schrodinger.application.desmond.packages.restraint.utils module¶
Module for utilities for restraint generation.
Copyright Schrodinger, LLC. All rights reserved.
- exception schrodinger.application.desmond.packages.restraint.utils.CrossLinkGenerationError[source]¶
Bases:
Exception
- __init__(*args, **kwargs)¶
- args¶
- with_traceback()¶
Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.
- schrodinger.application.desmond.packages.restraint.utils.clear_encoded_restraints(cms_sys: schrodinger.application.desmond.cms.Cms, keep_persistent: bool = True)[source]¶
Remove encoded restraints from the
cms_sys
- Parameters
cms_sys (
cms.Cms
) – “cms” to be processed.keep_persistent (bool) – “persistent” restraints disposition.
- schrodinger.application.desmond.packages.restraint.utils.get_encoded_restraints(cms_sys)[source]¶
Get encoded restraints from cms
- Return type
str
- schrodinger.application.desmond.packages.restraint.utils.set_encoded_restraints(cms_sys, restr)[source]¶
Store restraints in cms_sys object.
- schrodinger.application.desmond.packages.restraint.utils.b64_encode(input_string: str) str [source]¶
Encodes to a
str
rather thanbytes
so that the result can be set as a string property of a CT.- Parameters
input_string – string to be encoded
- Returns
base64 encoded input
- schrodinger.application.desmond.packages.restraint.utils.b64_decode(input_string: str) str [source]¶
- class schrodinger.application.desmond.packages.restraint.utils.PLInteractionAids(ligand_aid: int, receptor_n_aid: int, receptor_ca_aid: int, receptor_c_aid: int)[source]¶
Bases:
object
- ligand_aid: int¶
- receptor_n_aid: int¶
- receptor_ca_aid: int¶
- receptor_c_aid: int¶
- property receptor_aids: Tuple[int, int, int]¶
- __init__(ligand_aid: int, receptor_n_aid: int, receptor_ca_aid: int, receptor_c_aid: int) None ¶
- class schrodinger.application.desmond.packages.restraint.utils.CentroidData(aids: List[int], diff: numpy.ndarray, centroid: numpy.ndarray)[source]¶
Bases:
object
- aids: List[int]¶
- diff: numpy.ndarray¶
- centroid: numpy.ndarray¶
- __init__(aids: List[int], diff: numpy.ndarray, centroid: numpy.ndarray) None ¶