rid.task package

Submodules

rid.task.builder module

class rid.task.builder.ConstrainedMDTaskBuilder(conf: str, topology: Optional[str], label_config: Dict, cv_file: Optional[List[str]] = None, selected_atomid: Optional[List[int]] = None, sampler_type: str = 'gmx', plumed_output: str = 'plm.out', cv_mode: str = 'distance')

Bases: TaskBuilder

build() → Task

build_gmx()

build_lmp()

build_plumed()

get_task()

class rid.task.builder.EnhcMDTaskBuilder(conf: str, topology: Optional[str], exploration_config: Dict, cv_file: Optional[List[str]] = None, selected_resid: Optional[List[int]] = None, selected_atomid: Optional[List[int]] = None, sampler_type: str = 'gmx', trust_lvl_1: float = 1.0, trust_lvl_2: float = 2.0, model_list: List[str] = ['graph.pb'], plumed_output: str = 'plm.out', cv_mode: str = 'torsion', wall_list: Optional[List[str]] = None, iteration: Optional[str] = None)

Bases: TaskBuilder

build() → Task

build_gmx()

build_lmp()

build_plumed()

get_cv_dim()

get_task()

class rid.task.builder.RestrainedMDTaskBuilder(conf: str, topology: Optional[str], label_config: Dict, cv_file: Optional[List[str]] = None, selected_resid: Optional[List[int]] = None, selected_atomid: Optional[List[int]] = None, sampler_type: str = 'gmx', kappa: Union[int, float, List[Union[int, float]]] = 0.5, at: Union[int, float, List[Union[int, float]]] = 1.0, plumed_output: str = 'plm.out', cv_mode: str = 'torsion')

Bases: TaskBuilder

build() → Task

build_gmx()

build_lmp()

build_plumed()

get_task()

class rid.task.builder.TaskBuilder

Bases: ABC

abstract build()

rid.task.builder.build_gmx_constraint_dict(conf: str, topology: str, gmx_config: Dict, selected_atomid: Optional[List[int]] = None)

rid.task.builder.build_gmx_dict(conf: str, topology: str, gmx_config: Dict)

rid.task.builder.build_lmp_dict(conf: str)

rid.task.builder.build_plumed_constraint_dict(conf: Optional[str] = None, cv_file: Optional[str] = None, selected_atomid: Optional[List[int]] = None, stride: int = 100, output: str = 'plm.out', mode: str = 'distance')

rid.task.builder.build_plumed_dict(conf: Optional[str] = None, cv_file: Optional[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)

rid.task.builder.build_plumed_restraint_dict(conf: Optional[str] = None, cv_file: Optional[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')

rid.task.task module

class rid.task.task.Task

Bases: object

Define the files needed by an MD task. .. rubric:: Examples

>>> # this example dumps all files needed by the task.
>>> files = exploration_task.files()
... for file_name, file_content in files.items():
...     with open(file_name, 'w') as fp:
...         fp.write(file_content)

add_file(fname: str, fcont: Tuple[Optional[Union[str, bytes]], str])

Add file to the task

Parameters

• fname (str) – The name of the file

• fcont (str) – The content of the file.

add_property(properties: Dict)

property files: Dict

Get all files for the task.

Returns

files – The dict storing all files for the task. The file name is a key of the dict, and the file content is the corresponding value.

Return type

dict