oemdaffinity.cubes - Cube Documentation¶
- Affinity Analysis
- 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
- Free Energy Calculations
- 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
- IFP MD Simulations
- IFP Preparation
- Input Checker
- MD Analysis
- MD Simulations
- Simulation Flask Preparation
- Structure Based Design
- Unbound Simulation Preparation