Re: [Rdkit-discuss] ConstrainedEmbed and issues with overlapping Hs
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Re: [Rdkit-discuss] ConstrainedEmbed and issues with overlapping Hs
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From: Greg L. <gre...@gm...> - 2018-01-31 07:49:07
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Hi Susan,
This seems to be a bug in the embedding code. I will take a look and see if
I can figure out what's going on.
Best,
-greg
On Wed, Jan 17, 2018 at 4:45 PM, Susan Leung <sus...@st...
> wrote:
> 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
>
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