Dear all,
I am using Constrained embed to generate conformers. I AddHs before I use
ConstrainedEmbed but I am finding that some of the conformers have Hs which
overlap (have the same coordinates).
Here is one example below.
from rdkit import Chem
from rdkit.Chem import AllChem, rdFMCS
from rdkit.Chem.Draw import IPythonConsole
m = Chem.MolFromMolBlock("""
RDKit 3D
23 25 0 0 0 0 0 0 0 0999 V2000
68.3300 51.1910 11.2220 C 0 0 0 0 0 0 0 0 0 0 0 0
67.2290 50.0380 7.4130 N 0 0 0 0 0 0 0 0 0 0 0 0
69.1000 46.9130 6.3200 O 0 0 0 0 0 0 0 0 0 0 0 0
68.1740 52.1510 10.2210 C 0 0 0 0 0 0 0 0 0 0 0 0
66.6510 48.5160 5.8250 N 0 0 0 0 0 0 0 0 0 0 0 0
67.8070 51.7450 8.9400 C 0 0 0 0 0 0 0 0 0 0 0 0
70.2560 46.5410 8.2130 N 0 0 0 0 0 0 0 0 0 0 0 0
68.1130 49.8320 10.9440 C 0 0 0 0 0 0 0 0 0 0 0 0
67.7430 49.4420 9.6500 C 0 0 0 0 0 0 0 0 0 0 0 0
67.5850 50.4050 8.6490 C 0 0 0 0 0 0 0 0 0 0 0 0
67.0030 48.7500 7.0910 C 0 0 0 0 0 0 0 0 0 0 0 0
67.1430 47.7100 8.0530 C 0 0 0 0 0 0 0 0 0 0 0 0
67.5210 48.1000 9.3470 C 0 0 0 0 0 0 0 0 0 0 0 0
66.9080 46.1720 7.8280 C 0 0 0 0 0 0 0 0 0 0 0 0
68.1970 45.3010 7.7860 C 0 0 0 0 0 0 0 0 0 0 0 0
69.2630 46.2750 7.3670 C 0 0 0 0 0 0 0 0 0 0 0 0
70.3640 45.7820 9.4850 C 0 0 0 0 0 0 0 0 0 0 0 0
71.0660 47.6920 7.7870 C 0 0 1 0 0 0 0 0 0 0 0 0
71.1300 48.7910 8.8520 C 0 0 0 0 0 0 0 0 0 0 0 0
71.3550 50.1140 8.1030 C 0 0 0 0 0 0 0 0 0 0 0 0
72.4840 50.0120 7.0390 C 0 0 0 0 0 0 0 0 0 0 0 0
72.6270 48.6580 6.2850 C 0 0 0 0 0 0 0 0 0 0 0 0
72.4290 47.4350 7.1920 C 0 0 0 0 0 0 0 0 0 0 0 0
4 1 2 0
6 4 1 0
8 1 1 0
9 8 2 0
10 9 1 0
10 6 2 0
10 2 1 0
11 5 1 0
11 2 2 0
12 11 1 0
13 12 2 0
13 9 1 0
14 12 1 0
15 14 1 0
16 15 1 0
16 7 1 0
16 3 2 0
17 7 1 0
18 7 1 1
19 18 1 0
20 19 1 0
21 20 1 0
22 21 1 0
23 22 1 0
23 18 1 0
M END
""")
sm = "CN(C(=O)CCc1cc2ccccc2nc1N)C1CCCCC1CC"
res = rdFMCS.FindMCS([m, Chem.MolFromSmiles(sm)], completeRingsOnly=True,
ringMatchesRingOnly=True, matchValences=True)
core1 = AllChem.DeleteSubstructs(AllChem.ReplaceSidechains(m,
Chem.MolFromSmarts(res.smartsString)),
Chem.MolFromSmiles('*'))
confs = []
sm_H_mol = Chem.AddHs(Chem.MolFromSmiles(sm))
for i in xrange(10):
sm_H_conf = AllChem.ConstrainedEmbed(sm_H_mol, core1, randomseed=i)
confs.append(sm_H_conf)
print Chem.MolToMolBlock(confs[1])
>
RDKit 3D
54 56 0 0 0 0 0 0 0 0999 V2000
70.3134 45.7178 9.5447 C 0 0 0 0 0 0 0 0 0 0 0 0
70.3467 46.4946 8.2897 N 0 0 0 0 0 0 0 0 0 0 0 0
69.2899 46.2820 7.3349 C 0 0 0 0 0 0 0 0 0 0 0 0
69.2440 46.9503 6.2711 O 0 0 0 0 0 0 0 0 0 0 0 0
68.1131 45.3908 7.6445 C 0 0 0 0 0 0 0 0 0 0 0 0
66.8303 46.2273 7.8443 C 0 0 0 0 0 0 0 0 0 0 0 0
67.0755 47.7186 8.0943 C 0 0 0 0 0 0 0 0 0 0 0 0
67.4608 48.1061 9.3845 C 0 0 0 0 0 0 0 0 0 0 0 0
67.7033 49.4491 9.6830 C 0 0 0 0 0 0 0 0 0 0 0 0
68.0967 49.8458 10.9679 C 0 0 0 0 0 0 0 0 0 0 0 0
68.3350 51.1969 11.2372 C 0 0 0 0 0 0 0 0 0 0 0 0
68.1872 52.1531 10.2278 C 0 0 0 0 0 0 0 0 0 0 0 0
67.8127 51.7603 8.9409 C 0 0 0 0 0 0 0 0 0 0 0 0
67.5741 50.4115 8.6657 C 0 0 0 0 0 0 0 0 0 0 0 0
67.2187 50.0280 7.4186 N 0 0 0 0 0 0 0 0 0 0 0 0
66.9721 48.7322 7.0969 C 0 0 0 0 0 0 0 0 0 0 0 0
66.6333 48.4598 5.7410 N 0 0 0 0 0 0 0 0 0 0 0 0
71.4151 47.5160 8.1630 C 0 0 0 0 0 0 0 0 0 0 0 0
71.1074 48.8659 8.8420 C 0 0 0 0 0 0 0 0 0 0 0 0
71.2788 50.0894 7.9509 C 0 0 0 0 0 0 0 0 0 0 0 0
72.5203 49.9911 7.0632 C 0 0 0 0 0 0 0 0 0 0 0 0
72.4817 48.7307 6.1876 C 0 0 0 0 0 0 0 0 0 0 0 0
72.4676 47.4487 7.0184 C 0 0 0 0 0 0 0 0 0 0 0 0
72.4079 46.1960 6.1098 C 0 0 0 0 0 0 0 0 0 0 0 0
72.8476 44.9214 6.8308 C 0 0 0 0 0 0 0 0 0 0 0 0
69.3674 45.9082 10.0888 H 0 0 0 0 0 0 0 0 0 0 0 0
71.1204 45.9748 10.2614 H 0 0 0 0 0 0 0 0 0 0 0 0
70.4079 44.6341 9.3233 H 0 0 0 0 0 0 0 0 0 0 0 0
68.2620 44.7176 8.5091 H 0 0 0 0 0 0 0 0 0 0 0 0
67.9625 44.7142 6.7755 H 0 0 0 0 0 0 0 0 0 0 0 0
66.1401 46.0683 6.9939 H 0 0 0 0 0 0 0 0 0 0 0 0
66.2713 45.8132 8.7122 H 0 0 0 0 0 0 0 0 0 0 0 0
67.5457 47.3613 10.1663 H 0 0 0 0 0 0 0 0 0 0 0 0
68.2163 49.1169 11.7605 H 0 0 0 0 0 0 0 0 0 0 0 0
68.6345 51.5040 12.2309 H 0 0 0 0 0 0 0 0 0 0 0 0
68.3727 53.1977 10.4415 H 0 0 0 0 0 0 0 0 0 0 0 0
67.7110 52.5047 8.1608 H 0 0 0 0 0 0 0 0 0 0 0 0
66.5713 47.4964 5.3471 H 0 0 0 0 0 0 0 0 0 0 0 0
66.5713 47.4964 5.3471 H 0 0 0 0 0 0 0 0 0 0 0 0
72.1427 47.1639 8.9264 H 0 0 0 0 0 0 0 0 0 0 0 0
71.7567 49.0277 9.7362 H 0 0 0 0 0 0 0 0 0 0 0 0
70.0854 48.8441 9.2335 H 0 0 0 0 0 0 0 0 0 0 0 0
70.3813 50.1875 7.3012 H 0 0 0 0 0 0 0 0 0 0 0 0
71.3383 51.0053 8.5783 H 0 0 0 0 0 0 0 0 0 0 0 0
73.4344 49.9826 7.6967 H 0 0 0 0 0 0 0 0 0 0 0 0
72.5677 50.8875 6.4079 H 0 0 0 0 0 0 0 0 0 0 0 0
71.5753 48.7637 5.5431 H 0 0 0 0 0 0 0 0 0 0 0 0
73.3699 48.7384 5.5175 H 0 0 0 0 0 0 0 0 0 0 0 0
73.5013 47.4357 7.4535 H 0 0 0 0 0 0 0 0 0 0 0 0
73.1047 46.3372 5.2542 H 0 0 0 0 0 0 0 0 0 0 0 0
71.4064 46.0513 5.6681 H 0 0 0 0 0 0 0 0 0 0 0 0
73.8765 45.0386 7.2323 H 0 0 0 0 0 0 0 0 0 0 0 0
72.1608 44.6738 7.6613 H 0 0 0 0 0 0 0 0 0 0 0 0
72.8446 44.0727 6.1149 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
3 4 2 0
3 5 1 0
5 6 1 0
6 7 1 0
7 8 2 0
8 9 1 0
9 10 2 0
10 11 1 0
11 12 2 0
12 13 1 0
13 14 2 0
14 15 1 0
15 16 2 0
16 17 1 0
2 18 1 0
18 19 1 0
19 20 1 0
20 21 1 0
21 22 1 0
22 23 1 0
23 24 1 0
24 25 1 0
16 7 1 0
23 18 1 0
14 9 1 0
1 26 1 0
1 27 1 0
1 28 1 0
5 29 1 0
5 30 1 0
6 31 1 0
6 32 1 0
8 33 1 0
10 34 1 0
11 35 1 0
12 36 1 0
13 37 1 0
17 38 1 0
17 39 1 0
18 40 1 0
19 41 1 0
19 42 1 0
20 43 1 0
20 44 1 0
21 45 1 0
21 46 1 0
22 47 1 0
22 48 1 0
23 49 1 0
24 50 1 0
24 51 1 0
25 52 1 0
25 53 1 0
25 54 1 0
M END
Best,
Susan
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
