Hi, In a similarity search, obabel consider another molecule than the reference I'm giving.
My library being test.smi: C1(=CC2=C(C(C(C2)(C#N)C#N)(CC(=O)C)C#N)C(=O)N)C(=O)NC(=O)S1 A C1(=Cc2c(oc3c(cc(cc3)Br)c2=O)C(=O)N)C(=O)NC(=O)S1 B C1(=CC2=C(C(C(C2)(C#N)C#N)(C2CCCC2=O)C#N)C(=O)N)C(=O)NC(=O)S1 C after conversion in fs format: obabel test.smi -ofs The command: obabel test.fs -SA.smi -ofpt -at0.0 is giving: >C >A Tanimoto from C = 1 Possible superstructure of C >B Tanimoto from C = 0.278689 3 molecules converted A is _not_ the reference (first line). obabel is considering C instead. B as reference is ok: obabel test.fs -SB.smi -ofpt -at0.0 >B >C Tanimoto from B = 0.278689 >A Tanimoto from B = 0.278689 3 molecules converted C as reference is OK, and is producing the same result as if taking A as reference. Changing the order in test.smi (e.g. C, A, B), using C as reference returns A in the first line. Using A as reference is OK. I have 43 similar cases out of my 1579 compounds library. Any ideas apart from shuffling the smiles file? :) Regards, Pascal ------------------------------------------------------------------------------ Precog is a next-generation analytics platform capable of advanced analytics on semi-structured data. The platform includes APIs for building apps and a phenomenal toolset for data science. Developers can use our toolset for easy data analysis & visualization. Get a free account! http://www2.precog.com/precogplatform/slashdotnewsletter _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
