# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
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# 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 GNU Public Licence, v2 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
#
"""CRD structure files in MDAnalysis --- :mod:`MDAnalysis.coordinates.CRD`
===========================================================================
Read and write coordinates in CHARMM CARD coordinate format (suffix
"crd"). The CHARMM "extended format" is handled automatically.
"""
import itertools
import numpy as np
import warnings
from ..exceptions import NoDataError
from ..lib import util
from . import base
[docs]class CRDReader(base.SingleFrameReaderBase):
"""CRD reader that implements the standard and extended CRD coordinate formats
.. versionchanged:: 0.11.0
Now returns a ValueError instead of FormatError.
Frames now 0-based instead of 1-based.
"""
format = 'CRD'
units = {'time': None, 'length': 'Angstrom'}
def _read_first_frame(self):
# EXT:
# (i10,2x,a) natoms,'EXT'
# (2I10,2X,A8,2X,A8,3F20.10,2X,A8,2X,A8,F20.10)
# iatom,ires,resn,typr,x,y,z,segid,rid,wmain
# standard:
# (i5) natoms
# (2I5,1X,A4,1X,A4,3F10.5,1X,A4,1X,A4,F10.5)
# iatom,ires,resn,typr,x,y,z,segid,orig_resid,wmain
coords_list = []
with util.openany(self.filename) as crdfile:
extended = False
natoms = 0
for linenum, line in enumerate(crdfile):
if line.strip().startswith('*') or line.strip() == "":
continue # ignore TITLE and empty lines
fields = line.split()
if len(fields) <= 2:
# should be the natoms line
natoms = int(fields[0])
extended = (fields[-1] == 'EXT')
continue
# process coordinates
try:
if extended:
coords_list.append(np.array(line[45:100].split()[0:3], dtype=float))
else:
coords_list.append(np.array(line[20:50].split()[0:3], dtype=float))
except Exception:
errmsg = (f"Check CRD format at line {linenum}: "
f"{line.rstrip()}")
raise ValueError(errmsg) from None
self.n_atoms = len(coords_list)
self.ts = self._Timestep.from_coordinates(np.array(coords_list),
**self._ts_kwargs)
self.ts.frame = 0 # 0-based frame number
# if self.convert_units:
# self.convert_pos_from_native(self.ts._pos) # in-place !
# sanity check
if self.n_atoms != natoms:
raise ValueError("Found %d coordinates in %r but the header claims that there "
"should be %d coordinates." % (self.n_atoms, self.filename, natoms))
[docs] def Writer(self, filename, **kwargs):
"""Returns a CRDWriter for *filename*.
Parameters
----------
filename: str
filename of the output CRD file
Returns
-------
:class:`CRDWriter`
"""
return CRDWriter(filename, **kwargs)
[docs]class CRDWriter(base.WriterBase):
"""CRD writer that implements the CHARMM CRD coordinate format.
It automatically writes the CHARMM EXT extended format if there
are more than 99,999 atoms.
Requires the following attributes to be present:
- resids
- resnames
- names
- chainIDs
- tempfactors
.. versionchanged:: 0.11.0
Frames now 0-based instead of 1-based
"""
format = 'CRD'
units = {'time': None, 'length': 'Angstrom'}
fmt = {
#crdtype = 'extended'
#fortran_format = '(2I10,2X,A8,2X,A8,3F20.10,2X,A8,2X,A8,F20.10)'
"ATOM_EXT": ("{serial:10d}{totRes:10d} {resname:<8.8s} {name:<8.8s}"
"{pos[0]:20.10f}{pos[1]:20.10f}{pos[2]:20.10f} "
"{chainID:<8.8s} {resSeq:<8d}{tempfactor:20.10f}\n"),
"NUMATOMS_EXT": "{0:10d} EXT\n",
#crdtype = 'standard'
#fortran_format = '(2I5,1X,A4,1X,A4,3F10.5,1X,A4,1X,A4,F10.5)'
"ATOM": ("{serial:5d}{totRes:5d} {resname:<4.4s} {name:<4.4s}"
"{pos[0]:10.5f}{pos[1]:10.5f}{pos[2]:10.5f} "
"{chainID:<4.4s} {resSeq:<4d}{tempfactor:10.5f}\n"),
"TITLE": "* FRAME {frame} FROM {where}\n",
"NUMATOMS": "{0:5d}\n",
}
def __init__(self, filename, **kwargs):
"""
Parameters
----------
filename : str or :class:`~MDAnalysis.lib.util.NamedStream`
name of the output file or a stream
"""
self.filename = util.filename(filename, ext='crd')
self.crd = None
[docs] def write(self, selection, frame=None):
"""Write selection at current trajectory frame to file.
Parameters
----------
selection : AtomGroup
group of atoms to be written
frame : int (optional)
Move the trajectory to frame `frame`; by default, write
the current frame.
"""
try:
u = selection.universe
except AttributeError:
errmsg = "Input obj is neither an AtomGroup or Universe"
raise TypeError(errmsg) from None
if frame is not None:
u.trajectory[frame] # advance to frame
else:
try:
frame = u.trajectory.ts.frame
except AttributeError:
frame = 0 # should catch cases when we are analyzing a single PDB (?)
atoms = selection.atoms # make sure to use atoms (Issue 46)
coor = atoms.positions # can write from selection == Universe (Issue 49)
n_atoms = len(atoms)
# Detect which format string we're using to output (EXT or not)
# *len refers to how to truncate various things,
# depending on output format!
if n_atoms > 99999:
at_fmt = self.fmt['ATOM_EXT']
serial_len = 10
resid_len = 8
totres_len = 10
else:
at_fmt = self.fmt['ATOM']
serial_len = 5
resid_len = 4
totres_len = 5
# Check for attributes, use defaults for missing ones
attrs = {}
missing_topology = []
for attr, default in (
('resnames', itertools.cycle(('UNK',))),
# Resids *must* be an array because we index it later
('resids', np.ones(n_atoms, dtype=int)),
('names', itertools.cycle(('X',))),
('tempfactors', itertools.cycle((0.0,))),
):
try:
attrs[attr] = getattr(atoms, attr)
except (NoDataError, AttributeError):
attrs[attr] = default
missing_topology.append(attr)
# ChainIDs - Try ChainIDs first, fall back to Segids
try:
attrs['chainIDs'] = atoms.chainIDs
except (NoDataError, AttributeError):
# try looking for segids instead
try:
attrs['chainIDs'] = atoms.segids
except (NoDataError, AttributeError):
attrs['chainIDs'] = itertools.cycle(('',))
missing_topology.append(attr)
if missing_topology:
warnings.warn(
"Supplied AtomGroup was missing the following attributes: "
"{miss}. These will be written with default values. "
"".format(miss=', '.join(missing_topology)))
with util.openany(self.filename, 'w') as crd:
# Write Title
crd.write(self.fmt['TITLE'].format(
frame=frame, where=u.trajectory.filename))
crd.write("*\n")
# Write NUMATOMS
if n_atoms > 99999:
crd.write(self.fmt['NUMATOMS_EXT'].format(n_atoms))
else:
crd.write(self.fmt['NUMATOMS'].format(n_atoms))
# Write all atoms
current_resid = 1
resids = attrs['resids']
for i, pos, resname, name, chainID, resid, tempfactor in zip(
range(n_atoms), coor, attrs['resnames'], attrs['names'],
attrs['chainIDs'], attrs['resids'], attrs['tempfactors']):
if not i == 0 and resids[i] != resids[i-1]:
current_resid += 1
# Truncate numbers
serial = util.ltruncate_int(i + 1, serial_len)
resid = util.ltruncate_int(resid, resid_len)
current_resid = util.ltruncate_int(current_resid, totres_len)
crd.write(at_fmt.format(
serial=serial, totRes=current_resid, resname=resname,
name=name, pos=pos, chainID=chainID,
resSeq=resid, tempfactor=tempfactor))