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