5.12 OEGetSequenceAlignment

OESequenceAlignment OEGetSequenceAlignment(OEChem::OEMolBase &m1,
                                           OEChem::OEMolBase &m2,
                     unsigned int assume = OEAssumption::Default,
                     unsigned int method = OESeqAlignmentMethod::PAM250,
                     int gap = -10,
                     int extend = -2);

This function returns an OESequenceAlignment between two molecules. The first two parameters of the two protein molecules of interest. The remaining four parameters have default values and are thus optional. The method parameter indicates the method to be used to generate the alignment and should be one of the constants selected from the OESeqAlignmentMethod namespace. The gap and extend parameters indicate the gap and extention penalty to be used in the alignment respectively.

The assume argument is a bitmask that indicates whether the algorithm can assume that the molecule has perceived residues, has PDB ordered atoms, or as bonded residues (see the OEAssumption namespace for more information).

				OEChem - API Manual

				OEChem - API Manual