I am writing because I ran into an example where use of --gen3d apparently
changed the number of rotatable bonds from 12 to 3.
Is that to be expected or is it a possible bug? (If this indicates that
the compound is less flexible than might be inferred from the InChi or
SMILES that would be great. On the other hand, if the number of rotatable
bonds can increase with --gen3d, then that is less good.)
The compound is CHEMBL1096885
<https://www.ebi.ac.uk/chembl/compound/inspect/CHEMBL1096885>. ChemBL has
the number of rotatable bonds at 12, as does NumRotors() based on the InChi
key.
Here's is my test: (hopefully one can copy, paste and reproduce it)
echo
'InChI=1S/C34H36F3NO13/c1-4-5-9-21(40)49-13-20(39)33(47)11-16-24(19(12-33)51-22-10-17(27(41)14(2)50-22)38-32(46)34(35,36)37)31(45)26-25(29(16)43)28(42)15-7-6-8-18(48-3)23(15)30(26)44/h6-8,14,17,19,22,27,41,43,45,47H,4-5,9-13H2,1-3H3,(H,38,46)/t14-,17-,19-,22-,27+,33-/m0/s1'
> tmp.inchi; obabel -i inchi tmp.inchi --gen3d -o mol2 -O out.mol2 ;
python -c 'import pybel; import sys; import itertools; [
sys.stdout.write(str(mol.OBMol.NumRotors())+"\t"+str(mol)) for mol in
itertools.chain(pybel.readfile("inchi","tmp.inchi"),pybel.readfile("mol2",
"out.mol2"))];'
1 molecule converted
12 CCCCC(=O)OCC(=O)[C@@]1(Cc2c([C@H](C1)O[C@H]1C[C@@H]([C@@H]([C@H
](C)O1)O)N=C(C(F)(F)F)O)c(c1c(C(=O)c3cccc(c3C1=O)OC)c2O)O)O
3 C123CCCC(=O)OCC(=O)[C@
@]4(Cc5c([CH](C4)(O[CH]46C[CH]([CH]7([CH](C([H]6)[H]7)(O4)[H]1)O)(/N=C(\C(F)(F)F)/O)[H]2)[H]3)c(c1c(C(=O)c2cccc(c2C1=O)OC)c5O)O)O
*****
My version information:
obabel -V
Open Babel 2.3.90 -- Feb 26 2015 -- 00:48:45
Also, what does the "*****" mean from pybel's str(mol)?
Aaron Schweiger
p.s. I sent this to Geoff directly become becoming aware of the proper
etiquette; apologies if already discussed.
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