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#!/usr/bin/python
"""MMP and XYZ files share a common Atom definition. This will
make it easy to move information back and forth between the two
formats.
$Id$
"""
__author__ = "Will"
import re
import os
import sys
import string
import random
_PeriodicTable = [
"X", # our singlet has element number zero
"H", "He",
"Li", "Be", "B", "C", "N", "O", "F", "Ne",
"Na", "Mg", "Al", "Si", "P", "S", "Cl", "Ar",
"K", "Ca" #Sc,Ti,V,Cr,Mn,Fe....
]
_MmpAtomPattern = re.compile("^atom (\d+) \((\d+)\) " +
"\((\-?\d+), (\-?\d+), (\-?\d+)\)")
class NotAtomException(Exception):
pass
class Atom:
def fromMmp(self, line):
m = _MmpAtomPattern.match(line)
if m == None:
raise NotAtomException
groups = m.groups()
self.elem = elem = string.atoi(groups[1])
str = "atom %s" % groups[0]
str += " (%s)" % groups[1]
str += " (%d, %d, %d)"
str += line[m.span()[1]:] # anything after position
self._mmpstr = str
self.x = 0.001 * string.atoi(groups[2])
self.y = 0.001 * string.atoi(groups[3])
self.z = 0.001 * string.atoi(groups[4])
def clone(self):
"permit deep cloning of structure files"
a = Atom()
for key in self.__dict__.keys():
setattr(a, key, getattr(self, key))
return a
def fromXyz(self, element, x, y, z):
self.elem = _PeriodicTable.index(element)
self.x = x
self.y = y
self.z = z
def toMmpString(self):
return self._mmpstr % (int(self.x * 1000),
int(self.y * 1000),
int(self.z * 1000))
def toXyzString(self):
element = _PeriodicTable[self.elem]
return "%s %f %f %f" % (element, self.x, self.y, self.z)
def __repr__(self):
return "<" + self.toXyzString() + ">"
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