oemdaffinity.cubes - Cube DocumentationΒΆ
- Affinity Analysis
- Analysis
- Cluster Ligand Traj OEMol
- Compute BintScore for Initial Pose and Trajectory
- 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
- MD Analysis
- MD Simulations
- Simulation Flask Preparation
- Unbound Simulation Preparation