Tags
CDK, Java, SMSD, substructure
Today with the help of Egon the SMSD was successfully integrated with the CDK. The nightly build is available via nightly build. If you are interested in the source code then please visit GIT SMSD.
Q: How can I compute Substructure search between a query and target molecule?
A: An example for Substructure search:
//Turbo mode search
//Bond Sensitive is set true
SMSD comparison = new SMSD(Algorithm.SubStructure, true);
// set molecules and remove hydrogens
comparison.init(queryMol, targetMol, true, true);
// set chemical filter true
comparison.setChemFilters(true, true, true);
if (comparison.isSubgraph()) {
//Get similarity score
System.out.println(“Tanimoto coefficient: ” + comparison.getTanimotoSimilarity());
}
Q: How can I compute MCS search between a query and target molecule?
A: An example for MCS search:
//{ 0: Default SMSD Algorithm, 1: MCSPlus Algorithm, 2: VFLibMCS Algorithm, 3: CDKMCS Algorithm}
//Bond Sensitive is set true
SMSD comparison = new SMSD(Algorithm.DEFAULT, true);
// set molecules and remove hydrogens
comparison.init(queryMol, targetMol, true, true);
// set chemical filter true
comparison.setChemFilters(true, true, true);
//Get similarity score
System.out.println(“Tanimoto coefficient: ” + comparison.getTanimotoSimilarity());
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If you interested in the complete java code please refer to:
Ricardo Pino said:
I want to know how do this algorithm for n>2 molecules
greetings and thanks you
Ricardo
chembioinfo said:
please check my recent blog https://chembioinfo.wordpress.com/2011/03/01/mcs-between-n-molecules/
surajit ray said:
Awesome ! I was waiting for this ! Now some of my server code can get a new lease of life ! UIT was really bringing the server to a crawl.
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chembioinfo said:
Thanks, I use Enterprise layout designed by StudioPress. Good Luck with your blogging!