Re: [OpenBabel-scripting] Using fastsearch from Python

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

See http://openbabel.org/wiki/Install_%28source_code%29:
"""
If you are compiling directly from the Subversion repository, then you
need to create the Python/Perl bindings yourself. To do so, you need
to install the latest version of SWIG and to run configure as
"configure --enable-maintainer-mode"
"""

It should work then,

Noel

2008/5/27 Nick England <nic...@gm...>:
> Thanks Chris,
>
> When testing this new SVN version, I get the following error when
> trying to build the python bindings with
>
> python setup.py build
>
> file openbabel.py (for module openbabel) not found
> file openbabel.py (for module openbabel) not found
> running build_ext
> building '_openbabel' extension
> gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall
> -Wstrict-prototypes -fPIC -I../../include
> -I/home/nwe23/bin/include/python2.5 -c openbabel_python.cpp -o
> build/temp.linux-x86_64-2.5/openbabel_python.o
> gcc: openbabel_python.cpp: No such file or directory
> gcc: no input files
> error: command 'gcc' failed with exit status 1
>
> openbabel.py
> openbabel_python.cpp
>
> are missing from the /scripts/python dir in the SVN repository, but
> are listed in the MANIFEST file.
>
> Do these need to be built from SWIG or something?
>
> - Nick
>
> 2008/5/23 Chris Morley <c.m...@ds...>:
>> Nick England wrote:
>>> 2008/5/23 Noel O'Boyle <bao...@gm...>:
>>>> 2008/5/23 Chris Morley <c.m...@ds...>:
>>>>> I think Nick's suggestion is a good idea.
>>>>> There could be a C++ function
>>>>>
>>>>> bool OBConversion::OpenInAndOutFiles(std::string infilename, std::string
>>>>> outfilename);
>>
>> I've now added this to the development code. Here it is making an index
>> and then substructure searching it. (Note that my Python is rather shaky.)
>> I don't think the CloseOutFile() is necessary here but may be sometimes.
>> It is a bit tedious compared with the babel command line, but maybe
>> Pybel could help?
>>
>>  >>> import openbabel
>>  >>> conv=openbabel.OBConversion()
>>  >>> conv.OpenInAndOutFiles("1200mols.smi","index.fs")
>> True
>>  >>> conv.SetInAndOutFormats("smi","fs")
>> True
>>  >>> conv.Convert()
>> This will prepare an index of 1200mols.smi and may take some time...
>>  It took 6 seconds
>> 1192
>>  >>> conv.CloseOutFile()
>>  >>> conv.OpenInAndOutFiles("index.fs","results.smi")
>> True
>>  >>> conv.SetInAndOutFormats("fs","smi")
>> True
>>  >>> conv.AddOption("s",conv.GENOPTIONS,"C=CC#N")
>>  >>> conv.Convert()
>> 10 candidates from fingerprint search phase
>> 1202
>>  >>> f=open("results.smi")
>>  >>> f.read()
>> 'OC(=O)C(=Cc1ccccc1)C#N\t298\nN#CC(=Cc1ccccc1)C#N\t490\nO=N(=O)c1cc(ccc1)C=C(C#N
>> )C#N\t491\nClc1ccc(cc1)C=C(C#N)C#N\t492\nClc1ccc(c(c1)Cl)C=C(C#N)C#N\t493\nClc1c
>> cc(cc1Cl)C=C(C#N)C#N\t494\nBrc1ccc(cc1)C=C(C#N)C#N\t532\nClc1ccccc1C=C(C#N)C#N\t
>> 542\nN#CC(=CC=Cc1occc1)C#N\t548\nCCOC(=O)C(C#N)=C(C)C\t1074\n'
>>  >>>
>>
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