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
TM
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 Python
License for OpenEye Toolkits
Installation
Prerequisites
Linux
macOS
Windows
GPU Prerequisites
GPU-Related Requirements
Supported Platforms
Supported GPUs
NVIDIA Drivers
Performance Tuning
Installing Python on macOS and Linux
Linux & macOS
Installing OpenEye Python Toolkits as a Conda Package
Alternative Installation Strategies
Integration Testing
Windows
Installing Python on Windows
Installing OpenEye Python Toolkits As A Conda package
Alternative Installation Strategies
Integration Testing
Uninstallation
Uninstalling OpenEye Python Toolkits - Anaconda
Uninstalling OpenEye Python Toolkits - PIP
How to Develop with the OpenEye Python Toolkit in PyCharm
Create a New Project
Adding the OpenEye Python Toolkit to Your Project as a Package
Adding a module to your project
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
Appendix: Additional Examples in Python
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
Bioisostere TK
Theory
Theory
Bioisostere How to
Bioisostere Examples
Building Brood Database (CHOMP)
Creating Brood Query
Generating Brood Hits
Generating Brood Matches
Overlay between Fragments
Replacing a Fragment in a Molecule
Building and Using an External Compound Database
Creating Brood Query by Linking Two Molecules (Bridging)
API
OEBioisostere Classes
OEBioisostere Constants
OEBioisostere Functions
Release History
OEBioisostere TK 4.2.1
Bioisostere TK 4.2.0
Bioisostere TK 4.1.0
Bioisostere TK 4.0.0
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
Appendix: Additional Examples in Python
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
Eon TK
Introduction
Welcome to the Eon Toolkit Documentation
Theory
Theory
Eon Examples
Computing Eon Overlap
Simple Eon Overlay
Eon PB Overlay
API
OEEon Classes
OEEon Functions
OEEon Constants
Release History
Eon TK 3.1.2
EON TK 3.1.1
Eon TK 3.1.0
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
Appendix: Additional Examples in Python
Tutorials
Tutorial 0: Basic usage of
FastROCS TK
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
OEFF TK
Theory
Components
Force Field
Sheffield Model
OEFF Examples
Simple Functions and Optimization
Molecule Functions
Small Molecule Force fields
Protein-Ligand Complexes
Using adaptors
Custom Force Fields
OEFF API
OEOpt Classes
OEMolPotential Classes
OEMolPotential Constants
OEConstr Classes
OEMolMMFF Classes
OEMolMMFF Functions
OEMolSmirnoff Classes
OEMolSmirnoff Constants
OESheff Classes
OESheff Constants
OEFF Classes
OEFF Functions
OEFF Constants
Release History
OEFF TK 2.9.1
OEFF TK 2.9.0
OEFF TK 2.8.0
OEFF TK 2.7.1.3
OEFF TK 2.7.1
OEFF TK 2.7.0
OEFF TK 2.5.2.1
OEFF TK 2.5.2.0
OEFF TK 2.5.1
OEFF TK 2.5.0
OEFF TK 2.4.0
OEFF TK 2.3.1
OEFF TK 2.3.0
OEFF TK 2.2.0
OEFF TK 2.1.0
OEFF TK 2.0.4
OEFF TK 2.0.3
OEFF TK 2.0.2
OEFF TK 2.0.1
OEFF TK 2.0.0
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
Appendix: Additional Examples in Python
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
TM
TK 1.5.4
Grapheme
TM
TK 1.5.3
Grapheme
TM
TK 1.5.2
Grapheme
TM
TK 1.5.1.3
Grapheme
TM
TK 1.5.1.0
Grapheme
TM
TK 1.5.0
Grapheme
TM
TK` 1.4.7
Grapheme
TM
TK 1.4.6
Grapheme
TM
TK 1.4.5
Grapheme
TM
TK 1.4.4
Grapheme
TM
TK 1.4.3
Grapheme
TM
TK 1.4.2
Grapheme
TM
TK 1.4.1
Grapheme
TM
TK 1.4.0
Grapheme
TM
TK 1.3.7
Grapheme
TM
TK 1.3.6
Grapheme
TM
TK 1.3.5
Grapheme
TM
TK 1.3.4
Grapheme
TM
TK 1.3.3
Grapheme
TM
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
Appendix: Selected Examples in Python
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
Appendix: Additional Examples in Python
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
Appendix: Additional Examples in Python
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
Appendix: Additional Examples in Python
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
Appendix: Additional Examples in Python
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
Saiph TK
Examples
Traversing File with an OEMolFileConverter
Set Schema Record to Shape OERecord Extraction
OERecord to OEMol
OEMol to OERecord
OERecord to OEDesignUnit
File Records to Pandas DataFrame
OESaiph API
OESaiph Classes
OESaiph Functions
Release History
Saiph TK 1.0.0
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
SiteHopper TK
Introduction
GPU-Related Requirements
Supported Platforms
Supported GPUs
NVIDIA Drivers
Performance Tuning
Examples
SiteHopper Search
SiteHopper Database
Preliminary OESiteHopper API
OESiteHopper Classes
OESiteHopper Constants
OESiteHopper Functions
Release History
Sitehopper TK 2.1.3
SiteHopper TK 2.1.2
SiteHopper TK 2.1.1
SiteHopper TK 2.1.0
Sitehopper TK 2.0.4
Sitehopper TK 2.0.3
Sitehopper TK 2.0.2
Sitehopper TK 2.0.1
SiteHopper TK 2.0.0
Spicoli TK
Theory
Surfaces
Surface Generation
Atom Association and Surface Splitting
Surface Manipulation
Surface Storage
Appendix: Additional Examples in Python
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
Spruce TK
Introduction
Theory
Brief Definitions
Asymmetric Unit
Biological Unit
Biological Design Unit (BioDU)
Design Unit
Spruce TK Preparation Workflow
Proton Placement and Optimization
Protein Side Chain Modeling
Protein Loop Modeling
Protein Superposition
How to Correctly Read a Macromolecular File Format (mmCIF/PDB)
Iridium
Categorization
Advanced Macromolecular Preparation Workflow
Inputs
Filtering and Standardization
Generating the Biological Unit
Generating Packing Residues
Enumerating Alternate Locations
Componentizing the System
Building Missing Pieces
Optimizing the Hydrogen Bond Network
Assignment on Radii and Partial Charges
Prepared Biological Units (BioDUs)
Enumerating Sites / Pockets
Assigning an Iridium Category
Generating a Docking Receptor
Superposition to a Common Frame of Reference
Design Unit Validation
Examples
Spruce TK Examples
Appendix: Additional Examples in Python
OESpruce API
OESpruce Classes
OESpruce Constants
OESpruce Functions
Release History
Spruce TK 1.8.0
Spruce TK 1.7.0
Spruce TK 1.6.1.1
Spruce TK 1.6.1
Spruce TK 1.6.0
Spruce TK 1.5.3
Spruce TK 1.5.2
Spruce TK 1.5.1
Spruce TK 1.5.0
Spruce TK 1.4.0
Spruce TK 1.3.0
Spruce TK 1.2.0
Spruce TK 1.1.0
Spruce TK 1.0.0
Spruce TK 0.9.2
Spruce TK 0.9.1
Spruce TK 0.9.0
Szmap TK
Introduction
Licenses
Theory
Semi-continuum Solvation with SZMAP
Working with Szmap TK
The Szmap TK Standard Water Model
Examples
Szmap TK Examples
Appendix: Additional Examples in Python
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
freeform
Theory
API
OESz Classes
OESz Constants
OESz Functions
Preliminary API
OESz Classes
OESz Constants
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
Appendix: Additional Examples in Python
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
Szybki TK 2.3.0
Szybki TK 2.2.0
Szybki TK 2.1.0
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 TK
Theory and Examples
The What of Zap
The Why of Zap
The Way of Zap
Appendix: Additional Examples in Python
API
OEPB Classes
OEPB Constants
OEPB Functions
Release History
Zap TK 2.5.2
Zap TK 2.5.1
Zap TK 2.5.0
Zap TK 2.4.7
Zap TK 2.4.6
Zap TK 2.4.5
Zap TK 2.4.4
Zap TK 2.4.3
Zap TK 2.4.2
Zap TK 2.4.1
Zap TK 2.4.0
Zap TK 2.3.7
Zap TK 2.3.6
Zap TK 2.3.5
Zap TK 2.3.4
Zap TK 2.3.3
Zap TK 2.3.2
Zap TK 2.3.1
Zap TK 2.3.0
Zap TK 2.2.7
Zap TK 2.2.6
Zap TK 2.2.5
Zap TK 2.2.4
Zap TK 2.2.3
Zap TK 2.2.2
Zap TK 2.2.1
Zap TK 2.2.0
Zap TK 2.1.7
Zap TK 2.1.6
Zap TK 2.1.5
Zap TK 2.1.4
Zap TK 2.1.3
Zap TK 2.1.2
Zap TK 2.1.1
Zap TK 2.1.0
Zap TK 2.0.0
OpenEye Glossary of Terms
Bibliography
Toolkits--python
All OpenEye Documentation
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Grapheme Toolkit 1.5.4.1
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Release History
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Grapheme
TM
TK` 1.4.7
Grapheme
TM
TK` 1.4.7
Minor internal improvements have been made.