"Difficulty opening ..." Error Using Fastsearch Index
Why am I getting this "Difficulty opening ..." error using Fastsearch Index files?
When you are using a fastsearch index file as the input, you must keep the original molecule data files in the original location, because the index file has references to the original data files.
If those original data files are removed or moved to another location, "babel" will give this "Difficulty opening ..." error.
The following command session shows what happens, if you renamed the original data file after the index file was generated.
fyicenter$ babel molecules.sdf -o fs molecules-index.fs This will prepare an index of molecules.sdf and may take some time... It contains 409 molecules It took 0 seconds 409 molecules converted 37 audit log messages fyicenter$ mv molecules.sdf molecules-bck.sdf fyicenter$ babel -i fs molecules-index.fs -o smiles -s 'c1ccccc1' -at 0.2 -aa ============================== *** Open Babel Error in ReadChemObject Difficulty opening molecules.sdf 0 molecules converted 1 errors 24 audit log messages
⇒ "babel -i fs ... -s SMILES" - Substructure Search with Index
⇐ "babel -i fs ... -s ... -at score_range" - Similarity Search
⇑ Using Fastsearch Fingerprint Index
2020-08-25, 585👍, 0💬
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