OEToolkits 2021.1
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
Detailed Release Notes 2021.1
New features
Major bug fixes
Minor bug fixes
Documentation changes
New features
Minor bug fixes
Major bug fixes
New features
Major bug fixes
New features
Minor bug fixes
New features
Minor bug fixes
New features
New features
Major bug fixes
Minor bug fixes
Minor bug fixes
New features
Major bug fixes
Minor bug fixes
Major bug fixes
New features
Minor bug fixes
Documentation changes
New features
Getting Started
Introduction
Prerequisites
Windows
Linux
macOS
GPU Prerequisites
GPU-Related Requirements
Supported Platforms
Supported GPUs
NVIDIA Drivers
Performance Tuning
Licensing
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
Using Eclipse
Creating a new project
Adding a class to our project
Running our example inside Eclipse
Creating an executable JAR
Creating an Example on the command line
Creating a custom oejava jar file
Examples of creating a special jar
Third Party Licensing
Zstandard
InChI
Computational Crystallography Toolbox (CCTBX) / MolProbity
GEMMI - GEneral MacroMolecular I/O
OpenSSL
How to import the toolkits
Legal Notices
Sample Code
Citation
Best Practices for Java
How to Reduce Memory Fragmentation
When to Call close()
When to Call delete()
OEFloatArray vs float[]
OpenEye Defines
Keep in Mind
References
Introduction
Toolkit API
Release Cycle
OEChem Toolkit
Introduction
How to read this manual
OEChem and Informatics
Theory
OEChem Theory
OESystem Theory
OEBio Theory
OEGrid Theory
Examples
OEChem Examples
OEBio Examples
Python Cookbook Examples
API
OEChem API
Preliminary OEChem API
OESystem API
Preliminary OESystem API
OEPlatform API
OEMath API
OEBio API
Preliminary OEBio API
Release History
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
Glossary
Bibliography
Index
OEDepict Toolkit
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
Appendices
Appendix: Element coloring (CPK)
API
Release History
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
Glossary
Bibliography
Index
OEDocking Toolkit
Introduction
Welcome to the Docking Toolkit documentation
Theory
Receptors
Scoring
Docking
Pose Prediction
Using Multiple Receptors
Receptor Flexibility
OEDocking Examples
Docking and Scoring Examples
POSIT Examples
Receptor Examples
API
OEDocking Classes
OEDocking Constants
OEDocking Functions
OEDocking Classes (Deprecated)
OEDocking Functions (Deprecated)
Release History
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
Bibliography
Index
FastROCS Toolkit
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 2.2.0
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
Bibliography
Index
Grapheme Toolkit
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 1.4.3
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
Index
GraphSim Toolkit
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 2.5.2
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
Glossary
Bibliography
Index
Lexichem Toolkit
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 2.7.3
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
Bibliography
Index
OEMedChem Toolkit
Introduction
Theory
Molecule Fragmentation
Matched Molecule Pair Analysis
Examples
OEMedChem TK Examples
API
OEMedChem Classes
OEMedChem Constants
OEMedChem Functions
Release History
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
Bibliography
Index
MolProp Toolkit
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 2.5.6
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
Bibliography
Index
Omega Toolkit
Theory
OMEGA Theory
Macrocycle Conformations
GPU-Omega
GPU-Related Requirements
Usage
OMEGA Examples
Classic OEOmega Examples
StereoAndTorsion Examples
Generating Torsion Driven Conformation Examples
Fragment Library generation Examples
Macrocycle Examples
API
OEConfGen Classes
OEConfGen Constants
OEConfGen Functions
Release History
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
Bibliography
Index
Quacpac Toolkit
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
Release History
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
Bibliography
Index
Shape Toolkit
Theory
Theory
Examples
Calculating Overlap
ROCS
Overlay Optimization
Working with Shape Query
Shape from Hermite expansion
Advanced Examples
API
OEShape Classes
OEShape Constants
OEShape Functions
Deprecated OEShape Classes
Deprecated OEShape Constants
Release History
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
Bibliography
Index
Spicoli Toolkit
Theory
Surfaces
Surface Generation
Atom Association and Surface Splitting
Surface Manipulation
Surface Storage
API
OESpicoli Classes
OESpicoli Constants
OESpicoli Functions
Release History
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
Glossary
Bibliography
Index
Szmap Toolkit
Introduction
Licenses
Theory
Semi-continuum Solvation with SZMAP
Working with Szmap TK
The Szmap TK Standard Water Model
Examples
Szmap TK Examples
API
OESzmap Classes
OESzmap Constants
OESzmap Functions
Release History
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
Bibliography
Index
Szybki Toolkit
Theory
SZYBKI Theory
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
Release History
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
Bibliography
Index
Zap Toolkit
Theory and Examples
The What of Zap
The Why of Zap
The Way of Zap
API
OEPB Classes
OEPB Constants
OEPB Functions
Release History
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
Index
Toolkits--java
Docs
»
<no title>
»
OEDocking Toolkit 4.1.0.1
»
API
»
OEDocking Functions (Deprecated)
»
OEBoxYMid
OEBoxYMid
ΒΆ
float
OEBoxYMid
(
const
OEBoxBase
&
box
)
Returns the Y midpoint of the box.