Source code for MDAnalysis.topology.GROParser

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GRO topology parser

Read a list of atoms from a GROMOS/Gromacs GRO coordinate file to
build a basic topology.

Atom types and masses are guessed.

See Also


.. autoclass:: GROParser

import numpy as np

from ..lib.util import openany
from ..core.topologyattrs import (
from ..core.topology import Topology
from .base import TopologyReaderBase, change_squash
from . import guessers

[docs]class GROParser(TopologyReaderBase): """Reads a Gromacs GRO file Reads the following attributes: - resids - resnames - atomids - atomnames Guesses the following attributes - atomtypes - masses """ format = 'GRO'
[docs] def parse(self, **kwargs): """Return the *Topology* object for this file""" # Gro has the following columns # resid, resname, name, index, (x,y,z) with openany(self.filename) as inf: next(inf) n_atoms = int(next(inf)) # Allocate shizznizz resids = np.zeros(n_atoms, dtype=np.int32) resnames = np.zeros(n_atoms, dtype=object) names = np.zeros(n_atoms, dtype=object) indices = np.zeros(n_atoms, dtype=np.int32) for i, line in enumerate(inf): if i == n_atoms: break try: resids[i] = int(line[:5]) resnames[i] = line[5:10].strip() names[i] = line[10:15].strip() indices[i] = int(line[15:20]) except (ValueError, TypeError): errmsg = ( f"Couldn't read the following line of the .gro file:\n" f"{line}") raise IOError(errmsg) from None # Check all lines had names if not np.all(names): missing = np.where(names == '') raise IOError("Missing atom name on line: {0}" "".format(missing[0][0] + 3)) # 2 header, 1 based # Fix wrapping of resids (if we ever saw a wrap) if np.any(resids == 0): # find places where resid hit zero again wraps = np.where(resids == 0)[0] # group these places together: # find indices of first 0 in each block of zeroes # 1) find large changes in index, (ie non sequential blocks) diff = np.diff(wraps) != 1 # 2) make array of where 0-blocks start starts = np.hstack([wraps[0], wraps[1:][diff]]) # remove 0 in starts, ie the first residue **can** be 0 if starts[0] == 0: starts = starts[1:] # for each resid after a wrap, add 100k (5 digit wrap) for s in starts: resids[s:] += 100000 # Guess types and masses atomtypes = guessers.guess_types(names) masses = guessers.guess_masses(atomtypes) residx, (new_resids, new_resnames) = change_squash( (resids, resnames), (resids, resnames)) # new_resids is len(residues) # so resindex 0 has resid new_resids[0] attrs = [ Atomnames(names), Atomids(indices), Atomtypes(atomtypes, guessed=True), Resids(new_resids), Resnums(new_resids.copy()), Resnames(new_resnames), Masses(masses, guessed=True), Segids(np.array(['SYSTEM'], dtype=object)) ] top = Topology(n_atoms=n_atoms, n_res=len(new_resids), n_seg=1, attrs=attrs, atom_resindex=residx, residue_segindex=None) return top