Hi John,
thanks for the patch.
> I should also disclaim that I don't think the concept is in general
useful, may I ask why you need it?
You mean the daylight aromaticity concept?
We are migrating a pathway prediction system from chemaxon to cdk +
ambit-smarts. Chemaxon had apparently a similar aromaticity concept as
daylight, and the reaction rules have been defined accordingly. Some
cannot be applied when using the standard cdk aromaticity.
Regards,
Martin
Am 10.11.2015 um 16:12 schrieb John M:
Forwarding to list.
Regards,
John W May
john.wilkinson...@gmail.com <mailto:john.wilkinson...@gmail.com>
On 10 November 2015 at 15:04, John M <john.wilkinson...@gmail.com
<mailto:john.wilkinson...@gmail.com>> wrote:
Patch: https://github.com/cdk/cdk/pull/172
There is no default, you need to decide what's best. I'll admit
the naming 'cdkAromaticSet()' makes it sound useful for
aromaticity but it was basically just a restricted set of cycles
used in the old aromaticity model.
I tend to used *Cycles.all()* or *Cycles.or(Cycles.all(),
Cycles.edgeShort())* since the first one will fail for ring
systems like Fullerene C60. Some might think SSSR is sensible but
then in Fullerene C60, you'll have one ring in fullerene C60 which
isn't aromatic. Another common approach is to restrict the size of
the cycle (ala Open Babel) but it's easy to quickly find examples
with large aromatic rings.
I should also disclaim that I don't think the concept is in
general useful, may I ask why you need it?
John
Regards,
John W May
john.wilkinson...@gmail.com <mailto:john.wilkinson...@gmail.com>
On 10 November 2015 at 14:54, Martin Gütlein <guetl...@posteo.de
<mailto:guetl...@posteo.de>> wrote:
Hi John,
thanks for your response, so you will commit a fix for that?
That would be great, I would merge that fix into our cdk
1.5.11 build...
> Also you shouldn't use cdkAromaticSet() cycles...
So whats the default, .all() ?
Kind regards,
Martin
Am 10.11.2015 um 15:45 schrieb John M:
Hi Martin,
The daylight model should... but I some point I added a
valence constraint
(https://github.com/cdk/cdk/blob/master/base/standard/src/main/java/org/openscience/cdk/aromaticity/DaylightModel.java#L277).
Simple fix so will allow 4 and 6 for S and Se.
Also you shouldn't use cdkAromaticSet() cycles... that's
there for legacy reasons and doesn't handle porphyrin
correctly (for example).
John
Regards,
John W May
john.wilkinson...@gmail.com <mailto:john.wilkinson...@gmail.com>
On 10 November 2015 at 08:33, Martin Gütlein
<guetl...@posteo.de <mailto:guetl...@posteo.de>> wrote:
Hi,
is there an aromaticity model in CDK that works for this
structure:
O=s1cncc1 ?
This is what I tried:
String smiles = "O=s1cncc1";
IAtomContainer mol = new
SmilesParser(SilentChemObjectBuilder.getInstance()).parseSmiles(smiles);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
CycleFinder cycles = Cycles.cdkAromaticSet();
ElectronDonation model = ElectronDonation.cdk();
//.daylight()
Aromaticity aromaticity = new Aromaticity(model,
cycles);
System.out.println("is-aromatic: " +
aromaticity.apply(mol));
Kind regards,
Martin
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