Source code for vermouth.processors.tune_cystein_bridges

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright 2018 University of Groningen
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# See the License for the specific language governing permissions and
# limitations under the License.
Provides processors that can add and remove cystein bridges.

import functools

from ..selectors import proto_multi_templates
from .processor import Processor
from .add_molecule_edges import AddMoleculeEdgesAtDistance
from .. import edge_tuning

UNIVERSAL_BRIDGE_TEMPLATE = [{'resname': 'CYS', 'atomname': 'SG'}, ]

[docs] def remove_cystein_bridge_edges(molecule, templates=UNIVERSAL_BRIDGE_TEMPLATE): # pylint: disable=dangerous-default-value """ Remove all the edges that correspond to cystein bridges from a molecule. Cystein bridge edges link an atom from a cystein side chain to the same atom on an other cystein. Selecting the correct atom is done with a list of template node dictionaries. A template node dictionary functions in the same way as node matching in links. An atom that can be involved in a cystein bridge must match at least one of the templates of the list. The default template list selects the 'SG' bead of the residue 'CYS': ``[{'resname': 'CYS', 'atomname': 'SG'}, ]``. A template is a dictionary that defines the key:value pairs that must be matched in the atoms. Values can be instances of :class:`~vermouth.molecule.LinkPredicate`. Parameters ---------- molecule: networkx.Graph Molecule to modify in-place. templates: list[dict] A list of templates; selected atom must match at least one. """ selector = functools.partial(proto_multi_templates, templates=templates) edge_tuning.prune_edges_with_selectors(molecule, selector)
[docs] class RemoveCysteinBridgeEdges(Processor): """ Processor removing edges corresponding to cystein bridges. The edge for a cystein bridge is an edge between two atoms that match at least one template from a list of templates. Parameters ---------- template: list[dict] List of node templates. """ def __init__(self, template=UNIVERSAL_BRIDGE_TEMPLATE): # pylint: disable=dangerous-default-value self.template = template
[docs] def run_molecule(self, molecule): remove_cystein_bridge_edges(molecule, self.template) return molecule
[docs] class AddCysteinBridgesThreshold(AddMoleculeEdgesAtDistance): """ Add edges corresponding to cystein bridges on a distance criterion. The edge for a cystein bridge is an edge between two atoms that match at least one template from a list of templates if the two ends of the edge are closer than a given distance. Parameters ---------- threshold: float Distance in nanometers under which to consider an edge. template: list[dict] List of node templates. """ def __init__(self, threshold, # pylint: disable=dangerous-default-value template=UNIVERSAL_BRIDGE_TEMPLATE, attribute='position'): super().__init__( threshold, templates_from=template, templates_to=template, attribute=attribute, )