[MMTK] itopically pure molecules

Jochen Küpper jochen@jochen-kuepper.de
29 Sep 2001 23:39:16 -0400


I want to do calculations using isotopically pure molecules. To do so
I defined new atoms for all the isotopes I need like
,----[o16]
| # -*- Python -*-
| 
| name = 'oxygen 16'
| symbol = 'O16'
| 
| mass = [(15.9949146221, 100.0)]
| 
| color = 'blue'
`----
and then define the molecules like
,----[h2o]
| # -*- Python -*-
| 
| name = 'H2O'
| 
| structure = \
|    "  O\n" + \
|    " / \\\n" + \
|    "H   H\n"
| 
| O  = Atom('O16')
| H1 = Atom('H1')
| H2 = Atom('H1')
| 
| bonds = [Bond(O, H1), Bond(O, H2), Bond(H1, H2)]
| 
| pdbmap = [('HOH', {'O': O, 'H1': H1, 'H2': H2})]
| pdb_alternative = {'OH2': 'O'}
| 
| configurations = {
|     'default': Cartesian({H1: (-0.0756950327264, 0., -0.0520320595151),
|                           H2: (0.0756950327264, 0., -0.0520320595151),
|                           O: (0., 0., 0.00655616814675)})
|     }
`----

Well, I am wondering whether this is the best way to do it,
esp. considering the manual stating that the symbol must be exactly
equal to the IUPAC symbol.

Is there a better way to do this?

Greetings,
Jochen
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