Hello All,
When trying to find all the subgraph isomorphisms, one would anticipate from
the javadocs that the use of the
UniversalIsomorphismTester.getSubgraphAtomsMaps of CDK 1.2.5 would
return ALL the subgraph isomorphisms in a molecule of interest. However,
that is not the case. I am posting the code below to provide an example of
this behaviour: for the two molecules in question, we can see that there is
only one MCS from the MCSS code (as one would expect), but also only two
lists of RMaps from getSubgraphAtomsMaps, indicating only two subgraphs
identified.
Do you believe it would be possible to get ALL the subgraphs, no matter how
small, into the getSubgraphAtomsMaps, as one would anticipate from the
description, or is there another way to do this within (or outside CDK)?
Am I doing things correctly?
If the behaviour of getSubgraphAtomsMaps is intentionally such that it only
returns n biggest subgraph matches, may I kindly suggest that the javadoc
description be changed?
Regards,
Leonid Chepelev
***************************************************************
import java.util.Iterator;
import java.util.List;
import org.openscience.cdk.io.SMILESWriter;
import java.io.StringWriter;
import org.openscience.cdk.DefaultChemObjectBuilder;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.isomorphism.mcss.RMap;
import org.openscience.cdk.Molecule;
import org.openscience.cdk.smiles.SmilesParser;
import org.openscience.cdk.isomorphism.UniversalIsomorphismTester;
public class Main {
public static void main(String[] args) throws Exception {
SmilesParser smilesParser = new
SmilesParser(DefaultChemObjectBuilder.getInstance());
String referenceMolecule = "C1CCCCC1CC(=O)OCCCC";
String testmolecule = "C1CCCCC1CC(=O)O";
IAtomContainer molecule =
smilesParser.parseSmiles(referenceMolecule);
IAtomContainer lookup = smilesParser.parseSmiles(testmolecule);
List allthefragments =
UniversalIsomorphismTester.getOverlaps(molecule, lookup);
for (Iterator<IAtomContainer> i = allthefragments.iterator();
i.hasNext( ); ) {
IAtomContainer s = i.next( );
try {
StringWriter funna = new StringWriter();
SMILESWriter writemysmiles = new SMILESWriter();
writemysmiles.setWriter(funna);
Molecule themoleculetowrite = new Molecule(s);
writemysmiles.write(themoleculetowrite);
writemysmiles.close();
System.out.println(funna.toString());
funna.close();
} catch (Exception e) {
System.out.println(e.toString());
}
}
List<List<RMap>> atommappingsad =
UniversalIsomorphismTester.getSubgraphAtomsMaps(molecule, lookup);
for (List<RMap> j:atommappingsad) {
for (RMap estro:j){
try {
int firsta = estro.getId1();
int seconda = estro.getId2();
System.out.println("Atom " + firsta + " in G1 maps to
atom " + seconda + " in G2.");
} catch (Exception e) {
System.out.println(e.toString());
}
}
System.out.println("End of mapped fragment...");
}
}
}
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