Hi Noel,
it took me a while to find the time to compile the latest code from Git, but it
seems it all works great.
Thanks for the great news!
S
On 11/16/18 12:21 AM, Noel O'Boyle wrote:
> Have you tried the development version? This has been rewritten.
>
> On Fri, 16 Nov 2018, 00:19 Stefano Fo
Have you tried the development version? This has been rewritten.
On Fri, 16 Nov 2018, 00:19 Stefano Forli Hi,
>
> I've found a series of molecules that trigger what looks like a bug but I
> want to make sure there isn't something clearly wrong with the structures,
> before reporting it.
>
> The m
MOL files that represent molecules store kekule bond representations, not
aromatic bonds, so there is nothing to check.
First of all, if you are worried about aromaticity problems, you should use
the development version of Open Babel.
I wouldn't worry about the "-aa" option - it's only in the dev
I usually convert SMILES to SDF.
In my current project, I didn't call the flag -aa. Would that have affected
the aromaticity of the compounds or the default attempt would have worked?
I didn't see any warnings about failing attempts to fix the aromaticity.
What's the general rule of thumb here? Do
Here's a detail about Daylight's aromaticity detection that you might not
be able to deduce by looking at results. (This is not a trade secret; Dave
described this in public at several MUG meetings.)
1. Read the SMILES, SDF, or other format into an object.
2. Deduce the orbital configuration of EV
HI Jubilant,
The development version has rewritten handling of aromaticity, and as this
will be the next release, I will focus on this. The following talk gives an
overview of the process:
https://baoilleach.blogspot.co.uk/2017/08/my-acs-talk-on-kekulization-and.html
Your question didn't mention
El mié, 22-02-2012 a las 11:16 -0500, Geoffrey Hutchison escribió:
> > Im asking because I am using CDK and OpenBabel, and I am suffering of
> > interoperability problems, because both tools have different ways of
> > defining aromaticity.
>
> There is no unified aromaticity model in chemistry. I'
This is somewhat unrelated but I found that CDK has a well-documented
aromaticity algorithm. You could try looking at that before examining Open
Babel's implementation. They might be similar.
On Wed, Feb 22, 2012 at 8:16 AM, Geoffrey Hutchison <
ge...@geoffhutchison.net> wrote:
> > Im asking be
> Im asking because I am using CDK and OpenBabel, and I am suffering of
> interoperability problems, because both tools have different ways of
> defining aromaticity.
There is no unified aromaticity model in chemistry. I'm not sure the
aromaticity algorithm in Open Babel is publishable, and even
On Nov 22, 2010, at 6:24 PM, Craig A. James wrote:
> It appears that OpenBabel retains the original single/double bond assignment
> and uses that to determine aromaticity of the remaining part of the molecule
> after atoms are deleted. But depending on the original Kekule assignment of
> bonds
On 11/22/10 2:51 PM, Geoffrey Hutchison wrote:
>> Is there a way in OpenBabel 2.3 to standardise the bonds in molecules in
>> such way that the bond orders are no longer dependent on the way the
>> molecule was entered? For example, the two smiles representations of the
>> indole ring, N1C=CC2=C
> Is there a way in OpenBabel 2.3 to standardise the bonds in molecules in such
> way that the bond orders are no longer dependent on the way the molecule was
> entered? For example, the two smiles representations of the indole ring,
> N1C=CC2=C1C=CC=C2 and N1C=CC2=CC=CC=C12, lead to differences
> Is there a way in OpenBabel 2.3 to standardise the bonds in molecules in such
> way that the bond orders are no longer dependent on the way the molecule was
> entered? For example, the two smiles representations of the indole ring,
> N1C=CC2=C1C=CC=C2 and N1C=CC2=CC=CC=C12,
First off, I need
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