Looks like the -al1000000 tag (rather than -l 1000000) may have solved the
problem. Thanks for all your help! ~Jacob
On Fri, May 16, 2014 at 12:35 AM, Fredrik Wallner <fred...@wallner.nu>wrote:
> Hi,
>
> I don’t know if it will solve the problem, but your use of the l option is
> not entirely correct. Since you want the read option, you should specify it
> as -al1000000
>
> Kind regards,
> Fredrik
>
> 16 maj 2014 kl. 04:28 skrev Jacob Durrant <jacobdurr...@gmail.com>:
>
> I've been trying to get substructure searches working with Open Babel for
> some time. I always run into the same frustration.
>
> I have a SDF file with ~27,000 compounds. I first convert it to an fs file:
>
> -bash-4.1$ babel compounds.sdf -ofs
> This will prepare an index of compounds.sdf and may take some time...
> It contains 27036 molecules Estimated completion time 0 seconds
>
> It took 59 seconds
> 27036 molecules converted
> 37 audit log messages
>
> Now I try performing a substructure search:
>
> -bash-4.1$ babel compounds.fs -ifs -s"C(=O)O" results.smi
> *** Open Babel Warning in Find
> Stopped looking after 9778 molecules.
>
> 4000 candidates from fingerprint search phase
> 3895 molecules converted
> 1 warnings 134948 audit log messages
>
> I don't want it to stop looking after 9778 molecules. I want it to search
> through the entire file. The -l option seemed promising. From the help file:
>
> Read Options (when searching) e.g. -at0.7
> t# Do similarity search:#mols or # as min Tanimoto
> a Add Tanimoto coeff to title in similarity search
> l# Maximum number of candidates. Default<4000>
> e Exact match
> Alternative to using exact in ``-s`` parameter, see above
> n No further SMARTS filtering after fingerprint phase
>
> However, using this option doesn't resolve the problem.
>
> -bash-4.1$ babel compounds.fs -ifs -s"C(=O)O" results.smi -l 1000000
> *** Open Babel Warning in Find
> Stopped looking after 9778 molecules.
>
> 4000 candidates from fingerprint search phase
> 3895 molecules converted
> 1 warnings 134948 audit log messages
>
> Can anyone tell me how to instruct Open Babel to keep searching beyond the
> initial 9778 molecules? I'm using version 2.3.1 -- Oct 13 2011. Thanks.
>
> Thanks.
>
> ~Jacob
>
>
>
> --
> ==============================
> Jacob D. Durrant <https://amarolab.ucsd.edu/~jdurrant/>, PhD
> Rommie E. Amaro Research Group <https://amarolab.ucsd.edu/>
> University of California, San Diego
>
> Connect with me on LinkedIn<http://www.linkedin.com/profile/view?id=94290749>
> jacobdurr...@gmail.com
> jdurr...@ucsd.edu
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==============================
Jacob D. Durrant <https://amarolab.ucsd.edu/~jdurrant/>, PhD
Rommie E. Amaro Research Group <https://amarolab.ucsd.edu/>
University of California, San Diego
Connect with me on LinkedIn<http://www.linkedin.com/profile/view?id=94290749>
jacobdurr...@gmail.com
jdurr...@ucsd.edu
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