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#!/usr/bin/python
"""A common Atom definition to be shared by the classes for various
molecule file formats including MMP and XYZ. This will make it easy to
move information back and forth between 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])
self.bonds = [ ]
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 mmpBonds(self, line):
if line.startswith("bond"):
for b in line.split()[1:]:
self.bonds.append(string.atoi(b))
return True
return False
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() + ">"
class FileLineIterator:
def __init__(self, lines):
self.lines = lines
self.pointer = 0
def next(self):
pointer = self.pointer
lines = self.lines
if pointer >= len(lines):
raise StopIteration
self.pointer = pointer + 1
return lines[pointer]
def backup(self):
pointer = self.pointer
if pointer <= 0:
raise Exception, "can't back up"
self.pointer = pointer - 1
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