OEApplications 2023.1
Release Highlights 2023.1.0
Supported Platforms
Related Application Versions
General Notices
Detailed Release Notes 2023.1
AFITT 2.6.3
BROOD 3.2.1
EON 2.4.1
Zap TK 2.4.5
OEDOCKING 4.2.1
OEDocking TK 4.2.1
OMEGA 4.2.2
Omega TK 4.2.2
MolProp TK 2.6.2
PICTO 5.0.0
OEDepict TK 2.5.2
pKa-Prospector 1.2.1
QUACPAC 2.2.2
Quacpac TK 2.2.2
ROCS 3.6.0
Shape TK 3.6.0
SiteHopper 2.0.3
Sitehopper TK 2.0.3
SPRUCE 1.5.2
Spruce TK 1.5.2
Szmap TK 1.6.6
SZYBKI 2.6.0
Szybki TK 2.6.0
Previous Release Highlights
Release Highlights 2022.2.2
Release Highlights 2022.2.1
Release Highlights 2022.1
Release Highlights 2021.2
Release Highlights 2021.1
Release Highlights 2020.2.2
Release Highlights 2020.2
Release Highlights 2020.1.1
Release Highlights 2020.1
Release Highlights 2020.0
Release Highlights 2019.Nov
Release Highlights 2019.May
OEApplications 2018.Nov
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 2.6.3.0
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 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 3.2.1.0
Introduction
Applications
Utility Programs
Installing the BROOD Database
vBROOD
Overview
Build and Run
Build a New Query
Run BROOD
Filtering
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
Fragment similarity searching
Clash detection and selectivity
Strain energy
Fragment joining
Cyclization
Molecular complexity
Aromatic fragment comparison
Shape-based belief model
Abbott bioavailability score
CHOMP Theory
BROOD Fragment Database
ChEMBL31 Fragment Database
ChEMBL31_lite Fragment Database
brood-database-chembl-3.0.0
Release History
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 2.4.1.0
Introduction
Overview
Applications
EON
Overview
Example Commands
Report File
Command Line Help
Required Parameters
Optional Parameters
Theory
Release History
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 4.2.1.0
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
POSIT Theory
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
MakeReceptor
Overview
GUI Layout
Setting up a Receptor
Utilities
ReceptorInDU
OEB2DUReceptor
DockingReport
ScorePose
ReceptorToolbox
combine_receptors
DU2OEBReceptor
Release History
OEDOCKING 4.2.1
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 4.2.2.0
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 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 5.0.0.0
Introduction
Overview
Applications
PICTO
Overview
Sketcher
SMARTS
Implicit/Explicit Hydrogens
Atom Labeling, Aromatic Displays, Aromatic Modeling, and other Displays
Release History
PICTO 5.0.0
OEDepict TK 2.5.2
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 1.2.1.0
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 1.2.1
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 2.2.2.0
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 2.2.2
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 3.6.0.0
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 3.6.0
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 2.0.3.0
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 2.0.3
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 1.5.2.0
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
Release History
SPRUCE 1.5.2
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 1.6.6.0
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 1.6.6
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 2.6.0.0
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 2.6.0
Szybki TK 2.6.0
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 5.0.4.0
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 5.0.4
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
Glossary
Bibliography
Applications-
All OpenEye Documentation
»
Contents
»
AFITT 2.6.3.0
AFITT 2.6.3.0
ΒΆ
Overview
Applications
Utility Programs
FLYNN
Overview
Example Commands
Basic Usage
Generating Reports
Choosing box regions of density
Choosing density close to residues
Choosing MTZ columns
Fragment usage
Command Line Help
Required Parameters
Optional Parameters
Input Options
MTZ File Options
Advanced Options
Fragment Fitting Options
3D Construction Options
Usage Notes
Minimum Requirements
Types of input ligands
Stereochemistry Enumeration
Refinement Dictionaries
REFMAC5 refinement dictionaries
Looking up known residues
MMFF94 versus MMFF94s forcefields
FLYNN and writing CIF Files
Results on The Gold Test Set
Coot Integration
Overview
Using FLYNN
FLYNN Advanced Options
Using WriteDict
WriteDict Advanced Options
planarAniline option
Using RotFit
ROTFIT options
Installing Coot Interface
Coot
WinCoot 0.9.4.1+
WinCoot 0.3.3 to 0.8.9.2
Utilities
AlignGrid
Overview
Example Commands
Command Line Help
Required Parameters
Optional Parameters
RotFit
Overview
Example Commands
Command Line Help
Required Parameters
Optional Parameters
Rscc
Overview
Example Commands
Command Line Help
Required Parameters
Optional Parameters
WriteDict
Overview
Example Commands
Command Line Help
Required Parameters
Optional Parameters
Theory
Fragment Fitting
Release History
AFITT 2.6.3
AFITT 2.6.2
AFITT 2.6.1
AFITT 2.6.0
New features
AFITT 2.5.3
Minor Bug Fixes
Documentation Changes
AFITT 2.5.2.0
AFITT 2.5.1
AFITT 2.5.0
AFITT-CL 2.4.1
Platform Support
Coot Support
Bug Fixes
AFITT-CL 2.4.0
Platform Support
FLYNN
WRITEDICT
ROTFIT
AFITT-CL 2.3.0
Other
WRITEDICT
FLYNN
COOT Integration
AFITT-CL 2.2.0
WRITEDICT
FLYNN
AFITT-CL 2.1.1
WRITEDICT
FLYNN
AFITT-CL 2.1.0
WRITEDICT
FLYNN
AFITT-CL 2.0.1
WRITEDICT
FLYNN
FLYNN 2.0.0
Citation