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CanonicalizeMol may generate the mirror image of the starting coordinates
Discussed in https://github.com/rdkit/rdkit/discussions/5292
Originally posted by petrucci86 May 15, 2022
It was found that CanonicalizeMol() may generate the mirror image of the starting coordinates.
Here's a reproducible:
from rdkit import Chem
from rdkit.Chem import AllChem
compound = Chem.MolFromMolBlock("""CREYON GGG TRIMER
RDKit 3D
115123 0 0 0 0 0 0 0 0999 V2000
8.2042 -2.4634 3.1848 P 0 0 2 0 0 5 0 0 0 0 0 0
7.8494 -3.4834 2.1238 O 0 0 0 0 0 0 0 0 0 0 0 0
7.8138 -2.6951 4.6291 O 0 0 0 0 0 1 0 0 0 0 0 0
7.6396 -1.0063 2.7027 O 0 0 0 0 0 0 0 0 0 0 0 0
7.7680 0.1152 3.5679 C 0 0 0 0 0 0 0 0 0 0 0 0
7.3128 1.3872 2.8602 C 0 0 1 0 0 0 0 0 0 0 0 0
8.0988 1.5558 1.6567 O 0 0 0 0 0 0 0 0 0 0 0 0
7.2498 2.2325 0.6908 C 0 0 2 0 0 0 0 0 0 0 0 0
5.8832 2.4410 1.3458 C 0 0 1 0 0 0 0 0 0 0 0 0
5.8526 1.3516 2.3989 C 0 0 2 0 0 0 0 0 0 0 0 0
4.9584 1.6282 3.4643 O 0 0 0 0 0 0 0 0 0 0 0 0
3.4522 0.9784 3.4851 P 0 0 2 0 0 5 0 0 0 0 0 0
2.8200 1.3647 4.8079 O 0 0 0 0 0 0 0 0 0 0 0 0
3.5593 -0.4888 3.1199 O 0 0 0 0 0 1 0 0 0 0 0 0
2.6139 1.7212 2.2858 O 0 0 0 0 0 0 0 0 0 0 0 0
2.2464 3.0927 2.4139 C 0 0 0 0 0 0 0 0 0 0 0 0
1.5986 3.6604 1.1426 C 0 0 1 0 0 0 0 0 0 0 0 0
2.4788 3.5567 0.0163 O 0 0 0 0 0 0 0 0 0 0 0 0
1.6723 3.3375 -1.1641 C 0 0 2 0 0 0 0 0 0 0 0 0
0.2133 3.3102 -0.7152 C 0 0 1 0 0 0 0 0 0 0 0 0
0.3154 2.9161 0.7475 C 0 0 2 0 0 0 0 0 0 0 0 0
-0.8028 3.3390 1.5120 O 0 0 0 0 0 0 0 0 0 0 0 0
-2.0321 2.3004 1.8353 P 0 0 2 0 0 5 0 0 0 0 0 0
-2.9865 3.0192 2.7687 O 0 0 0 0 0 0 0 0 0 0 0 0
-1.4375 0.9747 2.2670 O 0 0 0 0 0 1 0 0 0 0 0 0
-2.8089 2.0481 0.4126 O 0 0 0 0 0 0 0 0 0 0 0 0
-3.5773 3.0909 -0.1820 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.1051 2.7174 -1.5726 C 0 0 1 0 0 0 0 0 0 0 0 0
-3.0592 2.4160 -2.4956 O 0 0 0 0 0 0 0 0 0 0 0 0
-3.5069 1.4069 -3.4170 C 0 0 2 0 0 0 0 0 0 0 0 0
-4.9474 1.0847 -3.0352 C 0 0 1 0 0 0 0 0 0 0 0 0
-5.0103 1.4902 -1.5683 C 0 0 2 0 0 0 0 0 0 0 0 0
-6.3259 1.8118 -1.1533 O 0 0 0 0 0 0 0 0 0 0 0 0
-7.2397 0.6938 -0.3787 P 0 0 2 0 0 5 0 0 0 0 0 0
-8.5428 1.3520 0.0250 O 0 0 0 0 0 0 0 0 0 0 0 0
-6.3938 -0.0082 0.6627 O 0 0 0 0 0 1 0 0 0 0 0 0
-7.5357 -0.3592 -1.5932 O 0 0 0 0 0 0 0 0 0 0 0 0
-8.3938 0.0106 -2.6592 C 0 0 0 0 0 0 0 0 0 0 0 0
-5.7829 1.9282 -3.8299 O 0 0 0 0 0 0 0 0 0 0 0 0
-2.6110 0.2634 -3.3539 N 0 0 0 0 0 0 0 0 0 0 0 0
-2.4041 -0.6383 -4.3635 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.4262 -1.4789 -3.8867 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.9536 -2.5536 -4.7147 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.0876 -3.3483 -4.3712 O 0 0 0 0 0 0 0 0 0 0 0 0
-1.6126 -2.5582 -5.9505 N 0 0 0 0 0 0 0 0 0 0 0 0
-2.6119 -1.6397 -6.3441 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.0283 -0.6667 -5.5644 N 0 0 0 0 0 0 0 0 0 0 0 0
-3.1227 -1.8316 -7.6012 N 0 0 0 0 0 0 0 0 0 0 0 0
-1.0178 -1.1344 -2.6346 N 0 0 0 0 0 0 0 0 0 0 0 0
-1.7444 -0.0735 -2.3431 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.2656 4.6518 -0.8403 O 0 0 0 0 0 0 0 0 0 0 0 0
2.0870 2.1015 -1.8143 N 0 0 0 0 0 0 0 0 0 0 0 0
1.7504 1.7238 -3.0873 C 0 0 0 0 0 0 0 0 0 0 0 0
2.3008 0.4731 -3.2379 C 0 0 0 0 0 0 0 0 0 0 0 0
2.1171 -0.2350 -4.4741 C 0 0 0 0 0 0 0 0 0 0 0 0
2.5844 -1.3440 -4.7000 O 0 0 0 0 0 0 0 0 0 0 0 0
1.3346 0.5106 -5.3647 N 0 0 0 0 0 0 0 0 0 0 0 0
0.8024 1.7932 -5.1035 C 0 0 0 0 0 0 0 0 0 0 0 0
1.0046 2.4283 -3.9705 N 0 0 0 0 0 0 0 0 0 0 0 0
0.0555 2.3352 -6.1164 N 0 0 0 0 0 0 0 0 0 0 0 0
2.9508 0.0592 -2.1156 N 0 0 0 0 0 0 0 0 0 0 0 0
2.7868 1.0548 -1.2666 C 0 0 0 0 0 0 0 0 0 0 0 0
5.9167 3.7336 1.9549 O 0 0 0 0 0 0 0 0 0 0 0 0
7.1601 1.4424 -0.5316 N 0 0 0 0 0 0 0 0 0 0 0 0
6.6121 1.8757 -1.7117 C 0 0 0 0 0 0 0 0 0 0 0 0
6.5983 0.7643 -2.5206 C 0 0 0 0 0 0 0 0 0 0 0 0
6.0300 0.8560 -3.8373 C 0 0 0 0 0 0 0 0 0 0 0 0
5.9802 -0.0802 -4.6250 O 0 0 0 0 0 0 0 0 0 0 0 0
5.5379 2.1446 -4.0800 N 0 0 0 0 0 0 0 0 0 0 0 0
5.5942 3.2226 -3.1684 C 0 0 0 0 0 0 0 0 0 0 0 0
6.1372 3.1160 -1.9760 N 0 0 0 0 0 0 0 0 0 0 0 0
5.0404 4.3950 -3.6119 N 0 0 0 0 0 0 0 0 0 0 0 0
7.1144 -0.3306 -1.8970 N 0 0 0 0 0 0 0 0 0 0 0 0
7.4228 0.1042 -0.6906 C 0 0 0 0 0 0 0 0 0 0 0 0
9.8135 -2.1697 3.1305 O 0 0 0 0 0 0 0 0 0 0 0 0
10.4457 -2.0051 1.8723 C 0 0 0 0 0 0 0 0 0 0 0 0
8.8215 0.2100 3.8504 H 0 0 0 0 0 0 0 0 0 0 0 0
7.1718 -0.0558 4.4697 H 0 0 0 0 0 0 0 0 0 0 0 0
7.5002 2.2436 3.5205 H 0 0 0 0 0 0 0 0 0 0 0 0
7.7453 3.1731 0.4234 H 0 0 0 0 0 0 0 0 0 0 0 0
5.0241 2.4145 0.6724 H 0 0 0 0 0 0 0 0 0 0 0 0
5.6160 0.3916 1.9270 H 0 0 0 0 0 0 0 0 0 0 0 0
1.5514 3.1876 3.2548 H 0 0 0 0 0 0 0 0 0 0 0 0
3.1441 3.6673 2.6474 H 0 0 0 0 0 0 0 0 0 0 0 0
1.3890 4.7240 1.3148 H 0 0 0 0 0 0 0 0 0 0 0 0
1.8905 4.1519 -1.8648 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.4500 2.6635 -1.2935 H 0 0 0 0 0 0 0 0 0 0 0 0
0.4591 1.8326 0.8245 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.9513 3.9803 -0.2596 H 0 0 0 0 0 0 0 0 0 0 0 0
-4.4175 3.3215 0.4813 H 0 0 0 0 0 0 0 0 0 0 0 0
-4.6509 3.5876 -1.9609 H 0 0 0 0 0 0 0 0 0 0 0 0
-3.4212 1.8275 -4.4257 H 0 0 0 0 0 0 0 0 0 0 0 0
-5.2480 0.0488 -3.2148 H 0 0 0 0 0 0 0 0 0 0 0 0
-4.5795 0.6944 -0.9505 H 0 0 0 0 0 0 0 0 0 0 0 0
-8.5550 1.0911 -2.6900 H 0 0 0 0 0 0 0 0 0 0 0 0
-9.3558 -0.4905 -2.5268 H 0 0 0 0 0 0 0 0 0 0 0 0
-7.9479 -0.3161 -3.6016 H 0 0 0 0 0 0 0 0 0 0 0 0
-6.6754 1.8983 -3.4495 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.3510 -3.2801 -6.6154 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.7963 -2.5853 -8.1959 H 0 0 0 0 0 0 0 0 0 0 0 0
-3.8446 -1.2235 -7.9721 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.6810 0.4802 -1.4179 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.1002 4.7142 -0.3501 H 0 0 0 0 0 0 0 0 0 0 0 0
1.1331 0.0944 -6.2690 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.3715 3.2501 -6.0209 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.0997 1.8359 -6.9852 H 0 0 0 0 0 0 0 0 0 0 0 0
3.1579 1.0652 -0.2523 H 0 0 0 0 0 0 0 0 0 0 0 0
5.1659 3.7905 2.5669 H 0 0 0 0 0 0 0 0 0 0 0 0
5.1024 2.3152 -4.9817 H 0 0 0 0 0 0 0 0 0 0 0 0
4.6182 4.4665 -4.5310 H 0 0 0 0 0 0 0 0 0 0 0 0
5.0285 5.2232 -3.0268 H 0 0 0 0 0 0 0 0 0 0 0 0
7.8362 -0.5082 0.0972 H 0 0 0 0 0 0 0 0 0 0 0 0
9.9754 -1.1901 1.3171 H 0 0 0 0 0 0 0 0 0 0 0 0
10.3844 -2.9333 1.2989 H 0 0 0 0 0 0 0 0 0 0 0 0
11.4973 -1.7597 2.0394 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0
1 3 1 1
1 4 1 0
4 5 1 0
5 6 1 0
6 7 1 0
7 8 1 0
8 9 1 0
9 10 1 0
10 11 1 0
11 12 1 0
12 13 2 0
12 14 1 6
12 15 1 0
15 16 1 0
16 17 1 0
17 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 2 0
23 25 1 1
23 26 1 0
26 27 1 0
27 28 1 0
28 29 1 0
29 30 1 0
30 31 1 0
31 32 1 0
32 33 1 0
33 34 1 0
34 35 2 0
34 36 1 1
34 37 1 0
37 38 1 0
31 39 1 0
30 40 1 0
40 41 1 0
41 42 2 0
42 43 1 0
43 44 2 0
43 45 1 0
45 46 1 0
46 47 2 0
46 48 1 0
42 49 1 0
49 50 2 0
20 51 1 0
19 52 1 0
52 53 1 0
53 54 2 0
54 55 1 0
55 56 2 0
55 57 1 0
57 58 1 0
58 59 2 0
58 60 1 0
54 61 1 0
61 62 2 0
9 63 1 0
8 64 1 0
64 65 1 0
65 66 2 0
66 67 1 0
67 68 2 0
67 69 1 0
69 70 1 0
70 71 2 0
70 72 1 0
66 73 1 0
73 74 2 0
1 75 1 0
75 76 1 0
10 6 1 0
21 17 1 0
32 28 1 0
50 40 1 0
47 41 1 0
62 52 1 0
59 53 1 0
74 64 1 0
71 65 1 0
5 77 1 0
5 78 1 0
6 79 1 1
8 80 1 6
9 81 1 6
10 82 1 6
16 83 1 0
16 84 1 0
17 85 1 1
19 86 1 6
20 87 1 6
21 88 1 6
27 89 1 0
27 90 1 0
28 91 1 6
30 92 1 6
31 93 1 1
32 94 1 1
38 95 1 0
38 96 1 0
38 97 1 0
39 98 1 0
45 99 1 0
48100 1 0
48101 1 0
50102 1 0
51103 1 0
57104 1 0
60105 1 0
60106 1 0
62107 1 0
63108 1 0
69109 1 0
72110 1 0
72111 1 0
74112 1 0
76113 1 0
76114 1 0
76115 1 0
M CHG 4 3 -1 14 -1 25 -1 36 -1
M END
""", removeHs=False)
Chem.AssignStereochemistryFrom3D(compound)
compound_canon = Chem.Mol(compound)
AllChem.CanonicalizeMol(compound_canon, normalizeCovar=True, ignoreHs=True)
Chem.AssignStereochemistryFrom3D(compound_canon)
print(AllChem.CalcRMS(compound_canon, compound))
5.352834539276516
chirality_compound = Chem.FindMolChiralCenters(compound, useLegacyImplementation=False)
chirality_compound_canon = Chem.FindMolChiralCenters(compound_canon, useLegacyImplementation=False)
print(chirality_compound == chirality_compound_canon)
False
print(chirality_compound)
print(chirality_compound_canon)
[(0, 'R'), (5, 'R'), (7, 'R'), (8, 'R'), (9, 'S'), (11, 'R'), (16, 'R'), (18, 'R'), (19, 'R'), (20, 'S'), (22, 'R'), (27, 'R'), (29, 'R'), (30, 'R'), (31, 'S'), (33, 'R')]
[(0, 'S'), (5, 'S'), (7, 'S'), (8, 'S'), (9, 'R'), (11, 'S'), (16, 'S'), (18, 'S'), (19, 'S'), (20, 'R'), (22, 'S'), (27, 'S'), (29, 'S'), (30, 'S'), (31, 'R'), (33, 'S')]
print(AllChem.GetAlignmentTransform(compound_canon, compound)[0])
3.8816982044141284
This is indeed a mirror image:
for i in range(compound_canon.GetConformer().GetNumAtoms()):
coord = compound_canon.GetConformer().GetAtomPosition(i)
coord.x = -coord.x
compound_canon.GetConformer().SetAtomPosition(i, coord)
Chem.AssignStereochemistryFrom3D(compound_canon)
chirality_compound_canon = Chem.FindMolChiralCenters(compound_canon, useLegacyImplementation=False)
print(chirality_compound == chirality_compound_canon)
True
print(AllChem.GetAlignmentTransform(compound_canon, compound)[0])
0.0
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