This class represents OESequenceAlignment.
This class contains information regarding a sequence alignment
between two molecules that have residue information. The class
includes information concerning the methods used to generate the
alignment as well as OEMatchBase information for either the alpha
carbons or all the backbone atoms that are paired by the
alignment. The OESequenceAlignment class can be passed to an
OERMSD function to generate
3D alignment based on the
sequence alignment, and can also be passed to the
function to generate a standard sequence alignment text output.
OESequenceAlignment(const OESequenceAlignment &rhs)
Default and copy constructors.
OESequenceAlignment &operator=(const OESequenceAlignment &rhs)
Default assignment operator
operator bool() const
An OESequenceAlignment object is considered invalid until its implementation is set.
Resets the object to the state in which it is default constructed.
const OEChem::OEMatchBase &GetBackboneMatch(unsigned idx1=0, unsigned idx2=1)
Returns an OEMatchBase that is the alignment of backbone atoms between the sequences indicated by ‘idx1’ and ‘idx2’. By default, the indices are 0 and 1 respectively, corresponding to a simple pairwise alignment.
const OEChem::OEMatchBase &GetCAlphaMatch(unsigned idx1=0, unsigned idx2=1)
Returns an OEMatchBase that is the alignment of alpha carbon atoms between the sequences indicated by ‘idx1’ and ‘idx2’. By default, the indices are 0 and 1 respectively, corresponding to a simple pairwise alignment.
char GetChainID(unsigned int idx) const;
Returns the chain id of the given sequence.
The index of the sequence. In a simple pairwise alignment this should be either 0 or 1.
int GetExtend() const
Returns an integer that is the extension penalty used in creating the sequence alignment.
int GetGap() const
Returns an integer that is the gap penalty used in creating the sequence alignment.
unsigned GetMaxSeqIdx() const
Returns a pointer that is the maximum index of any of the sequences used in the alignment.
unsigned GetMethod() const
Returns the unsigned integer that corresponds to one of the
constants in the namespace
This is the method that was used to create the alignment.
int GetScore() const
Returns an integer that is the score of the sequence alignment.
double GetSequenceIdentity() const;
Returns the percentage identity between the two sequences.