#!/usr/bin/env python
##############################################################################
#
# diffpy.structure by DANSE Diffraction group
# Simon J. L. Billinge
# (c) 2007 trustees of the Michigan State University.
# All rights reserved.
#
# File coded by: Pavol Juhas
#
# See AUTHORS.txt for a list of people who contributed.
# See LICENSE_DANSE.txt for license information.
#
##############################################################################
"""Parser for XYZ file format, where.
* First line gives number of atoms.
* Second line has optional title.
* Remaining lines contain element, `x, y, z`.
"""
import sys
from diffpy.structure import Structure
from diffpy.structure.parsers import StructureParser
from diffpy.structure.structureerrors import StructureFormatError
from diffpy.utils._deprecator import build_deprecation_message, deprecated
base = "diffpy.structure.P_xyz"
removal_version = "4.0.0"
parseLines_deprecation_msg = build_deprecation_message(
base,
"parseLines",
"parse_lines",
removal_version,
)
toLines_deprecation_msg = build_deprecation_message(
base,
"toLines",
"to_lines",
removal_version,
)
[docs]
class P_xyz(StructureParser):
"""Parser for standard XYZ structure format.
Attributes
----------
format : str
Format name, default "xyz".
"""
def __init__(self):
StructureParser.__init__(self)
self.format = "xyz"
return
@deprecated(parseLines_deprecation_msg)
def parseLines(self, lines):
"""This function has been deprecated and will be removed in
version 4.0.0.
Please use diffpy.structure.P_xyz.parse_lines instead.
"""
return self.parse_lines(lines)
[docs]
def parse_lines(self, lines):
"""Parse list of lines in XYZ format.
Parameters
----------
lines : list of str
List of lines in XYZ format.
Returns
-------
Structure
Parsed structure instance.
Raises
------
StructureFormatError
Invalid XYZ format.
"""
linefields = [line.split() for line in lines]
# prepare output structure
stru = Structure()
# find first valid record
start = 0
for field in linefields:
if len(field) == 0 or field[0] == "#":
start += 1
else:
break
# first valid line gives number of atoms
try:
lfs = linefields[start]
w1 = linefields[start][0]
if len(lfs) == 1 and str(int(w1)) == w1:
p_natoms = int(w1)
stru.title = lines[start + 1].strip()
start += 2
else:
emsg = "%d: invalid XYZ format, missing number of atoms" % (start + 1)
raise StructureFormatError(emsg)
except (IndexError, ValueError):
exc_type, exc_value, exc_traceback = sys.exc_info()
emsg = "%d: invalid XYZ format, missing number of atoms" % (start + 1)
e = StructureFormatError(emsg)
raise e.with_traceback(exc_traceback)
# find the last valid record
stop = len(lines)
while stop > start and len(linefields[stop - 1]) == 0:
stop -= 1
# get out for empty structure
if p_natoms == 0 or start >= stop:
return stru
# here we have at least one valid record line
nfields = len(linefields[start])
if nfields != 4:
emsg = "%d: invalid XYZ format, expected 4 columns" % (start + 1)
raise StructureFormatError(emsg)
# now try to read all record lines
try:
p_nl = start
for fields in linefields[start:]:
p_nl += 1
if fields == []:
continue
elif len(fields) != nfields:
emsg = ("%d: all lines must have " + "the same number of columns") % p_nl
raise StructureFormatError(emsg)
element = fields[0]
element = element[0].upper() + element[1:].lower()
xyz = [float(f) for f in fields[1:4]]
stru.add_new_atom(element, xyz=xyz)
except ValueError:
exc_type, exc_value, exc_traceback = sys.exc_info()
emsg = "%d: invalid number format" % p_nl
e = StructureFormatError(emsg)
raise e.with_traceback(exc_traceback)
# finally check if all the atoms have been read
if p_natoms is not None and len(stru) != p_natoms:
emsg = "expected %d atoms, read %d" % (p_natoms, len(stru))
raise StructureFormatError(emsg)
return stru
@deprecated(toLines_deprecation_msg)
def toLines(self, stru):
"""This function has been deprecated and will be removed in
version 4.0.0.
Please use diffpy.structure.P_xyz.to_lines instead.
"""
return self.to_lines(stru)
[docs]
def to_lines(self, stru):
"""Convert Structure stru to a list of lines in XYZ format.
Parameters
----------
stru : Structure
Structure to be converted.
Returns
-------
list of str
List of lines in XYZ format.
"""
lines = []
lines.append(str(len(stru)))
lines.append(stru.title)
for a in stru:
rc = a.xyz_cartn
s = "%-3s %g %g %g" % (a.element, rc[0], rc[1], rc[2])
lines.append(s)
return lines
# End of class P_xyz
# Routines -------------------------------------------------------------------
parsers_base = "diffpy.structure"
getParser_deprecation_msg = build_deprecation_message(
parsers_base,
"getParser",
"get_parser",
removal_version,
)
@deprecated(getParser_deprecation_msg)
def getParser():
"""This function has been deprecated and will be removed in version
4.0.0.
Please use diffpy.structure.P_xyz.get_parser instead.
"""
return get_parser()
[docs]
def get_parser():
"""Return new `parser` object for XYZ format.
Returns
-------
P_xcfg
Instance of `P_xyz`.
"""
return P_xyz()