"babel -i fs ... -s query_file" - Substructure Search
Why am I getting no results with "babel -i fs ... -s query_file" command? It should perform a substructure search in a fastsearch index file.
According to the "babel -H fs" help document, you can perform a substructure search in a fastsearch index file with the query molecule stored in a file in any format.
However, Open Babel 2.3.1 seems to have an issue to support this. Here is an example session:
fyicenter$ babel -V Open Babel 2.3.1 -- Oct 13 2011 -- 15:14:47 fyicenter$ babel -i fs molecules-index.fs -o smiles result.smi -s 'c1ccccc1' 210 candidates from fingerprint search phase 208 molecules converted 7241 audit log messages fyicenter$ ls -l result.smi -rw-r--r-- 1 fyicenter staff 13889 May 25 14:18 result.smi fyicenter$ babel -i fs molecules-index.fs -o smiles result.smi -s benzene.sdf 210 candidates from fingerprint search phase 0 molecules converted 3836 audit log messages fyicenter$ ls -l result.smi -rw-r--r-- 1 fyicenter staff 0 May 25 14:17 result.smi
As you can see, if the query molecule, benzene ring, is specified in a SMILES string in the command line, "babel" found 210 candidates in the first step, and confirmed/converted 208 molecules as the substructure match result.
However, if the query molecule, benzene ring, is specified in in a SDF file, "babel" found 210 candidates in the first step, and failed to confirm/convert any molecules as the substructure match result.
This is a bug in Open Babel 2.3.1. There is no problem, if you are using Open Babel 2.4.1.
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2020-05-25, 387👍, 0💬
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