> Any idea of the 2.3 schedule yet?
Considering I haven't switched to using trunk on a daily basis, I'd estimate we
need 2-3 months of stabilization, testing, documentation, and bug-fixing before
release. That puts us in February.
I'll certainly make more regular snapshot releases before that p
Geoffrey Hutchison wrote:
>> I need certain things fixed, and I have to do it now, using OpenBabel 2. I
>> need a pragmatic, short-term solution. The questions I'm asking are:
>> - Whether there's any interest by others in the work I'll be doing
>> - Whether the current aromaticity detection i
> I need certain things fixed, and I have to do it now, using OpenBabel 2. I
> need a pragmatic, short-term solution. The questions I'm asking are:
> - Whether there's any interest by others in the work I'll be doing
> - Whether the current aromaticity detection in OpenBabel is bad
>scienc
2009/10/30 Craig A. James :
> 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 mode
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
Andrew,
Thanks for reminding me about the "X" specification. You're absolutely right,
that's the way to do it. I'd forgotten about "X", which Daylight introduced
specifically because of the problems with the "D" notation.
If we ever get around to an OpenSMARTS specification, I think the "D" s
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
http://www.dalkescientific.com/
On Oct 29, 2009, at 6:33 PM, Craig A. James wrote:
> 1. The "D" or "degree" in SMARTS
>
> [#6D2] is supposed to mean a a carbon atom with two bonds.
I disagree. The SMARTS documentation at
http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html
says
D - degree - explicit connec
The SMILES definition of aromaticity would seem to be an excellent
solution.
The only concern with elimination of "atom-is-aromatic" property is
that I would want to be able to search for an aromatic atom e.g.
carboxylic acid attached to an aromatic atom. If I can still do this
then I'm ha
I'm looking forward to these fixes.
The current handling is wrong in many cases. I see no problem with
replacing that with some version of "right" before 3.0. My current
approach is to remove problematic molecules from my datasets.
- Noel
2009/10/29 Craig A. James :
> Geoff and I have had a shor
> 1. The "D" or "degree" in SMARTS
>
> [#6D2] is supposed to mean a a carbon atom with two bonds. However,
> it treats explicit hydrogens as a bond,
Well, that can be changed. You're the former Daylight guy -- is "D"
supposed to ignore explicit hydrogens?
> For OpenBabel 3, we should clarify
This is just a quick summary of the technical problems I've discovered. I'm
putting them here so that if I've overlooked something, or anyone has insights
that I've missed, we can discuss them.
1. The "D" or "degree" in SMARTS
[#6D2] is supposed to mean a a carbon atom with two bonds. However
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 py
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