Definition problem

[Andy Gimblett]

OK, forgot to attach the file...  Sorry!  :-)

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#!/usr/bin/env python

from MMTK import *
from MMTK import Bonds

class MyMolecule(Molecule):
    
    def __init__(self, name, atoms, bonds):
        
        self.atoms = []
        self.bonds = []
        self.groups = []
        self.name = name
        
        for element, position in atoms:
            self.atoms.append(Atom(element, position = position))
            
        for i1, i2 in bonds:
            self.bonds.append(Bonds.Bond((self.atoms[i1], self.atoms[i2])))

        self.bonds = Bonds.BondList(self.bonds)
        self.parent = None # top-level object
        self.type = None # no database type

h2 = MyMolecule('h2', [('h', Vector(0., 0., -0.05)),
                       ('h', Vector(0.,0., 0.05))], [(0, 1)])

h2.writeToFile('test.pdb')