Default aromatize mode

Hi, what is the defult mode to aromatize molecule for a GraphMolecule, in method molecule.aromatise(). I know you have basic/chemaxon (1), general/daylight (2), and loose mode(3). It does not look like is the basic (1) based on my test. Can you let me know?

Thanks

Dong

The method falls back to General (2) method. "Only single or double bonds are changed to aromatic, aromatic bonds are not changed."

Se more: Marvin API documentation

 

Regards:
Balázs

Thanks for confirming this. We are in the process of converting Tripos SLN's queries into smarts and found that the general mode aromaticity is quite different from the Tripos aromaticity rule. The basic is close to what Tripos is using still there are minor differences. I think aromaticity will affect the donor and acceptor counts. I  tried to call calculator plugin  using the basic mode of aromaticity, however looks like the calculator plugin such as TopologyAnalyser would disregard the setting and rollback to the general based on my observation of the calculation on aromatic ring count. In my mind it should not, it should take in the mode user set. Can you confirm this with your calculator plugin developer.

Thanks

Dong

Hi,

I think aromaticity will affect the donor and acceptor counts.

Yes, it is right. We use the basic aromatization method  for calculating of the donor-acceptor count.

 

...TopologyAnalyser would disregard the setting and 

rollback to the general based on my observation of the calculation on 

aromatic ring count. In my mind it should not, it should take in the 

mode user set.

Yes , I agree with this. The aromatization should  be adjustable  on user's demands. This  problem will be solved asap. 

 

Jozsi

Hi Jozsi,

Can you double check on last point, the TopologyAnalyzor will ignor the aromaticity setting user designated before calling its setMol method. Base on my test it is true. If it is so does this occur across the board on all your calculator plugins as of now?

Thanks

Dong

Hi,

If it is so does this occur across the board on all your calculator plugins as of now?

Yes, it is true.

This is done intentionally because the parameters of a calculation have been optimized under  a specific aromatization type, (basic or general). This is why  the user don't have permission to modifiy such kind of key parmater as aromatization type. 

 

The topology analyser seems to be an exception because the aromatic atom count depends only on the definition of the aromatization, therefore, in this plugin we have to provide an option for overwriting the default aromatization type. So we fix this problem now.

 

Jozsi

Hi Dong,

Sorry, my informaion was not adequate yesterday.

Probably there is an alternative  way to set  aromatization method in TopologyAnalyser. I was informed by a developer even now.

You will be informed soon how to do.

 

Jozsi

TopologyAnalyser.setMolecule(MoleculeGraph mol, int aromatizationMode) method can be used to set the aromatization method in topology analyser calculations. It is part of the public API and it's available right now.

In Marvin 6.0 this setting will be available in TopologyAnalyserPlugin API, in  MarvinSketch, in cxcalc, and in Chemical Terms too.

Thanks for the information. I am using Marvin 5.8.2 API, I just need to upgrade to 6.

Dong

6.0 is not released yet. Currently, in 5.11.4 only the TopologyAnalyser.setMolecule(MoleculeGraph mol, int aromatizationMode) method is available.

In 6.0 the listed additinal features will be available. 6.0 can be expected around May 2013.

Zsolt