Menu
▾
▴
[OpenBabel-scripting] Using Fastsearch from Python
|
From: Noel O'B. <bao...@gm...> - 2008-05-22 15:50:06
|
---------- Forwarded message ----------
From: Nick England <nic...@gm...>
Date: 2008/5/22
Subject: Re: [OpenBabel-scripting] Python bindings in 2.1.1 missing "fs" format
To: Noel O'Boyle <bao...@gm...>
Noel,
I am trying to perform a substructure search on a large number of
molecules. I can do the SMARTS matching from python, but would need
the fast search ideally.
Would it be possible for me to write a C++ class to call the
OBConversion with input and output streams, and call that from a
Python script instead?
Calling the babel executable directly from Python is an option, but I
believe that has issues with portability?
- Nick
2008/5/22 Noel O'Boyle <bao...@gm...>:
> There's no way to do streams in Python. That's why we have this whole
> ReadFile, Read, business. Can you describe what the overall problem is
> that you're working on, and maybe some of the wise heads on this list
> can suggest some alternative solutions...
>
> Noel
>
> 2008/5/22 Nick England <nic...@gm...>:
>> Chris,
>>
>> Would it be possible to do something like
>>
>> infile=open("input.smi","r")
>> outfile=open("index.fs","w")
>> obconversion = openbabel.OBConversion(infile,outfile) (although these
>> need to be wrapped into streams somehow, SWIG has a function for
>> this?)
>> obconversion.Convert()
>>
>> I am trying to be able to make and search an index from calls from a
>> scripting environment.
>>
>> Thanks,
>>
>> Nick
>>
>>
>> 2008/5/21 Chris Morley <c.m...@ds...>:
>>> When fs is used as an output format it makes an index of the input file.
>>> This is a list of the fingerprint of each molecule in the input file
>>> and the number of bytes it is from the beginning of that file. It wasn't
>>> written to be used like you are doing it, so the failure is not
>>> surprising. There is an API of C++ classes for fastsearch but even with
>>> scripting I think it would be easier to use the conversion framework to
>>> make an index (if that is what you are trying to do). On the command
>>> line it would be
>>> babel input.smi index.fs
>>> which would index all the molecules in input.smi
>>> To use the index
>>> babel index.fs -osmi -s"CO"
>>> which would display all the molecules match the SMARTS.
>>>
>>> The SMARTS actually has to be a valid SMILES (a molecular fragment)
>>> because in the searching its fingerprint is calculated (to be compared
>>> with all the fingerprints in the input file).
>>>
>>> If you are doing a simple SMARTS filter
>>> babel input.smi -osmi -s"[#6]O"
>>> you can use a full SMARTS.
>>>
>>> Coming back to scripting, the fastsearch only has any point if you do it
>>> all in one go, i.e. scan the index using compiled code. Looping in a
>>> scripting language is too slow. This probably applies also when
>>> indexing a file. Both would be best done by calling the conversion
>>> framework. I'm afraid I haven't thought how to recover the result
>>> molecules one by one.
>>>
>>> It may be that your best approach is not to use fastsearch and use an
>>> ordinary SMARTS search instead. From the command line this is probably
>>> the best way anyway for fewer than 10,000 molecules.
>>>
>>> Chris
>>>
>>> When
>>> Noel O'Boyle wrote:
>>>> Sounds like a bug. Could you file one?
>>>>
>>>> I didn't realise that 'fs' was a proper format. I always thought it
>>>> was just some sort of index used to search a large SDF file, or
>>>> something.
>>>>
>>>> Noel
>>>>
>>>> 2008/5/21 Nick England <nic...@gm...>:
>>>>> Noel,
>>>>>
>>>>> The "obconversion.SetInFormat("fs")" returns true, and the input file
>>>>> is valid in that it was made on this computer and works fine on the
>>>>> command line babel (both under linux)
>>>>>
>>>>> However, trying to do:
>>>>>
>>>>> import pybel
>>>>> allmols=[mol for mol in pybel.readfile("smi","input.smi")]
>>>>> smarts=pybel.Smarts("[#6]O")
>>>>> for mol in allmols:
>>>>> if(smarts.findall(mol)):
>>>>> print mol.write("fs")
>>>>>
>>>>> results in the mesage
>>>>>
>>>>> "Not a valid output format"
>>>>>
>>>>>
>>>>> using the interpreter:
>>>>>>>> obconversion.SetInFormat("fs")
>>>>> True
>>>>>>>> obconversion.SetOutFormat("fs")
>>>>> True
>>>>>
>>>>> This problem cannot be due to a problem with the input files, since it
>>>>> won't even output a simple CCCO smiles string to the fs format. The
>>>>> obconversion seems to understant the format though.
>>>>>
>>>>>
>>>>> 2008/5/21 Noel O'Boyle <bao...@gm...>:
>>>>>> 2008/5/21 Nick England <nic...@gm...>:
>>>>>>> Hello all,
>>>>>>>
>>>>>>> I am experiencing some odd behavoir with the python bindings. A simple
>>>>>>> program to read in an index file:
>>>>>>>
>>>>>>> #! /usr/bin/env python
>>>>>>> import openbabel
>>>>>>> import pybel
>>>>>>> allmols=[]
>>>>>>> obconversion = openbabel.OBConversion()
>>>>>>> obconversion.SetInFormat("fs")
>>>>>>> obmol = openbabel.OBMol()
>>>>>>>
>>>>>>> notatend = obconversion.ReadFile(obmol,"index.fs")
>>>>>>>
>>>>>>> while notatend:
>>>>>>>
>>>>>>> allmols.append(obmol)
>>>>>>> obmol=openbabel.OBMol()
>>>>>>> notatend=obconversion.Read(obmol)
>>>>>>> pybel.Molecule(obmol).write("smi","results.smi",True)
>>>>>>>
>>>>>>> is failing with the message:
>>>>>>> "Not a valid input format"
>>>>>> What line is failing? Try "success = obconversion.SetInFormat("fs")"
>>>>>> and check its value.
>>>>>>
>>>>>> If the value is True, then the problem is not setting the format, but
>>>>>> rather reading the file. Is the inputfile valid? Is it from the same
>>>>>> operating system? If so, it sounds like a bug. Can you file one and
>>>>>> provide the input file (use a short example, if possible).
>>>>>>
>>>>>>> However typing babel -Hfs and obconversion.GetSupportedInputFormat()
>>>>>>> both list the fastsearch format as being present. The command babel
>>>>>>> -ifs index.fs -osmi works fine, and the python program above works if
>>>>>>> the format isn't fs.
>>>>>>> I would also like to add the line
>>>>>>> obconversion.AddOption('s',openbabel.OBConversion::GENOPTIONS,searchstring)
>>>>>>> (but this is throwing a syntax error on the OBCoversion::GENOPTIONS
>>>>>>> part, this is my first attempt at using python however so its not
>>>>>>> unexpected!)
>>>>>> Try using the interactive Python prompt:
>>>>>>>>> dir(openbabel.OBConversion())
>>>>>> ['ALL', 'AddChemObject', 'AddOption', 'CloseOutFile', 'Convert', 'CopyOptions',
>>>>>> ...
>>>>>> GENOPTIONS', 'GetAuxConv', 'GetChemObject', 'GetDefaultFormat', 'GetInFilename',
>>>>>> 'GetInFormat', 'GetInLen', 'GetInPos', 'GetInStream', 'GetOptionParams', 'GetOp
>>>>>> ...
>>>>>> 'thisown']
>>>>>>>>> openbabel.OBConversion.GENOPTIONS
>>>>>> 2
>>>>>>
>>>>>>> Any help would be appreciated!
>>>>>>>
>>>>>>> -------------------------------------------------------------------------
>>>>>>> This SF.net email is sponsored by: Microsoft
>>>>>>> Defy all challenges. Microsoft(R) Visual Studio 2008.
>>>>>>> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
>>>>>>> _______________________________________________
>>>>>>> OpenBabel-scripting mailing list
>>>>>>> Ope...@li...
>>>>>>> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>>>>>>>
>>>>
>>>> -------------------------------------------------------------------------
>>>> This SF.net email is sponsored by: Microsoft
>>>> Defy all challenges. Microsoft(R) Visual Studio 2008.
>>>> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
>>>> _______________________________________________
>>>> OpenBabel-scripting mailing list
>>>> Ope...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>>>>
>>>
>>>
>>> -------------------------------------------------------------------------
>>> This SF.net email is sponsored by: Microsoft
>>> Defy all challenges. Microsoft(R) Visual Studio 2008.
>>> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
>>> _______________________________________________
>>> OpenBabel-scripting mailing list
>>> Ope...@li...
>>> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>>>
>>
>> -------------------------------------------------------------------------
>> This SF.net email is sponsored by: Microsoft
>> Defy all challenges. Microsoft(R) Visual Studio 2008.
>> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
>> _______________________________________________
>> OpenBabel-scripting mailing list
>> Ope...@li...
>> https://lists.sourceforge.net/lists/listinfo/openbabel-scripting
>>
>
|
