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MSAPlugin 3D cleans an input molecule when run from groovy
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Oleg

Joined: 21 May 2014
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Link to postPosted: Thu Feb 05, 2015 8:03 pmPost subject: MSAPlugin 3D cleans an input molecule when run from groovy Reply with quote

Dear all!

I'm trying to calculate molecular surface area 3D for several conformers with a groovy script. But it always return the same ASA for all (different) conformers. It seems that setInputMolecule(Molecule mol) always modifies the input structure, so MSAPlugin always gets the same (3D cleaned) structure instead of different structures of conformers.

When I run the MSA plugin manually in the Marvin interface, it works as expected, calculating the surface of the input molecule, but how do I run MSAPlugin for the input structure from the groovy code?

instantjchem 15.1.26.0; Marvin Sketch 14.9.1.0

Regards,

Oleg Miloserdov.

Gabor
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Joined: 29 May 2005
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Link to postPosted: Fri Feb 13, 2015 10:46 amPost subject: Reply with quote

Dear Oleg,

 

Could you please send the script you used and the input structure to reproduce the problem?

 

regards,

Gabor

Oleg

Joined: 21 May 2014
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Link to postPosted: Tue Feb 17, 2015 1:04 pmPost subject: Reply with quote

gimre wrote:

Dear Oleg,

 

Could you please send the script you used and the input structure to reproduce the problem?

 

regards,

Gabor

Dear Gabor,

Thank you for your reply.

I think that it would be better to send you the whole project as an example.

To reproduce the problem please launch the project attached. Then open Polymers -> Form view for Polymers.
Push "Surface area Calculator". Then refresh the form to see new Conformers generated (select another structure in Polymers block and then go back). 

In the Surface area block for each Conformer (from Conformers block) there must be calculated ASA, ASA+ etc.. ASA and others fields should be different for different Conformers, but they are the same and are equal to the surface areas of a 3d cleaned molecule. I think that it is not a prescribed behavior.

Regards, 
Oleg Miloserdov. 



Last edited by Oleg on Wed Jul 15, 2015 10:25 am; edited 1 time in total
Oleg

Joined: 21 May 2014
Posts: 7

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Link to postPosted: Thu Feb 19, 2015 11:07 amPost subject: Reply with quote

gimre wrote:

Dear Oleg,

 

Could you please send the script you used and the input structure to reproduce the problem?

 

regards,

Gabor

Dear Gabor,

The problem was solved by creation a new project, new tables and new forms.

But still there is a bug in the old project and I don't know how to solve it.

Regards,
Oleg Miloserdov 

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