Dear colleagues,
I used Chem.MolFromMolFile to read in an sd file with stereo info on some
atoms. But the stereo info seems to be lost. Could you spot what I missed?
The input file is attached. On the atom lines, the third column after the
element name should contain the stereo data. I simply used mol.Debug() to dump
out the atoms' info.
> mol = Chem.MolFromMolFile("r3.sdf", removeHs=False)
> mol.Debug()
Thank you for your insight.
Ling
2tmn
3D
Structure written by MMmdl.
22 21 0 0 1 0 999 V2000
35.4170 41.5840 -4.5590 N 0 3 0 0 0 0
36.4970 42.1070 -3.7400 C 0 0 2 0 0 0
37.8260 41.4200 -4.0320 C 0 0 0 0 0 0
38.8450 42.1020 -3.8700 O 0 0 0 0 0 0
36.2170 41.9220 -2.2430 C 0 0 0 0 0 0
37.2180 42.4800 -1.2800 C 0 0 0 0 0 0
37.4030 43.9860 -1.5290 C 0 0 0 0 0 0
36.5540 42.0260 0.0330 C 0 0 0 0 0 0
34.7201 42.3022 -4.6959 H 0 0 0 0 0 0
36.1182 40.8543 -2.0470 H 0 0 0 0 0 0
35.2586 42.3951 -2.0289 H 0 0 0 0 0 0
34.9967 40.7910 -4.0956 H 0 0 0 0 0 0
36.6040 43.1723 -3.9446 H 0 0 0 0 0 0
37.8752 40.3930 -4.3626 H 0 0 0 0 0 0
38.1720 41.9677 -1.4048 H 0 0 0 0 0 0
37.8230 44.4527 -0.6380 H 0 0 0 0 0 0
36.4373 44.4382 -1.7551 H 0 0 0 0 0 0
38.0798 44.1347 -2.3704 H 0 0 0 0 0 0
37.3222 41.7052 0.7366 H 0 0 0 0 0 0
35.9921 42.8557 0.4619 H 0 0 0 0 0 0
35.8777 41.1957 -0.1700 H 0 0 0 0 0 0
35.7836 41.2949 -5.4546 H 0 0 0 0 0 0
1 9 1 0 0 0
1 2 1 0 0 0
1 12 1 0 0 0
1 22 1 0 0 0
2 3 1 0 0 0
2 5 1 0 0 0
2 13 1 0 0 0
3 4 2 0 0 0
3 14 1 0 0 0
5 6 1 0 0 0
5 10 1 0 0 0
5 11 1 0 0 0
6 7 1 0 0 0
6 8 1 0 0 0
6 15 1 0 0 0
7 16 1 0 0 0
7 17 1 0 0 0
7 18 1 0 0 0
8 19 1 0 0 0
8 20 1 0 0 0
8 21 1 0 0 0
M CHG 1 1 1
M END
$$$$
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