Hi, Greg,
This is a bit of a meta-comment, so I hope it's appropriate here. I might
possibly make more comments on the github site.
After this discussion went dead (but before I retired from Schrödinger), I
looked into the origin of that bizarre multicyclic structure. It turned out
to have
This is reviving a long-dead thread because I just marked the associated
issue as "won't fix" and some of you might be interested in the reasons.
Here's the bug: https://github.com/rdkit/rdkit/issues/523
The comment explaining my thinking is here:
Hi,
I do not insist on using kekule forms. In fact, I said that using a
double bond between two aromatic atoms in a SMILES does not appear
problematic to me.
I was trying to say in the line you quoted that even if analysis of QM
results leads to a verdict of non-aromaticity, such a verdict
On 06/17/2015 08:36 AM, Peter Shenkin wrote:
We could consider some quantum-mechanical calculations
Yes! for the question of the true nature of the molecule. But that not
need not affect the way canonicalization is done.
Again, define canonical. If you insist on using kekule form in a
Hi, Greg,
Within the SMILES framework, it seems to me that if you allow the atoms to
be aromatic, then these are two Kekule structures of the same aromatic
system, and however you do the canonicalization, they ought to canonicalize
to the same structure, which the two examples did not do. I don't
We could consider some quantum-mechanical calculations ... well, I always
hated this discussion when I heard for my web service with millions of
structures, I should consider quantum-mechanical calculations as part of
the structure normalization/canonicalization ;-)
On Wed, Jun 17, 2015 at 8:22
We could consider some quantum-mechanical calculations
Yes! for the question of the true nature of the molecule. But that not
need not affect the way canonicalization is done.
These are two different forms of entertainment
-P.
On Wed, Jun 17, 2015 at 3:24 AM, Markus Sitzmann
On Jun 16, 2015, at 10:20 PM, Peter Shenkin wrote:
[N-]=[N+]=NC(=O)N1C(=O)N([N+]([O-])=O)C2(C13C4=C56)C4=C5C2=C36
[N-]=[N+]=NC(=O)N(C(=O)N1[N+]([O-])=O)C(c23)(c4c56)C16c3c5c24
rdkit canonicalizes the two to the following, respectively:
[N-]=[N+]=NC(=O)N1C(=O)N([N+]([O-])=O)C2(C13C4=C56)C4=C5C2=C36
[N-]=[N+]=NC(=O)N(C(=O)N1[N+]([O-])=O)C(c23)(c4c56)C16c3c5c24
rdkit canonicalizes the two to the following, respectively:
[N-]=[N+]=NC(=O)N1C(=O)N([N+](=O)[O-])C23c4c5c2c2c-5c4C213
Thanks, Andrew...
BTW, to help it out, you can ask RDKit to include all of the bond information,
as otherwise it will use the single-or-aromatic notation.
That's a nice feature.
I don't know how it is that RDKit adds a double bond to the second cubane,
given only aromatic carbons and
10 matches
Mail list logo
