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If a molecule contains variable attachment points with connected-atom indices lower than the atom indices found in a linknode, the enumeration fails.
Here's an example molecule where this happens:
And the actual reproducible:
>>> m = Chem.MolFromMolBlock('''
... Mrv2014 02182116082D
...
... 0 0 0 0 0 999 V3000
... M V30 BEGIN CTAB
... M V30 COUNTS 15 14 0 0 0
... M V30 BEGIN ATOM
... M V30 1 C -2.1474 10.0453 0 0
... M V30 2 C -3.481 9.2753 0 0
... M V30 3 C -3.481 7.7352 0 0
... M V30 4 C -2.1474 6.9652 0 0
... M V30 5 C -0.8137 7.7352 0 0
... M V30 6 C -0.8137 9.2753 0 0
... M V30 7 N 0.6334 9.802 0 0
... M V30 8 C 0.7204 7.3118 0 0
... M V30 9 C 1.5815 8.5885 0 0
... M V30 10 * -3.0365 9.0186 0 0
... M V30 11 O -3.0365 11.3286 0 0
... M V30 12 C 1.0579 11.2824 0 0
... M V30 13 O -0.0119 12.3901 0 0
... M V30 14 * 1.151 7.9501 0 0
... M V30 15 C 1.151 10.2601 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 9
... M V30 8 1 7 6
... M V30 9 1 5 8
... M V30 10 2 8 9
... M V30 11 1 10 11 ENDPTS=(3 2 3 1) ATTACH=ANY
... M V30 12 1 7 12
... M V30 13 1 12 13
... M V30 14 1 14 15 ENDPTS=(2 8 9) ATTACH=ANY
... M V30 END BOND
... M V30 LINKNODE 1 2 2 12 7 12 13
... M V30 END CTAB
... M END''')
>>> res = rdMolEnumerator.Enumerate(m)
Traceback (most recent call last):
File "<ipython-input-5-c7650297002a>", line 1, in <module>
res = rdMolEnumerator.Enumerate(m)
ValueError: bond not found between atoms in LINKNODE '1 2 2 12 7 12 13'
The text was updated successfully, but these errors were encountered:
If a molecule contains variable attachment points with connected-atom indices lower than the atom indices found in a linknode, the enumeration fails.
Here's an example molecule where this happens:
And the actual reproducible:
The text was updated successfully, but these errors were encountered: