Source code for parmed.charmm.charmmcrds

"""
Provides a class for parsing CHARMM-style coordinate files, namely CHARMM .crd
(coordinate) files and CHARMM .rst (restart) file. Uses CharmmFile class in
_charmmfile.py for reading files

Author: Jason Deckman
Contributors: Jason Swails
Date: June 19, 2015
"""
from __future__ import print_function, division, absolute_import

from contextlib import closing
import numpy as np
from parmed.utils import io
from parmed.formats.registry import FileFormatType
from parmed.exceptions import CharmmError
from parmed import unit as u
from parmed.utils.six import add_metaclass, string_types
from parmed.utils.six.moves import range
from parmed.vec3 import Vec3

CHARMLEN = 22
TIMESCALE = 4.888821E-14 * 1e12 # AKMA time units to picoseconds
ONE_TIMESCALE = 1 / TIMESCALE

@add_metaclass(FileFormatType)
[docs]class CharmmCrdFile(object): """ Reads and parses a CHARMM coordinate file (.crd) into its components, namely the coordinates, CHARMM atom types, resid, resname, etc. Parameters ---------- fname : str Name of the restart file to parse Attributes ---------- natom : int Number of atoms in the system resname : list of str List of all residue names in the system coordinates : np.ndarray with shape (1, natom, 3) Atomic coordinates in a numpy array positions : natom x 3 distance Quantity 2-D list of all coordinates with the appropriate distance unit attached. Has the format [ [x1, y1, z1], [x2, y2, z2], ... ] """ @staticmethod
[docs] def id_format(filename): """ Identifies the file type as a CHARMM coordinate file Parameters ---------- filename : str Name of the file to check format for Returns ------- is_fmt : bool True if it is a CHARMM coordinate file """ with closing(io.genopen(filename)) as f: line = f.readline() while line and len(line.strip()) == 0: # Skip whitespace line = f.readline() intitle = True while intitle: line = f.readline() if len(line.strip()) == 0: intitle = False elif line[0] != '*': intitle = False else: intitle = True while line and len(line.strip()) == 0: # Skip whitespace line = f.readline() try: natom = int(line.split()[0]) for row in range(min(natom, 3)): line = f.readline().split() int(line[0]) int(line[1]) float(line[4]) float(line[5]) float(line[6]) int(line[8]) float(line[9]) except (IndexError, ValueError): return False return True
[docs] def __init__(self, fname): self.atomno = [] # Atom number self.resno = [] # Residue number self.resname = [] # Residue name self.resid = [] # Residue ID self.atname = [] # Atom type self.coords = [] # 3N atomic coordinates self.title = [] # .crd file title block self.segid = [] # Segment ID self.weighting = [] # Atom weighting self.natom = 0 # Number of atoms specified in file self._parse(fname)
@property def positions(self): """ Atomic coordinates with units attached to them with the shape (natom, 3) """ return [Vec3(*xyz) for xyz in self.coordinates[0]] * u.angstroms @property def coordinates(self): return self.coords @property def box(self): return None def _parse(self, fname): with closing(io.genopen(fname, 'r')) as crdfile: line = crdfile.readline().strip() while len(line) == 0: # Skip whitespace, as a precaution line = crdfile.readline().strip() intitle = True while intitle: self.title.append(line) line = crdfile.readline().strip() if len(line) == 0: intitle = False elif line[0] != '*': intitle = False else: intitle = True while len(line) == 0: # Skip whitespace line = crdfile.readline().strip() try: self.natom = int(line.split()[0]) for row in range(self.natom): line = crdfile.readline().split() self.atomno.append(int(line[0])) self.resno.append(int(line[1])) self.resname.append(line[2]) self.atname.append(line[3]) self.coords.append(float(line[4])) self.coords.append(float(line[5])) self.coords.append(float(line[6])) self.segid.append(line[7]) self.resid.append(int(line[8])) self.weighting.append(float(line[9])) assert 3*self.natom == len(self.coords), '# atom mismatch' except (ValueError, IndexError): raise CharmmError('Error parsing CHARMM coordinate file') self.coords = np.array(self.coords).reshape((-1, self.natom, 3)) @staticmethod
[docs] def write(struct, dest): """ Writes a CHARMM coordinate file from a structure Parameters ---------- struct : :class:`parmed.structure.Structure` The input structure to write the CHARMM coordinate file from dest : str or file-like object The file name or file object to write the coordinate file to """ if isinstance(dest, string_types): dest = io.genopen(dest, 'w') own_handle = True else: own_handle = False dest.write('* GENERATED BY PARMED (HTTPS://GITHUB.COM/PARMED/PARMED)\n') dest.write('*\n') dest.write('%10d EXT\n' % len(struct.atoms)) add = 0 if struct.residues[0].number > 0 else 1-struct.residues[0].number for i, atom in enumerate(struct.atoms): res = atom.residue segid = res.segid.strip() or res.chain.strip() or 'SYS' dest.write('%10d%10d %-8s %-8s%20.10f%20.10f%20.10f %-8s ' '%-8s%20.10f\n' % (i+1, atom.residue.number+add, atom.residue.name, atom.name, atom.xx, atom.xy, atom.xz, segid, atom.residue.number, 0)) if own_handle: dest.close()
@add_metaclass(FileFormatType)
[docs]class CharmmRstFile(object): """ Reads and parses data, velocities and coordinates from a CHARMM restart file (.rst) of file name 'fname' into class attributes Parameters ---------- fname : str Name of the restart file to parse Attributes ---------- natom : int Number of atoms in the system resname : list of str Names of all residues in the system coordinates : np.ndarray shape(1, natom, 3) List of all coordinates in the format [x1, y1, z1, x2, y2, z2, ...] coordinatesold : np.ndarray shape(1, natom, 3) List of all old coordinates in the format [x1, y1, z1, x2, y2, z2, ...] velocities : np.ndarray shape(1, natom, 3) List of all velocities in the format [x1, y1, z1, x2, y2, z2, ...] positions : natom x 3 distance Quantity 2-D list of all coordinates with the appropriate distance unit attached. Has the format [ [x1, y1, z1], [x2, y2, z2], ... ] positionsold : natom x 3 distance Quantity 2-D list of all old coordinates with the appropriate distance unit attached. Has the format [ [x1, y1, z1], [x2, y2, z2], ... ] """ @staticmethod
[docs] def id_format(filename): """ Identifies the file type as a CHARMM restart file Parameters ---------- filename : str Name of the file to check format for Returns ------- is_fmt : bool True if it is a CHARMM restart file """ with closing(io.genopen(filename)) as f: line = f.readline() return line.startswith('REST')
[docs] def __init__(self, fname): self.header = [] self.title = [] self.enrgstat = [] self.coordsold = [] self.coords = [] self.vels = [] self.ff_version = 0 self.natom = 0 self.npriv = 0 self.nstep = 0 self.nsavc = 0 self.nsavv = 0 self.jhstrt = 0 self._parse(fname)
@property def coordinates(self): return self.coords @property def coordinatesold(self): return self.coordsold @property def positions(self): """ Atomic positions with units """ return [Vec3(*xyz) for xyz in self.coords[0]] * u.angstroms @property def positionsold(self): """ Old atomic positions with units """ return [Vec3(*xyz) for xyz in self.coordsold[0]] * u.angstroms @property def velocities(self): """ Atomic velocities in Angstroms/picoseconds """ return self.vels @property def box(self): return None def _parse(self, fname): with closing(io.genopen(fname, 'r')) as crdfile: readingHeader = True while readingHeader: line = crdfile.readline() if not len(line): raise CharmmError('Premature end of file') line = line.strip() words = line.split() if len(line) != 0: if words[0] == 'ENERGIES' or words[0] == '!ENERGIES': readingHeader = False else: self.header.append(line.strip()) else: self.header.append(line.strip()) for row in range(len(self.header)): if len(self.header[row].strip()) != 0: line = self.header[row].strip().split() if line[0][0:5] == 'NATOM' or line[0][0:6] == '!NATOM': try: line = self.header[row+1].strip().split() self.natom = int(line[0]) self.npriv = int(line[1]) # num. previous steps self.nstep = int(line[2]) # num. steps in file self.nsavc = int(line[3]) # coord save frequency self.nsavv = int(line[4]) # velocities " self.jhstrt = int(line[5]) # Num total steps? break except (ValueError, IndexError): raise CharmmError('Problem parsing CHARMM restart') self.scan(crdfile, '!XOLD') self._get_formatted_crds(crdfile, self.coordsold) self.coordsold = np.array(self.coordsold).reshape((-1,self.natom,3)) self.scan(crdfile, '!VX') self._get_formatted_crds(crdfile, self.vels) self.vels = np.array(self.vels).reshape((-1, self.natom, 3)) # Convert velocities to angstroms/ps self.vels *= ONE_TIMESCALE self.scan(crdfile, '!X') self._get_formatted_crds(crdfile, self.coords) self.coords = np.array(self.coords).reshape((-1, self.natom, 3))
[docs] def scan(self, handle, str, r=0): # read lines in file till 'str' is found scanning = True if(r): handle.seek(0) while scanning: line = handle.readline() if not line: raise CharmmError('Premature end of file') if len(line.strip()) != 0: if line.strip().split()[0][0:len(str)] == str: scanning = False
def _get_formatted_crds(self, crdfile, crds): for row in range(self.natom): line = crdfile.readline() if not line: raise CharmmError('Premature end of file') if len(line) < 3*CHARMLEN: raise CharmmError("Less than 3 coordinates present in " "coordinate row or coords may be " "truncated.") line = line.replace('D','E') # CHARMM uses 'D' for exponentials # CHARMM uses fixed format (len = CHARMLEN = 22) for crds in .rst's crds.append(float(line[0:CHARMLEN])) crds.append(float(line[CHARMLEN:2*CHARMLEN])) crds.append(float(line[2*CHARMLEN:3*CHARMLEN]))