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#!/usr/bin/python
import sys
import string
import Atom
class XyzFile:
"""Python class to contain information from an XYZ file"""
def __init__(self):
self.atoms = [ ]
def clone(self):
other = XyzFile()
other.atoms = [ ]
for a in self.atoms:
other.atoms.append(a.clone())
return other
def getAtom(self, i):
return self.atoms[i]
def __getitem__(self, i):
a = self.atoms[i]
return (a.x, a.y, a.z)
def __setitem__(self, i, xyz):
a = self.atoms[i]
a.x, a.y, a.z = xyz
def __len__(self):
return len(self.atoms)
def read(self, filename):
inf = open(filename)
self.readstring(inf.read())
inf.close()
def readstring(self, lines):
lines = lines.split("\n")
numAtoms = string.atoi(lines[0])
lines = lines[2:]
for i in range(numAtoms):
element, x, y, z = lines[i].split()
x, y, z = map(string.atof, (x, y, z))
a = Atom.Atom()
a.fromXyz(element, x, y, z)
self.atoms.append(a)
def write(self, title, outf=None):
if outf == None:
outf = sys.stdout
outf.write("%d\n%s\n" % (len(self.atoms), title))
for atm in self.atoms:
outf.write(atm.toXyzString() + "\n")
if __name__ == "__main__":
# do a little test
class StringCollector:
def __init__(self):
self.contents = ""
def write(self, x):
self.contents += x
import sys
example_xyz_file = """15
RMS=0.994508
C -0.193641 2.900593 -0.026523
X 0.093601 3.502437 0.394872
X -0.623522 3.154064 -0.637458
C -1.079249 2.005273 0.890906
X -1.803795 1.958430 0.584626
X -1.090331 2.310792 1.617200
C 0.986482 2.029986 -0.552402
X 0.945121 1.985940 -1.338110
X 1.667645 2.347089 -0.314849
C -0.443634 0.583852 0.936816
X -0.955793 0.061908 0.643109
X -0.248030 0.411844 1.680547
C 0.839719 0.603152 0.054672
X 1.466374 0.446893 0.504740
X 0.762053 0.079748 -0.528147
"""
xyz = XyzFile()
xyz.readstring(example_xyz_file)
# test 1
sc = StringCollector()
ss, sys.stdout = sys.stdout, sc
xyz.write("RMS=0.994508")
sys.stdout = ss
assert sc.contents == example_xyz_file
# test 2
for i in range(len(xyz)):
print xyz.getAtom(i)
print
for i in range(8):
xyz[i] = (1.0, 2.0, 3.0)
for i in range(len(xyz)):
print xyz.getAtom(i)
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