Hi all,
I have run across some errors when attempting to use RunReactants on
molecules with specified stereochemistry, as show in the below two example
cases:
I notice that the same molecules will run without errors using this
reaction specification if stereochemistry is turned off.
case 1:
>>> rxn2 =
AllChem.ReactionFromSmarts('[#1;D1R0:4][#8;H1D2R0:3][#6;H0D3R0:2](=[#8;H0D1R0:5])[#6;D4;H1,H0,H2:1]([#6:7])[#6,#1D1AR0,ClH0D1AR0,FH0D1AR0,BrH0D1AR0:6]>>[*:3]=[*:2]=[*:5].[*:4]-[*:1](-[*:6])-[*:7]')
>>> mol2 = AllChem.MolFromSmiles('CSCC[C@@H](N)C(=O)O')
>>> mol2 = AllChem.AddHs(mol2)
>>> rxn2.RunReactants([mol2])
[13:06:37]
****
Invariant Violation
expected reactant bond not found
Violation occurred on line 533 in file
/tmp/rdkit20150904-11712-k5lp6f/rdkit-Release_2015_03_1/Code/GraphMol/ChemReactions/ReactionRunner.cpp
Failed Expression: rBond
****
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
RuntimeError: Invariant Violation
>>> mol2 = AllChem.MolFromSmiles('CSCCC(N)C(=O)O')
>>> mol2 = AllChem.AddHs(mol2)
>>> rxn2.RunReactants([mol2])
((<rdkit.Chem.rdchem.Mol object at 0x1078822e8>, <rdkit.Chem.rdchem.Mol
object at 0x1078823c8>),)
case 2:
rxn =
AllChem.ReactionFromSmarts('[#1;D1R0:5][#6;H1D4:4]1[#6;H1D4:6][#6;H1D4:7]([#8;H1D2R0:8])[#6;H1D4:9][#8;H0D2:1][#6;H1D4:2]1[#8;H1D2R0:3]>>[*:3]-[*:2](-[*:5])-[*:4]-1-[*:1]-[*:9]-[*:7](-[*:8])-[*:6]-1')
>>> mol = AllChem.MolFromSmiles('OC[C@H]1OC(O)[C@H](O)[C@H](O)[C@@H]1O')
>>> mol = AllChem.AddHs(mol)
>>> rxn.RunReactants([mol])
[12:51:43]
****
Invariant Violation
expected reactant bond not found
Violation occurred on line 533 in file
/tmp/rdkit20150904-11712-k5lp6f/rdkit-Release_2015_03_1/Code/GraphMol/ChemReactions/ReactionRunner.cpp
Failed Expression: rBond
****
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
RuntimeError: Invariant Violation
>>> mol = AllChem.MolFromSmiles('OCC1OC(O)C(O)C(O)C1O')
>>> mol = AllChem.AddHs(mol)
>>> rxn.RunReactants([mol])
((<rdkit.Chem.rdchem.Mol object at 0x107882278>,),)
Would anyone be able to shed light on why this might be occurring?
Cheers,
Dante
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