On Wed, Nov 18, 2015 at 1:13 PM, Dante <dante.esgrimi...@gmail.com> wrote:
> 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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