[MMTK] Using MMTK

khinsen at cea.fr khinsen at cea.fr
Wed Jul 20 19:25:14 CEST 2005


On 20.07.2005, at 17:55, Matias Saavedra wrote:

>>      if hasattr(residue.peptide, 'H_3'):
>> 	new_residue_type += '_nt'
>>      elif hasattr(residue.peptide, 'O_2'):
>> 	new_residue_type += '_ct'
> Why do you make those tests?

To take the termini into account. The suffixes _nt and _ct indicate the  
terminal forms of the amino acids.

>> 		    try:
>> 			a = atom_mapping[a]
>> 			ao = getattr(g_old, a)
>> 		    except KeyError:
>> 			pass
> Why do you make the test with atom_mapping?

Because otherwise the program would crash if it hits an atom for which  
it doesn't have a substitute position. You may prefer an exception to  
an error message, so feel free to change this.

Konrad.
--
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Konrad Hinsen
Laboratoire Leon Brillouin, CEA Saclay,
91191 Gif-sur-Yvette Cedex, France
Tel.: +33-1 69 08 79 25
Fax: +33-1 69 08 82 61
E-Mail: khinsen at cea.fr
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