Re: [OpenBabel-scripting] split structures into new objects

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

I've filed a bug at https://sourceforge.net/p/openbabel/bugs/847/. It
should be fairly easy to copy the residue info to the separated
molecules; I've just done this for stereo info.

Please note for future reference that openbabel-scripting is obsolete.
Please send emails to openbabel-discuss instead.

- Noel

On 8 November 2012 12:37, Stefan Henrich <ste...@h-...> wrote:
> Hi Noel,
>
> Thank you for the fast answer. Actually, OBMol can be split into separated
> OBMol objects but the order of residues of a protein will be mixed up at
> least if unknown residue names are present or the protein is disconnected.
> Furthermore, for ligands the residue name, residue numbering and the atom
> names will not be copied to the new OBMol object. It seems that 'Separate'
> just copy atoms from one OBMol to a new ones.
>
> Best,
> Stefan
>
>
>
>
> On 11/07/2012 04:16 PM, Noel O'Boyle wrote:
>>
>> Does OBMol::Separate work for this? See the API at
>>
>> http://openbabel.org/api/2.3/classOpenBabel_1_1OBMol.shtml#a1e5c6955a32c0ec2317a8de12ab7ba5a
>>
>> - Noel
>>
>> On 7 November 2012 13:53, Stefan Henrich <ste...@h-...> wrote:
>>>
>>> Hi OpenBabel users,
>>>
>>> Is there an easy way to read a complex structure as a molecule using
>>> openbabel (python-API) and to split it afterwards into different
>>> molecules (e.g., protein, ligand, cofactor,...) to handle/write it as
>>> different objects? Here, it would be helpful not loosing information
>>> like residue names what happens if you just copy atoms to a new molecule
>>> object.
>>> Thank you for your help!
>>>
>>> Best,
>>> Stefan
>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> LogMeIn Central: Instant, anywhere, Remote PC access and management.
>>> Stay in control, update software, and manage PCs from one command center
>>> Diagnose problems and improve visibility into emerging IT issues
>>> Automate, monitor and manage. Do more in less time with Central
>>> http://p.sf.net/sfu/logmein12331_d2d
>>> _______________________________________________
>>> OpenBabel-scripting mailing list
>>> Ope...@li...
>>> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>
>
> --
> Dr. Stefan Henrich
> Research Associate
>
> HITS gGmbH Schloss-Wolfsbrunnenweg 35
> 69118 Heidelberg
> Germany
>
> phone: +49 6221 533 223
> fax:   +49 6221 533 298
> email:Ste...@h-...
> http://www.h-its.org
>
> Amtsgericht Mannheim / HRB 337446
> Managing Directors:
> Dr. h. c. Dr.-Ing. E. h. Klaus Tschira
> Prof. Dr.-Ing. Andreas Reuter
>