• 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
    • Licensing
      • Legal Notices
    • Installation
      • Prerequisites
      • GPU Prerequisites
      • GPU-Related Requirements
      • Installing Python on macOS and Linux
      • Linux & macOS
      • Windows
      • Uninstallation
    • Using PyCharm
      • Create a new project
      • Adding OpenEye Python package to your project
      • Adding a module to your project
    • Third Party Licensing
      • Zstandard
      • InChI
      • Computational Crystallography Toolbox (CCTBX) / MolProbity
      • GEMMI - GEneral MacroMolecular I/O
      • OpenSSL
      • GCC
    • How to import the toolkits
    • Legal Notices
      • Sample Code
      • Citation
  • 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 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 2.2.0
      • 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
  • OEFF Toolkit
    • Theory
      • Components
      • Force Field
    • 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
      • OEFF Classes
      • OEFF Functions
      • OEFF Constants
      • Preliminary API
    • Release History
      • 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
    • 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
      • 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
    • 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
  • Spruce Toolkit
    • Introduction
    • Theory
      • Definitions
      • Biological Unit
      • Design Unit
      • Proton Placement and Optimization
      • Protein Sidechain Modeling
      • Protein Loop Modeling
      • Protein Superposition
      • How to Correctly Read a PDB File
    • Iridium
      • Categorization
    • Examples
      • Spruce TK Examples
    • OESpruce API
      • OESpruce Classes
      • OESpruce Constants
      • OESpruce Functions
    • Preliminary OESpruce API
      • Preliminary OESpruce Classes
      • Preliminary OESpruce Functions
    • Release History
      • 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 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--python
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  • Spruce Toolkit 1.3.0.1 »
  • OESpruce API »
  • Preliminary OESpruce Classes

Preliminary OESpruce ClassesΒΆ

  • OECapBuilderOptions
    • Constructors
    • operator=
    • GetDeleteClashingSolvent
    • GetAllowTruncate
    • SetDeleteClashingSolvent
    • SetAllowTruncate
  • OELoopBuilderOptions
    • GetOptimizationStage2IterMultiplier
    • GetOptimizationUseSolventModel
    • GetOptimizationInclSurfaceAreaTerm
    • GetOptimizationMaxLoops
    • GetAllowBuildDisulfideBridges
    • GetSeqAlignMethod
    • GetSeqAlignGapPenalty
    • GetSeqAlignExtendPenalty
    • SetLoopDBFilename
    • SetUsePackingResidues
    • SetCropLength
    • SetTransformThreshold
    • SetStrictProlineMatch
    • SetConnectBufferDistance
    • SetBackboneClashRejectThreshold
    • SetLoopClashRejectThreshold
    • SetOptimizationShell
    • SetOptimizationTolerance
    • SetOptimizationStage1IterMultiplier
    • SetOptimizationStage2IterMultiplier
    • SetOptimizationUseSolventModel
    • SetOptimizationInclSurfaceAreaTerm
    • SetOptimizationMaxLoops
    • SetAllowBuildDisulfideBridges
    • SetSeqAlignMethod
    • SetSeqAlignGapPenalty
    • GetSeqAlignExtendPenalty
  • OEPocket
    • Constructors
    • operator=
    • GetSurfaceArea
    • GetLocalDensity
    • GetPocketPredicate
    • GetPocketSurface
    • GetAtoms
    • GetResidues
  • OEPocketOptions
    • Constructors
    • operator=
    • GetMinSurfaceArea
    • GetMaxSurfaceArea
    • GetBurialFactor
    • SetMinSurfaceArea
    • SetMaxSurfaceArea
    • SetBurialFactor
  • OESidechainBuilderOptions
    • Constructors
    • operator=
    • GetDeleteClashingSolvent
    • GetRotamerLibrary
    • GetStrictMode
    • SetRotamerCoverage
    • SetRotamerLibrary
    • SetDeleteClashingSolvent
    • SetStrictMode
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© Copyright 2021, OpenEye Scientific Software, Inc. Last updated on Jul 19, 2021.