Dear Reinis and dear all,
actually the aromaticity detection problem is only raised when dealing
with charged heterocyclic systems with formats which do not support
explicit formal charges (e.g., MOL2), while there are no problems with
SDF and MOL files. I was initially misled about this and I
Looking at blame online, it seems that Tim made the change to allow
ferrocene structures to be normalised for the eMolecule
canonicalisation tests:
http://openbabel.svn.sourceforge.net/viewvc/openbabel/openbabel/trunk/src/formats/smilesformat.cpp?r1=4033r2=4034;
IMO, structure normalisations
On Thu, May 24, 2012 at 6:03 AM, Noel O'Boyle baoille...@gmail.com wrote:
Looking at blame online, it seems that Tim made the change to allow
ferrocene structures to be normalised for the eMolecule
canonicalisation tests:
On Thu, May 24, 2012 at 7:45 AM, Craig James cja...@emolecules.com wrote:
On Thu, May 24, 2012 at 6:03 AM, Noel O'Boyle baoille...@gmail.comwrote:
Looking at blame online, it seems that Tim made the change to allow
ferrocene structures to be normalised for the eMolecule
canonicalisation
Here are my changes:
http://openbabel.svn.sourceforge.net/viewvc/openbabel/openbabel/trunk/src/formats/smilesformat.cpp?r1=4758r2=4763;
Craig
On Thu, May 24, 2012 at 8:00 AM, Craig James cja...@emolecules.com wrote:
On Thu, May 24, 2012 at 7:45 AM, Craig James cja...@emolecules.comwrote:
On
I should probably devise a test application to add to OpenBabel so that this
doesn't happen again. Is there some way to add a test to the system where
success is defined by performance rather than correct output?
There are a few ways. Probably the easiest is to add a small unit test (look
Hi,
Deleting the copying of the molecule should be no problem since the
ferrocene specific code is also gone. This code was added to make the
canonicalization of ferrocene-like structures possible. Since it
requires 10! labelings to be analysed, it took forever to find the
canonical labeling.
If I'm not mistaken, these two SMILES should represent the same molecule,
but OB thinks they're different:
c1n1
c1[n]1
According to the SMILES spec, putting the nitrogen in brackets only says
that its charge is zero and H-count is zero, which are the defaults when
the nitrogen is
Hi,
I've run into a case where one of my algorithms runs something like 10,000
time slower in 2.3.x than it did in 2.2.x, and running valgrind with the
callgrind tool seems to indicate that aromaticity detection is the
problem.
Here's the problem: Normally when you generate a SMILES, it detects
More information on this question...
On Wed, May 23, 2012 at 3:05 PM, Craig James cja...@emolecules.com wrote:
Hi,
I've run into a case where one of my algorithms runs something like 10,000
time slower in 2.3.x than it did in 2.2.x, and running valgrind with the
callgrind tool seems to
On Mon, Jul 5, 2010 at 5:56 PM, Craig A. James cja...@emolecules.com wrote:
On 7/2/10 4:44 AM, Tim Vandermeersch wrote:
Hi,
I have put the old aromaticity algorithm back since unit tests were
failing. I tried to debug the problem but didn't get far. When Craig
has time to look at this, I
Hi,
I have put the old aromaticity algorithm back since unit tests were
failing. I tried to debug the problem but didn't get far. When Craig
has time to look at this, I can merge this again.
Although electron counting isn't the problem with the failing unit
test, Craig has a point. There should
On 7/2/10 4:44 AM, Tim Vandermeersch wrote:
Hi,
I have put the old aromaticity algorithm back since unit tests were
failing. I tried to debug the problem but didn't get far. When Craig
has time to look at this, I can merge this again.
Although electron counting isn't the problem with the
Andrew Dalke wrote:
On Oct 29, 2009, at 7:49 PM, Chris Swain wrote:
The SMILES definition of aromaticity would seem to be an excellent
solution.
Except when it isn't. That's why different people and different
software have different aromaticity models.
I wrote some about this in
Geoff and I have had a short private conversation about aromaticity, and I had
some ideas that are better expressed here on the discussion board.
Currently, OpenBabel's aromaticity (typer.cpp) is pretty well broken. It seems
to accept most correct structures, ordinary stuff like benzenes and
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