Package Contents

• af2rave.alphafold module
  • af2rave.alphafold.colabfold module
• af2rave.feature module
  • FeatureSelection
    • FeatureSelection.apply_filter()
    • FeatureSelection.atom_pairs
    • FeatureSelection.feature_array
    • FeatureSelection.features
    • FeatureSelection.get_chimera_plotscript()
    • FeatureSelection.get_rmsd()
    • FeatureSelection.minimum_nonbonded_distance
    • FeatureSelection.nonbonded_pairs
    • FeatureSelection.pca()
    • FeatureSelection.pdb_name
    • FeatureSelection.peptide_bond_filter()
    • FeatureSelection.peptide_bond_stats
    • FeatureSelection.rank_feature()
    • FeatureSelection.ref_pdb
    • FeatureSelection.regular_space_clustering()
    • FeatureSelection.rmsd_filter()
    • FeatureSelection.steric_clash_filter()
    • FeatureSelection.top
    • FeatureSelection.traj
  • af2rave.feature.utils
    • atom_name()
    • chain()
    • chimera_representation()
    • representation()
    • resid()
    • resname()
• af2rave.simulation module
  • Utilities for creating simulation box
    • SimulationBox
      • SimulationBox.add_disulfide_bond()
      • SimulationBox.create_box()
      • SimulationBox.map_atom_index
      • SimulationBox.save_pdb()
    • TopologyMap
      • TopologyMap.map_atom_index()
  • Tools for unbiased simulation
    • UnbiasedSimulation
      • UnbiasedSimulation.pos
      • UnbiasedSimulation.restart()
      • UnbiasedSimulation.run()
      • UnbiasedSimulation.save_checkpoint()
      • UnbiasedSimulation.save_pdb()
  • OpenMM reporters
    • CVReporter
      • CVReporter.describeNextReport()
      • CVReporter.report()
    • MinimizationReporter
      • MinimizationReporter.report()
• af2rave.amino module
• af2rave.spib module
  • af2rave.spib.SPIBProcess
    • SPIBProcess
      • SPIBProcess.run()
  • af2rave.spib.SPIBResult
    • SPIBResult
      • SPIBResult.apparent_bias
      • SPIBResult.apparent_weight
      • SPIBResult.bias
      • SPIBResult.dt
      • SPIBResult.from_file()
      • SPIBResult.get_free_energy()
      • SPIBResult.get_latent_representation()
      • SPIBResult.get_probability_distribution()
      • SPIBResult.get_state_label()
      • SPIBResult.get_traj_label()
      • SPIBResult.n_converged_states
      • SPIBResult.n_input_labels
      • SPIBResult.n_traj
      • SPIBResult.project()
      • SPIBResult.project_colvar()
      • SPIBResult.project_state_label()
      • SPIBResult.to_file()
      • SPIBResult.weight
• af2rave.colvar module
  • Colvar
    • Colvar.choose()
    • Colvar.data
    • Colvar.from_file()
    • Colvar.header
    • Colvar.kappend()
    • Colvar.map()
    • Colvar.read()
    • Colvar.shape
    • Colvar.stride()
    • Colvar.tappend()
    • Colvar.time
    • Colvar.write()