Hello Vinay,
Perhaps example.sdf and example.smi represent different compounds.
- Noel
2010/1/25 Vinay M <[email protected]>
> Hi all
> I have been using babel for various molecular calculations and conversions.
>
> I have noticed an unexpected error during conversion and with obprop
> calculation. When i use cannonical smiles as input for obprop, I get a
> different canonical output, its entirely a different compund and if i use
> sdf as input, I got a different canonical string. The following is an
> example.
> SDF was converted to cannonicals by babel- Using babel -isdf filename -ocan
> filename.can
>
>
> Example one where, I have used Canonical smiles as the input for obprop.
>
> 1.
> [vi...@vinay_pc testing]$ ls
> can_from_sdf.can example.can example.sdf
>
> [vi...@vinay_pc testing]$ obprop example.can > obprop_can_input
> ==============================
> *** Open Babel Warning in InChI code
> ZINC20816447 :Accepted unusual valence(s): N(4); C(5); Proton(s)
> added/removed
>
>
> Example two, where in I have used sdf as input file for obprop
> 2.
>
> [vi...@vinay_pc testing]$ obprop example.sdf > obprop_sdf_input
> ==============================
> *** Open Babel Warning in InChI code
> ZINC20816447 :Proton(s) added/removed
>
>
> [vi...@vinay_pc testing]$ ls
> can_from_sdf.can example.can example.sdf obprop_can_input
> obprop_sdf_input
>
>
> Differences in canonical strings from different input files.
>
> [vi...@vinay_pc testing]$ more obprop_can_input
> name ZINC20816447
> formula C21H32N7O2
> mol_weight 414.524
> exact_mass 414.262
> canonical_SMILES C/C=C/CN1CC[NH+](CC1)CC[n]1c2nc3N(C)[C](=O)=[N](C[C]
> =O)=c3n2c(C)c1C ZINC20816447
>
> InChI
> InChI=1S/C21H31N7O2/c1-6-7-8-25-9-11-26(12-10-25)13-14-27-15(2)16(3)28-17-18(22-20(27)28)23(4)21(30)24(5)19(17)29/h6-7H,8-14H2,1-5H3/p+1/b7-6+
>
> num_atoms 62
> num_bonds 65
> num_residues 0
> sequence -
> num_rings 4
> logP 0.4349
> PSA 79.65
> MR 131.945
> $$$$
>
>
> This is sdf as input file,
>
> [vi...@vinay_pc testing]$ more obprop_sdf_input
> name ZINC20816447
> formula C21H32N7O2
> mol_weight 414.524
> exact_mass 414.262
> canonical_SMILES
> C/C=C/CN1CC[NH+](CC1)CCn1c2nc3c(c(=O)n(C)c(=O)n3C)n2c(C)c1C ZINC20816447
>
> InChI
> InChI=1S/C21H31N7O2/c1-6-7-8-25-9-11-26(12-10-25)13-14-27-15(2)16(3)28-17-18(22-20(27)28)23(4)21(30)24(5)19(17)29/h6-7H,8-14H2,1-5H3/p+1/b7-6+
>
> num_atoms 62
> num_bonds 65
> num_residues 0
> sequence -
> num_rings 4
> logP 0.5869
> PSA 73.91
> MR 128.186
> $$$$
>
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