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 orginal 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

⇑⇑ Open Babel Tutorials