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# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding: utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under the Lesser GNU Public Licence, v2.1 or any higher version
#
# Please cite your use of MDAnalysis in published work:
#
# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler,
# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein.
# MDAnalysis: A Python package for the rapid analysis of molecular dynamics
# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th
# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy.
# doi: 10.25080/majora-629e541a-00e
#
# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein.
# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
#
"""DL Poly format Topology Readers --- :mod:`MDAnalysis.topology.DLPolyParser`
==============================================================================
Read DL Poly_ format topology files
DLPoly files have the following Attributes:
- Atomnames
- Atomids
.. note::
By default, atomtypes and masses will be guessed on Universe creation.
This may change in release 3.0.
See :ref:`Guessers` for more information.
.. _Poly: http://www.stfc.ac.uk/SCD/research/app/ccg/software/DL_POLY/44516.aspx
Classes
-------
.. autoclass:: ConfigParser
.. autoclass:: HistoryParser
"""
import numpy as np
from .base import TopologyReaderBase
from ..core.topology import Topology
from ..core.topologyattrs import (
Atomids,
Atomnames,
Resids,
Resnums,
Segids,
)
from ..lib.util import openany
class ConfigParser(TopologyReaderBase):
"""DL_Poly CONFIG file parser
.. versionadded:: 0.10.1
.. versionchanged:: 2.8.0
Removed type and mass guessing (attributes guessing takes place now
through universe.guess_TopologyAttrs() API).
"""
format = "CONFIG"
def parse(self, **kwargs):
with openany(self.filename) as inf:
inf.readline()
levcfg, imcon, megatm = np.int64(inf.readline().split()[:3])
if not imcon == 0:
inf.readline()
inf.readline()
inf.readline()
names = []
ids = []
line = inf.readline().strip()
while line:
name = line[:8].strip()
names.append(name)
try:
idx = int(line[8:])
except ValueError:
pass
else:
ids.append(idx)
inf.readline()
if levcfg > 0:
inf.readline()
if levcfg == 2:
inf.readline()
line = inf.readline()
n_atoms = len(names)
if ids:
ids = np.array(ids)
names = np.array(names, dtype=object)
order = np.argsort(ids)
ids = ids[order]
names = names[order]
else:
ids = np.arange(n_atoms)
attrs = [
Atomnames(names),
Atomids(ids),
Resids(np.array([1])),
Resnums(np.array([1])),
Segids(np.array(["SYSTEM"], dtype=object)),
]
top = Topology(n_atoms, 1, 1, attrs=attrs)
return top
class HistoryParser(TopologyReaderBase):
"""DL_Poly History file parser
.. versionadded:: 0.10.1
"""
format = "HISTORY"
def parse(self, **kwargs):
with openany(self.filename) as inf:
inf.readline()
levcfg, imcon, megatm = np.int64(inf.readline().split()[:3])
names = []
ids = []
line = inf.readline()
while not (len(line.split()) == 4 or len(line.split()) == 5):
line = inf.readline()
if line == "":
raise EOFError("End of file reached when reading HISTORY.")
while line and not line.startswith("timestep"):
name = line[:8].strip()
names.append(name)
try:
idx = int(line.split()[1])
except ValueError:
pass
else:
ids.append(idx)
inf.readline()
if levcfg > 0:
inf.readline()
if levcfg == 2:
inf.readline()
line = inf.readline()
n_atoms = len(names)
if ids:
ids = np.array(ids)
names = np.array(names, dtype=object)
order = np.argsort(ids)
ids = ids[order]
names = names[order]
else:
ids = np.arange(n_atoms)
attrs = [
Atomnames(names),
Atomids(ids),
Resids(np.array([1])),
Resnums(np.array([1])),
Segids(np.array(["SYSTEM"], dtype=object)),
]
top = Topology(n_atoms, 1, 1, attrs=attrs)
return top
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