[chimera-dev] gaussian interface: getting nuts with connectivity
Eric Pettersen
pett at cgl.ucsf.edu
Fri Jul 17 10:43:21 PDT 2009
Hi JD,
I don't think you attached the right file. The file you attached is
just a Mol2 file. Nonetheless, from the format description you
provided I think you just want to loop through Molecule.atoms and then
for each atom its bondsMap in order to write your file. The major
stumbling block is that Chimera doesn't compute bond orders. The mol2
module guesstimates them using a few heuristics, but could certainly
get them wrong in complex situations. You could just conscript the
half page of code that does the estimation into your own module if you
felt that it was "good enough". Otherwise you're going to have to
write some code to generate bond orders consistent with the atoms'
types. If the systems you work with aren't too large that would be
feasible (though non-trivial) but for large systems would likely be
slow unless you coded it in a compiled language (urg!).
At any rate, assuming that you've obtained bond orders for bonds
somehow, the template for writing the format you need would be:
# may need to fetch m.atoms and sort it into Gaussian order
# instead of using m.atoms directly...
for a in m.atoms:
# 'identifer' dictionary maps atoms to Gaussian name
print>>outf, identifer[a],
for nb, b in a.bondsMap.items():
print>>outf, identifier[nb], order[b],
print>>outf
On Jul 17, 2009, at 8:01 AM, Jean Didier Pie Marechal wrote:
> Dear all,
>
> I am trying to make chimera an interface for the quantum mechanical
> program gaussian.
> Pretty much everything seems to go smooth but I am getting crazy
> (stupid?) because I can't reproduce the geometry connectivity
> gaussian wants. I used tools of chimera I know for bond mapping and
> connectivity. But I can't get to the right connectivity format.
>
> I join you here an input file of gaussian (a ARG-ALA dipeptide). If
> you look at the file, the connectivity between the atoms is at the
> end and is in the following form:
>
> atom 1, atom 2, bond_order, atoms 3, bond_order (etc for all atoms
> linked to atom 1)
> ...
>
>
> atom 31 (to 37 = all terminal atoms).
>
> I have been using the different atoms attributes I know like
> neighbors, bonds and bondMap, but I can't see how to proceed neither
> I see how to use the bond order calculations as in the mol2 module.
> If you have time and can give me a hint, I would be extremely greatful
>
> Thank you very much,
>
> best
> JD
>
>
> Dr. Jean-Didier Maréchal
> Lecturer
> Computational Biotechnological Chemistry @ Transmet
> Unitat de Química Física
> Departament de Química
> Universitat Autònoma de Barcelona
> Edifici C.n.
> 08193 Cerdanyola (Barcelona)
> Tel: +34.935814936
> e-mail: JeanDidier.Marechal at uab.es
>
> ----- Missatge original -----
> De: chimera-dev-request at cgl.ucsf.edu
> Data: Dijous, Juliol 9, 2009 9:00 pm
> Assumpte: Chimera-dev Digest, Vol 66, Issue 2
>
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>> Today's Topics:
>>
>> 1. Generating images in chimera with the --nogui option (Davide
>> Ba?) 2. Re: Generating images in chimera with the --nogui option
>> (Greg Couch)
>>
>>
>> --------------------------------------------------------------------
>> --
>>
>> Message: 1
>> Date: Thu, 9 Jul 2009 17:32:22 +0200
>> From: Davide Ba? <dbau at cipf.es>
>> Subject: [chimera-dev] Generating images in chimera with the --nogui
>> option
>> To: chimera-dev at cgl.ucsf.edu
>> Message-ID:
>> <3e4b67ca0907090832r4e46b826i5dfe81842b58685a at mail.gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Hi,
>>
>> my name is Davide and I'm currently working on Marc Marti-Renom's
>> group.
>> I'm trying to generate an image using chimera with the --nogui
>> option:
>>
>> chimera --nogui --nostatus --script cmd.py
>>
>>
>> The file cmd.py contains the following lines:
>>
>> from chimera import runCommand
>>> runCommand('open input.cmm')
>>> runCommand('copy file image.png png')
>>
>>
>> but I keep getting the following error message:
>>
>> Traceback (most recent call last):
>>> File "/usr/src/chimera/share/__main__.py", line 65, in <module>
>>> value = chimeraInit.init(sys.argv)
>>> File "CHIMERA/share/chimeraInit.py", line 384, in init
>>> chimera.openModels.open(a, prefixableType=1)
>>> File "CHIMERA/share/chimera/__init__.py", line 1344, in open
>>> File "CHIMERA/share/chimera/__init__.py", line 787, in _openPython
>>> File "cmd.py", line 3, in <module>
>>> runCommand('copy file image.png png')
>>> File "CHIMERA/share/chimera/__init__.py", line 2025, in runCommand
>>> File "CHIMERA/share/Midas/midas_text.py", line 62, in makeCommand
>>> File "CHIMERA/share/Midas/midas_text.py", line 563, in doCopy
>>> File "<string>", line 1, in <module>
>>> File "CHIMERA/share/Midas/__init__.py", line 908, in copy
>>> File "CHIMERA/share/chimera/printer.py", line 1182, in saveImage
>>> AttributeError: '_chimera.NoGuiViewer' object has no attribute
>> 'pilImages'> Error while processing cmd.py:
>>> AttributeError: '_chimera.NoGuiViewer' object has no attribute
>> 'pilImages'>
>> (see reply log for Python traceback info)
>>>
>>
>> cmd.py was generated from within chimera using the "record" command
>> of
>> chimera's "command line".
>> If I delete the line "runCommand('copy file image.png png')", the
>> scriptexecute with no error.
>>
>> Is it possible to generate images using the --nogui option?
>>
>> Thanks a lot for your help!
>>
>> Best regards,
>> Davide
>>
>> ____________
>> *Davide Ba?*
>> Structural Genomics Unit
>> Bioinformatics & Genomics Department, Prince Felipe Research Center
>> Avda. Autopista del Saler, 16 , 46012 Valencia, Spain
>> Tel: +34 96 328 96 80 (ext. 1021) Fax: +34 96 328 97 01
>> Email: *dbau at cipf.es*
>> Web: *http://sgu.bioinfo.cipf.es/dbau*
>> -------------- next part --------------
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>>
>> ------------------------------
>>
>> Message: 2
>> Date: Thu, 9 Jul 2009 10:04:53 -0700 (PDT)
>> From: Greg Couch <gregc at cgl.ucsf.edu>
>> Subject: Re: [chimera-dev] Generating images in chimera with the
>> --nogui option
>> To: Davide Ba? <dbau at cipf.es>
>> Cc: chimera-dev at cgl.ucsf.edu
>> Message-ID: <Pine.OSF.
>> 4.63.0907090956280.1975366 at guanine.cgl.ucsf.edu>
>> Content-Type: text/plain; charset="x-unknown"
>>
>> To generate chimera images with --nogui, you need to use a Headless
>> chimera. Currently, they are only available as chimera daily
>> builds and
>> only for Linux and Linux 64-bit.
>>
>> - Greg
>>
>> On Thu, 9 Jul 2009, Davide Ba?? wrote:
>>
>>> Hi,
>>>
>>> my name is Davide and I'm currently working on Marc Marti-Renom's
>> group.>
>>> I'm trying to generate an image using chimera with the --nogui
>> option:>
>>> chimera --nogui --nostatus --script cmd.py
>>>
>>>
>>> The file cmd.py contains the following lines:
>>>
>>> from chimera import runCommand
>>>> runCommand('open input.cmm')
>>>> runCommand('copy file image.png png')
>>>
>>>
>>> but I keep getting the following error message:
>>>
>>> Traceback (most recent call last):
>>>> File "/usr/src/chimera/share/__main__.py", line 65, in <module>
>>>> value = chimeraInit.init(sys.argv)
>>>> File "CHIMERA/share/chimeraInit.py", line 384, in init
>>>> chimera.openModels.open(a, prefixableType=1)
>>>> File "CHIMERA/share/chimera/__init__.py", line 1344, in open
>>>> File "CHIMERA/share/chimera/__init__.py", line 787, in
>> _openPython>> File "cmd.py", line 3, in <module>
>>>> runCommand('copy file image.png png')
>>>> File "CHIMERA/share/chimera/__init__.py", line 2025, in
>> runCommand>> File "CHIMERA/share/Midas/midas_text.py", line 62,
>> in makeCommand
>>>> File "CHIMERA/share/Midas/midas_text.py", line 563, in doCopy
>>>> File "<string>", line 1, in <module>
>>>> File "CHIMERA/share/Midas/__init__.py", line 908, in copy
>>>> File "CHIMERA/share/chimera/printer.py", line 1182, in saveImage
>>>> AttributeError: '_chimera.NoGuiViewer' object has no attribute
>> 'pilImages'>> Error while processing cmd.py:
>>>> AttributeError: '_chimera.NoGuiViewer' object has no attribute
>> 'pilImages'>>
>>> (see reply log for Python traceback info)
>>>>
>>>
>>> cmd.py was generated from within chimera using the "record"
>> command of
>>> chimera's "command line".
>>> If I delete the line "runCommand('copy file image.png png')",
>> the script
>>> execute with no error.
>>>
>>> Is it possible to generate images using the --nogui option?
>>>
>>> Thanks a lot for your help!
>>>
>>> Best regards,
>>> Davide
>>>
>>> ____________
>>> *Davide Ba??*
>>> Structural Genomics Unit
>>> Bioinformatics & Genomics Department, Prince Felipe Research Center
>>> Avda. Autopista del Saler, 16 , 46012 Valencia, Spain
>>> Tel: +34 96 328 96 80 (ext. 1021) Fax: +34 96 328 97 01
>>> Email: *dbau at cipf.es*
>>> Web: *http://sgu.bioinfo.cipf.es/dbau*
>>>
>>
>> ------------------------------
>>
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>> End of Chimera-dev Digest, Vol 66, Issue 2
>> ******************************************
>>
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>
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