(ccing the list)
That's strange. You might get weird effects if you alter the original
file, or move them around, after creating the .fs file, but if you
just create and use it, then it should work.
If you could file a bug report with a specific test case, we could look into it.
- Noel
On 21 March 2015 at 22:14, Stefano Forli <fo...@scripps.edu> wrote:
> The fs file was created using obabel:
>
> obabel mymols.mol2 -ofs
>
> About the escaping, I've tried several combinations of single and double
> quotes, and it didn't work. Actually, trying again with single quotes, it
> did what it was expected to do in Bash.
>
> By the way, in the meantime, I've also tried opening the fs using Pybel and
> while it is listed in the supported formats, it shows an error message:
>
> >>> m = pybel.readfile('fs', 'mol2_files_top50K.fs').next()
> HIER
> Not a valid input formatTraceback (most recent call last):
> File "<stdin>", line 1, in <module>
> StopIteration
> >>> 'fs' in pybel.informats
> True
>
>
> Thanks!
>
>
> On 03/21/2015 03:02 PM, Noel O'Boyle wrote:
>>
>> How did you create the .fs file? BTW, there should be no need to
>> escape if you use double quotation mark, i.e. ".
>>
>> On 21 March 2015 at 21:52, Stefano Forli <fo...@scripps.edu> wrote:
>>>
>>> I think there's an error either in the documentation or in the
>>> implementation of the
>>> filter by pattern in obabel (v2.3.2). The online help says:
>>>
>>> $ obabel -H
>>> ...
>>> -s"smarts" Convert only if match SMARTS or mols in file:
>>> ...
>>>
>>> as well as the documentation page here:
>>>
>>> http://openbabel.org/docs/dev/Fingerprints/fingerprints.html#substructure-searching
>>>
>>> Although, when trying the following example, I get an error message that
>>> implies the code
>>> is expecting a SMILES string:
>>>
>>> --------------------
>>> $ obabel -ifs mol2_files_top50K.fs
>>>
>>> -s'[#6]-1(=[#6](-[$([#1]),$([#6](-[#1])-[#1]),$([#6]=[#8])])-[#16]-[#6](-[#7]-1-[$([#1]),$([#6]-[#1]),$([#6]:[#6])])=[#7;\!R])-[$([#6](-[#1])-[#1]),$([#6]:[#6])]'
>>> -osmi -O first.smi
>>> ==============================
>>> *** Open Babel Error in ReadMolecule
>>> C-1(=C(-[$(H),$(C(-H)-H),$(C=O)])-S contained a character ',' which
>>> is invalid in SMILES
>>> ==============================
>>> *** Open Babel Error in ObtainTarget
>>> Cannot read the SMILES string
>>> 0 molecules converted
>>> ----------------------
>>>
>>> (note: I've escaped some characters in the pattern to avoid shell
>>> errors).
>>>
>>> Thanks,
>>>
>>> S
>>>
>>>
>>>
>>> --
>>> Stefano Forli, PhD
>>>
>>> Staff Scientist
>>> Molecular Graphics Laboratory
>>> Dept. of Integrative Structural
>>> and Computational Biology, MB-112F
>>> The Scripps Research Institute
>>> 10550 North Torrey Pines Road
>>> La Jolla, CA 92037-1000, USA.
>>>
>>> tel: +1 (858)784-2055
>>> fax: +1 (858)784-2860
>>> email: fo...@scripps.edu
>>> http://www.scripps.edu/~forli/
>>>
>>>
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>
>
> --
> Stefano Forli, PhD
>
> Staff Scientist
> Molecular Graphics Laboratory
> Dept. of Integrative Structural
> and Computational Biology, MB-112F
> The Scripps Research Institute
> 10550 North Torrey Pines Road
> La Jolla, CA 92037-1000, USA.
>
> tel: +1 (858)784-2055
> fax: +1 (858)784-2860
> email: fo...@scripps.edu
> http://www.scripps.edu/~forli/
------------------------------------------------------------------------------
Dive into the World of Parallel Programming The Go Parallel Website, sponsored
by Intel and developed in partnership with Slashdot Media, is your hub for all
things parallel software development, from weekly thought leadership blogs to
news, videos, case studies, tutorials and more. Take a look and join the
conversation now. http://goparallel.sourceforge.net/
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