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

#include <openeye.h>
#include <oesystem.h>
#include <oechem.h>
#include <oegraphsim.h>

using namespace OESystem;
using namespace OEChem;
using namespace OEGraphSim;

int main()
{
  OEGraphMol pmol;
  OESmilesToMol(pmol, "c1cnc2c(c1)CC(CC2O)CF");

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

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

  unsigned int idx = 0;
  for (OEIter<OEMatchBase> match = OEGetFPOverlap(pmol, tmol, fptype); match; ++match)
  {
    idx++;
    printf("match %2d:", idx);
    for (OEIter<OEMatchPair<OEAtomBase> > mpair = match->GetAtoms(); mpair; ++mpair)
    {
      printf(" %d%s-%d%s", mpair->pattern->GetIdx(), OEGetAtomicSymbol(mpair->pattern->GetAtomicNum()),
             mpair->target->GetIdx(), OEGetAtomicSymbol(mpair->target->GetAtomicNum()));
    }
    printf("\n");
  }
  return 0;
}

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: