I'm having a problem with the conversion of certain smiles structures to the
fastsearch format, followed by subsequent similarity searches. I'm
currently working with a large dataset (~160,000) compounds, and some
compounds that I know are in the FS file are not hitting in the output.
Here is a representative example.
Take the following smiles string:
c1cccc(c1)C(C(OC(=O)C)C[N+](=O)[O-])c1ccccc1
As far as I can tell, it is a valid smiles structure. It came from babel
conversion from an SDF file to SMI file, and pastes into chemdraw just
fine. If i put it into the tab-delimited file, test.smi, as:
c1cccc(c1)C(C(OC(=O)C)C[N+](=O)[O-])c1ccccc1 cmpd001
and then generate the fastsearch index:
>babel -ismi test.smi -ofs test.fs
The index appears to build without error (i.e. 1 molecule converted).
However, if I then probe that fs index with the exact input string:
>babel test.fs hitlist.smi -s'c1cccc(c1)C(C(OC(=O)C)C[N+](=O)[O-])c1ccccc1'
-at0.85
I get 0 molecules converted. I have also tried leaving it in the original
SDF format, but have the same problem. I'm currently using openbabel
2.3.0. I thought that the development version might contain some bugfixes,
however, I have not yet been successful in compiling from source (which is a
nightmare, btw).
Any ideas?
Chris
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