/usr/share/pyshared/ase/io/pdb.py is in python-ase 3.6.0.2515-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 | import numpy as np
from ase.atoms import Atom, Atoms
from ase.parallel import paropen
"""Module to read and write atoms in PDB file format"""
def read_pdb(fileobj, index=-1):
"""Read PDB files.
The format is assumed to follow the description given in
http://www.wwpdb.org/documentation/format32/sect9.html."""
if isinstance(fileobj, str):
fileobj = open(fileobj)
images = []
atoms = Atoms()
for line in fileobj.readlines():
if line.startswith('ATOM') or line.startswith('HETATM'):
try:
# Atom name is arbitrary and does not necessarily contain the element symbol.
# The specification requires the element symbol to be in columns 77+78.
symbol = line[76:78].strip().lower().capitalize()
words = line[30:55].split()
position = np.array([float(words[0]),
float(words[1]),
float(words[2])])
atoms.append(Atom(symbol, position))
except:
pass
if line.startswith('ENDMDL'):
images.append(atoms)
atoms = Atoms()
if len(images) == 0:
images.append(atoms)
return images[index]
def write_pdb(fileobj, images):
"""Write images to PDB-file.
The format is assumed to follow the description given in
http://www.wwpdb.org/documentation/format32/sect9.html."""
if isinstance(fileobj, str):
fileobj = paropen(fileobj, 'w')
if not isinstance(images, (list, tuple)):
images = [images]
if images[0].get_pbc().any():
from ase.lattice.spacegroup.cell import cell_to_cellpar
cellpar = cell_to_cellpar( images[0].get_cell())
# ignoring Z-value, using P1 since we have all atoms defined explicitly
format = 'CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f P 1\n'
fileobj.write(format % (cellpar[0], cellpar[1], cellpar[2], cellpar[3], cellpar[4], cellpar[5]))
# 1234567 123 6789012345678901 89 67 456789012345678901234567 890
format = 'ATOM %5d %4s MOL 1 %8.3f%8.3f%8.3f 1.00 0.00 %2s \n'
# RasMol complains if the atom index exceeds 100000. There might
# be a limit of 5 digit numbers in this field.
MAXNUM = 100000
symbols = images[0].get_chemical_symbols()
natoms = len(symbols)
for n,atoms in enumerate(images):
fileobj.write('MODEL '+str(n+1)+'\n')
p = atoms.get_positions()
for a in range(natoms):
x, y, z = p[a]
fileobj.write(format % (a % MAXNUM, symbols[a], x, y, z, symbols[a].rjust(2)))
fileobj.write('ENDMDL\n')
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