Data

AuxData

Bases: BaseModel

active: bool = Field(default=False) class-attribute instance-attribute

If this data should be calculated and monitored during simulations or analyzed.

compute_function: Callable[[Any], float | MutableSequence[float]] = Field(default=None, exclude=True) class-attribute instance-attribute

Function to compute the descriptor value.

f_ext: str = Field(default='txt') class-attribute instance-attribute

File extension if saving.

file_name: str property

label: str instance-attribute

Label used for any data structures or file names.

progress: bool = Field(default=False) class-attribute instance-attribute

If this auxillary data should be used for a progress coordinate

values: MutableSequence[float | MutableSequence[float]] = Field(default=[], exclude=True) class-attribute instance-attribute

Data values.

write: bool = Field(default=False) class-attribute instance-attribute

Flag to write file containing data.

compute_frame(atoms_frame, subpex_config, atoms_ref=None, *args, **kwargs)

Will use compute_function to compute and then append the value to values.

ContainerAuxData

Bases: BaseModel

backbone_rmsd: AuxData = Field(default_factory=lambda: AuxData(label='backbone_rmsd', compute_function=get_backbone_rmsd)) class-attribute instance-attribute

pocket_jd: AuxData = Field(default_factory=lambda: AuxData(label='pocket_jd', compute_function=get_pocket_jaccard_convenience)) class-attribute instance-attribute

pocket_rmsd: AuxData = Field(default_factory=lambda: AuxData(label='pocket_rmsd', compute_function=get_pocket_rmsd_convenience)) class-attribute instance-attribute

pocket_rog: AuxData = Field(default_factory=lambda: AuxData(label='pocket_rog', compute_function=get_pocket_rog_convenience)) class-attribute instance-attribute

pocket_volume: AuxData = Field(default_factory=lambda: AuxData(label='pocket_volume', compute_function=get_pocket_volume_convenience)) class-attribute instance-attribute

get_active()

Yields each attribute of type AuxData.

get_all()

Yields each attribute of type AuxData.

DataConfig

Bases: BaseModel

aux: ContainerAuxData = Field(default_factory=ContainerAuxData) class-attribute instance-attribute

composite_sigma: float | None = Field(default=None) class-attribute instance-attribute

Sigma to use for composite progress coordinate. If None, this defaults to

sigma = (
    1
    - len(reference.select_atoms(selection_alignment))
    / len(reference.select_atoms("backbone"))
) / 2

write_dir: str = Field(default='') class-attribute instance-attribute

Where to write any auxillary data that has write as True