Hi,
apparently the --gen3D option takes ages and does not work for
mixtures in most cases.
Does anyone know the reason and/or a workaround?
An Example:
obabel -:"CNC[C@@H](c1ccc(c(c1)O)O)O" -d --gen3d -osdf
works fine and takes about 8 seconds on my machine.
obabel -:"CNC[C@@H](c1ccc(c(c1)O)O)O" -d --gen3d -osdf
takes about 5 minutes, and produces an erroneous 3d-structure (see
below, one bond length is >3).
Kind regards,
Martin
OpenBabel12051311593D
14 13 0 0 1 0 0 0 0 0999 V2000
3.9989 -1.9308 1.8375 C 0 0 0 0 0 0 0 0 0 0 0 0
2.0251 0.6398 1.7787 N 0 0 0 0 0 0 0 0 0 0 0 0
2.9371 1.0089 0.6399 C 0 0 0 0 0 0 0 0 0 0 0 0
4.5034 1.0523 0.7544 C 0 0 1 0 0 0 0 0 0 0 0 0
5.0234 1.3564 -0.6361 C 0 0 0 0 0 0 0 0 0 0 0 0
5.2317 2.6820 -1.0552 C 0 0 0 0 0 0 0 0 0 0 0 0
5.5467 2.9543 -2.3874 C 0 0 0 0 0 0 0 0 0 0 0 0
5.6293 1.9100 -3.3219 C 0 0 0 0 0 0 0 0 0 0 0 0
5.4306 0.5812 -2.9034 C 0 0 0 0 0 0 0 0 0 0 0 0
5.1478 0.3112 -1.5637 C 0 0 0 0 0 0 0 0 0 0 0 0
5.4605 -0.4418 -3.7834 O 0 0 0 0 0 0 0 0 0 0 0 0
5.8749 2.1790 -4.6204 O 0 0 0 0 0 0 0 0 0 0 0 0
4.9499 2.0285 1.6597 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.0991 1.9461 3.0701 Cl 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
4 3 1 6 0 0 0
4 5 1 0 0 0 0
4 13 1 0 0 0 0
5 6 2 0 0 0 0
5 10 1 0 0 0 0
6 7 1 0 0 0 0
7 8 2 0 0 0 0
8 9 1 0 0 0 0
8 12 1 0 0 0 0
9 10 2 0 0 0 0
9 11 1 0 0 0 0
M END
$$$$
--
Dipl-Inf. Martin Gütlein
Phone:
+49 (0)761 203 8442 (office)
+49 (0)177 623 9499 (mobile)
Email:
[email protected]
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