OEGetSimpleAlignment

OESequenceAlignment OEGetSimpleAlignment(OEChem::OEMolBase& mol1,
                                         OEChem::OEMolBase& mol2,
                                         unsigned int assume = OEAssumption::Default,
                                         unsigned int method = OESeqAlignmentMethod::PAM250,
                                         int gap = -10,
                                         int extend = -2,
                                         bool nonStdToX = false)

Returns the alignment of two proteins in an OESequenceAlignment object. Only the first chain of each protein is considered.

mol1, mol2: The two proteins of which alignment is being calculated. No 3D coordinates are required for sequence alignment; however, if the returned OESequenceAlignment is passed to OERMSD, both molecules must have 3D coordinates assigned.
assume: 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.
method: This value has to be from the OESeqAlignmentMethod namespace and it defines the algorithm that is used to generate the molecule alignment.
gap, extend: The gap and extension penalty to be used in the alignment. See also Gap penalty in Wikipedia.
nonStdToX: Option to convert non-standard residues to an X, default is false.