Source code for MDAnalysis.topology.GMSParser

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GAMESS Topology Parser

.. versionadded:: 0.9.1

Reads a GAMESS_ output file (also Firefly_ and `GAMESS-UK`_) and pulls
element information from it.  Symmetrical assembly is read (not
symmetry element!).  Atom names are read from the GAMESS section.  Any
information about residues or segments will not be populated.

.. _Firefly:
.. _`GAMESS-UK`:


.. autoclass:: GMSParser

import re
import numpy as np

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

class AtomicCharges(AtomAttr):
    attrname = 'atomiccharges'
    singular = 'atomiccharge'
    per_object = 'atom'

[docs] class GMSParser(TopologyReaderBase): """GAMESS_ topology parser. Creates the following Attributes: - names - atomic charges Guesses: - types - masses .. versionadded:: 0.9.1 """ format = 'GMS'
[docs] def parse(self, **kwargs): """Read list of atoms from a GAMESS file.""" names = [] at_charges = [] with openany(self.filename) as inf: while True: line = inf.readline() if not line: raise EOFError if re.match(r'^\s+ATOM\s+ATOMIC\s+COORDINATES\s*\(BOHR\).*',\ line): break line = inf.readline() # skip while True: line = inf.readline() _m = re.match(\ r'^\s*([A-Za-z_][A-Za-z_0-9]*)\s+([0-9]+\.[0-9]+)\s+(\-?[0-9]+\.[0-9]+)\s+(\-?[0-9]+\.[0-9]+)\s+(\-?[0-9]+\.[0-9]+).*', line) if _m is None: break name = at_charge = int(float( names.append(name) at_charges.append(at_charge) #TODO: may be use coordinates info from ?? atomtypes = guessers.guess_types(names) masses = guessers.guess_masses(atomtypes) n_atoms = len(names) attrs = [ Atomids(np.arange(n_atoms) + 1), Atomnames(np.array(names, dtype=object)), AtomicCharges(np.array(at_charges, dtype=np.int32)), Atomtypes(atomtypes, guessed=True), Masses(masses, guessed=True), Resids(np.array([1])), Resnums(np.array([1])), Segids(np.array(['SYSTEM'], dtype=object)), ] top = Topology(n_atoms, 1, 1, attrs=attrs) return top