OESequenceAlignment OEGetAlignment(OEChem::OEMolBase &mol1, OEChem::OEMolBase &mol2, unsigned int assume = OEAssumption::Default, unsigned int method = OESeqAlignmentMethod::PAM250, int gap=-10, int extend=-2)
Returns the highest scored alignment of all pairwise chain alignments calculated by OEGetAlignments.
- 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 generate the molecule alignment.
- gap, extent
- The gap and extension penalty to be used in the alignment. See also Gap penalty in Wikipedia.