prepmd

• prepmd package
  • Subpackages
    • prepmd.lib package
      • Submodules
      • prepmd.lib.icp module
      • prepmd.lib.mdaCIF module
      • Module contents
  • Submodules
  • prepmd.add_modeller_license module
    • setup_license()
    • entry_point()
  • prepmd.align_together module
    • align_modeller()
    • get_gaps()
    • print_mask()
    • mark_missing_ends()
    • mark_innermost_gap()
    • get_ends_deletion()
    • remove_from_model()
    • align_together()
    • entry_point()
  • prepmd.analysis module
    • get_selection_traj()
    • dist()
    • get_ligand_centroid_traj()
  • prepmd.download module
    • get_em_map()
    • get_structure()
    • get_uniprot_sequence()
  • prepmd.fix module
    • fix_nonstandard_cif()
    • remove_hetatms_unk()
    • fix()
    • restore_metadata_pdb()
  • prepmd.get_residues module
    • get_residues_pdb()
    • get_fullseq_pdb()
  • prepmd.ligand module
    • load_universe()
    • pdb_back_to_mmcif()
    • split_pdb_ligand()
    • solvate_openff()
    • create_ligand_system()
  • prepmd.metadynamics module
    • StopSimulation
    • RMSDIncrease
    • RMSDReporter
      • RMSDReporter.describeNextReport()
      • RMSDReporter.report()
    • get_representative_rmsd_frames()
  • prepmd.model module
    • retitle_alignment()
    • fasta()
    • get_alignment_info()
    • get_objective_functions()
    • get_best_pdb()
    • fix_missing_residues()
  • prepmd.pdb2pqr module
    • run_pdb2pqr()
  • prepmd.point_cloud module
    • to_point_cloud()
    • score_pdb_map()
  • prepmd.prep module
    • id_generator()
    • prep()
    • entry_point()
  • prepmd.run module
    • make_forcefield()
    • check_platforms()
    • test_sim()
    • run()
    • entry_point()
  • prepmd.util module
    • is_residue()
    • is_residue_sequence()
    • three_to_one()
    • three_to_one_sequence()
  • Module contents