Hi, on reading the spectrophore docs linked to below, I see that they
employ the EEM method to generate partial charges. Out of curiosity,
how do these compare with say Gasteiger charges? Is there a way I can
generate EEM charges via the OB API? I did a quick Java implementation
and the results weren't too encouraging, so I was hoping to check
another implementation
On Thu, Nov 11, 2010 at 9:34 AM, Noel O'Boyle <baoille...@gmail.com> wrote:
> Hi Florian,
>
> Good to meet you at Goslar.
>
> You can access the spectrophore from Python as follows:
>
>>>> import pybel
>>>> spectromaker = pybel.ob.OBSpectrophore()
>>>> mol = pybel.readstring("smi", "CCC(=O)Cl")
>>>> mol.make3D()
>>>> myspec = spectromaker.GetSpectrophore(mol.OBMol)
>>>> print myspec
> (1.9188820873264936, 1.3779850156141404, 1.6545133998665147,
> 4.223289590168287,
> 7.0393209939670101, 6.9526389819350349, 5.0181681207236251,
> 5.1643466127719195,
> 5.59340805409634, 8.345298919520646, 9.7302501926297307, 5.420193132509139,
> 2.65
> 89584250555993, 4.2305867338533503, 5.2040184695128362, 7.3529734782986313,
> 8.43
> 16917599250072, 10.56621427956005, 5.5603086090040872, 9.0161014657760621,
> 10.21
> 3590898162922, 10.556235776440086, 12.699924307275969, 8.3723611206701829,
> 6.555
> 0897240361765, 12.196124593591096, 11.149397464069917, 25.575659087717039,
> 29.86
> 9553579053754, 33.025183660115289, 23.489782781676645, 16.246285821014279,
> 26.17
> 6007787036561, 36.740589304516156, 43.705358401245142, 28.046290240485249,
> 0.547
> 30055623006191, 0.89174725011169631, 2.1830656346397137, 2.194336074284025,
> 0.99
> 119077568489211, 1.2875748624433234, 0.76040377919922997, 2.4829098627372299,
> 2.
> 3394221112921088, 1.4695456992744806, 1.5850520074712673, 2.0654417047802762)
>>>>
>
> For information on what all of these numbers are, see the API documentation
> at:
> http://openbabel.org/api/2.3/classOpenBabel_1_1OBSpectrophore.shtml
>
> With this, you should be able to iterate over all of the molecules in
> a file, and calculate the spectrophore for each.
>
> - Noel
>
> On 10 November 2010 10:23, Florian Kölling <florian.koell...@tu-bs.de> wrote:
>> Hi Folks,
>>
>> I wanted to start working with the new OB Spectrophore Class (ideally
>> using python).
>> Currently, I'm doing so using an os.system call:
>>
>> obspectrophore = "/usr/local/bin/obspectrophore"
>> template_call = "obspectrophore +' -i 1eve_ligand.mol > template.txt"
>> os.system(template_call)
>>
>> My Questions:
>> 1) Is there a more convenient way to get an output file than the
>> '>template.txt' option?
>>
>> 2) How can I handle (large) multi conformational sdf files? Just doing
>> the same way as mentioned above? I tried but stopped after quite a long
>> time (inefficient?!) -- Can I read in the sdf file via pybel and iterate
>> over every molecule separately and create the spectrophores?
>>
>> Thanks and best regards,
>>
>> flo
>>
>> --
>> --------------------------------------
>> Florian Koelling
>> Institut fuer Pharmazeutische Chemie
>> AK Baumann - Molecular Modelling Group
>> Technische Universitaet Braunschweig
>> Beethovenstrasse 55
>> D-38106 Braunschweig
>> Tel.: ++49 531 391-8451
>> florian.koell...@tu-braunschweig.de
>> --------------------------------------
>>
>>
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--
Rajarshi Guha
NIH Chemical Genomics Center
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