update docs as part of #432

This commit is contained in:
Greg Landrum
2015-02-22 04:57:02 +01:00
parent 6015efb370
commit dab18279dc
3 changed files with 25 additions and 1 deletions

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@@ -20,7 +20,6 @@ The rules are relatively straightforward.
Aromaticity is a property of atoms and bonds in rings.
An aromatic bond must be between aromatic atoms, but a bond between aromatic atoms does not need to be aromatic.
For example the fusing bonds here are not considered to be aromatic by the RDKit:
.. image:: images/picture_9.png
@@ -83,6 +82,31 @@ True
>>> m.GetBondBetweenAtoms(6,7).GetIsAromatic()
False
A special case, heteroatoms with radicals are not considered candidates for aromaticity:
.. image:: images/picture_10.png
>>> m = Chem.MolFromSmiles('C1=C[N]C=C1')
>>> m.GetAtomWithIdx(0).GetIsAromatic()
False
>>> m.GetAtomWithIdx(2).GetIsAromatic()
False
>>> m.GetAtomWithIdx(2).GetNumRadicalElectrons()
1
Carbons with radicals, however, are still considered:
.. image:: images/picture_11.png
>>> m = Chem.MolFromSmiles('C1=[C]NC=C1')
>>> m.GetAtomWithIdx(0).GetIsAromatic()
True
>>> m.GetAtomWithIdx(1).GetIsAromatic()
True
>>> m.GetAtomWithIdx(1).GetNumRadicalElectrons()
1
**Note:** For reasons of computation expediency, aromaticity perception is only done for fused-ring systems where all members are at most 24 atoms in size.

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