Hi,
I have a .rxn file that I read using ReactionFromRxnFile().
Then I loop through the Products/Reactants and parse those according to my
needs.
One of those functions used inside this loop is EmbedMolecule()
However for some reactions I get the following error:
RuntimeError: Invariant Violation
bad lower bound
Violation occurred on line 190 in file
Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.cpp
Failed Expression: lb > DIST12_DELTA || clb > DIST12_DELTA
RDKIT: 2018.09.1
BOOST: 1_68
Can somebody help me out why this error is happening and how/if I can fix it?
This error is reproducible for me with the following code:
from rdkit.Chem import AllChem as Chem
rxn = Chem.ReactionFromRxnFile(‚Reaction.rxn')
for mol in rxn.GetProducts():
Chem.EmbedMolecule(mol)
The Reactions.rxn file is from RHEA:53958 from the RHEA-DB
Best,
Martin
$RXN
Rhea rhea-util112620181400 53958
RHEA:release=100
2 2
$MOL
CHEBI:137997
Ketcher 09291716412D 1 1.00000 0.00000 0
35 34 0 0 0 999 V2000
-19.1585 1.6569 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-18.2597 1.1577 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-20.0230 1.1577 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-20.8874 1.6569 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-21.7520 1.1577 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-19.9886 3.1542 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-20.8874 2.6551 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-19.9886 4.1525 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-21.7176 4.1525 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-20.8532 4.6517 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-19.1241 5.6500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-20.4878 7.0135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-19.9886 6.1491 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-19.4895 7.0135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-20.8532 5.6500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-21.7177 6.1491 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-18.2597 6.1491 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-16.2632 6.1491 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-17.2614 7.1474 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-17.2614 5.1509 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-17.2614 6.1491 0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0
-17.3951 1.6569 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
-15.3986 6.6482 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-14.5342 6.1491 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-13.6697 6.6482 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-12.8051 6.1491 0.0000 * 0 0 0 0 0 0 0 0 0 0 0 0
-14.5342 5.1509 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-13.6697 7.6465 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-15.3986 4.6517 0.0000 * 0 0 0 0 0 0 0 0 0 0 0 0
-16.5306 1.1577 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-15.6662 1.6569 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-16.5307 0.1595 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-14.8016 1.1577 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-13.9371 1.6567 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-13.0726 1.1576 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
7 4 1 0 0 0
4 3 1 0 0 0
3 1 1 0 0 0
1 2 1 0 0 0
2 22 1 0 0 0
4 5 2 0 0 0
6 8 1 0 0 0
10 8 1 0 0 0
7 6 1 0 0 0
10 9 2 0 0 0
10 15 1 0 0 0
15 13 1 0 0 0
13 11 1 0 0 0
11 17 1 0 0 0
13 12 1 0 0 0
13 14 1 0 0 0
15 16 1 6 0 0
17 21 1 0 0 0
21 18 1 0 0 0
21 19 2 0 0 0
21 20 1 0 0 0
18 23 1 0 0 0
23 24 1 0 0 0
24 25 1 0 0 0
25 26 1 0 0 0
24 27 1 1 0 0
25 28 2 0 0 0
27 29 1 0 0 0
22 30 1 0 0 0
30 31 1 0 0 0
30 32 2 0 0 0
31 33 1 0 0 0
33 34 1 0 0 0
34 35 1 0 0 0
M CHG 2 20 -1 35 1
M END
$MOL
CHEBI:16526
Ketcher 01291817112D 1 1.00000 0.00000 0
3 2 0 0 0 999 V2000
3.8434 -32.8314 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
3.8434 -31.8314 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.8434 -30.8314 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0 0 0
2 3 2 0 0 0
M END
$MOL
CHEBI:15378
Marvin 11160515022D
1 0 0 0 0 0 999 V2000
0.0000 0.0000 0.0000 H 0 3 0 0 0 0 0 0 0 0 0 0
M CHG 1 1 1
M END
$MOL
CHEBI:137996
Ketcher 09291716372D 1 1.00000 0.00000 0
38 37 0 0 0 999 V2000
-19.1613 1.6571 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-18.2624 1.1579 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-20.0259 1.1579 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-20.8905 1.6571 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-21.7552 1.1579 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-19.9916 3.1547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-20.8905 2.6555 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-19.9916 4.1531 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-21.7208 4.1531 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-20.8562 4.6524 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-19.1269 5.6508 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-20.4908 7.0145 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-19.9916 6.1500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-19.4924 7.0145 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-20.8562 5.6508 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-21.7209 6.1500 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-18.2624 6.1500 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-16.2656 6.1500 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-17.2640 7.1484 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-17.2640 5.1516 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-17.2640 6.1500 0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0
-17.3977 1.6571 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
-15.4009 6.6492 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-14.5364 6.1500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-13.6717 6.6492 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-12.8070 6.1500 0.0000 * 0 0 0 0 0 0 0 0 0 0 0 0
-14.5364 5.1516 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-13.6717 7.6476 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-15.4009 4.6524 0.0000 * 0 0 0 0 0 0 0 0 0 0 0 0
-16.5330 1.1579 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-15.6685 1.6571 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-16.5331 0.1595 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-14.8038 1.1579 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-13.9391 1.6570 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-13.0746 1.1578 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-12.2099 1.6570 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-13.0746 0.1594 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-13.9391 2.6554 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
7 4 1 0 0 0
4 3 1 0 0 0
3 1 1 0 0 0
1 2 1 0 0 0
2 22 1 0 0 0
4 5 2 0 0 0
6 8 1 0 0 0
10 8 1 0 0 0
7 6 1 0 0 0
10 9 2 0 0 0
10 15 1 0 0 0
15 13 1 0 0 0
13 11 1 0 0 0
11 17 1 0 0 0
13 12 1 0 0 0
13 14 1 0 0 0
15 16 1 6 0 0
17 21 1 0 0 0
21 18 1 0 0 0
21 19 2 0 0 0
21 20 1 0 0 0
18 23 1 0 0 0
23 24 1 0 0 0
24 25 1 0 0 0
25 26 1 0 0 0
24 27 1 1 0 0
25 28 2 0 0 0
27 29 1 0 0 0
22 30 1 0 0 0
30 31 1 0 0 0
30 32 2 0 0 0
31 33 1 0 0 0
33 34 1 0 0 0
34 35 1 0 0 0
35 36 2 0 0 0
35 37 1 0 0 0
34 38 1 6 0 0
M CHG 3 20 -1 37 -1 38 1
M END
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