[MMTK] Ignoring side chains

khinsen@cea.fr khinsen at cea.fr
Tue Jan 24 18:25:30 CET 2006


On Jan 24, 2006, at 14:14, Peter wrote:

> No, I'm "only" trying to parse 494 PDB files.
>
> I want to extract (just) the protein backbone psi/phi angles, but  
> I'm beginning to appreciate just how nasty some PDB files can be.

Indeed. It seems that the PDB/XML files are in better shape, even  
though they were probably machine-generated from the PDB files. For  
example, 1BTY.xml has alternate code 'C' instead of the empty one in  
Ser61. PDB/XML support is on my to-do list, though not yet quite ready.

> I understand that this something you may not want to add to MMTK/ 
> Scientific, but what I propose is adding the following methods in  
> Scientific/IO/PDB.py to do this, based on the existing  
> deleteHydrogens() method:

That looks a bit too specific for my taste... And a more general  
variant would be no more complex:

def deleteAllExcept(self, atom_names):
	...

to be called as

	conf.deleteAllExcept(['N','CA','C','O'])


> In addition, I would also make the following change so that we can  
> delete "duplicate entries" without causing a key error (see also my  
> email about 1BTY and deleteHydrogens):

I don't think that's a good approach to duplicate entries, because  
such entries should never exist. Within a residue, atom names should  
be unique. So I'd rather add code to raise an exception when a  
duplicate is being created.

Konrad.
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