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

#!/usr/bin/env python
from openeye.oechem import *
from openeye.oegraphsim import *

pmol = OEGraphMol()
OESmilesToMol(pmol, "c1cnc2c(c1)CC(CC2O)CF")

tmol = OEGraphMol()
OESmilesToMol(tmol, "c1cc2c(cc1)CC(CCl)CC2N")

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

for idx, match in enumerate(OEGetFPOverlap(pmol, tmol, fptype)):
    ostring = "match %2d: " % (idx + 1)
    for mpair in match.GetAtoms():
        p = mpair.pattern
        t = mpair.target
        ostring += "%d%s-%d%s " % (p.GetIdx(), OEGetAtomicSymbol(p.GetAtomicNum()),
                                   t.GetIdx(), OEGetAtomicSymbol(t.GetAtomicNum()))
    print(ostring)

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: