[Open Babel] How to split a protein into different OBMols each with one residue? (Was Breaking PDB files into separate molecules)

[Noel O'B. <bao...@gm...>]

Hello Kirk,

One possibility is to iterate over the atoms in the original residue,
and create a new atom as part of the new molecule where you set the
coordinates and atom numbers the same. I'm not sure whether you can
directly copy a residue from one molecule to another.

I've retitled this thread to summarise your question in the hope that
someone will know the answer to that question.

- Noel

P.S. It should be "newres = openbabel.OBResidue(res)" as "newres =
res" doesn't copy anything (unlike the C++ API). This still doesn't
solve your problem.

2009/8/6 Robert DeLisle <rkd...@gm...>:
> Geoff (et al),
>
> To clarify the issue a bit and provide an actual working (non-working)
> example, I've attached a very short Python script.  Essentially all that I'm
> doing is to open a PDB file (also attached), get the first residue, create a
> new molecule and copy the residue into the new molecule.  Ultimately I'd
> like to write out the molecule in SDF format, but I think that step is
> trivial.  Notice from the output of the print statements (noted in the code)
> I end up with a new molecule containing one residue but no atoms.  Where did
> the atoms go?  Have a failed an initialization or construction step?
>
> -Kirk DeLisle
>
>
>
> On Tue, Aug 4, 2009 at 5:20 PM, Geoffrey Hutchison
> <ge...@ge...> wrote:
>>
>> On Aug 4, 2009, at 6:44 PM, rkd...@gm... wrote:
>>
>>> Ultimately, I would like to get rid of all protein derived portions. This
>>> is simple with larger pieces (filter by molecular weight), but I've yet to
>>> come up with a way to filter smaller portions and particularly the multiple
>>> rotamers. I tried to interrogate any data objects attached to resulting
>>> molecules - I'm told that there are from 6 to 9 OBGenericData objects
>>> attached, however if I try to get a list of the keys for those data objects,
>>> I'm told that none exist.
>>
>> So if I understand, you want to keep only atoms / fragments which are
>> HETATM records?
>>
>> My suggestion is first to iterate through the residues. For each residue,
>> you can iterate through the atoms and query OBResidue::IsHetAtom:
>>
>> http://openbabel.org/api/2.2.0/classOpenBabel_1_1OBResidue.shtml#cbf3d5f13bc263f0957a70dedca072c8
>>
>> If it's not a HETATM record, mark the atom for deletion. After that, call
>> OBMol::Separate.
>>
>> Now, I use the C++ code directly, so I'm not sure about all of this in
>> Python. In particular, you'd want to save a pointer to the OBAtom in a list
>> and then delete everything in the list. Others can comment on whether that's
>> currently possible in Python.
>>
>> Hope that helps,
>> -Geoff
>
>
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