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How to integrate Lee&Richards algorithm to Instant JChem
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Oleg

Joined: 21 May 2014
Posts: 7

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Link to postPosted: Fri Feb 03, 2017 9:53 pmPost subject: How to integrate Lee&Richards algorithm to Instant JChem Reply with quote

Dear all!

I need to calculate SASA using Lee&Richards algorithm for a big set of structures. Please help me to choose the fastest and the easiest way to integrate this algorithm to Instant JChem. For example I can make a plugin for this purpose (using netbeans) and include it to the program, but it would be better, if I can base on the code of a standard algorithm in molecular surface area plugin. 

Regards,
Oleg Miloserdov.

Daniel
ChemAxon personnel
Joined: 22 Jan 2012
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Link to postPosted: Mon Feb 06, 2017 4:56 pmPost subject: Reply with quote

Dear Oleg, 

The ChemAxon SASA calculator in the MSA plugin doesn't use the Lee-Richards algorithm, but the Hasel-type atom increment method. You can find the reference of this method here:

http://www.sciencedirect.com/science/article/pii/0898552988900152

Regarding integrating the Lee-Richards algorithm into JChem, I can't give you a technical answer. I rather move this topic to the Instant JChem team, they will help you with this issue.

Best regards, 

Daniel

Oleg

Joined: 21 May 2014
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Link to postPosted: Tue Feb 07, 2017 4:05 pmPost subject: Reply with quote

Dear Daniel,

Thank you for your help and the reference! I'll wait for a response from the Instant JChem team.

Regards,
Oleg Miloserdov.

Ondrej
ChemAxon personnel
Joined: 04 Jan 2016
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Link to postPosted: Wed Feb 08, 2017 11:08 amPost subject: Reply with quote

Dear Oleg,

there are several ways how to implement this in instant jchem. Java plugin which you suggest might be the most elegant, but also the most complicated way. Another option is to use calculated fields. This can be used as an interface for some simple groovy code. Yet another possibility is to call external program from the groovy script. This may be the easiest and least error-prone possibility.

That said, I encourage you also to assess whether you really need to use Lee and Richards algorithm. If this is for validation or reproducibility reasons, then go for it. In other cases, I am less sure. If you simply went for speed, you could go along with one of ChemAxon's current algorithms. If you were after accuracy, then you should probably go for some simulation tool.

Ondrej

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