OESystem::OEIterBase<OEBio::OESequenceAlignment>* OEGetAlignments(OEChem::OEMolBase &mol1,
               OEChem::OEMolBase &mol2,
               unsigned int assume = OEAssumption::Default,
               unsigned int method = OESeqAlignmentMethod::PAM250,
               int gap = -10,
               int extend = -2);

Returns an iterator over all pair-wise chain alignments of two proteins. The returned alignments are not sorted.

mol1, mol2
The two proteins of which alignment is being calculated.
A bitmask that indicates whether the algorithm can assume that the given proteins have perceived residues, have PDB ordered atoms, or have bonded residues. See the OEAssumption namespace for more information.
This value has to be from the OESeqAlignmentMethod namespace and it defines the algorithm that is used to gerenerate the molecule alignment.
gap, extent
The gap and extension penalty to be used in the alignment. See also Gap penalty in Wikipedia.

See also