Source code for vermouth.rcsu.go_utils

# Copyright 2023 University of Groningen
# Licensed under the Apache License, Version 2.0 (the "License");
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Utilities for Go model processors.
from vermouth.molecule import attributes_match

[docs] def get_go_type_from_attributes(molecule, prefix, **kwargs): """ Find all nodes that satisfy a number of attributes specified as kwargs and have a specific atomtype prefix. Parameters ---------- molecule: :class:`vermouth.molecule.Molecule` prefix: str the atom-type prefix of the Go virtual side kwargs: any number of attributes Yields ------ str the atom-type Raises ------ KeyError If no node can be found that matches attributes and prefix an KeyError is raised. """ for node in molecule.nodes: attrs = molecule.nodes[node] if attributes_match(attrs, kwargs) and attrs['atype'].startswith(prefix): yield attrs['atype'] else: resid = kwargs['resid'] chain = kwargs['chain'] raise KeyError(f"Could not find GoVs with resid {resid} in chain {chain}.")
def _in_resid_region(resid, regions): """ Check if resid falls in regions interval. Parameters ---------- resid: int the resid of a molecule regions: list[tuple(int, int)] a list of the intervals Returns ------- bool """ for limits in regions: # perhaps someone gives them as reversed low, up = sorted(limits) if low <= resid <= up: return True return False def _get_bead_size(atype): if atype.startswith("S"): bead_size = "small" elif atype.startswith("T"): bead_size = "tiny" else: bead_size = "regular" return bead_size