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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