rid.common package

Subpackages

• rid.common.gromacs package
  • Submodules
  • rid.common.gromacs.command module
    • get_grompp_cmd()
    • get_mdrun_cmd()
  • rid.common.gromacs.gmx_constant module
  • rid.common.gromacs.mdp module
    • check_basic_argument()
    • make_md_mdp_from_config()
    • make_md_mdp_string()
    • make_mdp_from_json()
    • modify_define()
    • modify_output()
  • rid.common.gromacs.trjconv module
    • generate_coords()
    • generate_forces()
    • slice_trjconv()
• rid.common.lammps package
  • Submodules
  • rid.common.lammps.command module
    • final_dump()
  • rid.common.lammps.lmp_constant module
• rid.common.plumed package
  • Submodules
  • rid.common.plumed.check_plumed module
    • check_deepfe_input()
  • rid.common.plumed.make_plumed module
    • get_cv_name()
    • make_constraint_plumed()
    • make_deepfe_bias()
    • make_deepfe_plumed()
    • make_distance()
    • make_distance_list()
    • make_distance_list_from_file()
    • make_distance_name()
    • make_print()
    • make_print_bias()
    • make_restraint()
    • make_restraint_list()
    • make_restraint_plumed()
    • make_torsion()
    • make_torsion_list()
    • make_torsion_list_from_file()
    • make_torsion_name()
    • make_wall_list()
    • make_wholemolecules()
    • user_plumed_def()
  • rid.common.plumed.plumed_constant module
• rid.common.sampler package
  • Submodules
  • rid.common.sampler.command module
    • get_grompp_cmd()
    • get_mdrun_cmd()
• rid.common.tensorflow package
  • Submodules
  • rid.common.tensorflow.graph module

Submodules

rid.common.mol module

rid.common.mol.distance(r1, r2)

rid.common.mol.get_dihedral_from_resid(file_path: str, selected_resid: List[int]) → Dict

rid.common.mol.get_dihedral_info(file_path: str)

rid.common.mol.get_distance_from_atomid(file_path: str, selected_atomid: List[int]) → Dict

rid.common.mol.slice_xtc(xtc: str, top: str, walker_idx: int, selected_idx, output: str, style: str = 'gmx')

rid.common.mol.slice_xtc_mdtraj(xtc: str, top: str, walker_idx: int, selected_idx: Sequence, output_format: str)

rid.common.mol_dpdata module

rid.common.mol_dpdata.slice_dump(dump: str, walker_idx: int, selected_idx, output: str, type_map: List = [], style: str = 'dpdata')

rid.common.mol_dpdata.slice_dump_dpdata(dump: str, walker_idx, selected_idx, output_format: str, type_map: List = [])