OESystem::OEIterBase<OEChem::OEAtomBondSet>* OEGetRingLinkerSideChainFragments( const OEChem::OEMolBase& mol, const OEBemisMurckoOptions& options = OEBemisMurckoOptions());
The following function is deprecated. Please use the more generic function above.
OESystem::OEIterBase<OEChem::OEAtomBondSet>* OEGetRingLinkerSideChainFragments( const OEChem::OEMolBase& mol, unsigned perceiveType)
The OEBemisMurckoOptions class can be used to specify both the OERegionType and also add additional functional groups to fragments. The perceiveType parameter only allows modification of the OERegionType of the fragments returned.
It returns an iterator over OEAtomBondSet objects where each OEAtomBondSet container stores the atoms and the bonds of an identified fragment. See example in Figure: Example of fragments returned by the OEGetRingLinkerSideChainFragments function where each fragment returned by the OEGetRingLinkerSideChainFragments function is highlighted with a different color.
The perceived regions are based upon the heavy atoms in the molecule. If the molecule contains explicit hydrogen atoms, those explicit hydrogens will be returned in the same perception set(s) as their alpha heavy atom neighbor. If the perception set(s) returned are used to subset or fragment the molecule, a mixture of implicit and explicit hydrogens may result, so care should be taken to normalize the structure for subsequent use.
Definitions from [Bemis-1996]:
- ring systems
- Cycles within the graph representation of molecules and cycles sharing an edge (a connection between two atoms or a bond).
- linker atoms
- Atoms that are on the direct path connecting two ring systems are defined as linker atoms.
- side chain atoms
- Any nonring, nonlinker atoms are defined as side chain atoms.
The molecule argument is const, so this function requires that the OEFindRingAtomsAndBonds perception activity has been performed prior to calling this function.