> Message: 4
> Date: Sun, 10 Mar 2013 21:02:41 +0000
> From: Chris Morley <c.mor...@gaseq.co.uk>
> Subject: Re: [Open Babel] obabel and fingerprints
> To: openbabel-discuss@lists.sourceforge.net
> Message-ID: <513cf4f1.2000...@gaseq.co.uk>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> On 10/03/2013 12:45, Chris Swain wrote:
>> I'm moving to use obabel rather than babel and I'm having a few problems
>> working out the syntax
>>
>> obabel /Users/swain/obsmiles.smiles -osmi -s "c1ccccc1" -xt
>>
>> Gives a list of 907 molecule names
>>
>> I've created the fastsearch index
>>
>> obabel /Users/swain/obsmiles.smiles -ofs
>>
>> this created /Users/swain/obsmiles.fs as expected.
>>
>> I then tried
>>
>> obabel /Users/swain/obsmiles.fs -ifs -s "c1ccccc1" -osmi
>> 907 candidates from fingerprint search phase
>> OC1C2NC(C1O)CC(C2)(F)FF)001377cc1c1371O 001376
>> 1 molecule converted
>>
>> Any help appreciated.
>
> I don't see anything wrong with the syntax. (The -ifs is actually not
> needed.) Something similar works ok for me on Windows with both v2.3.2
> and trunk.
>
> You could try
> obabel /Users/swain/obsmiles.fs -osmi
> which should give info on the .fs index, in case it hasn't been made
> properly. Otherwise I'm stumped.
>
> Chris
Thanks
obabel /Users/swain/obsmiles.fs -osmi
Shows the index to be formed correctly, but I think I've found a potential
problem. This is a very old smiles file I use for testing, it seems to have the
old Mac line endings, if I convert to unix it all runs fine. Is it possible
that everything works fine with the old Mac line endings except the fs search?
This is probably not a big issue since I think all files created now will have
Unix line endings.
Cheers
Chris
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