Hi Igor,
On Mon, Aug 27, 2012 at 11:17 PM, Igor Filippov
wrote:
> I'd like to pitch in about the changes in aromaticity perception - it
> looks like the more recent version of OB (2.3.1) is not recognizing one
> of the rings in the attached image as aromatic. I set atomic numbers for
> Z and D to
I'd like to pitch in about the changes in aromaticity perception - it
looks like the more recent version of OB (2.3.1) is not recognizing one
of the rings in the attached image as aromatic. I set atomic numbers for
Z and D to 0. I think the behavior was different before.
I would much prefer to see
One more interesting (and related) case: pleiadene
Carbons 3 and 8 are labelled as radical centers. Clearly this is a consequence
of the xyz format as you point out below.
Tom
-
30
C 0.0308731391 1.4691736561 0.0066435902
C 0.0509994911 -0.0014052265
I am happy to send you the entire test set if you are interested. Just reply to
me off list.
Tom
--
Dr. Thomas C. Allison, NIST
thomas.alli...@nist.gov
301-975-2216
On Apr 17, 2012, at 10:11 AM, Geoffrey Hutchison wrote:
>> Let me start with a little more background on the problem. I am usin
On Tue, Apr 17, 2012 at 7:56 AM, Noel O'Boyle wrote:
> Well, Geoff, if you're going to be working on this I've recently been
> subjecting ChEMBL to some canonicalisation tests, and can supply a good few
> more test cases. I'll wrap them up and email them to you off list tomorrow.
Would it be poss
Well, Geoff, if you're going to be working on this I've recently been
subjecting ChEMBL to some canonicalisation tests, and can supply a good few
more test cases. I'll wrap them up and email them to you off list tomorrow.
- Noel
On 17 April 2012 15:11, Geoffrey Hutchison wrote:
> > Let me start
> Let me start with a little more background on the problem. I am using Pybel
> to extract the information I need about a set of ~875 PAH molecules
> (including alkyl substituted and radical PAHs).
...
> "signature" of an error is typically that a C atom is labelled as sp3
> hybridized when it o
Oops, I forgot to reply to the list…Noel,Thank you for your email. I appreciate your help on this.Let me start with a little more background on the problem. I am using Pybel to extract the information I need about a set of ~875 PAH molecules (including alkyl substituted and radical PAHs). I gave th
As you've found, the aromacticity detection algorithm is not 100%
foolproof. If you could collect samples of failure, I'll file a bug report
on your behalf.
- Noel
On 6 April 2012 22:30, Tom Allison wrote:
> Hi all:
>
> When I use the following file named ("2175908.xyz")
>
> 32
>
> C -0
Hi all:
When I use the following file named ("2175908.xyz")
32
C -0.291523 0.3160533892 0.391375
C -0.0001205266 1.6897724142 -0.354856
C -1.1476732403 2.5783557540 -0.2608024912
C -0.7134957259 3.8662394928
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