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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