schrodinger.application.desmond.packages.restraint.utils module¶

Module for utilities for restraint generation.

exception schrodinger.application.desmond.packages.restraint.utils.CrossLinkGenerationError[source]¶

Bases: Exception

__init__(*args, **kwargs)¶: Initialize self. See help(type(self)) for accurate signature.

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 than bytes 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¶

__init__(ligand_aid: int, receptor_n_aid: int, receptor_ca_aid: int, receptor_c_aid: int) → None¶: Initialize self. See help(type(self)) for accurate signature.

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¶: Initialize self. See help(type(self)) for accurate signature.