• OEApplications 2024.2
    • 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
    • Detailed Release Notes 2024.2
    • AFITT 3.0.1
    • BROOD 4.1.0
    • Bioisostere TK 4.1.0
      • New features
      • Major bug fixes
      • Minor bug fixes
    • EON 3.1.0
      • New Features
      • Bug Fixes
    • Eon TK 3.1.0
      • New features
    • Zap TK 2.5.0
    • OEDocking 4.3.2
    • OEDocking TK 4.3.2
      • New features
      • Major bug fixes
      • Minor bug fixes
    • OMEGA 6.0.0
      • New Features
      • Minor Bug Fixes
    • Omega TK 6.0.0
      • New features
      • Minor bug fixes
    • MolProp TK 2.6.5
    • PICTO 5.1.2
      • New features
    • OEDepict TK 2.5.5
    • pKa-Prospector 1.2.4
    • QUACPAC 2.2.5
    • Quacpac TK 2.2.5
      • Minor bug fixes
    • ROCS 3.7.0
      • New Features
      • Minor Bug Fixes
    • Shape TK 3.7.0
      • New features
      • Minor bug fixes
    • SiteHopper 2.1.1
    • SiteHopper TK 2.1.1
      • Minor bug fixes
    • SPRUCE 1.6.1
      • New features
    • Spruce TK 1.6.1.1
      • Major bug fixes
    • Spruce TK 1.6.1
      • New features
      • Major bug fixes
      • Minor bug fixes
      • Documentation changes
    • SZMAP 1.7.1
    • Szmap TK 1.7.1
    • SZYBKI 2.8.0
    • Szybki TK 2.8.0
      • New features
    • VIDA 5.0.7
  • Previous Release Highlights
    • 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 3.0.1.1
    • 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
      • 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 4.1.0.1
    • 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 4.1.0
      • 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 3.1.0.1
    • Introduction
      • Overview
      • Applications
    • EON
      • Overview
      • Example Commands
      • Report File
      • Command Line Help
      • Required Parameters
      • Optional Parameters
    • Theory
    • Release History
      • 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 4.3.2.1
    • 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 4.3.2
      • 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 6.0.0.1
    • 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 6.0.0
      • 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 5.1.2.1
    • Introduction
      • Overview
      • Applications
    • PICTO
      • Overview
      • Sketcher
      • SMARTS
      • Implicit/Explicit Hydrogens
      • Atom Labeling, Aromatic Displays, Aromatic Modeling, and other Displays
    • Release History
      • PICTO 5.1.2
      • 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 1.2.4.1
    • 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 1.2.4
      • 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 2.2.5.1
    • 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 2.2.5
      • 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 3.7.0.1
    • 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 3.7.0
      • 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 2.1.1.1
    • 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 2.1.1
      • 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 1.6.1.1
    • 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 1.6.1
      • 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 1.7.1.1
    • 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 1.7.1
      • 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 2.8.0.1
    • 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
      • Freeform Theory
    • Utilities
      • OptLigandInDU
      • OptimizeDU
    • Release History
      • 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 5.0.7.1
    • 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 »
  • VIDA 5.0.7.1 »
  • Menus

Menus¶

This chapter contains a listing of the menu options available in VIDA. Where possible, each section also contains a listing of the Python code that is run when that option is selected. All Python menu commands are wrapped in a standard exception handling block:


    try: exec(<command>)
    except Exception, e:
        if 'Canceled' not in str(e):
            DoMenuError(e)
            raise;

File¶

Open¶


    Open(PromptFilenames([], 'molecule,grid,surface,query,python,state'))

Open State¶


    Open(PromptFilename('','Open','state'))

Open Special¶

From PDB…¶


    LoadMoleculesFromPDB(PromptString('Enter PDB code(s)'))

Script…¶


    Open(PromptFilename('', 'Open', 'python')

MTZ…¶


    DoOpenMTZ()

Clear¶

Marked¶


    DeleteScoped(MarkedScope, True)

Not Marked¶


    DeleteScoped(MarkedScope, False)

Visible¶


    DeleteScoped(VisibleScope, True)

Not Visible¶


    DeleteScoped(VisibleScope, False)

Clear All¶


    DeleteAll()

Save¶


    try:
        _tmp_keys = PromptKeys()
        if _tmp_keys:
            _tmp_sname = PromptSaveFilename(_tmp_keys)
            if _tmp_sname:
                Save(_tmp_sname, _tmp_keys)
    except:
        pass

Save Marked¶


    try:
        _tmp_keys  = GetMoleculesScoped(MarkedScope)
        _tmp_keys += GetGridsScoped(MarkedScope)
        _tmp_keys += GetSurfacesScoped(MarkedScope)
        if _tmp_keys:
            _tmp_sname = PromptSaveFilename(_tmp_keys)
            if _tmp_sname:
                Save(_tmp_sname, _tmp_keys)
    except:
        pass

Save State¶


    try:
          _tmp_filters = 'OpenEye State Version 2 ( *.oes ) ;;'      \
          				 'OpenEye Mini State Version 2 ( *.oes ) ;;' \
          				 'OpenEye State Version 1 ( *.oes ) '
          _tmp_results = PromptSaveFilename(_tmp_filters)
          if len(_tmp_results) == 2:
              SaveStateFilter(_tmp_results[0], _tmp_results[1])
    except:
        pass

New List¶

From AND¶


    try:
        _tmp_ids = PromptIDs(['Lists'], 0)
        if _tmp_ids:
            ListNewAnd(_tmp_ids)
    except:
        pass

From OR¶


    try:
        _tmp_ids = PromptIDs(['Lists'], 0)
        if _tmp_ids:
            ListNewOr(_tmp_ids)
    except:
        pass

From XOR¶


    try:
        _tmp_ids = PromptIDs(['Lists'], 0)
        if _tmp_ids:
            ListNewXor(_tmp_ids)
    except:
        pass

From Marked¶


    ListNewMarked()

New Molecule¶

From Name¶


    try:
        _tmp_smiles = PromptSmiles('New Molecule')
        if _tmp_smiles:
            _tmp_mol = MoleculeNew(_tmp_smiles)
            if _tmp_mol:
                MoleculeGenerateCoords(_tmp_mol, 1)
                Active(_tmp_mol)
    except:
        pass

From Merge¶

All three options under this menu (Scoped, Marked, and Visible) execute the following code.


    try:
        _tmp_name = PromptString('Name:')
        if _tmp_name:
            _tmp_id = MoleculeMergeScoped(SCOPE, _tmp_name)
            if _tmp_id:
                Active(_tmp_id)
    except:
        pass

The SCOPE parameter is assigned a value according to which option was selected (SelectedScope, MarkedScope, and VisibleScope respectively).

From Split¶

Components


    ids = MoleculeNewSubsetScoped(0,ActiveThenVisibleScope,1)
    if ids:
        Active(ids[0])

Selected


    ids = MoleculeNewSubsetScoped(0,ActiveThenVisibleScope,SelectedScope,1)
    if ids:
        Active(ids[0])

Marked


    ids = MoleculeNewSubsetScoped(0,ActiveThenVisibleScope,MarkedScope,1)
    if ids:
        Active(ids[0])

Import¶

Spreadsheet¶


    _tmp_fname = ''
    try:
        _tmp_fname = PromptFilename('', 'Open', 'data')
        if _tmp_fname:
            eval( SpreadsheetPromptImport(_tmp_fname) or 'None' )
    except:
        pass

Export¶

Script History¶


    try:
        _tmp_fname = PromptFilename('journal.py', 'Save', 'python')
        if _tmp_fname:
            AppScriptSave(_tmp_fname)
    except:
        pass

Screenshot¶


    MainWindowScreenshotPrompt()

Spreadsheet¶


    try:
        _tmp_fname = PromptFilename('', 'Save', 'data')
        if _tmp_fname:
            eval( SpreadsheetPromptExport(_tmp_fname) or 'None' )
    except:
        pass

POV-Ray¶


    try:
        _tmp_fname = PromptFilename('', 'Save', '')
        if _tmp_fname:
            ViewerExportPOVRAY(_tmp_fname)
    except:
        pass

Recents¶

All of the options in this menu call the following command:


    OpenWithRecents(FILENAME)

The FILENAME parameter is assigned to the filename specified in the option that was selected under this menu.

Recent Directories¶

All of the options in this menu call the following command:


    PromptOpenWithRecents('molecule,grid,surface,query,python,state', FILENAME)

The FILENAME parameter is assigned to the filename specified in the option that was selected under this menu.

Exit¶


    Quit()

Edit¶

Undo¶


    Undo()

Undo History¶

Redo¶


    Redo()

Redo History¶

Copy¶


    Copy()

Copy Image¶


    MainWindowScreenshot()

Paste¶


    PasteMolecules()

Select¶

All Visible¶


    SelectAllMolecules()

Expression¶


    try:
        _tmp_selexpr = PromptString('Selection Expression')
        if _tmp_selexpr:
            Select(_tmp_selexpr)
    except:
        pass

Query¶


    try:
        _tmp_query = PromptQuery()
        if _tmp_query:
            SelectByQuery(_tmp_query, False, VisibleScope)
    except:
        pass

Invert¶


    SelectInvert()

None¶


    ClearSelection()

Mark¶

All Visible¶


    MarkObjectsByScope(VisibleScope)

Query¶


    try:
        _tmp_query = PromptQuery()
        if _tmp_query:
            SelectByQuery(_tmp_query, True)
    except:
        pass

None¶


    ClearMarked()

Hide¶

All¶


    ClearVisible()

Selected¶


    HideScoped(SelectedScope, True)

Marked¶


    HideScoped(MarkedScope, True)

Not Selected¶


    HideScoped(SelectedScope, False)

Not Marked¶


    HideScoped(MarkedScope, False)

None¶


    HideNoneScoped()

Find¶

By LINGO Similarity¶

Creates a new list of molecules, based on the LINGO similarity measure to a query molecule. LINGO is a fast text-based similarity measure that uses the canonical, isomeric SMILES strings of molecules for comparisons.

See also

  • [Vidal-2005]


    try:
        _tmp_key    = PromptKey()
        _tmp_cutoff = PromptFloat('Similarity Cutoff', 0.4)
        if _tmp_key.IsValid() and _tmp_cutoff > 0.0:
            ListNew('Find Results', FindBySimilarityScoped(_tmp_key, _tmp_cutoff))
    except:
        pass

By SMARTS¶


    try:
        _tmp_query = PromptQuery()
        if _tmp_query:
            ListNew('Find Results', FindBySMARTSScoped(_tmp_query))
    except:
        pass

By Query Molecule¶


    try:
        _tmp_key = PromptKey()
        if _tmp_key.IsValid():
            ListNew('Find Results', FindByQueryScoped(_tmp_key))
    except:
        pass

By Title¶


    try:
        _tmp_title = PromptString('Title Search')
        if _tmp_title:
            ListNew('Find Results', FindByTitleScoped(_tmp_title))
    except:
        pass

Find on Disk¶


    FindOnDisk()

Clear Scripting Log¶


    InterpreterClear()

Extensions¶


    ExtensionsEdit()

Preferences¶


    PreferencesEdit()

View¶

Fullscreen¶


    if AppShowGet() == 'fullscreen':
        AppShowSet('normal')
    else:
        AppShowSet('fullscreen')

Data¶

Sort Spreadsheet¶


    eval( SpreadsheetPromptSort() or 'None' )

Filter Spreadsheet¶


    eval( SpreadsheetPromptFilter() or 'None' )

Create Column¶


    eval( SpreadsheetPromptColumnExpression() or 'None' )

Create Empty Column¶


    _tmp_col   = PromptString("Column Name")
    _tmp_table = DataGetTable( DatatableCurrent() )
    if _tmp_table.GetColumn( _tmp_col ) > _tmp_table.NumCols():
        DatatableSetExpression( DatatableCurrent(), _tmp_col, "" )
    else:
        PromptError("Column %s already exists"%repr(_tmp_col))

Format Columns¶


    for x in SpreadsheetPromptFormat()[:-1].split(';'):
        eval(x or 'None')

Organize Columns¶


    SpreadsheetColumnController()

Advanced Depiction Options¶


    SpreadsheetPromptGraphemeOpts()

Show Statistics¶


    SpreadsheetShowStatsSet(SpreadsheetCurrent(), \
    			not SpreadsheetShowStatsGet(SpreadsheetCurrent()))

Style¶

Color¶

Palette¶


    try:
        _tmp_color = PromptColor()
        ColorSetScoped(_tmp_color)
    except:
        pass

Unique¶


    ColorUniqueScoped()

Restore¶


    MoleculeColorsResetScoped()

Molecules¶

All but two of the options (Carbon and Reference) in this menu call the following function.


    MoleculeColorByScoped(SCHEME)

The SCHEME parameter is assigned based on which menu option was selected according to the table below.

Color schemes¶

Amino

‘amino’

Alternate Locations

‘alt location’

BFactor

‘bfactor’

Chain

‘chain’

CPK

‘cpk’

CPKNew

‘cpknew’

Element

‘element’

Formal Charge

‘formal charge’

Group

‘group’

Partial Charge

‘partial charge’

Residue

‘residue’

Shapely

‘shapely’

The Carbon menu option calls the following function.


    try:
        _tmp_color = PromptColor()
        AtomColorSetScoped(6, _tmp_color)
    except:
        pass

The Reference menu option calls the following function.


    AtomColorReferenceScoped()

Surfaces¶

All of the options in this menu call the following function.


    SurfaceColorByScoped(SCHEME, PARAMS)

Both the SCHEME and PARAMS parameters are assigned based on which option was selected according to the table below.

Color schemes and parameters¶

Atom Color

‘atom’

‘’

Curvature

‘curvature’

‘’

Distance

‘distance’

‘’

Electrostatic

‘electrostatics’

‘’

Hydrogen Bond Potential

‘hydrogen bonds’

‘’

Hydrophobicity

‘hydrophobicity’

‘’

Surface Potential

‘potential’

‘’

The Grid menu options calls the following function.


    try:
        id = PromptID(['g'], False)
        SurfaceColorByScoped('grid', str(id))
    except:
        pass

Transparency¶

All of the options in this menu call the following function.


    SurfaceTransparencySetScoped(N)

The N parameter is assigned to a value between 0 and 255 based on which option was selected. A value of 255 corresponds to 0 percent transparency and a value of 0 corresponds with 100 percent transparency. The specific values used in the menu are: 255, 230, 204, 179, 153, 128, 102, 77, 61, 26, 0.

Selection¶

Crop Selected¶


    SurfaceCropScribedScoped()

Crop Unselected¶


    SurfaceCropUnscribedScoped()

Display¶

Molecules¶

All of the options in this menu call the following function.


    MoleculeStyleSetScoped(STYLE)

The STYLE parameter is assigned based on which option was selected according to the table below.

Molecule Styles¶

Wireframe

‘wireframe’

Stick

‘stick’

Ball and Stick

‘ball and stick’

CPK

‘cpk’

Stars

‘stars’

Hidden

‘hidden’

Hydrogens

All of the options in this menu call the following function.


    AtomHydrogenStyleSetScoped(STYLE)

The STYLE parameter is assigned based on which option was selected according to the table below.

Hydrogen Styles¶

All

2

Polar

1

None

0

Non-Bonded Atoms

Both of the options in this menu call the following function with the HIDE parameter assigned based on which option was selected (Show assigns HIDE to False and Hide assigns HIDE to True).


    BondHideNonbondedSet(HIDE)

C-Alpha Trace

Both of the options in this menu call the following function with the DRAW parameter assigned based on which option was selected (Show assigns DRAW to True and Hide assigns DRAW to False).


    DrawCATracesSetScoped(DRAW)

Ribbons

Both of the options in this menu call the following function with the DRAW parameter assigned based on which option was selected (Show} assigns DRAW to True and Hide} assigns DRAW to False).


    DrawRibbonsSetScoped(DRAW)

Atom Labels

The Atom Labels submenu provides a variety of labeling of options. The “Custom…” option launches a dialog which allows the user to build up more complex and customized labels. This dialog is launched using the following Python command:


    ViewerLabelDialog('Atoms')

All of the other options in the submenu all call the following Python command but with different string arguments:


    AtomLabelSetScoped('')

The arguments used can be found in the table below:

Atom Label Arguments¶

Name

‘%n’

Index

‘%i’

Element

‘%e’

Isotope

‘%iso’

Type

‘%t’

Integer Type

‘%it’

Implicit H Count

‘%h’

Map Idx

‘%m’

Partial Charge

‘%p’

Formal Charge

‘%f’

Atom Radius

‘%rad’

Residue Info

‘%r’

Residue Info (CA)

‘%car’

B-Factor

‘%bf’

C-Alpha B-Factor

‘%cab’

Degree

‘%d’

Is Chiral

‘%c’

Chirality

‘%chi’

Hybridization

‘%hy’

Has Stereo Specified

‘%sts’

Is In Ring

‘%rng’

OEChem Idx

‘%oei’

Symmetry Class

‘%sy’

Atom Comment

‘%cm’

Atom Occupancy

‘%occ’

MMFF Atom Type

‘%mmff’

Generic Data

‘%gd(<GENERIC_DATA_TAG>)’

None

‘’

Bond Labels

The Bond Labels submenu provides a variety of labeling of options. The “Custom…” option launches a dialog which allows the user to build up more complex and customized labels. This dialog is launched using the following Python command:


    ViewerLabelDialog('Bonds')

All of the other options in the submenu all call the following Python command but with different string arguments:


    BondLabelSetScoped('')

The arguments used can be found in the table below:

Bond Label Arguments¶

Name

‘%n’

Index

‘%i’

Type

‘%t’

Integer Type

‘%it’

Order

‘%o’

Length

‘%l’

Is Chiral

‘%c’

Chirality

‘%chi’

Has Stereo Specified

‘%sts’

OEChem Idx

‘%oei’

Generic Data

‘%gd(<GENERIC_DATA_TAG>)’

None

‘’

Electrostatic Potential

Both of the options in this menu call the following function with the DRAW parameter assigned based on which option was selected (Show assigns DRAW to True and Hide assigns DRAW to False).


    ShowESGridScoped(DRAW)

Molecular Surface

Both of the options in this menu call the following function with the DRAW parameter assigned based on which option was selected (Show assigns DRAW to True and Hide assigns DRAW to False).


    ShowSurfaceScoped('molecular', DRAW)

Accessible Surface

Both of the options in this menu call the following function with the DRAW parameter assigned based on which option was selected (Show assigns DRAW to True and Hide assigns DRAW to False).


    ShowSurfaceScoped('accessible', DRAW)

Hydrogen Bonds

Add Targets


    HBondAddTargetsScoped()

Remove Targets


    HBondRemoveTargetsScoped()

External Hydrogen Bonds


    HBondShowExternalSet(not HBondShowExternalGet())

Internal Hydrogen Bonds


    HBondShowInternalSet(not HBondShowInternalGet())

Grids¶

Solid


    ContourDrawAsSurfaceSetScoped(True)

Mesh


    ContourDrawAsSurfaceSetScoped(False)

Cloud


    ContourDrawStyleSetScoped('cloud')

Grid Corners


    GridShowCornersSet(not GridShowCornersGet())

Electrostatic


    GridTypeSetScoped(1)

ET


    GridTypeSetScoped(5)

FRED


    GridTypeSetScoped(2)

Generic


    GridTypeSetScoped(0)

Difference Map


    GridTypeSetScoped(4)

Regular Map


    GridTypeSetScoped(3)

Add Contour


    ContourTypedAddScoped()

Delete Contour


    ContourTypedRemoveScoped()

Surfaces¶

All of the options in this menu except one (Restore) call the following function.


    SurfaceStyleSetScoped(STYLE)

The STYLE parameter is assigned based on which option was selected according to the table below.

Surface Style Arguments¶

Solid

‘solid’

Mesh

‘mesh’

Points

‘points’

The Restore option calls the following function.


    SurfaceRestoreScoped()

Graphics¶

Depth Cue¶


    ViewerDepthcueSet(not ViewerDepthcueGet())

Slabbing¶


    ViewerSlabEnableSet(not ViewerSlabEnableGet())

Mirror Slabs¶


    ViewerMirrorSlabsSet(not ViewerMirrorSlabsGet())

Slab Level¶

All of the options in this menu call the following function.


    ViewerSlabEnableSet(True)
    ViewerSlabFarSet(50+N/2)

The N parameter is assigned to a value between 10 and 80 corresponding to the desired percent of the scene to be contained within the slabbing planes.

Render Quality¶

All of the options in the menu call the following function.


    ViewerLODSet(LOD)

The LOD parameter is assigned based on which option was selected according to the table below.

Level of Detail Parameters¶

Fastest

1

Fast

2

Good

3

Better

4

Best

5

Presentation

6

Note: Presentation quality is optimized for creating output images with a white background.

Stereo¶

Off


    ViewerStereoEnableSet(False)

Splitscreen


    ViewerStereoEnableSet(True)
    ViewerStereoHardwareSet(False)

Stencil


    ViewerStereoStyleSet(2)
    ViewerStereoEnableSet(True)

Angle


    try:
        angle = PromptFloat('Stereo Angle')
        ViewerStereoAngleSet(angle)
    except:
      pass

Separation


    try:
        sep = PromptFloat('Stereo Separation')
        ViewerStereoSeparationSet(sep)
    except:
        pass

Cross-Eyed


    ViewerStereoCrossEyedSet(not ViewerStereoCrossEyedGet())

Symmetry¶

Edit Cell¶


    XRayEditCrystalParams(ActiveID())

Show Unit Cell¶


    DrawUnitCellSet(OEInternal.MenuVal)

Show Symmetry¶


    DrawSymmetrySet(OEInternal.MenuVal)

Realize Symmetry In Cell¶


    DoSymmetryRealize(True)

Realize Symmetry¶


    DoSymmetryRealize(False)

Symmetry Radius¶


    SymmetryRadiusSet(PromptFloat('Symmetry radius',SymmetryRadiusGet()))

Symmetry Operators¶

No Symmetry Color¶


    SymmetryColorHelper(0,OEInternal.MenuVal)

Single Symmetry Color¶


    SymmetryColorHelper(1,OEInternal.MenuVal)

Color By Operator¶


    SymmetryColorHelper(2,OEInternal.MenuVal)

Unique Color¶


    SymmetryColorHelper(3,OEInternal.MenuVal)

Bookmarks¶

Add¶


    try:
        _tmp_name = PromptString('Bookmark name', 'Bookmark ' + str(1 + len(Bookmarks())))
        if _tmp_name:
            BookmarkSave(_tmp_name)
    except:
        pass

Organize¶


    exec(BookmarkOrganizeDialog())

Animated¶


    ViewerBookmarksSetAnimated(not ViewerBookmarksGetAnimated())

Tools¶

FRED View¶


    CustomViewFRED()

EON View¶


    CustomViewEON()

ROCS View¶


    CustomViewROCS()

Select¶

The Select menu provides a number of ways to select groups of atoms for use in various tasks, like coloring atoms, creating surfaces, etc. Most selection operations involve only molecules which are visible in the 3D Window. The Select menu also provides the ability to name sets of atoms and store them for later retrieval. These sets can be combined with the current selection through logical operations, allowing a high degree of flexibility in creating selection sets.

Clear¶

Clears all selected atoms and bonds.

All¶

Selects all visible atoms and bonds.

Invert¶

Inverts the current selection with respect to visible atoms.

Protein¶

Operations in this menu are protein-centric.

Backbone¶

Selects backbone atoms only.

Sidechains¶

Selects side chain atoms.

C-Alphas¶

Selects alpha carbon atoms in a protein.

Residue #…¶

Allows selection of atoms by residue number. A dialog will prompt for residue numbers and chain ID’s to include in the selection.

Residue Type…¶

Selects standard amino and nucleic acid residues by type. A dialog will prompt for residue names to be included in the selection.

Complete Residues¶

Selects all atoms in any residue that has at least one atom selected.

Zero Occupancy¶

Selects all atoms with an occupancy value of zero.

Partial Occupancy¶

Selects all atoms with an occupancy value less than 1.0.

Alt Locations¶

Selects all residues with alternate location specifiers.

Waters¶

Selects all water molecules.

Atom Numbers…¶

Selects atoms by their OEChem index value. A dialog will prompt for the atom numbers to include in the selection.

By Distance…¶

Selects residues within a specified distance of the currently selected atoms. A dialog will appear to allow the distance to be specified with a slider. A checkbox in this dialog provides an option to exclude the originally selected atoms from the final selection.

Heteroatoms¶

Selects all atoms that are not carbon or hydrogen.

Charged¶

Selects all atoms with a non-zero formal charge.

SMARTS Pattern…¶

Selects all atoms matching a SMARTS query pattern. A dialog will prompt for the SMARTS pattern to use.

Expression…¶

Selects atoms using an expression from VIDA’s selection language. A dialog will prompt for the expression to use.

Store¶

These options allow the storage of the current selection into a new or existing atom set.

New Set…¶

Creates a new atom set after prompting for a set name.

Into <Set_Name>¶

Replaces the contents of the named set Set_Name with the current selection.

Recall¶

From <Set_Name>¶

Selects the atoms in the named set Set_Name.

Combine¶

Combines the current selection with named sets.

Include¶

Adds the atoms from the named set to the current selection (a logical OR operation).

Exclude¶

Removes atoms from the named set from the current selection (logical NOT operation).

Intersect¶

Selects the atoms that are in both the named set and the current selection (logical AND operation).

Delete Set¶

Deletes the named set. This does not delete any atoms.

Hide Selected¶

Turns off the visibility of all selected atoms.

Hide Unselected¶

Turns off the visibility of all unselected atoms in visible molecules.

Window¶

Main Window¶

2D Viewer¶


    if OEInternal.MenuVal:
        AppMainWindowSet('2D Viewer')

3D Viewer¶


    if OEInternal.MenuVal:
        AppMainWindowSet('3D Viewer')

Spreadsheet¶


    if OEInternal.MenuVal:
        AppMainWindowSet('Spreadsheet')

2D Preview¶


    WindowVisibleSet('2D Preview')

2D Viewer¶


    WindowVisibleSet('2D Viewer')

3D Viewer¶


    WindowVisibleSet('3D Viewer')

List Window¶


    WindowVisibleSet('List Window')

Process Manager¶


    WindowVisibleSet('Process Manager')

Scripting Window¶


    WindowVisibleSet('Scripting Window')

Spreadsheet¶


    WindowVisibleSet('Spreadsheet')

Style Control¶


    WindowVisibleSet('Style Control')

Help¶

About¶


    About()

Documentation¶

All of the items in this menu open a specific document. The script to open the document can be found below:


    AppOpenUrl('file:' + AppDocDir() + FILE_PATH)

The actual document path that is used is:

  • User Manual (HTML) <https://docs.eyesopen.com/applications/vida/index.html>_.

License¶

Open¶


    AppOpenUrl('file:' + AppLicenseFile())

Set¶


    AppLicenseUpdate(True)

Update¶


    AppLicenseUpdate(False)

Open Examples Directory¶


    AppOpenUrl('file:' + AppExamplesDir())

Open User Directory¶


    AppOpenUrl('file:' + AppUserDir())

File Bug Report¶


    AppOpenUrl('mailto:support@eyesopen.com')

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© Copyright 2025, Cadence Design Systems, Inc. (Cadence). Last updated on Feb 09, 2025.