Molecule FragmentationΒΆ

The OEMedChem TK currently provides four ways to partition a molecule into fragments:

These functions return an iterator over OEAtomBondSet objects that store the atoms and the bonds of the fragments.

The following examples (Listing 1, Listing 2) show how to fragment a molecule into ring and chain components. The code loops over the OEAtomBondSet objects returned by the OEGetRingChainFragments. Each OEAtomBondSet object is used to initialize an atom and a bond predicates. These predicates specify which atoms and bonds have to be considered when creating a subset of the molecule, i.e the fragment, when calling the OESubsetMol function. See the depiction of the input molecule and the generated fragments in Figure: Example of fragmentation.

Listing 1: Example of molecule fragmentation

from __future__ import print_function
from openeye import oechem
from openeye import oemedchem

mol = oechem.OEGraphMol()
oechem.OESmilesToMol(mol, "COc1ccc(cc1)CC(=O)N")

for frag in oemedchem.OEGetRingChainFragments(mol):
    fragatompred = oechem.OEIsAtomMember(frag.GetAtoms())
    fragbondpred = oechem.OEIsBondMember(frag.GetBonds())

    fragment = oechem.OEGraphMol()
    adjustHCount = True
    oechem.OESubsetMol(fragment, mol, fragatompred, fragbondpred, adjustHCount)
    print(oechem.OEMolToSmiles(fragment))

The output of Listing 1 is the following:

CO
c1ccccc1
CC(=O)N
../_images/Fragmentation.png

Example of fragmentation (A) input molecule (B) fragments returned by the OEGetRingChainFragments function

See also

The following example (Listing 2) shows how to fragment a molecule into ring and chain components with annotations. See the depiction of the input molecule and the generated fragments in Figure: Example of Bemis Murcko fragmentation.

Listing 2: Example of molecule fragmentation with annotations

from __future__ import print_function
from openeye import oechem
from openeye import oemedchem

mol = oechem.OEGraphMol()
oechem.OESmilesToMol(mol, "CCOc1ccc(cc1)CC(OC)c2ccccc2CC(=O)N")

adjustHCount = True
for frag in oemedchem.OEGetBemisMurcko(mol):
    fragment = oechem.OEGraphMol()
    oechem.OESubsetMol(fragment, mol, frag, adjustHCount)
    print(".".join(r.GetName() for r in frag.GetRoles()), oechem.OEMolToSmiles(fragment))

The output of Listing 2 is the following:

Framework c1ccc(cc1)CCc2ccccc2
Ring c1ccccc1.c1ccccc1
Linker CC
Sidechain CCO.CC(=O)N.CO
../_images/OEGetBemisMurcko.png

Example of Bemis Murcko fragmentation