#!/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 raw XYZ file format.
Raw XYZ is a 3 or 4 column text file with cartesian coordinates
of atoms and an optional first column for atom types.
"""
import sys
from diffpy.structure import Structure
from diffpy.structure.parsers import StructureParser
from diffpy.structure.structureerrors import StructureFormatError
from diffpy.structure.utils import isfloat
[docs]
class P_rawxyz(StructureParser):
"""Parser --> StructureParser subclass for RAWXYZ format.
Attributes
----------
format : str
Format name, default "rawxyz".
"""
def __init__(self):
StructureParser.__init__(self)
self.format = "rawxyz"
return
[docs]
def parseLines(self, lines):
"""Parse list of lines in RAWXYZ format.
Parameters
----------
lines : list of str
List of lines in RAWXYZ format.
Returns
-------
Structure
Parsed structure instance.
Raises
------
StructureFormatError
Invalid RAWXYZ 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
# 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 start >= stop:
return stru
# here we have at least one valid record line
# figure out xyz layout from the first line for plain and raw formats
floatfields = [isfloat(f) for f in linefields[start]]
nfields = len(linefields[start])
if nfields not in (3, 4):
emsg = "%d: invalid RAWXYZ format, expected 3 or 4 columns" % (start + 1)
raise StructureFormatError(emsg)
if floatfields[:3] == [True, True, True]:
el_idx, x_idx = (None, 0)
elif floatfields[:4] == [False, True, True, True]:
el_idx, x_idx = (0, 1)
else:
emsg = "%d: invalid RAWXYZ format" % (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 = el_idx is not None and fields[el_idx] or ""
xyz = [float(f) for f in fields[x_idx : x_idx + 3]]
if len(xyz) == 2:
xyz.append(0.0)
stru.addNewAtom(element, xyz=xyz)
except ValueError:
emsg = "%d: invalid number" % p_nl
exc_type, exc_value, exc_traceback = sys.exc_info()
e = StructureFormatError(emsg)
raise e.with_traceback(exc_traceback)
return stru
[docs]
def toLines(self, stru):
"""Convert Structure stru to a list of lines in RAWXYZ format.
Parameters
----------
stru : Structure
Structure to be converted.
Returns
-------
list of str
List of lines in RAWXYZ format.
"""
lines = []
for a in stru:
rc = a.xyz_cartn
s = "%s %g %g %g" % (a.element, rc[0], rc[1], rc[2])
lines.append(s.lstrip())
return lines
# End of class P_rawxyz
# Routines -------------------------------------------------------------------
[docs]
def getParser():
"""Return new `parser` object for RAWXYZ format.
Returns
-------
P_rawxyz
Instance of `P_rawxyz`.
"""
return P_rawxyz()