haddock.modules.base_cns_module module

Functionalities related to CNS modules.

class haddock.modules.base_cns_module.BaseCNSModule(order: int, path: Path, initial_params: str | Path, cns_script: str | Path)

Bases: BaseHaddockModule

Operation module for CNS.

Contains additional functionalities excusive for CNS modules.

default_envvars() → dict[str, str]

Return default env vars updated to envvars (if given).

get_ambig_fnames(prev_ambig_fnames: list[Union[NoneType, str, pathlib.Path]]) → list[Union[str, pathlib.Path]] | None

Get the correct ambiguous restraint names.

Parameters:

prev_ambig_fnames (list) – list of ambig_fname files encoded in previous models

Returns:

ambig_fnames (list or None) – list of ambig_fname files to be used by the CNS module

make_self_contained() → None

Create folders to make run self-contained.

name: str

run(**params: Any) → None

Execute the module.

save_envvars(filename: str | Path = 'envvars') → None

Save envvars needed for CNS to a file in the module’s folder.