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# -*- coding: utf-8 -*-
#
# Copyright (c) 2017, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""A reader for XYZ (Cartesian coordinate) files."""
from cclib.io import filereader
from cclib.parser.data import ccData
from cclib.parser.utils import PeriodicTable
class XYZ(filereader.Reader):
"""A reader for XYZ (Cartesian coordinate) files."""
def __init__(self, source, *args, **kwargs):
super(XYZ, self).__init__(source, *args, **kwargs)
self.pt = PeriodicTable()
def parse(self):
super(XYZ, self).parse()
self.generate_repr()
return self.data
def generate_repr(self):
"""Convert the raw contents of the source into the internal representation."""
assert hasattr(self, 'filecontents')
it = iter(self.filecontents.splitlines())
# Ordering of lines:
# 1. number of atoms
# 2. comment line
# 3. line of at least 4 columns: 1 is atomic symbol (str), 2-4 are atomic coordinates (float)
# repeat for numver of atoms
# (4. optional blank line)
# repeat for multiple sets of coordinates
all_atomcoords = []
comments = []
while True:
try:
line = next(it)
if line.strip() == '':
line = next(it)
tokens = line.split()
assert len(tokens) >= 1
natom = int(tokens[0])
comments.append(next(it))
lines = []
for _ in range(natom):
line = next(it)
tokens = line.split()
assert len(tokens) >= 4
lines.append(tokens)
assert len(lines) == natom
atomsyms = [line[0] for line in lines]
atomnos = [self.pt.number[atomsym] for atomsym in atomsyms]
atomcoords = [line[1:4] for line in lines]
# Everything beyond the fourth column is ignored.
all_atomcoords.append(atomcoords)
except StopIteration:
break
attributes = {
'natom': natom,
'atomnos': atomnos,
'atomcoords': all_atomcoords,
'metadata': {"comments": comments},
}
self.data = ccData(attributes)
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