Hi RDKiters,
I am trying to output EZ configurations ('/', '\') in SMARTS syntax. While it
is possible to do it for SMILES with ease (using the MolToSmiles() method), I
didn't succeed for SMARTS. Below an example:
zbut = Chem.MolFromInchi('InChI=1S/C4H8/c1-3-4-2/h3-4H,1-2H3/b4-3-')
ebut = Chem.MolFromInchi('InChI=1S/C4H8/c1-3-4-2/h3-4H,1-2H3/b4-3+')
Chem.SanitizeMol(zbut)
Chem.SanitizeMol(ebut)
Chem.AssignStereochemistry(zbut)
Chem.AssignStereochemistry(ebut)
print('zbut', Chem.MolToSmarts(zbut), Chem.MolToSmiles(zbut))
# zbut [#6H3]-[#6H]=[#6H]-[#6H3] C/C=C\C
print('ebut', Chem.MolToSmarts(ebut), Chem.MolToSmiles(ebut))
# ebut [#6H3]-[#6H]=[#6H]-[#6H3] C/C=C/C
I also did try to build an "atomQuery" object, but without the expected result:
smarts = "[*]/[*]"
qb = Chem.MolFromSmarts(smarts).GetBondWithIdx(0)
print(qb.HasQuery())
# True
print(qb.GetBondDir())
# ENDUPRIGHT
print('SMARTS:', qb.GetSmarts())
# SMARTS: -
Any tip and help are welcome, thank you by advance,
Best wishes,
Thomas
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