Hi JP,
If you have also a SMILES of the molecule you want to read from PDB, you
can assign the bond orders based on this template:
tmp = Chem.MolFromPDBFile(yourfilename)
template = Chem.MolFromSmiles(yoursmiles)
mol = AllChem.AssignBondOrdersFromTemplate(template, tmp)
Is this what you're looking for?
Best,
Sereina
2014/1/13 JP <jeanpaul.ebe...@inhibox.com>
> RDKitters!
>
> Finally back on the mailing list!
>
> I am sure we've been through this at the UGM (my mind must have wandered
> off!), but a quick question about the PDB reader and bond perception. Is
> this supported with the current PDB reader? I remember that someone
> (PaulE, perhaps?) was saying bond perception was painful, but there was
> some dictionary for PDB ligands which helps (any idea the name of this
> dictionary?).
>
> To the technical details.
>
> I am reading in the following PDB file with a simple MolFromPDBFile() call:
>
> HETATM 1 O1P 84T A1862 -27.016 9.387 -72.564 1.00 20.81
> O
> HETATM 2 P 84T A1862 -27.282 9.818 -73.968 1.00 19.65
> P
> HETATM 3 O2P 84T A1862 -27.881 11.176 -74.182 1.00 21.49
> O
> HETATM 4 N 84T A1862 -25.869 9.583 -74.813 1.00 19.78
> N
> HETATM 5 C 84T A1862 -25.759 10.010 -76.075 1.00 19.97
> C
> HETATM 6 CA 84T A1862 -24.493 9.748 -76.807 1.00 19.75
> C
> HETATM 7 CB 84T A1862 -24.794 8.678 -77.847 1.00 19.73
> C
> HETATM 8 CG 84T A1862 -23.571 8.324 -78.681 1.00 19.70
> C
> HETATM 9 CD2 84T A1862 -23.309 9.519 -79.611 1.00 18.49
> C
> HETATM 10 CD1 84T A1862 -23.863 6.932 -79.305 1.00 18.60
> C
> HETATM 11 OHB 84T A1862 -25.210 7.467 -77.223 1.00 19.17
> O
> HETATM 12 OH 84T A1862 -23.549 9.127 -75.984 1.00 20.33
> O
> HETATM 13 O 84T A1862 -26.672 10.517 -76.692 1.00 20.26
> O
> HETATM 14 O5' 84T A1862 -28.377 8.861 -74.619 1.00 19.39
> O
> HETATM 15 C5' 84T A1862 -28.002 7.536 -74.954 1.00 18.47
> C
> HETATM 16 C4' 84T A1862 -28.909 7.000 -76.012 1.00 18.24
> C
> HETATM 17 C3' 84T A1862 -28.901 7.826 -77.298 1.00 18.28
> C
> HETATM 18 C2' 84T A1862 -30.318 7.610 -77.768 1.00 18.69
> C
> HETATM 19 O2' 84T A1862 -30.789 8.641 -78.581 1.00 19.64
> O
> HETATM 20 O4' 84T A1862 -30.262 6.951 -75.529 1.00 18.80
> O
> HETATM 21 C1' 84T A1862 -31.152 7.470 -76.521 1.00 19.01
> C
> HETATM 22 N9 84T A1862 -31.753 8.732 -76.009 1.00 20.08
> N
> HETATM 23 C4 84T A1862 -33.033 9.013 -76.158 1.00 21.10
> C
> HETATM 24 N3 84T A1862 -34.018 8.339 -76.786 1.00 21.58
> N
> HETATM 25 C2 84T A1862 -35.263 8.846 -76.830 1.00 21.95
> C
> HETATM 26 C8 84T A1862 -31.223 9.701 -75.291 1.00 20.27
> C
> HETATM 27 N7 84T A1862 -32.173 10.618 -75.019 1.00 21.28
> N
> HETATM 28 C5 84T A1862 -33.315 10.213 -75.563 1.00 21.81
> C
> HETATM 29 C6 84T A1862 -34.624 10.702 -75.627 1.00 22.85
> C
> HETATM 30 N1 84T A1862 -35.550 10.010 -76.285 1.00 22.44
> N
> HETATM 31 N6 84T A1862 -35.008 11.862 -75.052 1.00 23.86
> N
> TER
> END
>
> But I am losing all the double bond (and aromatic) information:
>
> m = Chem.MolFromPDBFile(sys.argv[1])
> print Chem.MolToSmiles(m)
>
> Gives me:
>
> CC(C)C(O)C(O)C(O)NP(O)(O)OCC1CC(O)C(N2CNC3C2NCNC3N)O1
>
> As usual, many thanks for your time,
>
> -
> Jean-Paul Ebejer
> Early Stage Researcher
>
>
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