• OEApplications 2025.1.1
    • Release Highlights 2025.1.1
      • FastROCS: Grid Query Support
      • Bioisostere TK: Feature Extensions
      • SZYBKI: Robust Protein–Ligand Optimization
    • Supported Platforms
    • Related Application Versions
    • Detailed Release Notes 2025.1
    • FLYNN 3.0.2
    • BROOD 4.2.0
      • New Features
    • Bioisostere TK 4.2.0
      • New Features
      • Minor Bug Fixes
    • EON 3.1.1
    • EON TK 3.1.1
    • Zap TK 2.5.1
    • OEDocking 4.3.3
    • OEDocking TK 4.3.3
    • OMEGA 6.1.0
    • Omega TK 6.1.0
      • New Features
      • Minor Bug Fixes
    • MolProp TK 2.6.6
    • PICTO 5.1.3
    • OEDepict TK 2.5.6
    • pKa-Prospector 1.2.5
    • Quacpac 2.2.6
    • Quacpac TK 2.2.6
    • ROCS 3.8.0
    • Shape TK 3.8.0
      • New Features
    • SiteHopper 2.1.2
    • SiteHopper TK 2.1.2
    • SPRUCE 1.7.0
    • Spruce TK 1.7.0
      • New Features
      • Major Bug Fixes
      • Minor Bug Fixes
    • SZMAP 1.7.2
    • Szmap TK 1.7.2
    • SZYBKI
      • New Features
      • Minor Bug Fixes
    • Szybki TK 2.9.0
      • New Features
      • Major Bug Fixes
      • Minor Bug Fixes
  • Previous Release Highlights
    • Release Highlights 2024.2.1
    • Release Highlights 2024.2.0
      • OMEGA: Thompson Sampling for Torsion Driving
      • BROOD: Bioisosteric Fragment Replacement in Macrocyclic Peptides
      • Eon TK: New Toolkit for Overlay Optimization with Shape and Charge Density
    • Supported Platforms
    • Related Application Versions
    • Release Highlights 2024.1.3
    • Release Highlights 2024.1.0
      • EON: Overlay Optimization with Shape and Charge Density
      • FLYNN: Ligand fitting for Cryo-EM
      • Hydrogen Placement Updates in SPRUCE
      • Bioisostere TK: New Toolkit for Bioisosteric Fragment Replacement
    • Supported Platforms
    • Related Application Versions
    • Release Highlights 2023.2.3
      • Supported Platforms
      • Related Application Versions
    • Release Highlights 2023.1.1
    • Release Highlights 2023.1.0
      • Supported Platforms
      • Related Application Versions
    • Release Highlights 2022.2.2
    • Release Highlights 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
      • Supported Platforms
      • Related Application Versions
      • General Notices
    • Release Highlights 2022.1
      • Enhanced Stereo Information Support
      • Sheffield Solvation Model for Proteins
      • Spruce Filter and Design Unit Validation
      • Multistate Heuristic pKa Model
      • Supported Platforms
      • Related Application Versions
      • General Notices
    • Release Highlights 2021.2
      • SiteHopper: New Toolkit for Protein Binding Site Comparison
      • SZYBKI: OpenFF-Sage force field support
      • OEChem: MMCIF and CIF writers
      • Supported Platforms
      • Related Application Versions
      • General Notices
    • Release Highlights 2021.1
      • OESiteHopper: Application Suite for Rapid Protein Binding Site Comparison
      • OEDocking: Make Receptor (Receptors in Design Unit)
      • VIDA 5: Major Update and OEDesignUnit support
      • Supported Platforms
      • Related Application Versions
      • General Notices
    • Release Highlights 2020.2.2
    • Release Highlights 2020.2
      • OMEGA: New fragment library
      • OEDOCKING: Improved receptors
      • SZYBKI: A new protein force field
      • Supported Platforms
      • Related Application Versions
      • General Notices
    • Release Highlights 2020.1.1
    • Release Highlights 2020.1
    • Release Highlights 2020.0
      • OMEGA: GPU-OMEGA - GPU-accelerated torsion driving
      • SPRUCE: Protein Loop Modeling
      • SZYBKI: Custom SMIRNOFF
      • General Notices
    • Release Highlights 2019.Nov
      • SPRUCE: Application Suite for Biomolecular Structure Preparation
      • SZMAP: Simplified Workflow
      • SZYBKI: SMIRNOFF
      • General Notices
      • Platform Support
    • Release Highlights 2019.May
      • Windows Installer
      • OEZ Compressed File Format
      • General Notices
      • Platform Support
    • OEApplications 2018.Nov
      • First release of all OpenEye Applications as a single package
      • ROCS: ROCS
      • QUACPAC: Tautomers
      • General Notices
      • Platform Support
  • Getting Started
    • Installation and Platform Notes
      • Licenses for OpenEye Software
      • Installation
      • Example and Tutorial Data
      • MPI
      • Uninstallation
    • Release Cycle
    • Legal Notices
      • Copyright and Trademarks
      • Sample Code
      • Citation
      • Technology Licensing
  • AFITT 3.0.2.1
    • Overview
    • Applications
    • Utility Programs
    • FLYNN
      • Overview
      • Example Commands
      • Command Line Help
      • Required Parameters
      • Optional Parameters
      • Usage Notes
    • Coot Integration
      • Overview
      • Using FLYNN
      • Using WriteDict
      • Using RotFit
      • Installing Coot Interface
    • Utilities
      • AlignGrid
      • RotFit
      • Rscc
      • WriteDict
    • Theory
      • Fragment Fitting
    • Release History
      • FLYNN 3.0.2
      • AFITT 3.0.1
      • AFITT 3.0.0
      • AFITT 2.6.5
      • AFITT 2.6.4
      • AFITT 2.6.3
      • AFITT 2.6.2
      • AFITT 2.6.1
      • AFITT 2.6.0
      • AFITT 2.5.3
      • AFITT 2.5.2.0
      • AFITT 2.5.1
      • AFITT 2.5.0
      • AFITT-CL 2.4.1
      • AFITT-CL 2.4.0
      • AFITT-CL 2.3.0
      • AFITT-CL 2.2.0
      • AFITT-CL 2.1.1
      • AFITT-CL 2.1.0
      • AFITT-CL 2.0.1
      • FLYNN 2.0.0
    • Citation
  • BROOD 4.2.0.1
    • Introduction
      • Applications
      • Utility Programs
      • Installing the BROOD Database
    • vBROOD
      • Overview
      • Build and Run
      • Build a New Query
      • Run BROOD
      • View Results
      • Viewing Results in VIDA
    • BROOD
      • Overview
      • Input Files
      • Example Commands
      • Command Line Help
      • Parameters
      • Output Files
    • CHOMP
      • Overview
      • Example Commands
      • Command Line Help
      • Required Parameters
      • Optional Parameters
    • Utilities
      • Overview
      • Command Line Help
      • Example Commands
      • Required Parameters
      • Optional Parameters
    • Overview
    • Human Complement C3a Receptor Example
      • Specifying the Database
      • Loading a Molecule
      • Editing the Query
      • Selecting Properties
      • Setting Up the BROOD Search
      • Opening and Viewing Results
      • Exploring the Results
    • Fragment Joining Tutorial
      • BROOD Database
      • Loading Two Molecules
      • Loading the Protein
      • Choosing a Query
      • Setting up a Search
      • Examining the Log Files
      • Viewing Results in a Protein Site
    • Generating a Database with Crystallographic Conformations
      • Preparing Data Sources
      • Generating a Database
      • Advanced Topic: Editing the Fragments at an Intermediate Step
    • Theory
      • Theory
      • Fragment joining
      • Cyclization
      • BROOD Database Generation (CHOMP)
    • BROOD Fragment Database
      • ChEMBL31 Fragment Database
      • ChEMBL31_lite Fragment Database
      • brood-database-chembl-3.0.0
    • Release History
      • BROOD 4.2.0
      • Bioisostere TK 4.2.0
      • BROOD 4.1.0
      • Bioisostere TK 4.1.0
      • BROOD 4.0.0
      • Bioisostere TK 4.0.0
      • BROOD 3.2.2
      • BROOD 3.2.1
      • BROOD 3.2.0
      • BROOD 3.1.7
      • BROOD 3.1.6
      • BROOD 3.1.5
      • BROOD 3.1.4.0
      • BROOD 3.1.3
      • BROOD 3.1.2
      • BROOD 3.1.1
      • BROOD 3.1.0
      • BROOD 3.0.0
      • BROOD 2.0.0
      • BROOD 1.1.2
      • BROOD 1.1.1
      • BROOD 1.1.0
      • BROOD 1.0.1
      • BROOD 1.0.0
      • BROOD 0.9.b2
      • BROOD 0.9.b1
    • Citation
  • EON 3.1.1.1
    • Introduction
      • Overview
      • Applications
    • EON
      • Overview
      • Example Commands
      • Report File
      • Command Line Help
      • Required Parameters
      • Optional Parameters
    • Theory
    • Release History
      • EON 3.1.1
      • EON TK 3.1.1
      • Zap TK 2.5.1
      • EON 3.1.0
      • Eon TK 3.1.0
      • Zap TK 2.5.0
      • EON 3.0.0.3
      • EON 3.0.0.0
      • Zap TK 2.4.7
      • EON 2.4.2
      • Zap TK 2.4.6
      • EON 2.4.1
      • Zap TK 2.4.5
      • EON 2.4.0
      • Zap TK 2.4.4
      • EON 2.3.7
      • Zap TK 2.4.3
      • EON 2.3.6
      • Zap TK 2.4.2
      • EON 2.3.5
      • Zap TK 2.4.1
      • EON 2.3.4.0
      • Zap TK 2.4.0
      • EON 2.3.3
      • EON 2.3.2
      • EON 2.3.1
      • EON 2.3.0
      • EON 2.2.0
      • EON 2.1.0
      • EON 2.0.0
    • Citation
  • OEDocking 4.3.3.1
    • Introduction
      • Overview
      • Applications
      • Utility Programs
    • Tutorials
      • Overview
      • Receptor Preparation Tutorial
      • CombineReceptors tutorial
      • FRED tutorial
      • HYBRID tutorial
      • POSIT tutorial
      • POSIT MPI tutorial
    • Theory
      • Receptors
      • FRED Theory
      • HYBRID Theory
      • Scoring Functions
      • POSIT Theory
      • Posit How to
    • FRED
      • Overview
      • Input Preparation
      • Example Commands
      • Command Line Help
      • Required Parameters
      • Optional Parameters
    • HYBRID
      • Overview
      • Input Preparation
      • Example Commands
      • Command Line Help
      • Required Parameters
      • Optional Parameters
    • POSIT
      • Overview
      • Input Preparation
      • Example Commands
      • Command Line Help
      • Required Parameters
      • Optional Parameters
    • Make Receptor
      • Overview
      • GUI Layout
      • Setting up a Receptor
    • Utilities
      • ReceptorInDU
      • OEB2DUReceptor
      • DockingReport
      • ScorePose
      • ReceptorToolbox
      • combine_receptors
      • DU2OEBReceptor
    • Release History
      • OEDocking 4.3.3
      • OEDocking TK 4.3.3
      • OEDocking 4.3.2
      • OEDocking TK 4.3.2
      • OEDocking 4.3.1
      • OEDocking TK 4.3.1.3
      • OEDocking TK 4.3.1.0
      • OEDOCKING 4.3.0
      • OEDocking TK 4.3.0
      • OEDOCKING 4.2.1.1
      • OEDOCKING 4.2.1.0
      • OEDocking TK 4.2.1
      • OEDOCKING 4.2.0
      • OEDocking TK 4.2.0
      • OEDOCKING 4.1.2
      • OEDocking TK 4.1.2
      • OEDOCKING 4.1.2
      • OEDocking TK 4.1.2
      • OEDOCKING 4.1.0
      • OEDocking TK 4.1.0
      • OEDOCKING 4.0.0.2
      • OEDOCKING 4.0.0.0
      • OEDocking 3.5.0
      • OEDocking 3.4.0
      • OEDocking 3.3.1
      • OEDocking 3.3.0
      • OEDocking 3.2.0
      • OEDocking 3.0.1
      • OEDocking 3.0.0
      • POSIT 3.1.0
      • POSIT 1.0.3
      • POSIT 1.0.2
      • POSIT 1.0.1
      • POSIT 1.0.0
      • FRED 2.2.5
      • FRED 2.2.4
      • FRED 2.2.3
      • FRED 2.2.2
      • FRED 2.2.1
      • FRED 2.2.0
    • Citation
  • OMEGA 6.1.0.1
    • Introduction
      • Overview
      • Applications
      • Utility Programs
    • FILTER
      • Overview
      • Example Commands
      • Command Line Help
      • Required Parameters
      • Optional Parameters
      • Filter Files
    • OMEGA
      • Overview
      • GPU-Omega
      • Example Commands
      • Command Line Help
      • Required Parameters
      • Optional Parameters
      • Additional specifications
    • Utilities
      • Flipper
      • MakeFraglib
      • Oeb2SdConf
    • Theory
      • OMEGA Theory
      • Macrocycle Conformations
      • Filtering Theory
    • Release History
      • OMEGA 6.1.0
      • Omega TK 6.1.0
      • MolProp TK 2.6.6
      • OMEGA 6.0.0
      • Omega TK 6.0.0
      • MolProp TK 2.6.5
      • OMEGA 5.1.0
      • Omega TK 5.1.0
      • MolProp TK 2.6.4
      • OMEGA 5.0.0
      • Omega TK 5.0.0
      • MolProp TK 2.6.3
      • OMEGA 4.2.2
      • Omega TK 4.2.2
      • MolProp TK 2.6.2
      • OMEGA 4.2.1
      • OMEGA 4.2.0
      • Omega TK 4.2.0
      • MolProp TK 2.6.0
      • OMEGA 4.1.2
      • Omega TK 4.1.2
      • MolProp TK 2.5.7
      • OMEGA 4.1.1
      • Omega TK 4.1.1
      • MolProp TK 2.5.6
      • OMEGA 4.1.0.0
      • Omega TK 4.1.0
      • MolProp TK 2.5.5
      • OMEGA 4.0.0.6
      • OMEGA 4.0.0
      • OMEGA 3.1.2
      • OMEGA 3.1.1
      • OMEGA 3.1.0
      • OMEGA 3.0.1
      • OMEGA 3.0.0
      • OMEGA 2.5.1
      • OMEGA 2.4.6
      • OMEGA 2.4.3
      • OMEGA 2.4.1
      • OMEGA 2.4.0
      • OMEGA 2.3.3
      • OMEGA 2.3.2
      • OMEGA 2.3.1
      • OMEGA 2.3.0
      • OMEGA 2.2.2
      • OMEGA 2.2.1
    • Citation
  • PICTO 5.1.3.1
    • Introduction
      • Overview
      • Applications
    • PICTO
      • Overview
      • Sketcher
      • SMARTS
      • Implicit/Explicit Hydrogens
      • Atom Labeling, Aromatic Displays, Aromatic Modeling, and other Displays
    • Release History
      • PICTO 5.1.3
      • OEDepict TK 2.5.6
      • PICTO 5.1.2
      • OEDepict TK 2.5.5
      • PICTO 5.1.1
      • OEDepict TK 2.5.4
      • PICTO 5.1.0
      • OEDepict TK 2.5.3
      • PICTO 4.6.0
      • OEDepict TK 2.5.1
      • PICTO 4.5.4
      • OEDepict TK 2.5.0
      • PICTO 4.5.3
      • OEDepict TK 2.4.7
      • PICTO 4.5.2
      • OEDepict TK 2.4.6
      • PICTO 4.5.1.0
      • OEDepict TK 2.4.5
      • PICTO 4.5.0
    • Citation
  • pKa-Prospector 1.2.5.1
    • Introduction
      • Overview
      • Applications
    • pKa-Prospector
      • Overview
      • QuickStart
      • Query Molecule
      • Property Filters
      • Search Buttons
      • Results View
      • Preferences
      • Result Report
      • Menu Items
      • Appending Data
      • Selecting an Imported Database
    • Release History
      • pKa-Prospector 1.2.5
      • pKa-Prospector 1.2.4
      • pKa-Prospector 1.2.3
      • pKa-Prospector 1.2.2
      • pKa-Prospector 1.2.1
      • pKa-Prospector 1.2.0
      • pKa-Prospector 1.1.7
      • pKa-Prospector 1.1.6
      • pKa-Prospector 1.1.5
      • pKa-Prospector 1.1.4.0
      • pKa-Prospector 1.1.3
      • pKa-Prospector 1.1.2
      • pKa-Prospector 1.1.1
      • pKa-Prospector 1.1.0
      • pKa-Prospector 1.0.0
    • Citation
  • QUACPAC 2.2.6.1
    • Introduction
      • Overview
      • Applications
    • FixpKa
      • Overview
      • Example Commands
      • Command Line Help
      • Required Parameters
      • Optional Parameters
    • MolCharge
      • Overview
      • Example Commands
      • Command Line Help
      • Required Parameters
      • Optional Parameters
    • pKaTyper
      • Overview
      • Example Commands
      • Command Line Help
      • Required Parameters
      • Optional Parameters
    • Tautomers
      • Overview
      • Example Commands
      • Command Line Help
      • Required Parameters
      • Optional Parameters
    • MolCharge Theory
      • Introduction
      • Marsili-Gasteiger Partial Charges
      • MMFF94 Partial Charges
      • AM1 Charges
      • AM1BCC Charges
      • ELF Conformer Selection
      • Amber ff94, ff96, ff99, ff99sb, and ff99sbc0 Partial Charges
    • Release History
      • Quacpac 2.2.6
      • Quacpac TK 2.2.6
      • QUACPAC 2.2.5
      • Quacpac TK 2.2.5
      • QUACPAC 2.2.4
      • Quacpac TK 2.2.4
      • QUACPAC 2.2.3
      • Quacpac TK 2.2.3
      • QUACPAC 2.2.2
      • Quacpac TK 2.2.2
      • QUACPAC 2.2.1
      • Quacpac TK 2.2.1
      • QUACPAC 2.2.0
      • Quacpac TK 2.2.0
      • QUACPAC 2.1.3
      • Quacpac TK 2.1.3
      • QUACPAC 2.1.2
      • Quacpac TK 2.1.2
      • QUACPAC 2.1.1.0
      • Quacpac TK 2.1.1.2
      • Quacpac TK 2.1.1
      • QUACPAC 2.1.0
      • QUACPAC 2.0.2
      • QUACPAC 2.0.1
      • QUACPAC 2.0.0
      • QUACPAC 1.7.0
      • QUACPAC 1.6.3
      • QUACPAC 1.5.0
      • QUACPAC 1.3.1
      • QUACPAC 1.3.0
      • QUACPAC 1.1.0
    • molcharge Appendix: Complete list of -method options
    • Citation
  • ROCS 3.8.0.1
    • Introduction
      • Overview
      • Applications
      • Utility Programs
    • ROCS
      • Overview
      • Input Files
      • Example Commands
      • Report File
      • Command Line Help
      • Required Parameters
      • Optional Parameters
    • vROCS
      • Overview
      • Setup a simple run and a validation run
      • Results visualization and analysis
      • Statistics metrics
      • Saving ROCS data
      • ROCS shape query sources
      • Editing ROCS queries in vROCS
      • vROCS menus
    • Utilities
      • CheckCff
      • Chunker
      • HLMerge
      • MakeRocsDB
      • ROCSReport
    • ROCS Tutorials
      • Introduction
      • Build/edit a query using the Wizard
      • Build/edit a query manually
      • Perform a ROCS validation run
      • Perform a simple ROCS run
      • Perform a ROCS run from the command line
    • Theory
      • Shape Theory
      • Color Features
      • Color Force Field
      • Similarity Measures
    • Release History
      • ROCS 3.8.0
      • Shape TK 3.8.0
      • ROCS 3.7.0
      • Shape TK 3.7.0
      • ROCS 3.6.2
      • Shape TK 3.6.2
      • ROCS 3.6.1
      • Shape TK 3.6.1
      • ROCS 3.6.0
      • Shape TK 3.6.0
      • ROCS 3.5.1
      • Shape TK 3.5.1
      • ROCS 3.4.3
      • Shape TK 3.4.3
      • ROCS 3.4.2
      • Shape TK 3.4.2
      • ROCS 3.4.1.0
      • Shape TK 3.4.1
      • ROCS 3.4.0
      • ROCS 3.3.2
      • ROCS 3.3.1
      • ROCS 3.3.0
      • ROCS 3.2.2
      • ROCS 3.2.1
      • ROCS 3.2.0
      • ROCS 3.1.2
      • ROCS 3.1.1
      • ROCS 3.1.0
      • ROCS 3.0.0
      • ROCS 2.4.2
      • ROCS 2.4.1
      • ROCS 2.3.1
      • ROCS 2.3.0
      • ROCS 2.2.0
    • List of selected ROCS publications
    • Citation
  • SiteHopper 2.1.2.1
    • Introduction
      • Overview
      • Applications
    • SiteHopper Search
      • Overview
      • GPU Prerequisites
      • Example Commands
      • Command Line Help
      • Required Parameters
      • Optional Parameters
    • SiteHopper build
      • Overview
      • Example Commands
      • Command Line Help
      • Required Parameters
      • Optional Parameters
    • Release History
      • SiteHopper 2.1.2
      • SiteHopper TK 2.1.2
      • SiteHopper 2.1.1
      • SiteHopper TK 2.1.1
      • SiteHopper 2.1.0
      • SiteHopper TK 2.1.0
      • SiteHopper 2.0.4
      • Sitehopper TK 2.0.4
      • SiteHopper 2.0.3
      • Sitehopper TK 2.0.3
      • SiteHopper 2.0.2
      • Sitehopper TK 2.0.2
      • SiteHopper 2.0.1
      • Sitehopper TK 2.0.1
      • SiteHopper 2.0.0
      • SiteHopper TK 2.0.0
      • SiteHopper 1.0.0
    • Citation
  • SPRUCE 1.7.0.1
    • Introduction
      • Overview
      • Applications
      • Utility Programs
      • Utilizing a Loop Template Database
    • SPRUCE
      • Overview
      • Spruce Output Naming Conventions
      • Example Commands
      • Command Line Help
      • Required Parameters
      • Optional Parameters
    • Superposition
      • Overview
      • Example Commands
      • Command Line Help
      • Required Parameters
      • Optional Parameters
    • EnumSites
      • Overview
      • Example Commands
      • Command Line Help
      • Required Parameters
      • Optional Parameters
    • GetStructure
      • Overview
      • Example Commands
    • LoopDBBuilder
      • Overview
      • Example Commands
      • Command Line Help
      • Required Parameters
      • Optional Parameters
    • DU2PDB
      • Overview
      • Example Commands
      • Command Line Help
      • Required Parameters
      • Optional Parameters
    • du2mmcif
      • Overview
      • Example Commands
      • Command Line Help
      • Required Parameters
      • Optional Parameters
    • Release History
      • SPRUCE 1.7.0
      • Spruce TK 1.7.0
      • SPRUCE 1.6.1
      • Spruce TK 1.6.1.1
      • Spruce TK 1.6.1
      • SPRUCE 1.6.0
      • Spruce TK 1.6.0
      • SPRUCE 1.5.3
      • Spruce TK 1.5.3
      • SPRUCE 1.5.2.1
      • SPRUCE 1.5.2.0
      • Spruce TK 1.5.2
      • SPRUCE 1.5.1
      • Spruce TK 1.5.1
      • SPRUCE 1.5.0
      • Spruce TK 1.5.0
      • SPRUCE 1.4.0
      • Spruce TK 1.4.0
      • SPRUCE 1.3.0
      • Spruce TK 1.3.0
      • SPRUCE 1.2.0.2
      • SPRUCE 1.2.0.0
      • Spruce TK 1.2.0
      • SPRUCE 1.1.0
      • SPRUCE 1.1.0
      • SPRUCE 1.0.0
    • Citation
  • SZMAP 1.7.2.1
    • Introduction
      • Overview
      • Applications
      • Utility Programs
      • A Word About Pronunciation
    • Spruce Before Szmap
      • Overview
    • SZMAP
      • Overview
      • SZMAP Input and Output
      • Example Commands
      • Command Line Help
      • Required Parameters
      • Optional Parameters
    • GamePlan
      • Overview
      • Example Commands
      • Command Line Help
      • Required Parameters
      • Optional Parameters
    • Utilities
      • SzmapGrid
      • GridComp
      • SzmapReport
    • VIDA Extensions
      • Introduction
      • Installing VIDA Extensions
      • WaterColor VIDA Extension
      • Water Orientation VIDA Extension
      • Color By Atom Properties
    • Tutorials
      • SZMAP Workflow
      • Protein and Ligand Preparation
      • Running SZMAP Stabilization Calculations
      • Analyzing SZMAP Results
      • Running SZMAP at Coordinates
      • Running Gameplan
    • Theory
      • Philosophy and Design
      • Technical Details
    • Release History
      • SZMAP 1.7.2
      • Szmap TK 1.7.2
      • SZMAP 1.7.1
      • Szmap TK 1.7.1
      • SZMAP 1.7.0
      • Szmap TK 1.7.0
      • SZMAP 1.6.7
      • SZMAP 1.6.6
      • SZMAP 1.6.5
      • Szmap TK 1.6.5
      • SZMAP 1.6.4
      • Szmap TK 1.6.4
      • SZMAP 1.6.3
      • Szmap TK 1.6.3
      • SZMAP 1.6.2
      • Szmap TK 1.6.2
      • SZMAP 1.6.1.0
      • Szmap TK 1.6.1
      • SZMAP 1.6.0
      • SZMAP 1.5.0
      • SZMAP 1.4.1
      • SZMAP 1.4.0
      • SZMAP 1.3.0
      • SZMAP 1.2.1
      • SZMAP 1.2.0
      • SZMAP 1.1.1
      • SZMAP 1.1.0
      • SZMAP 1.0.0
    • Appendix 1: SZMAP Grids
      • Protein + Ligand Complex
      • Ligand Only
      • Protein Only
      • (Complex - Protein - Ligand) Stabilization
    • Appendix 2: SZMAP Atom Properties
      • Complex, Apo or Ligand
      • (Complex - Protein - Ligand) Stabilization
    • Citation
  • SZYBKI 2.9.0.1
    • Overview
    • Applications
    • Utility Programs
    • SZYBKI
      • Overview
      • Example Commands
      • Command Line Help
      • Required Parameters
      • Optional Parameters
    • FREEFORM
      • Overview
      • Example Commands
      • Command Line Help
      • Required Parameters
      • Optional Parameters
    • Theory
      • SZYBKI Theory
      • Nonplanar Aromatic Rings in Protein-Bound Ligands
      • Freeform Theory
    • Utilities
      • OptLigandInDU
      • OptimizeDU
    • Release History
      • SZYBKI
      • Szybki TK 2.9.0
      • SZYBKI 2.8.0
      • Szybki TK 2.8.0
      • SZYBKI 2.7.1
      • Szybki TK 2.7.1.3
      • Szybki TK 2.7.1.0
      • SZYBKI 2.7.0
      • Szybki TK 2.7.0
      • SZYBKI 2.6.0
      • Szybki TK 2.6.0.1
      • Szybki TK 2.6.0.0
      • SZYBKI 2.5.1
      • Szybki TK 2.5.1.2
      • Szybki TK 2.5.1.1
      • SZYBKI 2.5.0
      • Szybki TK 2.5.0
      • SZYBKI 2.4.0
      • SZYBKI 2.3.1
      • Szybki TK 2.3.1
      • SZYBKI 2.3.0.2
      • SZYBKI 2.3.0.0
      • Szybki TK 2.3.0
      • SZYBKI 2.2.0
      • SZYBKI 1.11.0
      • SZYBKI 1.10.1
      • SZYBKI 1.10.0
      • SZYBKI 1.9.0
      • SZYBKI 1.8.0
      • SZYBKI 1.7.0
      • SZYBKI 1.5.2
      • SZYBKI 1.5.1
      • SZYBKI 1.5.0
      • SZYBKI 1.3.4
      • SZYBKI 1.3.3
      • SZYBKI 1.3.2
      • SZYBKI 1.3.1
      • SZYBKI 1.3.0
      • SZYBKI 1.2.2
    • Citation
  • VIDA 5.1.0.a.1
    • Introduction
      • General Concepts
      • Scope
      • Layout
      • Undo / Redo
      • Mouse Map
      • User Directory
      • Help
    • Installation and Platform Notes
      • Enterprise Installation for Windows
    • File I/O
      • Opening Files
      • Closing Files
      • Saving Files
      • Importing Files
      • Exporting Files
      • Drag and Drop
      • Copy and Paste
    • 3D Display
      • User Interaction
      • Rendering
      • Stereo
      • Viewpoint
      • Bookmarks
      • Tiled Display
      • Toolbars
      • Display Widgets
      • Molecular Visualization
      • Grid Visualization
      • Grid Types
      • Reentrant Grids
      • Surface Visualization
      • Symmetry
    • 2D Display
      • Preview vs. Viewer
      • Interaction
      • Advanced Depiction Options
    • Spreadsheet
      • Basic Usage
      • Sorting
      • Displaying Data
      • Organizing Columns
      • Creating New Columns
      • Filtering
      • Statistics
      • Formatting Columns
      • Advanced Depiction Options
      • Importing/Exporting
      • Atom Spreadsheet
      • Residue Spreadsheet
    • List Management
      • Introduction
      • Browsing
      • Views
      • List Columns
      • List Manipulation
    • Processes
      • Processes
      • Pipes
    • Molecule Manipulation
      • Creating Molecules
      • Editing Molecules
    • Custom Views
      • FRED View
      • EON View
      • ROCS View
    • Selection Language
      • Introduction
      • Operators
      • Lists and Ranges
      • Properties
      • Macros/Pre-defined sets
      • Scripting with ScratchScope
    • Scripting
      • Journal File
      • Startup File
      • Scripts Directory
      • Scripting API
      • Scripting Window
      • OpenEye Toolkits
      • Customizing the User Interface
    • Extensions
      • Example Extensions
      • Extension Manager
      • Creating Extensions
      • Distributing Extensions
    • Preferences
    • Menus
      • File
      • Edit
      • View
      • Data
      • Style
      • Bookmarks
      • Tools
      • Select
      • Window
      • Help
    • Examples
      • Data
      • Scripts
    • VIDA Python API
      • General Functions
      • Scope Functions
      • User Interface Functions
      • Display Functions
      • Object Functions
      • Molecule Builder Functions
      • Data Analysis Functions
      • Deprecated Functions
    • Release History
      • VIDA 5.0.7
      • VIDA 5.0.6
      • VIDA 5.0.5
      • VIDA 5.0.4
      • VIDA 5.0.3
      • VIDA 5.0.2
      • VIDA 5.0.1
      • VIDA 5.0.0
      • VIDA 4.4.0
      • VIDA 4.3.0
      • VIDA 4.2.0
      • VIDA 4.1.1
      • VIDA 4.1.0
      • VIDA 4.0.3
      • VIDA 4.0.0
      • VIDA 3.0.0
      • VIDA 2.1.2
      • VIDA 2.1.1
      • VIDA 2.1.0
      • VIDA 2.0.2
    • Citation
  • OpenEye Glossary of Terms
  • Bibliography
Applications-
  • All OpenEye Documentation »
  • Contents »
  • SiteHopper 2.1.2.1

SiteHopper 2.1.2.1¶

  • Introduction
    • Overview
    • Applications
  • SiteHopper Search
    • Overview
      • Basic Search Process
      • Output from sitehopper_search
      • Scoring in sitehopper_search
      • Binding site surface visualization
      • Pre-Built SiteHopper Database
    • GPU Prerequisites
      • Supported Platforms
      • Supported GPUs
      • NVIDIA Drivers
    • Example Commands
    • Command Line Help
    • Required Parameters
    • Optional Parameters
      • Input/Output
      • SiteHopper Search Options
      • Logging
  • SiteHopper build
    • Overview
    • Example Commands
    • Command Line Help
    • Required Parameters
    • Optional Parameters
      • Input/output
      • Database options
      • Logging
  • Release History
    • SiteHopper 2.1.2
    • SiteHopper TK 2.1.2
    • SiteHopper 2.1.1
    • SiteHopper TK 2.1.1
      • Minor bug fixes
    • SiteHopper 2.1.0
    • SiteHopper TK 2.1.0
      • New features
    • SiteHopper 2.0.4
    • Sitehopper TK 2.0.4
    • SiteHopper 2.0.3
    • Sitehopper TK 2.0.3
    • SiteHopper 2.0.2
    • Sitehopper TK 2.0.2
    • SiteHopper 2.0.1
    • Sitehopper TK 2.0.1
      • Python-specific changes
    • SiteHopper 2.0.0
      • New Features
    • SiteHopper TK 2.0.0
    • SiteHopper 1.0.0
  • Citation
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