The new rdkit 2020.03 has stricter bond checks (maybe incorrect) and the code to merge molecules fails and gives the following error. A temporary workaround is to use ReplaceBond() instead of AddBond().
>>> from rdchiral.main import *
>>> rdchiralRunText("([#16;a:3]:[c:4]:[c:5](:[#7;a:6])-[CH2;D2;+0:7]-[CH2;D2;+0:8]-[c:9].[NH2;D1;+0:1]-[c:2])>>O=[N+;H0;D3:1](-[O-])-[c:2].[#16;a:3]:[c:4]:[c:5](:[#7;a:6])/[CH;D2;+0:7]=[CH;D2;+0:8]\\[c:9]", "[CH3:1][C:2](=[O:3])[NH:4][c:5]1[n:6][c:7]([CH2:21][CH2:22][c:23]2[cH:24][cH:25][c:26]([NH2:29])[cH:27][cH:28]2)[c:8]([CH2:10][c:11]2[cH:12][cH:13][cH:14][c:15]([S:17]([CH3:18])(=[O:19])=[O:20])[cH:16]2)[s:9]1")
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/ljn/lab_jensen/rdchiral/rdchiral/main.py", line 94, in rdchiralRunText
return rdchiralRun(rxn, reactants, **kwargs)
File "/home/ljn/lab_jensen/rdchiral/rdchiral/main.py", line 261, in rdchiralRun
merged_mol.GetBondBetweenAtoms(
RuntimeError: Pre-condition Violation
Stereo atoms should be specified before specifying CIS/TRANS bond stereochemistry
Violation occurred on line 288 in file /usr/local/rdkit/include/rdkit/GraphMol/Bond.h
Failed Expression: what <= STEREOE || getStereoAtoms().size() == 2
RDKIT: 2020.03.4
BOOST: 1_67
ReplaceBond() workaround, replace the code between line 259-266 with
The new rdkit 2020.03 has stricter bond checks (maybe incorrect) and the code to merge molecules fails and gives the following error. A temporary workaround is to use ReplaceBond() instead of AddBond().
ReplaceBond() workaround, replace the code between line 259-266 with