Fingerprint OverlapΒΆ

The OEGetFPOverlap function provides access to the fragments of two molecules that are considered equivalent based on a specific fingerprint type. This means that the returned fragment-pairs set the same bit “on” when fingerprints are generated. The following example shows how to retrieve the common five bond-length patterns of two molecules.

Listing 18: Example of accessing common patterns based on a fingerprint

package openeye.docexamples.oegraphsim;

import openeye.oechem.*;
import openeye.oegraphsim.*;

public class FPOverlap    {

    public static void main(String argv[]) {

        OEGraphMol pmol = new OEGraphMol();
        oechem.OESmilesToMol(pmol, "c1cnc2c(c1)CC(CC2O)CF");

        OEGraphMol tmol = new OEGraphMol();
        oechem.OESmilesToMol(tmol, "c1cc2c(cc1)CC(CCl)CC2N");

        OEFPTypeBase fptype = oegraphsim.OEGetFPType("Tree,ver=2.0.0,size=4096,bonds=5-5,atype=AtmNum|HvyDeg|EqHalo,btype=Order");

        int idx = 0;
        for (OEMatchBase match : oegraphsim.OEGetFPOverlap(pmol, tmol, fptype)) {
            idx++;
            System.out.printf("match %2d:", idx);
            for (OEMatchPairAtom mpair : match.GetAtoms()) {
                System.out.printf(" %d%s-%d%s", mpair.getPattern().GetIdx(), oechem.OEGetAtomicSymbol(mpair.getPattern().GetAtomicNum()),
                        mpair.getTarget().GetIdx(), oechem.OEGetAtomicSymbol(mpair.getTarget().GetAtomicNum()));
            }
            System.out.printf("\n");
        }
    }
}

The first three matches returned by the Listing 18 are depicted in the next table. The output of code is the following:

match  1: 3C-2C  9C-11C  4C-3C  8C-10C  7C-7C  11C-8C
match  2: 3C-2C  4C-3C  5C-4C  6C-6C  7C-7C  8C-8C
match  3: 3C-2C  4C-3C  5C-4C  6C-6C  7C-7C  8C-10C
match  4: 3C-2C  4C-3C  5C-4C  6C-6C  7C-7C  11C-8C
match  5: 3C-2C  4C-3C  5C-4C  6C-6C  7C-7C  11C-10C
match  6: 3C-2C  9C-11C  4C-3C  6C-6C  7C-7C  11C-8C

... truncated  ...
Example of matches returned by the OEGetFPOverlap function. The numbers depicted next to the atoms are the atom indices.
../_images/FPOverlap-01.png
../_images/FPOverlap-02.png
../_images/FPOverlap-03.png

Warning

Even though the OEGetFPOverlap function returns an iterator of OEMatchBase objects, they are not matches in the traditional sense, i.e. the atom-pair and bond-pair correspondences between the pattern and the target atoms and bonds are not guaranteed. See example depicted below.

../_images/FPOverlap-NonPair-01.png

The two highlighted patterns set the same bit when fingerprints are generated, but the returned match is not pair-wise. The numbers depicted next to the atoms are the atom indices.

See also

Hint

The OEGetFPOverlap can be used to visualize molecule similarity based on a given fingerprint type. See more details in: