#!/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() + ">"