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