Source code for MDAnalysis.coordinates.CRD

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"""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 .. versionchanged:: 2.2.0 CRD extended format can now be explicitly requested with the `extended` keyword """ 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 extended : bool (optional) By default, noextended CRD format is used [``False``]. However, extended CRD format can be forced by specifying `extended` ``=True``. Note that the extended format is *always* used if the number of atoms exceeds 99,999, regardless of the setting of `extended`. .. versionadded:: 2.2.0 """ self.filename = util.filename(filename, ext='crd') self.crd = None # account for explicit crd format, if requested self.extended = kwargs.pop("extended", False)
[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 self.extended or 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 self.extended or 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))