rid.common.plumed package
Submodules
rid.common.plumed.check_plumed module
rid.common.plumed.make_plumed module
- rid.common.plumed.make_plumed.get_cv_name(conf: Optional[str] = None, cv_file: Optional[List[str]] = None, selected_resid: Optional[List[int]] = None, selected_atomid: Optional[List[int]] = None, stride: int = 100, mode: str = 'torsion')[source]
- rid.common.plumed.make_plumed.make_constraint_plumed(conf: Optional[str] = None, cv_file: Optional[List[str]] = None, selected_atomid: Optional[List[int]] = None, stride: int = 100, output: str = 'plm.out', mode: str = 'distance')[source]
- rid.common.plumed.make_plumed.make_deepfe_bias(cv_list: List[str], trust_lvl_1: float = 1.0, trust_lvl_2: float = 2.0, model_list: List[str] = ['graph.pb']) str[source]
- rid.common.plumed.make_plumed.make_deepfe_plumed(conf: Optional[str] = None, cv_file: Optional[List[str]] = None, selected_resid: Optional[List[int]] = None, selected_atomid: Optional[List[int]] = None, trust_lvl_1: float = 1.0, trust_lvl_2: float = 2.0, model_list: List[str] = ['graph.pb'], stride: int = 100, output: str = 'plm.out', mode: str = 'torsion', wall_list: Optional[List[str]] = None, iteration: Optional[str] = None)[source]
- rid.common.plumed.make_plumed.make_distance(name: str, atom_list: List[Union[int, str]]) str[source]
- rid.common.plumed.make_plumed.make_distance_list_from_file(file_path: str, selected_atomid: List[int]) Tuple[List, List][source]
- rid.common.plumed.make_plumed.make_print_bias(name_list, stride, file_name, model_list) str[source]
- rid.common.plumed.make_plumed.make_restraint(name: str, arg: str, kappa: Union[str, int, float], at: Union[str, int, float])[source]
- rid.common.plumed.make_plumed.make_restraint_list(cv_list: List[str], kappa: List[Union[int, float, str]], at: List[Union[int, float, str]]) Tuple[List, List][source]
- rid.common.plumed.make_plumed.make_restraint_plumed(conf: Optional[str] = None, cv_file: Optional[List[str]] = None, selected_resid: Optional[List[int]] = None, selected_atomid: Optional[List[int]] = None, kappa: Union[int, float, Sequence, ndarray] = 0.5, at: Union[int, float, Sequence, ndarray] = 1.0, stride: int = 100, output: str = 'plm.out', mode: str = 'torsion')[source]
- rid.common.plumed.make_plumed.make_torsion(name: str, atom_list: List[Union[int, str]]) str[source]