• Release 2024.1
    • Small Molecule Highlights
    • Antibody Highlights
    • General Release Notes
      • AbXtract™ - NGS Antibody Discovery
        • Introduction to AbXtract
        • Tutorials
        • How to Guides
        • Frequently Asked Questions
        • Abxtract Floes - Documentation
        • abxtract - Cube Documentation
        • Key Fields
        • Release Notes
      • AI Fold Floes
        • AI Fold Floes - Documentation
        • Release Notes
      • 3D Antibody Modeling Package
        • 3D Antibody Modeling Tutorial
        • Antibody MD Simulations Tutorial
        • Understanding Antibody Surfaces and Annotations
        • Antibody SiteHopper-based Clustering Tutorial
        • OpenEye 3D Antibody Modeling - Documentation
        • Release Notes
        • Bibliography
      • Cryptic Pocket Detection
        • Introduction
        • Tutorials
        • OpenEye Cryptic Pocket Detection Floes - Documentation
        • Release Notes
        • Bibliography
      • Molecular Dynamics Affinity Package
        • Introduction
        • How-To Guide and Tutorials
        • MD Affinity Floes - Documentation
        • oemdaffinity.cubes - Cube Documentation
        • Release Notes
      • Molecular Dynamics Core Package
        • Installation
        • orionmdcore.cubes - Cube Documentation
        • MD DataRecord
        • Release Notes
  • 3D QSAR Models
    • Introduction
    • Theory
      • A Model of Multiple Models
      • Model Descriptors
      • Machine Learning Methods
        • Gaussian Process Regression (GPR)
        • Kernel Partial Least Squares (kPLS)
      • 3D Conformer Generation
        • Stereoisomer Handling
      • Applicability Domain and Prediction Confidence
      • Model Interpretation
    • Tutorials
      • Datasets
      • 3D QSAR Model: Builder Floe
        • Running the Floe with Provided Pre-aligned Conformers
        • Running the Floe Using Posit as Conformer Generation and Alignment Method
      • 3D QSAR Model: Predictor Floe
      • 3D QSAR Model: Validation Floe
      • 3D QSAR Model: Interpretation Floe
    • OpenEye 3D QSAR Models - Floe Documentation
      • 3D QSAR Model: Builder
      • 3D QSAR Model: Interpretation
      • 3D QSAR Model: Predictor
      • 3D QSAR Model: Validation
    • OpenEye 3D QSAR Models - Cube Documentation
      • Descriptor Calculation
        • Descriptors Calculated for Bulk Storage
        • Model Descriptors
        • PLIF IntHint
      • Hyperparameter Optimization
        • Model Optimization: ROCS and Kernel-PLS Regression
      • Ligand Preparation
        • Pose Generation with Flexible Overlay
        • Pose Generation with Hybrid
        • OMEGA
      • Model Building
        • Model Builder: 3D Regression (Features Parameter)
        • Model Builder: 3D Regression (Features Port)
        • Model Validation: Average
      • Model Interpretation
        • Generate Probe Atoms
        • Generate Probe Surfaces
      • Model Prediction
        • Model Consensus Validation: 3D
        • Model Cross Validation
        • Model Predictor: 3D Regression
        • Model Predictor: Kernel-PLS Regression
      • Report Generation
        • Cross Validation Statistics Report
        • External Validation Statistics Report
        • Generate KPLS Optimization report
        • Model Report
      • Statistics
        • Calculate Validation Statistics
      • Utility
        • Add Ref Title
        • Add Tag to Record
        • Auto Choose Pose Generation Method
        • Check Potency Data
        • Check if Stereo Specified
        • Distribute KPLS Optimization
        • Filter Records by Posit Probability
        • Find Query Molecule
        • Generate Index
        • KPLS Optimum Number of Features Merge
        • Load External Descriptors
        • Merge KPLS Optimization Records
        • Merge Records to a Vector
        • Model Reader: Molecules Information
        • Model Reader: Receptor Information
        • Model Selector
        • Pick Best Stereo Conformer
        • Pick Optimal Feature for KPLS
        • Pick Pose Generation Method
        • Pick Pose Generation Method (Port Input)
        • Probe Generation Distributor
        • Probe Generation Switch
        • Receptor Selection for Pose Mode Auto
        • Remove DU
        • Sort Records by Index
        • Split Records for Training and Test
        • Split Records from Vector
    • Benchmark Results
      • Comparison to 3rd-party Software
        • BACE-1
        • Sutherland Datasets
    • Release Notes
      • v1.0.0 February 2024
        • General Notice
        • New Floes
    • Bibliography
  • AI Fold Floes
    • AI Fold Floes - Documentation
      • Protein Sequence to AI Folded Structure Prediction
    • Release Notes
      • v0.1.1 April 2024
        • General Notice
        • Floe Updates
      • v0.1.0 February 2024
        • General Notice
  • Biomolecular Modeling
    • Tutorials
      • Search for Similar Binding Sites with SiteHopper
        • Create a Tutorial Project
        • Prepare Patch Dataset
        • Prepare Query Protein
        • Search Patch Dataset
    • Biomodeling Floes - Documentation
      • Build Sidechains
      • Cap Chain Breaks
      • DU to Mol
      • DU to PDB
      • Enumerate Pockets on Design Units
      • Extract Biological Units
      • Make SiteHopper Patch Database
      • Minimize Design Unit
      • Mutate Residue(s)
      • Protein Loop Modeling or Re-modeling
      • Protonate DU and structures
      • Residue State Changer
      • Rotamers of a Residue
      • SiteHopper Search
      • Subset Design Unit
      • Subset Design Unit Within
      • Subset Design Unit to Smallest Binding Unit
      • Superpose DUs
      • Swap Metal(s)
      • Update DU Content
    • Release Notes
      • v0.3.9 February 2024
        • General Notice
        • Floe Updates
      • v0.3.8 July 2023
        • General Notice
        • Floe Updates
      • v0.3.6 December 2022
        • General Notice
        • Floe Updates
      • v0.3.5 September 2022
        • General Notice
        • Floe Updates
      • v0.3.2 July 2022
        • General Notice
        • Floe Updates
      • v0.3.1 December 2021
        • General Notice
        • Floe Updates
        • Data Updates
        • Documentation Updates
      • v0.2.1 June 2021
        • General Notice
        • Floe Updates
        • Documentation Updates
      • v0.2.0 November 2020
        • General Notice
        • Documentation Updates
        • Floe Updates
      • v0.1.1 August 2020
        • General Notice
        • Floe Updates
      • v0.1.0 April 2020
        • General Notice
  • Cheminformatics
    • Tutorials
      • Deciding on Clustering Method
        • Floes used in this Tutorial
        • Decision Tree
        • Size Constraints
        • Application-Based Clustering
        • Small Scale Clustering
      • Clustering Methods Overview
        • DBSCAN Clustering
        • K-Medoids Clustering
        • Hierarchical Clustering
        • Large Scale Clustering
        • Hitlist Clustering
        • Diverse Subset Floes
        • Large Scale Clustering
      • Diverse Subset
        • Floes used in this Tutorial
        • Required Inputs
        • Outputs
        • Troubleshooting
      • Creating and Applying Molecule Filters
        • Floes used in this Tutorial
        • Create a Custom Filter
        • Filter Customization
        • Parameter Settings
        • Functional Group Parameters
        • Create Custom Filter Floe Output
        • Run a Custom Filter
        • Troubleshooting
      • Hitlist Clustering
        • Floes used in this Tutorial
        • Required Inputs
        • Floe Report
        • Troubleshooting
      • Large Scale Clustering
        • Floes used in this Tutorial
        • Input Size
        • Algorithm: Directed Sphere Exclusion
        • Step 1: Generate N new cluster heads
        • Step 2: Assign cluster members to existing cluster heads
        • Sphere Exclusion Radius
        • Troubleshooting
        • Floe Runtime is Too High
        • Floe Cost is Too High
        • Memory Limit Exceeded
        • Advanced Parameter Descriptions
        • References
    • cheminfo - Documentation
      • 2D Diverse Subset
      • 2D Hitlist Clustering
      • 3D Diverse Subset
      • 3D Hitlist Clustering
      • Calculate Average Precision
      • Count Molecules in Fast Substructure Search Collection
      • DBSCAN 2D Similarity Clustering
      • DBSCAN 3D Similarity Clustering
      • Dataset Append – Generating SMILES Field
      • Dataset Classification – Bemis-Murcko
      • Dataset Deduplication – Based on Molecule, String, Integer, or Float Field
      • Dataset Deduplication – Merge
      • Dataset Filtering – Create Custom Filter
      • Dataset Filtering – Custom or Built-in Filter Types
      • Dataset Manipulation – Add Molecule Title Field
      • Dataset Manipulation – Add Title to Molecule Field
      • Dataset Manipulation – Concatenation
      • Dataset Manipulation – Field Rename
      • Dataset Manipulation – Field Type Conversion
      • Dataset Subsetting – Random Splitting Or Selection
      • Dataset Subsetting Based on Dataset, Numerical, String, or Regex Field
      • Dataset Subsetting Based on String Keys
      • Fast Fingerprint Similarity Search
      • Fast Substructure Search with SMARTS
      • Fast Substructure Search with an MDL Query
      • Generate 2D Similarity Matrix
      • Generate 3D Similarity Matrix
      • Generate Fingerprints
      • Generate User-Defined Fingerprints
      • Generate and Deduplicate SMILES for One or More Datasets
      • Hierarchical 2D Similarity Clustering
      • Hierarchical 3D Similarity Clustering
      • K-Medoids 2D Similarity Clustering
      • K-Medoids 3D Similarity Clustering
      • Large Scale 2D Similarity Clustering
      • Large Scale 3D Similarity Clustering
      • MultistatePKaModel Based Ionization States Enumeration Floe
      • Prepare Collection for Fast Similarity or Substructure Search from Dataset
      • Prepare Collection for Fast Similarity or Substructure Search from File
    • Release Notes
      • v1.3.0 February 2024
        • General Notice
        • Floe Updates
      • v1.2.0 July 2023
        • General Notice
        • New Floes
        • Floe Updates
      • v1.1.0 December 2022
        • General Notice
        • New Floes
        • Floe Updates
      • v1.0.0 July 2022
        • General Notice
        • New Floes
        • Floe Updates
      • v0.2.4 December 2021
        • General Notice
        • New Floes
        • Floe Updates
      • v0.2.3 June 2021
        • General Notice
        • New Floes
        • Floe Updates
      • v0.2.2 December 2020
        • General Notice
      • v0.2.1 November 2020
        • General Notice
      • v0.2.0 August 2020
        • General Notice
      • v0.1.1 April 2020
        • General Notice
        • New Floes
  • Classic Floes - OpenEye Applications in Orion
    • Tutorials
      • BROOD Floe Tutorial
        • Floes Used in the Tutorials
        • Input Parameters
        • BROOD Query Preparation
        • Running in ET and linkOnly modes
        • Interpretation of Results
      • CHOMP Floe Tutorial
        • Floes Used in the Tutorials
        • Input and Output Parameters
        • Fragment Filtering Parameters
        • Guidelines for Control Parameters
        • Interpretation of Results
      • Spruce Prep Tutorial
        • Floes Used in the Tutorials
        • Run the Protein Preparation Floes
        • Run the Protein Preparation Floes Using a Reference Design Unit
        • Reviewing the Floe Reports
        • Analyzing the Results
        • Next Steps
      • Gameplan Tutorial
        • Floes used in the Tutorials
        • Prepare Protein and Bound Ligand from PDB Codes
        • Run the Gameplan Floe
        • Gameplan Results
        • Next Steps
      • Filtering Docking Hits by Interactions Tutorial
        • Floes used in the Tutorial
        • Run the Floe
        • Exploring the Interaction Fingerprints
        • Filtering the Docked Poses
        • Next steps
    • How To Guides
      • How to Guides for Spruce Floes
        • How can I provide Spruce information about the bound ligand?
        • How can I generate a prepared design unit for an un-liganded structure?
        • How do I edit a prepared design unit?
    • Frequently Asked Questions
      • Frequently Asked Questions for Spruce Floes
        • What input formats does Spruce accept, and what are the requirements?
        • What is a reference design unit (DU) used for, and when should I provide one?
        • Spruce generated multiple design units from a structure, which one should I pick?
    • OpenEye Classic Floes - Documentation
      • Assign Partial Charges
      • BROOD - 3D Fragment Replacement
      • BROOD - DB File to Collection
      • BROOD - Query Builder
      • CHOMP - Generate BROOD Fragment Database
      • Calculate Atropisomerism
      • Calculate Dipole Moment
      • EON - Shape Alignment and Electrostatic Similarity Scoring
      • Filter Docking Hits by Interactions
      • Fingerprint Search - Small Scale 2D Similarity
      • FreeForm - Aqueous Ligand Configurational Free Energies with SZYBKI
      • FreeForm - Bound Ligand Configurational Free Energies with SZYBKI
      • FreeForm - Ligand Solvation Energies with SZYBKI
      • GamePlan - Ligand Design with Water Analysis using SZMAP
      • OEDocking - Dock into an Active Site for Virtual Screening
      • OMEGA - 3D Conformer Ensemble Generation
      • OMEGA - Conformer Generation for Macrocycles
      • OMEGA - Generate a Single 3D Conformer
      • POSIT - Ligand Guided Small Molecule Posing
      • ROCS - Shape Based Alignment for Virtual Screening
      • ROCS Query Model Builder
      • ROCS, FastROCS - Import Shape Query to Record
      • Receptor In DU
      • SPRUCE - Import Prepared PDB Files
      • SPRUCE - OEDesignUnit Format Type Updater
      • SPRUCE - Protein Preparation
      • SZYBKI - Ligand Minimization in a Flexible Active Site
      • SZYBKI - Ligand Minimization in a Rigid Active Site
      • SZYBKI - Single point MMPBSA
      • SZYBKI - Small Molecule Hydrogen-Only Minimization
      • SZYBKI - Small Molecule Minimization
      • Substructure Search - Small Scale Substructure Matching
    • Release Notes
      • v0.13.1 February 2024
        • General Notice
        • Floe Updates
      • v0.12.1 September 2023
        • General Notice
      • v0.12.0 July 2023
        • General Notice
        • Floe Updates
      • v0.11.2 December 2022
        • General Notice
        • Floe Updates
      • v0.10.1 September 2022
        • General Notice
        • Floe Updates
      • v0.10.0 July 2022
        • General Notice
        • New Floes
        • Floe Updates
      • v0.9.0 December 2021
        • General Notice
        • New Floes
        • Floe Updates
      • v0.8.3 June 2021
        • General Notice
        • New Floes
        • Floe Updates
      • v0.7.1 November 2020
        • General Notice
        • Floe Updates
      • v0.6.2 August 2020
        • General Notice
      • v0.6.1 August 2020
        • General Notice
        • New Floes
        • Floe Updates
        • Removed Floes
      • v0.5.2 April 2020
        • General Notice
        • New Floes
        • Floe Updates
      • v0.4.0 November 2019
        • General Notice
        • New Floes
        • Floe Updates
      • v0.3.6 September 2019
        • General Notice
        • New Floes
        • Floe Updates
      • v0.3.3 July 2019
        • General Notice
      • v0.3.1 June 2019
        • General Notice
        • New Floes
        • Floe Updates
      • v0.2.5 March 2019
        • General Notice
        • New Floes
        • Floe Updates
      • v0.2.2 September 2018
        • General Notice
        • Floe Updates
  • Cryptic Pocket Detection
    • Introduction
    • Tutorials
      • Preparing Input
        • Design Unit Preparation using a MMDS Reference Structure (Option 1)
        • Design Unit Preparation without a MMDS Reference Structure (Option 2)
        • Subset the Design Unit
      • Basic Tutorial: Automated Cryptic Pocket Detection with Probe Occupancy Analysis
        • Search and Run the Floe in Orion
        • Visualize Cryptic Pocket Analysis Report and Pocket Receptors
        • Failure Report
      • Advanced Tutorials
        • Solvate and Equilibrate Target Protein
        • Calculate Normal Modes
        • Run a Weighted Ensemble MD Simulation
        • Perform Weighted Ensemble MD Analysis
        • Dynamic Probe Analysis
        • Exposon Analysis
        • Probe Occupancy Analysis
    • OpenEye Cryptic Pocket Detection Floes - Documentation
      • Automated Cryptic Pocket Detection with Probe Occupancy Analysis
      • Calculate Normal Modes
      • Continue a Weighted Ensemble MD Simulation
      • Dynamic Probe Binding Analysis
      • Exposon Analysis
      • Perform Weighted Ensemble MD Analysis
      • Probe Occupancy Analysis
      • Run a Weighted Ensemble MD Simulation
      • Solvate and Equilibrate Target Protein
    • Release Notes
      • v0.2.2 April 2024
        • General Notice
        • Major Changes
        • Minor Changes
      • v0.1.2 September 2023
        • General Notice
        • Minor Changes
      • v0.1.0 July 2023
        • General Notice
    • Bibliography
  • Format Conversion
    • Orion ETL Floes - Documentation
      • Archive Import
      • Dataset Copy
      • Dataset to Collection Export
      • Dataset to File Export
      • Dataset to Record File Export
      • File to Dataset Import
      • Record Collection to Dataset Import
      • Record File to Dataset Import
      • URL to File Import
    • Release Notes
      • v6.1.2 February 2024
      • v6.0.0 September 2023
      • v2.3.0 July 2023
      • v2.1.3 February 2023
      • v2.1.2 November 2022
      • v2.1.1 September 2022
      • v2.1.0 July 2022
      • v2.0.2 February 2022
      • v2.0.1 December 2021
      • v2.0.0 November 2021
      • v1.2.9 November 2021
      • v1.2.8 October 2021
      • v1.2.7 October 2021
      • v1.2.6 June 2021
      • v1.2.5 June 2021
      • v1.2.4 November 2020
      • v1.2.3 August 2020
      • v1.2.2 April 2020
      • v1.2.1 March 2020
      • v1.2.0 February 2020
      • v1.1.1 October 2019
      • v1.1.0 August 2019
      • v1.0.0 July 2019
      • v0.1.29 April 2019
      • v0.1.28 February 2019
        • Bugfixes
      • v0.1.27 February 2019
      • v0.1.26 February 2019
        • Bugfixes
      • v0.1.25 January 2019
      • v0.1.24 December 2018
      • v0.1.23 November 2018
      • v0.1.22 November 2018
      • v0.1.21 October 2018
      • v0.1.20 October 2018
      • v0.1.19 October 2018
      • v0.1.18 September 2018
      • v0.1.17 September 2018
      • v0.1.16 September 2018
      • v0.1.15 September 2018
      • v0.1.14 September 2018
  • Generative Chemistry
    • Generative Structure Floes - Documentation
      • Apply Simple Reaction
      • Focused Library - Core Input
      • Focused Library - Core Input (Parallel)
      • Focused Library - Molecule Input
        • General Considerations
      • Focused Library - Reagent Join
      • Focused Library - Synthon Analogs
        • General Considerations
      • Generative Structure Floe
      • Generative Structure Floe (classic)
      • Generative Structure Floe - Site selection
      • Generative Structure Floe - Site selection (classic)
      • Generative Structure Indexing - Graft Database Generator
      • Generative Structure Indexing - MMP Molecule Indexer
      • Generative Structure Indexing - MMP Transform Extractor
      • MaaS Available Analogs
      • MaaS Resource List
      • MaaS Substructure Search
      • Reaction & Reagent Database - Create from Dataset
        • Launching the Floe
      • Reaction & Reagent Database - Create from SMILES
        • Launching the Floe
      • Reaction & Reagent Database - Create from ZINC Download
        • ZINC Subset Selection
        • Launching the Floe
      • Reaction & Reagent Database - Directory Listing
      • Reaction & Reagent Database - Half Reaction Generator
      • Reaction & Reagent Database - Launch Product Enumerations
      • Reaction & Reagent Database - Product Enumeration Summary
      • Reaction & Reagent Database - Reaction Definition Validator
      • Reaction & Reagent Database - Reagent Definition Generator
      • Reaction & Reagent Database - Reagent Molecule Classification
      • Reaction & Reagent Database - Retrieve Reaction Reagents
    • Release Notes
      • v0.7.1 September 2023
        • Updates to the Generative Design Floes - Base & Advanced Packages
      • v0.7.0 July 2023
        • Updates to the Generative Design Floes - Advanced Package
        • Bug fixes and features
      • v0.6.0 December 2022
        • Bug fixes and features
      • v0.5.1 September 2022
        • Bug fixes and features
      • v0.5.0 July 2022
        • Enhancements to reaction definitions
        • General enhancements
        • Updates to the Generative Design Floes package
        • Updates to the Generative Design Floes - Advanced package
        • Updates to the Generative Design Floes - MaaS package
      • v0.4.0 December 2021
        • Enhancements to reaction definitions
        • Additional enhancements
        • Updates to the Generative Design Floes package
        • Updates to the Reaction Floes - Advanced package
      • v0.3.2 July 2021
      • v0.3.1 June 2021
      • v0.2.14 November 2020
      • v0.2.13 November 2020
      • v0.2.12 August 2020
      • v0.2.11 May 2020
  • Large Scale Floes
    • Tutorials
      • Dock Ten Million Molecules with Gigadock Warp and Analysis with Freeform Consensus
        • Create a Tutorial Project and Working Directory
        • Prepare Design Unit / Receptor
        • View Prepared Design Unit / Receptor
        • Dock Molecules to Site
        • Compute Freeform Delta G of the Hit List Molecules
        • Compute Consensus of Docking Score and Freeform Delta G
        • View Results
      • Dock One Million Molecules with Gigadock Floe
        • Create a Tutorial Project and Working Directory
        • Prepare Design Unit / Receptor
        • View Prepared Design Unit / Receptor
        • Prepare One Million Input Molecules
        • Dock Molecules to Site
        • Cluster Hit List Poses from Gigadock
        • View Results
      • FastROCS Plus with Freeform Analysis
        • Create a Tutorial Project and Working Directory
        • Create a Dataset with Revlimid
        • Run the FastROCS Plus Floe
        • Compute Freeform Delta G of the Hit List Molecules
        • View hit list results
      • FastROCS Plus with Docking and Consensus Score of Top Molecules
        • Create a Tutorial Project and Working Directory
        • Prepare Design Unit / Receptor
        • View Prepared Design Unit / Receptor
        • Run the FastROCS Plus Floe
        • View Consensus Result
      • Prepare Vendor Database for Giga Docking and FastROCS
        • Create a Tutorial Project and Working Directory
        • Import Mcule Database into Orion
        • Create GigaDocking and FastROCS collections
        • View Collection Properties
        • View of Random Sample of the Collection
    • How-to Guides
      • Run Giga Docking on Billions of Molecules
        • Context
        • Procedure
      • Estimate the cost of a Giga Docking Run
        • Context
        • Procedure
      • Determine if Giga Docking Will Give Good Results with a Given Receptor
        • Context
        • Procedure
      • Edit a Receptor
        • Context
        • Procedure
      • Generate a Giga Docking Hit List Datast of More Than 10K Molecule
        • Context
        • Procedure
      • Prepare Molecules in a CSV File for GigaDocking and FastROCS
        • Context
        • Procedure 1 : Identify the title column
        • Procedure 2 : Prepare the molecules without titles
      • Restart a Giga Docking Job That Stopped Due to Cost
        • Context
        • Procedure
      • Get Access To Full Vendor Giga Docking Collections Prepared by OpenEye
        • Context
        • Procedure
    • Floe Reference Material
      • Gigadock
        • Description
        • Details
        • Parameters
      • FastROCS Plus
        • Description
        • Details
        • Parameters
      • Batch FastROCS
        • Description
        • Details
        • Parameters
      • Prepare Giga Collections
        • Description
        • Details
        • Parameters
      • Filter Collection
        • Description
        • Details
        • Parameters
      • Collection to Hitlist Dataset
        • Description
        • Details
        • Parameters
      • FreeForm Pose
        • Description
        • Details
        • Parameters
      • Cluster Poses
        • Description
        • Details
        • Parameters
      • Collection Info
        • Description
        • Details
        • Parameters
      • Sample Collection
        • Description
        • Details
        • Parameters
      • Collection to File
        • Description
        • Details
        • Parameters
      • Gigadock Collection to Hi-res FastROCS Collection
        • Description
        • Details
        • Parameters
      • Pareto Frontier Consensus
        • Description
        • Details
        • Parameters
      • Gigadock Warp
        • Description
        • Details
        • Parameters
      • Multi Query 2D Similarity
        • Description
        • Details
        • Parameters
    • Explanations
      • Gigadock Warp Details
        • Overview
        • Method
        • Performance Compared to floe_#01_large_scale_docking_floe
      • Datasets vs. Files. vs. Collections
        • Datasets
        • Files
        • Collections
      • Control the Cost of a Giga Docking Run
        • Context
        • Receptor / Design Unit
        • Docking Mode
        • Docking Molecules
      • Giga Docking Cost Threshold
      • FastFred
      • Pareto Frontier Explanation
    • Release Notes
      • 4.1.0 January 2024
        • Highlights
        • Features
        • Changes
        • Bugfixes
      • 4.0.2 September 2023 (Large Scale Floes Hotfix)
        • Changes
        • Bugfixes
      • 4.0.0 July 2023 (Orion Floe 2023.1 Release)
        • Highlights
        • Changes
        • Bugfixes
      • 3.4.5 December 2022 (Orion 2022.4 Release)
        • New Features
        • Bugfixes
      • 3.3.4 September 2022
        • Bugfixes
      • 3.3.0 June 2022 (Orion 2022.2 release)
        • Features
        • Changes
        • Bugfixes
      • 3.2.0 April 2022 (Orion 2022.1 release)
        • Changes
        • Minor Features
        • Bugfixes
      • 3.1.7 Dec 2021 (Orion 2021.2.1 release)
        • Highlights
        • General Notice
        • New Features
        • Changes
        • Fixes
      • 3.0.3 Oct 2021 (hotfix)
        • Fixes
      • 3.0.2 Jun 2021 (Orion 2021.1 release)
        • General Notice
        • New Features
        • Fixes
      • 2.0.6 April 2021 (hotfix)
        • Fixes
      • 2.0.0 Nov 2020 (Orion 2020.3 release)
        • General Notice
        • New Features
        • Fixes
      • 0.1.0 August 2020 (Orion 2020.2 release)
        • General Notice
        • New Features
        • Fixes
  • Machine Learning Model Building Floes
    • Introduction and Tutorials
      • Introduction and Layout of Machine Learning Model Building package
        • 1 Data-preprocessing Floe
        • 2 Machine Learning Model Building
        • 3 Molecule Property Prediction using built models
      • Tutorial: Building Machine Learning Regression Models for Property Prediction of Small Molecules
        • Create a Tutorial Project
        • Floe Input
        • Run OEModel Building Floe
        • Analysis of Output and Floe Report
      • Tutorial: Use Pretrained Model to Predict Generic Property of Molecules
        • Create a Tutorial Project
        • Floe Input
        • Run Generic Property Prediction Floe
        • Analyze OEModel Floe Report
        • Analyze Output
      • Tutorial: Cheaper and Faster Version of Building Machine Learning Regression Models for Physical Property Prediction of Small Molecules
        • Create a Tutorial Project
        • Floe Input
        • Run OEModel-Building Floe
        • Analysis of Output and Floe Report
      • Tutorial: Building Machine Learning Classifier Fingerprint Models for Physical Property Prediction of Small Molecules
        • Create a Tutorial Project
        • Floe Input
        • Run OEModel Building Floe
        • Analysis of Output and Floe Report
      • Tutorial: Use Pretrained Classification Fingerprint Model to Predict Generic Property of Molecules
        • Create a Tutorial Project
        • Floe Input
        • Run Classification Property Prediction Floe
        • Analyze OEModel Floe Report
        • Analyze Output
      • Tutorial: Building Machine Learning Regression Models on Feature Vector Input
        • Create a Tutorial Project
        • Floe Input
        • Run OEModel Building Floe
        • Analysis of Output and Floe Report
      • Tutorial: Use Custom Feature Input to predict regression properties
        • Create a Tutorial Project
        • Floe Input
        • Run Generic Property Prediction Floe
        • Analyze OEModel Floe Report
        • Analyze Output
      • Tutorial: Use Small Molecule Data Processing Floe to Preprocess ML Data
        • Create a Tutorial Project
        • Floe Input
        • Run Generic Property Prediction Floe
        • Analyze Output
        • Analyze OEModel Floe Report
      • Tutorial: Predict Solubility of Druglike Molecules
        • Create a Tutorial Project
        • Floe Input
        • Run OEModel-Apply Floe
        • Analyze OEModel Floe Report
        • Analyze Output
      • Tutorial: Predict hERG Toxicity of Drug-Like Molecules
        • Create a Tutorial Project
        • Floe Input
        • Run the hERG Toxicity Floe
        • Analyze the OEModel Floe Report
        • Analyze the Output
      • Tutorial: Use Transfer Learning to Rebuild Previous Machine Learning Model Builds Using New Data
        • Create a Tutorial Project
        • Floe Inputs
        • Run OEModel Building Floe
        • Analysis of Output and Floe Report
    • How-To Guides
      • How-to: Build an Optimal Property Predicting Machine Learning Model by Tweaking Neural Network Architecture
        • Fully Connected Feed Forward Neural Network (Fnn)
      • How-to: Use LIME Explainer to Understand and Analyze Machine Learning Predictions
        • Explaining Predictions Using LIME
      • How-to: Use Built Machine Learning Model for Property Prediction/Verification of Unseen Molecules
        • Library Details of the Floe
    • Floe Reference Documentation
      • ML Build: Regression Model with Tuner Using Fingerprints for Small Molecules
      • ML Predict: Regression Using Fingerprints for Small Molecules
      • Solubility Prediction for Small Molecules Using ML and Cheminfo Fingerprints
      • ML Build: Classification Model with Tuner Using Fingerprints for Small Molecules
      • ML Predict: Classification Using Fingerprints for Small Molecules
      • ML Build: Regression Model Using Feature Input
      • ML Predict: Regression Using Feature Input
      • Data Processing of Small Molecule for ML Model Building
      • ML ReBuild: Transfer Learn ML Regression Model Using Fingerprints for Small Molecules
      • hERG Toxicity Prediction for Small Molecules Using ML and Cheminfo Fingerprints
    • Release Notes
      • Release Notes
        • v0.11.1 July 2023
        • v0.10.5 March 2023
        • v0.10.0 December 2022
        • v0.9.2 September 2022
        • v0.9.0 July 2022
    • FAQs
      • Frequently Asked Questions
        • For model building floes, how do we compare multiple models to decide which one is the best?
        • How good is the solubility model?
        • Does the model use or train on 3D features?
        • The inputs are based on expert parameters such as fingerprints, which are all biased by the rules that are defined by the expert user. Any insights into how to overcome this flaw?
        • Are the predictions for crystalline solubility? Is the data for crystals?
        • Why do you prefer NNs instead of something like XGBoost?
        • Neural networks don’t always show good performance in low data regimes. What measures can you take to improve performance?
        • How are the confidences computed?
        • What methods are most effective to eliminate overfitting of your models?
        • How many percentages can the solubility prediction have for high/med confidences?
        • In the model builder floe, am I restricted to fingerprints, or can I add other descriptors, such as molecular properties or other calculated or experimental parameters?
  • Molecular Dynamics Affinity Package
    • Introduction
      • MD Affinity Floes
      • Induced-Fit Posing (Confined) Floe
    • How-To Guide and Tutorials
      • MD Affinity Floes
        • Bespoke and Custom Force Field
        • Short Trajectory MD with Analysis
        • Nonequilibrium Switching
        • Edge Mapper for RBFE Calculations
        • Plain MD
      • Induced-Fit Posing (Confined) Floe
        • Induced-Fit Posing (Confined)
    • MD Affinity Floes - Documentation
      • Analyze Protein-Ligand MD [MDAnalysis]
      • Associate Force Field Offxml Files With Ligand Record [Utility]
      • Bound Protein-Ligand MD [MDPrep] [MDRun]
      • Compare Experimental Affinity with End Point Analysis Results [Utility]
      • Compare Induced-Fit Posing (IFP) Results to Target Receptor [IFP]
      • Convert MD Analysis results to Cluster-Centric Dataset [Utility]
      • Edge Mapper for RBFE calculations [FECalc]
      • Equilibration and Nonequilibrium Switching [MDPrep] [MDRun] [FECalc]
      • Extract Short Trajectory MD Results for Download [Utility]
      • Induced-Fit Posing (Confined) [IFP]
      • Induced-Fit Posing (IFP) Prep: Pruning reference receptor for docking [IFP]
      • Ligand Bound and Unbound Equilibration for NES [MDPrep] [MDRun]
      • MD API Dataset Converter [Utility]
      • NES Result Utilities [Utility] [FECalc]
      • Nonequilibrium Switching Recovery [Utility] [FECalc]
      • Nonequilibrium Switching [MDRun] [FECalc]
      • Plain Gromacs [MDRun]
      • Plain Molecular Dynamics [MDRun]
      • Short Trajectory MD with Analysis [MDPrep] [MDRun] [MDAnalysis] [STMD]
      • Solvate and Run MD [MDPrep] [MDRun]
    • oemdaffinity.cubes - Cube Documentation
      • Affinity Analysis
        • Affinity Plot
      • Analysis
        • 2-traj MMPBSA
        • Cluster Ligand Traj OEMol
        • Compute BintScore for Initial Pose and Trajectory
        • Concatenate Trajectory BintScor Components
        • Concatenate Trajectory MMPBSA Energy Components
        • Conf Trajs To Ligand Traj
        • Generate Ligand Floe Report HTML from Protein-Ligand MD Traj Analysis.
        • MD Conformer Gathering Data
        • MDExtractDataCube
        • MDFloeReportCube
        • MDFloeWriteClusterCentricDataset
        • Make Cluster Protein and Ligand average and median OEMols
        • NMax Waters
        • Population Analysis of Traj Clusters
        • Prepare the Traj Analysis Dataset for Reporting
        • STMD Result to File
        • STMD Result to Tarball File
        • Traj to OEMol Cube
        • Trajectory Interaction Energies
        • Trajectory Poisson-Boltzmann and Surface Area Energies
        • Unbound Cluster Ligand Traj OEMol
        • Unbound Conf Trajs To Ligand Traj
        • Unbound MD Conformer Gathering Data
        • Unbound Population Analysis of Traj Clusters
        • Unbound Traj MMPBSA
        • Unbound Traj to OEMol Cube
      • Flask Preparation
        • Ligand Preparation For Pytest
      • Free Energy Calculations
        • BARoverlapTest
        • DDGAggregator
        • LigandClusterSelection
        • NESAnalysis
        • NESEdgeFloeReport
        • NESGMX
        • NESGMXChimera
        • NESResultToFile
        • OEMapper
        • OEMapperFloeReport
        • OEMapperResultToFile
        • PlotNESResults
        • PredictDGFromDDG
        • RBFECEdgeGathering
        • ReadChimeraMCSTests
        • TestChimeraMCS
      • IFP Analysis
        • Add Receptor Type Cube
        • Cluster Cube
        • Compute BintScore for Initial Pose and Trajectory (IFP)
        • Compute Score Cube
        • Compute Step1 Score Cube
        • Concatenate Trajectory BintScore Components (IFP)
        • Docking Checker Detection
        • Extract Clus Avg
        • Generate Ligand Floe Report HTML for IFP summary.
        • IFD Output Prep Cube
        • IFP Order Output Records Cube
        • IFP Rank Setting Cube
        • IFP Report Info Gather Cube
        • IFP Update Info Dict Cube
        • MDCompToDuCube
        • Minimized Pose Gathering Cube
        • POSIT Gathering Cube
        • Population Analysis of Traj Clusters (IFP)
        • Pose MMPBSA and BintScore
        • Reset AtomIdx Cube
      • IFP Input Checker
        • Optional Pruned Receptor Input Checker
        • Target Receptor Input Checker Cube
      • IFP MD Simulations
        • Minimization Cube for IFD
      • IFP Preparation
        • Active Site Detection
        • Active Site Pruning
        • Additional POSIT Switch
        • Set MapIdx Cube
      • Input Checker
        • PL Traj Analysis Input Checker Cube
        • Solvate and Run MD Input Checker Cube
      • MD Analysis
        • MD End Point Analysis Results to File
      • MD Simulations
        • Bound Protein Ligand MD Health Checker
        • MD ProxyCube
        • MD Recover Restart for ProxyCube
        • Specify Protein Tumbling Restraints
      • Simulation Flask Preparation
        • Bound and UnBound Splitting Cube
        • Simulation Flask ID Setting
      • Structure Based Design
        • Posit
      • Unbound Simulation Preparation
        • FreeForm Output Ligand Setting
        • Unbound FreeForm
        • Unbound Ligand Preparation
      • Unclassified
        • SMIRNOFF Force Field Files Loader
    • Release Notes
      • v 6.3.6 April 2024
        • General Notice
        • Floe Updates
        • New Cubes
        • Cube Updates
      • v 6.2.1 February 2024
        • General Notice
        • New Floes
        • Floe Updates
        • New Cubes
        • Cube Updates
      • v 6.1.7 September 2023
        • General Notice
      • v 6.1.4 September 2023
        • General Notice
        • Floe Updates
        • Cube Updates
      • v 6.1.2 July 2023
        • General Notice
        • New Floes
        • Floe Updates
        • New Cubes
        • Cube Updates
      • v 6.0.3 April 2023
        • General Notice
        • Floe Updates
        • New Cubes
        • Cube Updates
      • v 5.6.1 December 2022
        • General Notice
        • Floe Updates
        • New Cubes
        • Cube Updates
      • v 5.5.3 September 2022
        • General Notice
        • Cube Updates
        • Compatibility Notice
      • v 5.5.0 July 2022
        • General Notice
        • New Floes
        • Floe Updates
        • New Cubes
        • Cube Updates
      • v 5.0.5 April 2022
        • New Floes
        • Floe Updates
        • New Cubes
        • Cube Updates
      • v 5.0.3 December 2021
        • General Notice
        • New Floes
        • Floe Updates
        • New Cubes
        • Cube Updates
      • v 4.0.1 June 2021
        • General Notice
        • New Floes
        • Floe Updates
        • New Cubes
        • Cube Updates
      • v3.0.1 November 2020
        • General Notice
      • v2.0.0 September 2020
        • General Notice
        • New Floes
        • Floe Updates
        • New Cubes
        • Cube Updates
      • v1.0.0
        • General Notice
        • New Floes
        • Floe Updates
        • New Cubes
        • Cube Updates
      • v0.9.6
        • General Notice
        • New Floes
        • Floe Updates
        • New Cubes
        • Cube Updates
      • v0.9.4
        • General Notice
        • New Floes
        • Floe Updates
        • New Cubes
        • Cube Updates
  • Molecular Dynamics Core Package
    • Installation
    • orionmdcore.cubes - Cube Documentation
      • Flask Preparation
        • Collection Setting
        • Complex Preparation
        • Ligand Charge
        • Ligand Setting
        • Receptor Components
        • Record Size Checking
        • Solvation
      • Force Field
        • Apply Force Field
      • MD Simulations
        • Delete MD Stages
        • Iterative NPT Cube
        • MD Cycle Checkpoint
        • MD ProxyCube
        • MD Recover Restart for ProxyCube
        • MD Speed Checker Cube
        • Minimization Cube
        • NPT Cube
        • NVT Cube
      • Simulation Flask Preparation
        • Bound and UnBound Switching Cube
        • Simulation Flask ID Setting
      • Utility
        • MD API Dataset Converter Cube
    • MD DataRecord
      • MD DataRecord a brief overview
        • MD DataRecord structure
        • Code snippets
      • MDDatatecord API Documentation
    • Release Notes
      • v2.4.0 April 2024
        • Cube Updates
        • Bug Fixes
        • General Notice
      • v2.3.1 February 2024
        • API-Breaking Changes
        • New Features
        • Bug Fixes
        • General Notice
      • v2.1.2 September 2023
        • Bug Fixes
      • v2.1.1 September 2023
        • New Features
      • v2.1.0 July 2023
        • General Notice
        • Cube Updates
      • v2.0.1 April 2023
        • General Notice
        • New Cubes
        • Cube Updates
      • v1.1.6 June 2022
        • General Notice
        • New Cubes
        • Cube Updates
      • v1.1.5 April 2022
        • General Notice
        • New Cubes
        • Cube Updates
      • v1.1.2 December 2021
        • General Notice
        • New Cubes
        • Cube Updates
  • Permeability Floes
    • Tutorials
      • A Small Molecule Membrane Permeability Calculation
        • Create a Tutorial Project
        • Launch a Permeability Simulation Job
        • Analyze the Permeability Simulation
        • Calculate the Auxiliary Coordinates
    • OpenEye Permeability Floes - Documentation
      • Permeability - Analyze Permeability Simulation
      • Permeability - Calculate Auxiliary Coordinates (Optional)
      • Permeability - Run Permeability Simulation
    • permeability.cubes - Cube Documentation
      • Conformational Analysis
        • Conformational Analysis
      • Conformational Selection
        • Conformational Selection
        • Shard Extraction
      • Molecule Extraction
        • Molecule Extraction
      • Permeability
        • Calculate Permeability
      • Simulation
        • Convergence Checker
      • System Preparation
        • Calculate Simulation Box
        • Clean Up Preparation Data
        • Combine Membrane and Molecule
        • Continuation Check
        • Extract Molecule from Record
        • Ligand Identifier Reader Cube
        • Record Merger
        • Simulation Switch
        • Solvate Molecule
        • System Setup
      • Trajectory
        • Path Ensemble Writer
        • Permeation Path Tracer
      • Unclassified
        • Auxiliary Dataset Registry
        • Index Molecules
        • Merge Molecules
        • System Subset Setup
      • Utility
        • Post Process
        • Process Every N records
      • WESTPA
        • Auxiliary Calculation Setup
        • Auxiliary Calculation Switch
        • Rate Calculation Switch
        • Symmetrize Segments
        • Target State Optimizer
        • MD
        • Permeability
    • Release Notes
      • v0.1.5 September 2023
        • General Notice
        • Floe Updates
        • Documentation Updates
      • v0.1.4 July 2023
        • General Notice
        • Floe Updates
        • Documentation Updates
      • v0.1.3 December 2022
        • General Notice
        • Floe Updates
        • Documentation Updates
        • Minor Changes
      • v0.1.2 September 2022
        • General Notice
      • v0.1.1 July 2022
        • General Notice
        • Floe Updates
        • Documentation Updates
        • Minor Changes
      • v0.1.0 April 2022
        • General Notice
  • Quantum Mechanics Psi4 Floes
    • Psi4 QM Floes
      • Psi4 HF3c Dipole Moment
      • Psi4 QM Complete Molecule Torsion Scan
      • Psi4 QM Conformer Ensemble
      • Psi4 QM Fragmentation and Torsion Scanning
      • Psi4 QM Geometry Optimization
      • Psi4 QM Interaction Energy
      • Psi4 QM Local Minima Search
      • Psi4 QM Property Calculation
      • Psi4 QM SMARTS Torsion Scan
      • Psi4 QM Tautomer Floe
      • Psi4 QM UI Atom Selection Torsion Scanning
      • Psi4 QM Vacuum Entropy Floe
    • How-To Guides
      • How to Generate Conformers with a Custom Torsion Library
        • Create an Input Dataset
        • Run the Fragmentation and Torsion Scanning Floe
        • Understanding the Torsion Scan Floe Report
        • Generate Conformers with Your Custom Torsion Rules
        • Understanding the Conformer Ensemble Floe Report
      • How to Run Benchmark Floes for Cost Estimation
        • Benchmark Torsion Scanning Floes
        • Benchmark Conformer Generating Floes
        • Benchmark Property Calculation and Geometry Optimization Floes
    • Frequently Asked Questions
      • When should I change the memory or thread count?
      • How do I check the metrics (memory, CPU usage) in a QM calculation?
      • How much will my floe cost?
      • What method and basis set should I use?
      • Why are my calculations failing due to the presence of implicit hydrogens?
    • Release Notes
      • v1.2.0 July 2023
        • Floe Updates
      • v1.1.4 December 2022
        • Floe Updates
      • v1.0.0 (Orion Release 2022.2)
        • Floe Updates
        • Deleted Floes
        • Cube Updates
      • v0.6.0 (Orion Release 2021.2)
        • Floe Updates
        • New Cubes
        • Cube Updates
      • v0.5.1 (Orion Release 2021.1)
        • New Floes
        • Floe Updates
        • New Cubes
        • Cube Updates
      • v0.4.0 (Orion Release 2020.3)
        • New Floes
        • Floe Updates
        • New Cubes
        • Cube Updates
        • Deleted Cubes
      • v0.3.0 (Orion Release 2020.2)
        • New Floes
        • Floe Updates
        • New Cubes
        • Cube Updates
      • v0.2.0 (Orion Release 2020.1)
        • General Notice
        • New Floes
        • Floe Updates
        • New Cubes
        • Cube Updates
        • Removed Cubes
    • Bibliography
  • Reagent Enumeration
    • Large Scale Reaction Enumeration - Documentation
      • Reagent Archive - Create from tarfile
      • Reagent Archive - Directory Listing
      • Reagent Archive - Extract Enumeration Products to Dataset
      • Reagent Archive - Launch Reaction Enumerations
      • Reagent Archive - Product Enumeration Summary
    • Release Notes
      • v0.2.0 July 2023
      • v0.1.11 December 2022
      • v0.1.10 July 2022
      • v0.1.9 December 2021
      • v0.1.8 June 2021
      • v0.1.6 November 2020
      • v0.1.4 August 2020
  • Snowball - The Primary OpenEye Cube Library
    • Definitions of Floe Classifications
    • snowball - Cube Documentation
      • 2D Depiction
        • Molecule Annotation
        • Molecule Depiction
        • Molecule Highlighting
        • Molecule Similarity Depiction
        • Property Depiction
        • Protein-Ligand Visualization
        • Shape and Color Overlap Visualization
        • Visualizing 3D Information
      • 2D Similarity
        • 2D Fingerprint
      • 3D Similarity
        • Electrostatics
        • RMSD
        • Shape
      • Cheminformatics
        • Bemis Murcko Scoring
        • Mol Title from String Field
        • Rename A Field
        • Atom-Bond Typing
        • Atropisomerism
        • Dipole Moment Calculation
        • InChI
        • Maximum Common Substructure Search
        • Molecular Complexity
        • Molecular Descriptor
        • Molecule Alignment
        • Molecule Annotation and Tagging
        • Molecule Filtering
        • Molecule Manipulation
        • Molecule Naming
        • Molecule Processing
        • Molecule Property Calculation
        • SMILES
        • Substructure Search
      • Conformations
        • Conformer Manipulation
      • Debugging
        • Count Records
        • Log Record Fields
      • Examples
        • Index Generator
      • Floe Report
        • Brood Report Cube
        • Gameplan Report Cube
        • Brood
      • IO
        • Writers
      • Library Design
        • Apply ChEMBL Solubility Transformations
      • Ligand Modeling
        • EON
        • ForceField
        • Freeform Conf
        • Freeform Conf Advanced
        • Freeform Solv
        • Hermite
        • Kriging
        • PB-Electrostatics
        • Quacpac
        • ROCS
      • Ligand Preparation
        • Check for Partial Charges
        • Charging
        • OMEGA
        • Quacpac-prep
        • ROCS-prep
        • Szybki
        • Zap
      • Logic
        • Chunk
        • Classification
        • Field Conversion
        • Field Manipulation
        • Hit Lists
        • Numeric Comparison
        • Random Selection
        • Record Manipulation
        • String Comparison
        • Switches
      • MMDS
        • Data Load
        • Data Preparation
      • Models
        • Sorting Records by Index
        • ShapeQuery
      • Protein Ligand
        • Szybki
      • SiteHopper
        • Prep
        • Search
      • Spruce
        • Biomodeling
        • Format conversion
        • Structure Preparation
      • Structure Based Design
        • BintScore
        • Brood
        • Chemgauss4
        • Dock
        • Posit
        • Szmap
      • Surface
        • Invert Surface
        • Is Surface Open
        • Make Grid From Surface
        • Make Spherical Surface
        • Molecular Surface
        • Polar Surface Area
        • Rotate Surface
        • Smooth Surface
        • Split Surface By Atoms
        • Surface Area
        • Surface To Molecule Distance
        • Surface Volume
        • Transform Surface
        • Translate Surface
      • Unclassified
        • 2D Fragment Picker
        • 2D Torsion Picker
        • Assign design unit partial charges
        • Bound Ligand Entropy
        • Brood Fragment Selector
        • Freeform Conf Restriction Energies
        • Generate Targets Mixin
        • MDL Query Editor
        • Macrocycle Filter Cube
        • Multistate pKaModel-based Ionization States Enumeration
        • Numeric Field To Constant Value Comparison
        • Read Structure Collection Mixin
        • Valence Screening Cube
      • Utility
        • Add Boolean Field
        • Add Design Unit Field
        • Add Query Style
        • Check Design Unit
        • Convert Conformers to Mols
        • Convert Shape Query to Record
        • Dataset Reader Optional
        • Dataset Size Router
        • Design Unit Exception Handler
        • Exception Handler
        • Failure Report
        • Failure Report
        • Field Type Conversion Cube
        • Find Ligand
        • Find Protein
        • Find Receptor
        • Find ShapeQuery
        • Loop Database File Look-up
        • Molecule Counter
        • Named Collection Reader
        • Named Dataset Reader
        • Named File Reader
        • Pass Query molecules to top of output
        • Pass Query to top of output
        • Process Every N records
        • Process N records
        • Protein Preparation Issues Detector
        • Protein Preparation Report
        • Shard Reader Optional
        • Single File Reader
        • String Parameter to String Field
        • Success Counter
        • Success Counter
        • Success Counter Shard
    • Release Notes
      • v0.27.0 February 2024
        • General Notice
        • New Cubes
        • Cube Updates
      • v0.26.1 September 2023
        • General Notice
      • v0.26.0 July 2023
        • General Notice
        • New Cubes
        • Cube Updates
      • v0.25.3 December 2022
        • General Notice
        • New Cubes
        • Cube Updates
      • v0.24.1 September 2022
        • General Notice
        • Cube Updates
      • v0.24.0 July 2022
        • General Notice
        • New Cubes
        • Cube Updates
      • v0.23.1 December 2021
        • General Notice
        • New Cubes
        • Cube Updates
        • Deprecated Cubes
      • v0.20.1 June 2021
        • New Cubes
        • Cube Updates
      • v0.20.1 November 2020
        • New Cubes
        • Cube Updates
      • v0.19.3 August 2020
        • Cube Updates
      • v0.19.1 August 2020
        • New Cubes
        • Cube Updates
        • Removed Cubes
      • v0.18.2 April 2020
        • General Notice
        • New Cubes
        • Cube Updates
        • Removed Cubes
      • v0.17.2 November 2019
        • General Notice
        • New Cubes
        • Cube Updates
      • v0.16.6 September 2019
        • General Notice
        • New Cubes
        • Cube Updates
      • v0.16.0 July 2019
        • General Notice
      • v0.15.0 June 2019
        • General Notice
      • v0.14.0 June 2019
        • General Notice
        • New Cubes
        • Cube Updates
      • v0.13.6 March 2019
        • General Notice
        • New Cubes
        • Cube Updates
      • v0.13.4 November 2018
        • General Notice
        • Cube Updates
      • v0.13.3 September 2018
        • General Notice
        • New Cubes
        • Cube Updates
      • v0.13.0 August 2018
        • General Notice
  • Crystal Structure Prediction & Properties
    • Theory
      • Crystal structure predictions
        • Random packing
        • Force field
        • Quantum Methods
      • Intrinsic Solubility
    • Tutorials
      • Crystal Structure Predictions using Crystal Math Floes
        • Introduction
        • Main Floes in the CSP Protocol
        • Additional Optional Floes
    • Crystal Math Floes - Documentation
      • Automated Force Field Solubility
      • Automated QM Solubility
      • CIF Reader
      • Cost Estimation for Crystal Structure Prediction
      • Crystal RMSD Deduplication Floe
      • Crystal RMSD Floe
      • Filtering of Crystal Structures Based on Powder Diffraction Pattern
      • Force Field Crystal Entropy with a Cluster Expansion Method
      • Force Field Optimization of Crystal Structures in the Dimer Expansion Approach
      • Loose Quantum Optimization of Crystal Structures (Part IIIA of CSP Protocol)
      • Polymorph Filtering Based on IEFF Energies (Part II’ of CSP Protocol: Filtering)
      • Polymorph Search with IEFF Crystal Force Field (Part II of CSP Protocol: Generation and Filtering)
      • Psi4 Combined Tautomer and Torsion Sampling Conformer Floe
      • Psi4 QM Conformer Ensemble (Part I of CSP Protocol)
      • QM Crystal Entropy with a Cluster Expansion Method (Part IV of CSP Protocol)
      • Quantum Optimization of Crystal Structures (Part IIIB of CSP Protocol)
      • Solubility from Crystal Entropy and Enthalpy
      • Water Sampling Floe
    • Release Notes
      • v2.9.2 December 2022
        • Required Dependency Changes
        • Floe Updates
      • v2.8.1 July 2022
        • General Notice
        • Floe Updates
      • v2.7.1 December 2021
        • General Notice
        • Floes in this package
        • Floe Updates
      • v2.5.0 November 2020
        • General Notice
        • New Floes
        • Floe Updates
      • v2.0.0 August 2020
        • General Notice
        • New Floes
        • Floe Updates
      • v1.8.4 April 2020
        • General Notice
        • Floe Updates
    • Bibliography
  • Gaussian Documentation
    • Gaussian Floe Tutorials
      • Introduction
        • Content of these Tutorials
        • Tutorial Data on Orion
      • Gaussian QM Conformer Ensemble Tutorial
      • Gaussian QM Torsion Scan Tutorial
      • Gaussian QM Run Input Files Successful Calculation
        • Locate and Run the Floe
        • Download and Analyze Results
      • Gaussian QM Run Input Files Failed Calculation
        • Understanding Failure Reports
      • Gaussian QM Single-Point Energy Tutorial
      • Gaussian QM Geometry Optimization Tutorial
    • Frequently Asked Questions
      • When should hardware requirements be changed?
      • How should hardware metrics be checked in QM calculations?
      • How much will a Floe cost?
      • What method and basis set should be used?
      • How can Gaussian log files be used to understand failures?
      • Why are there multiple serial cubes instead of a parallel cube?
      • How do you create datasets on Orion?
      • Why are my calculations failing due to the presence of implicit hydrogens?
      • How do you rerun a Gaussian calculation from a checkpoint file?
      • Can GPUs be used with Gaussian on Orion?
      • How should files for the Run Gaussian Input File Floe be created and organized?
      • Why did the Gaussian input file change after running on Orion?
      • What should you know before running a large calculation with a Gaussian input file?
    • OpenEye Gaussian QM Floes - Documentation
      • Gaussian QM Conformer Ensemble
      • Gaussian QM Fragmentation and Torsion Scan
      • Gaussian QM Geometry Optimization
      • Gaussian QM Parallel Run Input Files
      • Gaussian QM Run Input Files
      • Gaussian QM SMARTS Torsion Scan
      • Gaussian QM Single Point Energy
      • Gaussian QM UI Torsion Scan
    • Release Notes
      • v0.4.0 July 2023
        • New Floes
        • Floe Updates
      • v0.3.3 December 2022
        • Floe Updates
      • v0.2.0 (Orion Release 2022.2)
        • New Floes
        • Floe Updates
      • v0.1.0 (Orion Release 2022.1)
        • New Floes
        • New Cubes
  • 3D Antibody Modeling Package
    • 3D Antibody Modeling Tutorial
      • Floes Used in This Tutorial
      • Importing Sequences
      • Antibody Model Generation
        • Starting with Sequences
        • Starting with Experimental Structures
      • Modeling Results
    • Antibody MD Simulations Tutorial
      • Antibody Molecular Dynamics Simulations
    • Understanding Antibody Surfaces and Annotations
      • Surface Patches
      • Structure Annotations
    • Antibody SiteHopper-based Clustering Tutorial
      • Result Analysis
    • OpenEye 3D Antibody Modeling - Documentation
      • Antibody CDR Loop Ensemble Generation
      • Antibody Experimental Structure Prep
      • Antibody MD Simulations with Conformational Analysis
      • Antibody Mutate Residue(s)
      • Antibody Sequences to 3D Models
      • Antibody SiteHopper-based Clustering
      • Antibody Structure Relaxation
      • Antibody Subset System
      • Antibody Surface Patch Generation
      • Import Antibody FASTA Files
      • Renumber and Restyle Antibody
    • Release Notes
      • v0.1.6 April 2024
        • General Notice
    • Bibliography
  • AbXtract™ - NGS Antibody Discovery
    • Introduction to AbXtract
    • Tutorials
      • Tutorial 1: NGS Pipeline with Custom Interactive Selection (PacBio), In-Vitro Library
        • Background
        • STEP 1 - Log in to Orion, Set Up a Directory, and Locate Tutorial Files
        • STEP 2 - Select the NGS Pipeline Floe
        • STEP 3 - Prepare PacBio Run and Start Job
        • STEP 4 - Open the Floe Report to Get a General Idea About the Population
        • STEP 5 - Activate the Dataset
        • STEP 6 - Plot Relative Abundance Versus Desired Overlap Population and Select Population with Analyze Tool
        • STEP 7 - Select the Enriched Population Using the Analyze Tool and Send to the Automated Top Lead Selection Floe
        • STEP 8 - Subset the Number of Fields for Output and Download CSV
      • Tutorial 2: NGS Pipeline with Automated Top Lead Selection (PacBio), In-Vitro Library
        • Background
        • STEP 1 - Log in to Orion, Set Up a Directory, and Locate Tutorial Files
        • STEP 2 - Select the NGS Pipeline with Automated Lead Selection Floe
        • STEP 3 - Prepare PacBio Run and Start Job
        • STEP 4 - Open the Floe Report to Get a Detailed Understanding of the Selected Population
        • STEP 5 - Select Populations with Net Negative Charge of the CDRs
        • STEP 6 - Subset the Output Fields
        • STEP 7 - Download the CSV
      • Tutorial 3: NGS and Sanger Pipeline with Automated Top Lead Selection (PacBio), In-Vitro Library
        • Background
        • STEP 1 - Login to Orion, Set-Up Directory, Locate Tutorial Files
        • STEP 2 - Select the ‘NGS and Sanger Pipeline with Automated Top Lead Selection’ Floe
        • STEP 3 - Prepare Sanger Files
        • STEP 4 - Prepare PacBio Files and Start Job
        • STEP 5 - Open the Floe Report to Get a Detailed Understanding of the Selected or ‘Picked’ Population
        • STEP 6 - Subset NGS Only Population by Cluster and Overlap_Population
      • Tutorial 4: NGS and Sanger Pipeline with Automated Top Lead Selection (Illumina), In-Vitro Library
        • Background
        • STEP 1 - Login to Orion, Set-Up Directory, Upload Files
        • STEP 2 - Select the ‘NGS and Sanger Pipeline with Automated Top Lead Selection’ Floe
        • STEP 3 - Prepare Sanger Files
        • STEP 4 - Prepare Illumina Files and Start Job
      • Tutorial 5: NGS Pipeline with Automated Top Lead Selection (PacBio), Patient Library
        • Background
        • STEP 1 - Login to Orion, Set-Up Directory, Upload Files
        • STEP 2 - Select the ‘NGS Pipeline with Automated Lead Selection’ Floe
        • STEP 3 - Prepare PacBio Run and Start Job
        • STEP 4 - Select Different Clonotyping Method
        • STEP 5 - Identify both the Picked and the Downstream Population
      • Tutorial 6: NGS UMIs Extract and Annotation Floe
        • Background
        • STEP 1 - Login to Orion, Set-Up Directory, Upload Files
        • STEP 2 - Select the ‘NGS Pipeline with Automated Lead Selection’ Floe
        • STEP 3 - Prepare PacBio Run and Start Job
        • STEP 4 - Select Different Clonotyping Method
        • STEP 5 - Identify both the Picked and the Downstream Population
      • Video Tutorials Featuring AbXtract
    • How to Guides
      • How to Use the Floe Report and NGS Select to Select Population of Interest
      • How to Use the Floe Report and SANGER Select to Pick Population of Interest
      • How to Condense a Dataset with Too Many Records
      • I Performed Enrichment. How Do I Know which Population of My Given Sequence was Found?
      • How to Reduce the Number of Fields in the Output
      • How to Download the CSV of the Dataset of Records
      • How to Visualize Custom Experimental Metrics
      • How to upload data from an AIRR-compatible file
      • How to export any dataset to an AIRR-compatible file
    • Frequently Asked Questions
      • Frequently Asked Questions about AbXtract Floes
        • What is the difference between upstream and downstream chain designations, _1 and _2?
        • What is the difference between upstream and downstream AbXtract floe processing?
        • What input formats do the AbXtract upstream processing floes accept, and what are the requirements?
        • What is the region of interest (ROI)?
        • Where are the liabilities tabulated in AbXtract?
        • There are several overlap options available. What are the differences among the different overlap options?
        • What input formats do the AbXtract downstream processing floes accept, and what are the requirements?
        • How many sequences can the platform process, and what is the output?
        • Why is the number of picked representatives below the total number of full-length when using the Automated Top Lead Selection Floe?
        • The clustering is taking quite a while with my inputs. Is there a way to bypass clustering in the NGS (PacBio/Illumina) Pipeline Floe?
        • I do not need the Floe Report. Can I bypass this option?
        • What is a barcode file, barcode_group, barcode_round, and sample_name? How do you format this table?
        • What is a customized DNA or AA Database?
        • How is relative enrichment calculated?
        • How is relative abundance calculated?
        • What is meaning of the cluster vocabulary? What is a cluster? What is the difference between cluster and cluster_numeric?
        • I have selected the Levenshtein or Hamming Distance Clustering Method. Where do I modify the edit distance?
        • How are liabilities quantified, and what do the different liability fields mean?
        • What is a customized liabilities table/database, how is it formatted, and does it override the floe parameters?
        • How many records are typically handled by the Analyze tool?
        • How long does it take to load the Floe Report? Where in Orion can the Floe Reports be found?
        • I am having difficulty uploading my FASTQ file or Orion logs out before process is complete, how do I overcome this?
        • Why is my download taking so long?
        • My floe fails due to a memory allocation issue. How do I overcome this?
        • My floe is stalling for more than 48 hours in the NGS (PacBio/Illumina) Pipeline Floe, or beyond the cost level acceptable for this job?
        • What happens if I want to change a barcode group after the FASTQ has already been processed or I did not add a barcode group?
        • I am having difficulty downloading my file from the dropdown option for my given dataset?
        • I processed an AIRR-compatible file and want to link the AbXtract values to the original input values. How can I do that?
        • Will annotating my sequences using the NGS (PacBio/Illumina) IgMatcher, Annotation Only - AbXtract Floe give me the same result as my AIRR-compatible file?
        • Why are there twice as many records/rows output when I convert a PacBio input to an AIRR-compatible file?
    • Abxtract Floes - Documentation
      • AbXtract/AIRR File to Orion Dataset - AbXtract
      • Archive To Files
      • Automated Top Lead Selection - AbXtract
      • Cluster (AbScan) Antibody Binding Regions - AbXtract
      • Condense Dataset by Region of Interest by Most Abundant - AbXtract
      • Convert floe report to html files
      • Custom NGS Select by Seq ID of Additional NGS Representatives by Group - AbXtract
      • Custom SANGER Select of Additional NGS Representatives by Group - AbXtract
      • Export AIRR Fields for Dataset - AbXtract
      • Liability Quantification Across CDRs - AbXtract
      • Logomaker for Antibody CDRs - AbXtract
      • Modify Sample Name/Barcode Group for Downstream Processing - AbXtract
      • Multiple Round Relative Abundance and Enrichment Calculation by Region of Interest (ROI) - AbXtract
      • NGS IgMatcher, Annotation Only - AbXtract
      • NGS Pipeline - AbXtract
      • NGS Pipeline Efficiency - AbXtract
      • NGS Pipeline with Automated Top Lead Selection - AbXtract
      • NGS UMIs Extract and Annotation - AbXtract
      • NGS and Sanger Pipeline - AbXtract
      • NGS and Sanger Pipeline with Automated Top Lead Selection - AbXtract
      • Overlap Among Different Datasets - AbXtract
      • Quick Sanger from ABI Traces - AbXtract
      • Quick Sanger from DNA or Amino Acid Sequence Files - AbXtract
      • Single Round Relative Abundance and Enrichment Calculation by Region of Interest (ROI) - AbXtract
      • Subset the Number of Fields for Export - AbXtract
    • abxtract - Cube Documentation
      • AbXtract, Liabilities
      • AbXtract, Sanger
      • AbXtract - Biophysical
        • Sequence-Based Biophysical Sequence Calculation
      • AbXtract - Downstream Processing
        • AbXtract Processing, NGS Only
        • AbXtract Processing, NGS and SANGER
        • Binary Enrichment and Relative Abundance Calculation
        • Binary Input to Cluster
        • Binary Liability Calculation
        • Clustering by AbScan, Edit Distance, or 100% Homology
        • Condense Total Number of Sequences by Region of Interest (ROI)
        • Enrichment and Depletion Tracing of Clones
        • Enrichment and Relative Abundance Calculation
        • Export AIRR fields for dataset
        • Liabilities Quantification
        • Liabilities Quantification, Improved
        • Overlap Among Different NGS Barcode Populations
      • AbXtract - SANGER Processing
        • Inputting SANGER File (Excel, TSV, CSV)
        • Inputting SANGER File (Excel, TSV, CSV)
        • Inputting SANGER File (Excel, TSV, CSV) - BETA
        • Inputting SANGER Records - BETA
        • Write Consolidated AbXtract Dataset
      • AbXtract - Upstream Processing
        • Input File from NovaSeq
        • Inputting FASTQ for Illumina
        • Inputting FASTQ for Illumina
        • Inputting FASTQ for Illumina
        • Inputting FASTQ for PacBio
        • Inputting FASTQ for PacBio with Compressed Files
        • Inputting FASTQ for PacBio with Compressed Files
        • NovaSeq Binary Handler
        • Sequence Annotation with IgMatcher for Illumina
        • Sequence Annotation with IgMatcher for PacBio
        • Sequence Annotation with IgMatcher for PacBio
      • Automated Lead Selection
        • Custom Select NGS Leads by Sequence ID with File
        • Select NGS Leads Matching SANGER
        • Select X Number of Non-Redundant Sequences by Cluster or ROI
        • Select X Number of Non-Redundant Sequences by Cluster or ROI
        • Select X Number of Non-Redundant Sequences by Cluster or ROI
        • Write Consolidated AbXtract Dataset
        • Write Consolidated AbXtract Dataset
        • Write Consolidated AbXtract Dataset
      • Converting dataframe to blob.
        • Loads Cluster Assignment by Region of Interest
        • RecordToDataFrameBlob
        • Write Top Ranked Clusters
      • Long-Read
        • Full-Chain
      • Unclassified
        • Read Collections and Condense Data
        • Read Collections and Condense Data
        • Reads in Collection and Output Individual Record
        • Record Field Initializer Cube
      • Upload, Modify or Subset
        • Modify Sample Name or Barcode Group in AbXtract Dataset
        • Subset AbXtract Fields
        • Upload AbXtract Compatible File
      • Writing Reports and Datasets
        • Consolidating and Writing Datasets
        • Consolidating and Writing Datasets, Illumina
        • Consolidating and Writing Datasets, PacBio
        • Consolidating and Writing Datasets, Sanger
        • Long or Short-Read Sequence Identifier
    • Key Fields
      • Liability Metric Fields
      • Biophysical Metric Fields
      • Identifier Fields
      • Overlap Fields of NGS to SANGER or NGS
      • Enrichment, Abundance and Relative Abundance Fields
      • Scaffold / Germline Call Fields
      • Clustering Fields
      • Annotation Fields
      • Sequence Quality Fields
      • Special Fields to Add to Upload (Use in Analyze Tool Only)
      • AIRR Fields
    • Release Notes
      • v0.1.6 April 2024
      • v0.1.5 October 2023
      • v0.1.4 December 2022
      • v0.1.3 June 2022
      • v0.1.2 April 2022
      • v0.1.1 March 2022
      • v0.1.0 December 2021
        • General Notice
  • OpenEye Glossary of Terms
  • Legal Notices
    • Copyright and Trademarks
    • Sample Code
    • Citation
      • Orion ® Floes
      • Toolkits and Applications
      • OpenEye Web Services
    • Technology Licensing
    • GCC
      • GCC RUNTIME LIBRARY EXCEPTION
      • GNU GENERAL PUBLIC LICENSE
Suites and Modules User Guide
  • All OpenEye Documentation »
  • Contents »
  • OpenEye Permeability Floes Documentation »
  • permeability.cubes - Cube Documentation »
  • Unclassified

Unclassified¶

  • Auxiliary Dataset Registry
  • Index Molecules
  • Merge Molecules
  • System Subset Setup
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