oemdaffinity.cubes - Cube Documentation

• 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
• FEC Analysis
  • NES Analysis
  • PredictDG FromDDG Plot
• Free Energy
  • NES GMX
• MD Simulations
  • MD ProxyCube
  • MD Recover Restart for ProxyCube
• RBFE Analysis
  • RBFE Plot
  • RBFE Result to File
• Relative Free Energy
  • GMX Chimera
  • RBFEC Edge Gathering
  • RBFEC Mapper Cube
  • RBFEC Mapper Floe Report Cube
  • RBFEC Mapper Result to File