Hi all,
I wanted to contribute sth (instead of just sending bugs and feature
requests): here is how I used UniversalIsomorphismTester.getOverlaps to
compute the MCS for more than just 2 Molecules (runtime is of course
O(n^2)).
(I hope its not yet included in CDK, havent found it, though).
Best regards,
Martin
org.openscience.cdk.isomorphism.MultiMCSComputer
[[[
package org.openscience.cdk.isomorphism;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Comparator;
import java.util.List;
import org.openscience.cdk.Molecule;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
public class MultiMCSComputer
{
public static IAtomContainer computeMCS(IAtomContainer mols[]) throws
CDKException
{
// sort according to number of atoms in ascending order to reduce
computational effort
Arrays.sort(mols, new Comparator<IAtomContainer>()
{
@Override
public int compare(IAtomContainer o1, IAtomContainer o2)
{
return new Integer(o1.getAtomCount()).compareTo(new
Integer(o2.getAtomCount()));
}
});
List<IAtomContainer> candidates = new ArrayList<IAtomContainer>();
// iterate over compounds
for (IAtomContainer mol : mols)
{
mol = new
Molecule(AtomContainerManipulator.removeHydrogens(mol));
if (candidates.size() == 0)
{
// if == first compound, add compound to candidates
candidates.add(mol);
}
else
{
// else compute mcs of all candidates with this compound,
use results as new candidates
List<IAtomContainer> newCandiates = new
ArrayList<IAtomContainer>();
for (IAtomContainer can : candidates)
{
List<IAtomContainer> canMCS =
UniversalIsomorphismTester.getOverlaps(can, mol);
for (IAtomContainer m : canMCS)
if (m.getAtomCount() > 0)
newCandiates.add(m);
}
candidates = newCandiates;
if (candidates.size() == 0)
return null;
}
}
IAtomContainer max = null;
for (IAtomContainer mol : candidates)
if (max == null || mol.getAtomCount() > max.getAtomCount())
max = mol;
return max;
}
}
]]]
--
Dipl-Inf. Martin Gütlein
Phone:
+49 (0)761 203 7633 (office)
+49 (0)177 623 9499 (mobile)
Email:
[email protected]
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