split structures into new objects

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split structures into new objects

Stefan Henrich
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


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Re: split structures into new objects

Noel O'Boyle
Administrator
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 <[hidden email]> 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
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> OpenBabel-scripting mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting

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Re: split structures into new objects

Stefan Henrich
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 <[hidden email]> 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
>> [hidden email]
>> 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:[hidden email]
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


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Re: split structures into new objects

Noel O'Boyle
Administrator
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 <[hidden email]> 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 <[hidden email]> 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
>>> [hidden email]
>>> 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:[hidden email]
> 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
>

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