye MMDS Web Service
      • Technology Licensing
        • GCC
  • Informatics and Modeling Toolkits
    • OEChem TK
      • Introduction
        • How to read this manual
        • OEChem and Informatics
      • Theory
        • OEChem Theory
        • OESystem Theory
        • OEBio Theory
        • OEGrid Theory
      • Examples
        • OEChem Examples
        • OEBio Examples
        • OEMath Examples
        • Python Cookbook Examples
      • API
        • OEChem API
        • Preliminary OEChem API
        • OESystem API
        • Preliminary OESystem API
        • OEPlatform API
        • OEMath API
        • OEBio API
      • Release History
        • OEChem TK 4.3.0
        • OEBio TK 4.3.0
        • OEGrid 4.3.0
        • OEChem TK 4.2.0
        • OEBio TK 4.2.0
        • OEChem TK 4.1.1.1
        • OEChem TK 4.1.1.0
        • OEPlatform TK 4.1.1
        • OEBio TK 4.1.1
        • OEChem TK 4.1.0
        • OESystem TK 4.1.0
        • OEMath TK 4.1.0
        • OEBio TK 4.1.0
        • OEGrid TK 4.1.0
        • OESystem TK 4.1.0
        • OEMath TK 4.1.0
        • OEChem TK 4.0.0
        • OEBio TK 4.0.0
        • OESystem TK 4.0.0
        • OEPlatform TK 4.0.0
        • OEGrid TK 4.0.0
        • OEChem TK 3.4.0
        • OESystem TK 3.3.1
        • OEPlatform TK 3.3.1
        • OEChem TK 3.3.1
        • OEBio TK 3.3.1
        • OESystem TK 3.3.1
        • OEPlatform TK 3.3.1
        • OEChem TK 3.3.0
        • OEBio TK 3.3.0
        • OESystem TK 3.3.0
        • OEPlatform TK 3.3.0
        • OEGrid TK 3.3.0
        • OEChem TK 3.2.0
        • OEBio TK 3.2.0
        • OESystem TK 3.2.0
        • OEPlatform TK 3.2.0
        • OEGrid TK 3.2.0
        • OEMath TK 3.2.0
        • OEChem TK 3.1.1
        • OEBio TK 3.1.1
        • OESystem TK 3.1.1
        • OEPlatform TK 3.1.1
        • OEGrid TK 3.1.1
        • OEMath TK 3.1.1
        • Version 3.1.0.2
        • Version 3.1.0
        • Version 3.0.0.6
        • Version 3.0.0.5
        • Version 3.0.0
        • Version 2.3.0
        • Version 2.2.0
        • Version 2.1.5
        • Version 2.1.4
        • Version 2.1.3
        • Version 2.1.2
        • Version 2.1.1
        • Version 2.1.0
        • Version 2.0.7
        • Version 2.0.6
        • Version 2.0.5
        • Version 2.0.4
        • Version 2.0.3
        • Version 2.0.2
        • Version 2.0.1
        • Version 2.0.0
        • Version 1.9.3
        • Version 1.9.2
        • Version 1.9.1
        • Version 1.9.0
        • Version 1.8.0
        • Version 1.7.7
        • Version 1.7.6
        • Version 1.7.5
        • Version 1.7.4
        • Version 1.7.3
        • Version 1.7.2
        • Version 1.7.1
        • Version 1.7.0
        • Version 1.6.1
        • Version 1.6.0
        • Version 1.5.1
        • Version 1.5.0
        • Version 1.4.2
        • Version 1.4.1
        • Version 1.4.0
        • Version 1.3.4
        • Version 1.3.3
        • Version 1.3.2
        • Version 1.3.1
        • Version 1.3.0
    • OEDepict TK
      • Introduction
      • Theory
        • Basic Drawing Primitives
        • Molecule Depiction
        • Highlighting
        • Molecule Layouts
        • Multi Page Images
        • MDL Query Depiction
        • MDL Reaction Depiction
        • Molecule Alignment
        • Generating Interactive SVG Images
      • Examples
        • OEDepict Examples
        • Python Cookbook Examples
      • API
        • OEDepict Classes
        • OEDepict Constants
        • OEDepict Functions
      • Appendices
        • Appendix: Element coloring (CPK)
      • Release History
        • OEDepict TK 2.6.0
        • OEDepict TK 2.5.6
        • OEDepict TK 2.5.5
        • OEDepict TK 2.5.4
        • OEDepict TK 2.5.3
        • OEDepict TK 2.5.2
        • OEDepict TK 2.5.1
        • OEDepict TK 2.5.0
        • OEDepict TK 2.4.7
        • OEDepict TK 2.4.6
        • OEDepict TK 2.4.5
        • OEDepict TK 2.4.4
        • OEDepict TK 2.4.3
        • OEDepict TK 2.4.2
        • OEDepict TK 2.4.1
        • OEDepict TK 2.4.0
        • OEDepict TK 2.3.6
        • OEDepict TK 2.3.5
        • OEDepict TK 2.3.4
        • OEDepict TK 2.3.3
        • OEDepict TK 2.3.2
        • OEDepict TK 2.3.1
        • OEDepict TK 2.3.0
        • OEDepict TK 2.2.6
        • OEDepict TK 2.2.5
        • OEDepict TK 2.2.4
        • OEDepict TK 2.2.3
        • OEDepict TK 2.2.2
        • OEDepict TK 2.2.1
        • OEDepict TK 2.2.0
        • OEDepict TK 2.1.0
        • OEDepict TK 2.0.4
        • OEDepict TK 2.0.3
        • OEDepict TK 2.0.2
        • OEDepict TK 2.0.1
        • OEDepict TK 2.0.0
    • OEDocking TK
      • Introduction
        • Welcome to the Docking Toolkit documentation
      • Theory
        • Receptors
        • Scoring
        • Docking
        • ShapeFit
        • POSIT Theory
        • Posit How to
      • OEDocking Examples
        • Docking and Scoring Examples
        • OEShapeFit Examples
        • POSIT Examples
        • Receptor Examples
      • OEModels Examples
        • Building ROCS Query Model
      • API
        • OEDocking API
        • Preliminary OEDocking API
        • Deprecated OEDocking API
        • OEModels API
      • Release History
        • OEDocking TK 4.3.4
        • OEDocking TK 4.3.3
        • OEDocking TK 4.3.2
        • OEDocking TK 4.3.1.3
        • OEDocking TK 4.3.1.0
        • OEDocking TK 4.3.0
        • OEDocking TK 4.2.1
        • OEDocking TK 4.2.0
        • OEDocking TK 4.1.2
        • OEDocking TK 4.1.1
        • OEDocking TK 4.1.0
        • OEDocking TK 4.0.0.2
        • OEDocking TK 4.0.0
        • OEDocking TK 3.5.0.5
        • OEDocking TK 3.5.0
        • OEDocking TK 1.4.1
        • OEDocking TK 1.4.0
        • OEDocking TK 1.3.7
        • OEDocking TK 1.3.6
        • OEDocking TK 1.3.5
        • OEDocking TK 1.3.4
        • OEDocking TK 1.3.3
        • OEDocking TK 1.3.2
        • OEDocking TK 1.3.1
        • OEDocking TK 1.3.0
        • OEDocking TK 1.2.7
        • OEDocking TK 1.2.6
        • OEDocking TK 1.2.5
        • OEDocking TK 1.2.4
        • OEDocking TK 1.2.3
        • OEDocking TK 1.2.2
        • OEDocking TK 1.2.1
        • OEDocking TK 1.2.0
        • OEDocking TK 1.1.4
        • OEDocking TK 1.1.3
        • OEDocking TK 1.1.2
        • OEDocking TK 1.1.1
        • OEDocking TK 1.1.0
        • OEDocking TK 1.0.0
    • FastROCS™ TK
      • Introduction
      • FastROCS vs ROCS
      • Installation
        • Prerequisites
        • Hardware Performance Comparison
      • FastROCS Architecture
        • Memory Usage
        • Multi-GPU Scaling
        • Multi-Node Scaling
      • Examples
        • FastROCS Example Suite
      • Tutorials
        • Tutorial 1: Alternative Starts
        • Tutorial 2: How to prepare a database for faster load speeds
      • API
        • OEFastROCS Classes
        • OEFastROCS Constants
        • OEFastROCS Functions
        • Using a Custom Color ForceField in FastROCS
        • OEFastROCS ShapeDatabaseServer XMLRPC API
      • Release History
        • FastROCS TK 2.3.1
        • FastROCS TK 2.3.0
        • FastROCS TK 2.2.7
        • FastROCS TK 2.2.6
        • FastROCS TK 2.2.5
        • FastROCS TK 2.2.4
        • FastROCS TK 2.2.3
        • FastROCS TK 2.2.2
        • FastROCS TK 2.2.1
        • FastROCS TK 2.2.0
        • FastROCS TK 2.1.0
        • FastROCS TK 2.0.0
        • FastROCS TK 1.10.1
        • FastROCS TK 1.10.0
        • FastROCS TK 1.9.0
        • FastROCS TK 1.8.4
        • FastROCS TK 1.8.3
        • FastROCS TK 1.8.2
        • FastROCS TK 1.8.1
        • FastROCS TK 1.8.0
        • FastROCS TK 1.7.0
        • FastROCS TK 1.6.0
        • FastROCS TK 1.5.1
        • FastROCS TK 1.5.0
        • FastROCS TK 1.4.0
        • FastROCS TK 1.3.1
        • FastROCS TK 1.3.0
        • FastROCS TK 1.2.1
        • FastROCS TK 1.1.1
        • FastROCS TK 1.1.0
        • FastROCS TK 1.0.1
        • FastROCS TK 1.0.0
        • FastROCS TK 0.4.0
        • FastROCS TK 0.3.1
        • FastROCS TK 0.3.0
        • FastROCS TK 0.2.3
        • FastROCS TK 0.2.2
        • FastROCS TK 0.2.1
        • FastROCS TK 0.2.0
        • FastROCS TK 0.1.1
        • FastROCS TK 0.1.0
    • Grapheme™ TK
      • Introduction
      • Theory
        • Annotating Atoms and Bonds
        • Drawing a Molecule Surface
        • Drawing a Ligand-Protein Complex Surface
        • Depicting Property Maps
      • Examples
        • Grapheme Examples
        • Python Cookbook Examples
      • Preliminary API
        • OEDrawIridiumData
      • API
        • OEGrapheme Classes
        • OEGrapheme Basic Arc Drawing Classes
        • OEGrapheme Constants
        • OEGrapheme Functions
        • OEGrapheme Basic Circle and Arc Drawing Functions
      • Release History
        • Grapheme TK 1.5.4
        • Grapheme TK 1.5.3
        • Grapheme TK 1.5.2
        • Grapheme TK 1.5.1.3
        • Grapheme TK 1.5.1.0
        • Grapheme TK 1.5.0
        • Grapheme TK 1.4.7
        • Grapheme TK 1.4.6
        • Grapheme TK 1.4.5
        • Grapheme TK 1.4.4
        • Grapheme TK 1.4.3
        • Grapheme TM TK 1.4.2
        • Grapheme TM TK 1.4.1
        • Grapheme TM TK 1.4.0
        • GraphemeTM TK 1.3.7
        • GraphemeTM TK 1.3.6
        • GraphemeTM TK 1.3.5
        • GraphemeTM TK 1.3.4
        • GraphemeTM TK 1.3.3
        • GraphemeTM TK 1.3.2
        • Grapheme TK 1.3.1
        • Grapheme TK 1.3.0
        • Grapheme TK 1.2.3
        • Grapheme TK 1.2.2
        • Grapheme TK 1.2.1
        • Grapheme TK 1.2.0
        • Grapheme TK 1.1.3
        • Grapheme TK 1.1.2
        • Grapheme TK 1.1.1
        • Grapheme TK 1.1.0
        • Grapheme TK 1.0.6
        • Grapheme TK 1.0.5
        • Grapheme TK 1.0.4
        • Grapheme TK 1.0.3
        • Grapheme TK 1.0.2
        • Grapheme TK 1.0.1
        • Grapheme TK 1.0.0
    • GraphSim TK
      • Introduction
        • Visualizing Molecule Similarity
      • Theory
        • Fingerprint Generation
        • Fingerprint Types
        • Storage and Retrieval
        • Similarity Measures
        • Fingerprint Database
        • User-defined Fingerprint
        • Fingerprint Coverage
        • Fingerprint Overlap
        • Fingerprint Patterns
      • GPU Fast Fingerprints
        • Prerequisites
        • Usage
      • Examples
        • GraphSim TK Examples
        • Python Cookbook Examples
      • API
        • OEGraphSim Classes
        • OEGraphSim Constants
        • OEGraphSim Functions
      • Release History
        • GraphSim TK 2.7.0
        • GraphSim TK 2.6.2
        • GraphSim TK 2.6.1
        • GraphSim TK 2.6.0
        • GraphSim TK 2.5.7
        • GraphSim TK 2.5.6
        • GraphSim TK 2.5.5
        • GraphSim TK 2.5.4
        • GraphSim TK 2.5.3
        • GraphSim TK 2.5.2
        • GraphSim TK 2.5.1
        • GraphSim TK 2.5.0
        • GraphSim TK 2.4.3
        • GraphSim TK 2.4.2
        • GraphSim TK 2.4.1
        • GraphSim TK 2.4.0
        • GraphSim TK 2.3.1
        • GraphSim TK 2.3.0
        • GraphSim TK 2.2.6
        • GraphSim TK 2.2.5
        • GraphSim TK 2.2.4
        • GraphSim TK 2.2.3
        • GraphSim TK 2.2.2
        • GraphSim TK 2.2.1
        • GraphSim TK 2.2.0
        • GraphSim TK 2.1.1
        • GraphSim TK 2.1.0
        • GraphSim TK 2.0.7
        • GraphSim TK 2.0.6
        • GraphSim TK 2.0.5
        • GraphSim TK 2.0.4
        • GraphSim TK 2.0.3
        • GraphSim TK 2.0.2
        • GraphSim TK 2.0.1
        • GraphSim TK 2.0.0
        • GraphSim TK 1.0.1
        • GraphSim TK 1.0.0
    • Lexichem TK
      • Theory
        • Input Name Representation
        • Output Name Representation
        • Output Name Styles
        • Examples of Name Style Differences
      • Examples
        • Lexichem TK Examples
      • API
        • OEIUPAC Constants
        • OEIUPAC Functions
      • Release History
        • Lexichem TK 2.9.4
        • Lexichem TK 2.9.3
        • Lexichem TK 2.9.2
        • Lexichem TK 2.9.1
        • Lexichem TK 2.9.0
        • Lexichem TK 2.8.1
        • Lexichem TK 2.8.0
        • Lexichem TK 2.7.5
        • Lexichem TK 2.7.4
        • Lexichem TK 2.7.3
        • Lexichem TK 2.7.2
        • Lexichem TK 2.7.1
        • Lexichem TK 2.7.0
        • Lexichem TK 2.6.7
        • Lexichem TK 2.6.6
        • Lexichem TK 2.6.5
        • Lexichem TK 2.6.4
        • Lexichem TK 2.6.3
        • Lexichem TK 2.6.2
        • Lexichem TK 2.6.1
        • Lexichem TK 2.6.0
        • Lexichem TK 2.5.2
        • Lexichem TK 2.5.1
        • Lexichem TK 2.5.0
        • Lexichem TK 2.4.2
        • Lexichem TK 2.4.1
        • Lexichem TK 2.4.0
        • Lexichem TK 2.3.2
        • Lexichem TK 2.3.0
        • Lexichem TK 2.2.3
        • Lexichem TK 2.2.2
        • Lexichem TK 2.2.0
        • Lexichem TK 2.1.2
        • Lexichem TK 2.1.1
        • Lexichem TK 2.1.0
        • Lexichem TK 2.0.2
        • Lexichem TK 2.0.0
        • Lexichem TK 1.9
        • Lexichem TK 1.8
        • Lexichem TK 1.7
        • Lexichem TK 1.6
        • Lexichem TK 1.5
        • Lexichem TK 1.4
        • Lexichem TK 1.3
        • Lexichem TK 1.2
        • Lexichem TK 1.1
        • Lexichem TK 1.0
    • OEMedChem TK
      • Introduction
      • Theory
        • Molecule Fragmentation
        • Matched Molecule Pair Analysis
      • Examples
        • OEMedChem TK Examples
      • API
        • OEMedChem API
      • Release History
        • OEMedChem TK 1.2.5
        • OEMedChem TK 1.2.4
        • OEMedChem TK 1.2.3
        • OEMedChem TK 1.2.2
        • OEMedChem TK 1.2.1
        • OEMedChem TK 1.2.0
        • OEMedChem TK 1.1.7
        • OEMedChem TK 1.1.6
        • OEMedChem TK 1.1.5
        • OEMedChem TK 1.1.4
        • OEMedChem TK 1.1.3
        • OEMedChem TK 1.1.2
        • OEMedChem TK 1.1.1
        • OEMedChem TK 1.1.0
        • OEMedChem TK 1.0.7
        • OEMedChem TK 1.0.6
        • OEMedChem TK 1.0.5
        • OEMedChem TK 1.0.4
        • OEMedChem TK 1.0.3
        • OEMedChem TK 1.0.2
        • OEMedChem TK 1.0.1
        • OEMedChem TK 1.0.0
        • OEMedChem TK 0.9.6
        • OEMedChem TK 0.9.5
        • OEMedChem TK 0.9.4
        • OEMedChem TK 0.9.3
        • OEMedChem TK 0.9.2
        • OEMedChem TK 0.9.1
        • OEMedChem TK 0.9.0
    • MolProp TK
      • Theory
        • Filtering Theory
        • Filter Preprocessing
        • Molecular Properties and Predictors
        • Filter Files
      • Examples
        • MolProp TK Examples
        • Python Cookbook Examples
      • API
        • OEMolProp Classes
        • OEMolProp Constants
        • OEMolProp Functions
      • Release History
        • MolProp TK 2.6.7
        • MolProp TK 2.6.6
        • MolProp TK 2.6.5
        • MolProp TK 2.6.4
        • MolProp TK 2.6.3
        • MolProp TK 2.6.2
        • MolProp TK 2.6.1
        • MolProp TK 2.6.0
        • MolProp TK 2.5.7
        • MolProp TK 2.5.6
        • MolProp TK 2.5.5
        • MolProp TK 2.5.4
        • MolProp TK 2.5.3
        • MolProp TK 2.5.2
        • MolProp TK 2.5.1
        • MolProp TK 2.5.0
        • MolProp TK 2.4.7
        • MolProp TK 2.4.6
        • MolProp TK 2.4.5
        • MolProp TK 2.4.4
        • MolProp TK 2.4.3
        • MolProp TK 2.4.2
        • MolProp TK 2.4.1
        • MolProp TK 2.4.0
        • MolProp TK 2.3.0
        • MolProp TK 2.2.2
        • MolProp TK 2.2.1
        • MolProp TK 2.2.0
        • MolProp TK 2.1.7
        • MolProp TK 2.1.6
        • MolProp TK 2.1.5
        • MolProp TK 2.1.4
        • MolProp TK 2.1.3
        • MolProp TK 2.1.2
        • MolProp TK 2.1.1
        • MolProp TK 2.1.0
    • Omega TK
      • Theory
        • OMEGA Theory
        • Macrocycle Conformations
      • GPU-Omega
        • GPU-Related Requirements
        • Usage
      • OMEGA Examples
        • Classic OEOmega Examples
        • Flipper Examples
        • Generating Torsion Driven Conformation Examples
        • Fragment Library generation Examples
        • Macrocycle Examples
      • API
        • OEConfGen Classes
        • OEConfGen Constants
        • OEConfGen Functions
      • Preliminary API
        • Preliminary OEConfGen Classes
      • Release History
        • Omega TK 6.1.1
        • Omega TK 6.1.0
        • Omega TK 6.0.0
        • Omega TK 5.1.0
        • Omega TK 5.0.0
        • Omega TK 4.2.2
        • Omega TK 4.2.1
        • Omega TK 4.2.0
        • Omega TK 4.1.2
        • Omega TK 4.1.1
        • Omega TK 4.1.0
        • Omega TK 4.0.0.6
        • Omega TK 4.0.0
        • Omega TK 2.9.1
        • Omega TK 2.9.0
        • Omega TK 2.8.0
        • Omega TK 2.7.0
        • Omega TK 2.6.7
        • Omega TK 2.6.6
        • Omega TK 2.6.5
        • Omega TK 2.6.4
        • Omega TK 2.6.3
        • Omega TK 2.6.2
        • Omega TK 2.6.1
        • Omega TK 2.6.0
        • Omega TK 2.5.7
        • Omega TK 2.5.6
        • Omega TK 2.5.5
        • Omega TK 2.5.4
        • Omega TK 2.5.3
        • Omega TK 2.5.2
        • Omega TK 2.5.1
        • Omega TK 2.5.0
        • Omega TK 2.4.6
        • Omega TK 2.4.5
        • Omega TK 2.4.4
        • Omega TK 2.4.1
        • Omega TK 2.4.0
        • Omega TK 2.3.3
        • Omega TK 2.3.2
        • Omega TK 2.3.1
        • Omega TK 2.3.0
        • Omega TK 2.2.2
        • Omega TK 2.2.1
    • Quacpac TK
      • Theory
        • Introduction to Quacpac TK
        • tautomers
        • pkatyper - Ligand pKa
        • molcharge - Partial Charges
        • Wiberg bond orders
      • Examples
        • Quacpac TK Examples
      • API
        • OEProton Classes
        • OEProton Constants
        • OEProton Functions
        • OEMolAM1 Classes
        • OEMolAM1 Constants
        • OEMolAM1 Constants
        • OEAM1BCC Functions
      • Preliminary API
        • Preliminary OEProton Class
        • Preliminary OEProton Constants
        • Preliminary OEProton Functions
      • Release History
        • Quacpac TK 2.2.7
        • Quacpac TK 2.2.6
        • Quacpac TK 2.2.5
        • Quacpac TK 2.2.4
        • Quacpac TK 2.2.3
        • Quacpac TK 2.2.2
        • Quacpac TK 2.2.1
        • Quacpac TK 2.2.0
        • Quacpac TK 2.1.4
        • Quacpac TK 2.1.3
        • Quacpac TK 2.1.2
        • Quacpac TK 2.1.1.2
        • Quacpac TK 2.1.1
        • Quacpac TK 2.1.0
        • Quacpac TK 2.0.2
        • Quacpac TK 2.0.1
        • Quacpac TK 2.0.0
        • Quacpac TK 1.9.3
        • Quacpac TK 1.9.2
        • Quacpac TK 1.9.1
        • Quacpac TK 1.9.0
        • Quacpac TK 1.8.6
        • Quacpac TK 1.8.5
        • Quacpac TK 1.8.4
        • Quacpac TK 1.8.3
        • Quacpac TK 1.8.2
        • Quacpac TK 1.8.1
        • Quacpac TK 1.8.0
        • Quacpac TK 1.7.2
        • Quacpac TK 1.7.1
        • Quacpac TK 1.7.0
        • Quacpac TK 1.6.4
        • Quacpac TK 1.6.2
        • Quacpac TK 1.6.1
        • Quacpac TK 1.6.0
        • Quacpac TK 1.5.2
        • Quacpac TK 1.5.1
        • Quacpac TK 1.5.0
        • Quacpac TK 1.4.1
        • Quacpac TK 1.4.0
        • Quacpac TK 1.3.1
        • Quacpac TK 1.3.0
        • Quacpac TK 1.1.0
    • Shape TK
      • Theory
        • Theory
      • Examples
        • Calculating Overlap
        • ROCS
        • Overlay Optimization
        • Working with Shape Query
        • Shape from Hermite expansion
        • Flexible Overlay with Shape, Color, and Forcefield
        • Advanced Examples
      • API
        • OEShape Classes
        • OEShape Constants
        • OEShape Functions
      • Preliminary API
        • Preliminary OEShape Classes
        • Preliminary OEShape Constants
      • Deprecated API
        • Deprecated OEShape Classes
        • Deprecated OEShape Constants
      • Release History
        • Shape TK 3.9.0
        • Shape TK 3.8.0
        • Shape TK 3.7.0
        • Shape TK 3.6.2
        • Shape TK 3.6.1
        • Shape TK 3.6.0
        • Shape TK 3.5.1
        • Shape TK 3.5.0
        • Shape TK 3.4.3
        • Shape TK 3.4.2
        • Shape TK 3.4.1
        • Shape TK 3.4.0
        • Shape TK 2.0.4
        • Shape TK 2.0.3
        • Shape TK 2.0.2
        • Shape TK 2.0.1
        • Shape TK 2.0.0
        • Shape TK 1.11.0
        • Shape TK 1.10.4
        • Shape TK 1.10.3
        • Shape TK 1.10.2
        • Shape TK 1.10.1
        • Shape TK 1.10.0
        • Shape TK 1.9.7
        • Shape TK 1.9.6
        • Shape TK 1.9.5
        • Shape TK 1.9.4
        • Shape TK 1.9.3
        • Shape TK 1.9.2
        • Shape TK 1.9.1
        • Shape TK 1.9.0
        • Shape TK 1.8.3
        • Shape TK 1.8.2
        • Shape TK 1.8.1
        • Shape TK 1.8.0
        • Shape TK 1.7.2
        • Shape TK 1.7.1
        • Shape TK 1.7.0
        • Shape TK 1.6.2
        • Shape TK 1.6.1
        • Shape TK 1.6
        • Shape TK 1.5
    • Spicoli TK
      • Theory
        • Surfaces
        • Surface Generation
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      • API
        • OESpicoli Classes
        • OESpicoli Constants
        • OESpicoli Functions
      • Release History
        • Spicoli TK 1.6.3
        • Spicoli TK 1.6.2
        • Spicoli TK 1.6.1
        • Spicoli TK 1.6.0
        • Spicoli TK 1.5.7
        • Spicoli TK 1.5.6
        • Spicoli TK 1.5.5
        • Spicoli TK 1.5.4
        • Spicoli TK 1.5.3
        • Spicoli TK 1.5.2
        • Spicoli TK 1.5.1
        • Spicoli TK 1.5.0
        • Spicoli TK 1.4.7
        • Spicoli TK 1.4.6
        • Spicoli TK 1.4.5
        • Spicoli TK 1.4.4
        • Spicoli TK 1.4.3
        • Spicoli TK 1.4.2
        • Spicoli TK 1.4.1
        • Spicoli TK 1.4.0
        • Spicoli TK 1.3.7
        • Spicoli TK 1.3.6
        • Spicoli TK 1.3.5
        • Spicoli TK 1.3.4
        • Spicoli TK 1.3.3
        • Spicoli TK 1.3.2
        • Spicoli TK 1.3.1
        • Spicoli TK 1.3.0
        • Spicoli TK 1.2.2
        • Spicoli TK 1.2.1
        • Spicoli TK 1.2.0
        • Spicoli TK 1.1.3
        • Spicoli TK 1.1.2
        • Spicoli TK 1.1.1
        • Spicoli TK 1.1.0
        • Spicoli TK 1.0.2
        • Spicoli TK 1.0.1
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      • Introduction
        • Licenses
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        • Szmap TK Examples
      • API
        • OESzmap Classes
        • OESzmap Constants
        • OESzmap Functions
      • Release History
        • Szmap TK 1.7.3
        • Szmap TK 1.7.2
        • Szmap TK 1.7.1
        • Szmap TK 1.7.0
        • Szmap TK 1.6.7
        • Szmap TK 1.6.6
        • Szmap TK 1.6.5
        • Szmap TK 1.6.4
        • Szmap TK 1.6.3
        • Szmap TK 1.6.2
        • Szmap TK 1.6.1
        • Szmap TK 1.6.0
        • Szmap TK 1.4.6
        • Szmap TK 1.4.5
        • Szmap TK 1.4.4
        • Szmap TK 1.4.3
        • Szmap TK 1.4.2
        • Szmap TK 1.4.1
        • Szmap TK 1.4.0
        • Szmap TK 1.3.7
        • Szmap TK 1.3.6
        • Szmap TK 1.3.5
        • Szmap TK 1.3.4
        • Szmap TK 1.3.3
        • Szmap TK 1.3.2
        • Szmap TK 1.3.1
        • Szmap TK 1.3.0
    • Szybki TK
      • Introduction
      • Theory
        • SZYBKI Theory
        • Nonplanar Aromatic Rings in Protein-Bound Ligands
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        • OESz Classes
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      • Preliminary API
        • OESz Classes
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      • Examples: Working with Szybki TK
        • Ligand Energetics and Optimization
        • Protein-Ligand Energetics and Optimization
        • DU Protein-Ligand Optimization with FF14SB-Parsley
        • Entropy estimation
        • Solvation free energy estimation
        • Conformations free energy estimation
      • Release History
        • Szybki TK 2.9.1
        • Szybki TK 2.9.0
        • Szybki TK 2.8.0
        • Szybki TK 2.7.1.3
        • Szybki TK 2.7.1.0
        • Szybki TK 2.7.0
        • Szybki TK 2.6.0.1
        • Szybki TK 2.6.0.0
        • Szybki TK 2.5.1.2
        • Szybki TK 2.5.1.1
        • Szybki TK 2.5.0
        • Szybki TK 2.4.0
        • Szybki TK 2.3.1
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        • Szybki TK 2.0.4
        • Szybki TK 2.0.3
        • Szybki TK 2.0.2
        • Szybki TK 2.0.1
        • Szybki TK 2.0.0
        • Szybki TK 1.9.2
        • Szybki TK 1.9.1
        • Szybki TK 1.9.0
        • Szybki TK 1.8.7
        • Szybki TK 1.8.6
        • Szybki TK 1.8.5
        • Szybki TK 1.8.4
        • Szybki TK 1.8.3
        • Szybki TK 1.8.2
        • Szybki TK 1.8.1
        • Szybki TK 1.7.5
        • Szybki TK 1.7.4
        • Szybki TK 1.7.3
        • Szybki TK 1.7.2
        • Szybki TK 1.7.1
        • Szybki TK 1.7.0
        • Szybki TK 1.6.0
        • Szybki TK 1.5.0
        • Szybki TK 1.4.0
        • Szybki TK 1.3.4
    • Zap Toolkit
      • Theory and Examples
        • The What of Zap
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      • API
        • OEPB Classes
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      • Release History
        • Zap TK 2.5.2
        • Zap TK 2.5.1
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  • OpenEye Glossary of Terms
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Toolkits--java
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  • Matched Pair analysis and listing of transformations related to probe structures

Matched Pair analysis and listing of transformations related to probe structures

A program that loads a previously generated Matched Pair index, then prints the transformations and matched pairs found from the analysis that are related to the provided probe structure(s). If an (optional, numeric) data field is provided, the returned transformations can also be ranked by the largest increase in the delta property found from the matched pairs that define it.

See also

  • OEMatchedPairAnalyzer class

  • OEMatchedPairAnalyzerOptions class

  • OEMatchedPairGetTransforms function

Command Line Interface

prompt> MatchedPairTransformProbe [ -datafield sdDataField ] index.mmpidx probe_molecules.sdf

Code

Download code

MatchedPairTransformProbe.java

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