Source code for vermouth.processors.rename_modified_residues

# -*- 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
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# distributed under the License is distributed on an "AS IS" BASIS,
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# limitations under the License.
Provides a processor that renames residues based on their current residue names
and identified modifications, such as PTMs.

from .processor import Processor

[docs] def rename_modified_residues(mol): """ Renames residue names based on the current residue name, and the found modifications. The new names are found in `force_field.renamed_residues`, which should be a mapping of ``{(rename, [modification_name, ...]): new_name}``. Parameters ---------- mol : Molecule The molecule whose residue names should be changed. Is modified in-place. """ rename_map_ff = mol.force_field.renamed_residues rename_map = {} # Sort the list of modifications, so that the order does not matter. Don't # make a frozenset, because it might be possible to have the same # modification multiple times? # This should probably be done as the list is parsed. Also, as we parse it, # make sure we actually recognize all the modification names. for (resname, mods), new_name in rename_map_ff.items(): rename_map[resname, tuple(sorted(mods))] = new_name for node_key in mol: node = mol.nodes[node_key] modifications = node.get('modifications', []) resname = node.get('resname', '') if not modifications: continue modifications = tuple(sorted(mod.graph['name'] for mod in modifications)) try: new_name = rename_map[(resname, modifications)] except KeyError: # We don't know how to rename this residue, so continue to the next # node. continue node['resname'] = new_name
[docs] class RenameModifiedResidues(Processor):
[docs] def run_molecule(self, molecule): rename_modified_residues(molecule) return molecule