Dear friends,
I am facing a similar problem.With open babel tutorial I could
able to generate a fast-search index (znd_unique) for 30 thousand molecule.
I have tried searching matches > 0.5 tanimoto similarity with one molecule
and the fast search index it worked well. The command line argument for the
same as follows -
babel znd_unique.fs similar0.5_CID5310786.sdf
-s"O=[P@@](O)(O[C@@H]1[C@H](O)[C@H](O)[C@@H](O)[C@@H](O1)C)O[P@](=O)(O)OC[C@H]1O[C@H](C[C@@H]1O)n1c(=O)[nH]c(=O)c(C)c1"
-at0.5
55 molecules converted
1152 audit log messages
But, when I tried with another molecule
SCCCn1c2c([nH]c1=O)cccc2)c1nc2n(c3c(c2nn1)cccc3)CC it did not work. The
command line argument and error message for the same is -
babel znd_unique.fs similar0.5_CID5310786.sdf
-s"SCCCn1c2c([nH]c1=O)cccc2)c1nc2n(c3c(c2nn1)cccc3)CC" -at0.5
==============================
*** Open Babel Error in ObtainTarget
Cannot read the SMILES string
0 molecules converted
1 errors 3 audit log messages
Please help me out.
Jyoti Prakash Rath
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