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qry = Chem.MolFromMolBlock('''
Mrv2108 08012107372D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 11 11 0 0 0
M V30 BEGIN ATOM
M V30 1 C -2.4167 7.8734 0 0
M V30 2 C -3.7503 7.1034 0 0
M V30 3 C -3.7503 5.5633 0 0
M V30 4 N -2.4167 4.7933 0 0
M V30 5 C -1.083 5.5633 0 0
M V30 6 C -1.083 7.1034 0 0
M V30 7 N 0.3973 7.5279 0 0
M V30 8 N 0.3104 5.0377 0 0
M V30 9 C 1.2585 6.2511 0 0
M V30 10 * 0.3539 6.2828 0 0
M V30 11 C 1.5089 8.2833 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 1 1 2
M V30 2 2 2 3
M V30 3 1 3 4
M V30 4 2 4 5
M V30 5 1 5 6
M V30 6 2 1 6
M V30 7 1 7 6
M V30 8 1 5 8
M V30 9 1 8 9
M V30 10 2 7 9
M V30 11 1 10 11 ENDPTS=(2 8 7) ATTACH=ANY
M V30 END BOND
M V30 END CTAB
M END
''')
which corresponds to this molecule:
The SMARTS generated indicate that the N atom which doesn't get the attachment point ends up an implicit H:
for m in rdMolEnumerator.Enumerate(qry):
print(Chem.MolToSmarts(m))
produces:
[#6]1:[#6]:[#6]:[#7]:[#6]2:[#6]:1:[#7]:[#6]:[#7H]:2-[#6]
[#6]1:[#6]:[#6]:[#7]:[#6]2:[#6]:1:[#7](:[#6]:[#7H]:2)-[#6]
Describe the bug
When enumerating this query:
which corresponds to this molecule:
The SMARTS generated indicate that the N atom which doesn't get the attachment point ends up an implicit H:
Expected behavior
The SMARTS for those should be:
Configuration (please complete the following information):
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