OESequenceAlignment

class OESequenceAlignment

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 OEWriteAlignment function to generate a standard sequence alignment text output.

Constructors

OESequenceAlignment()
OESequenceAlignment(const OESequenceAlignment &rhs)

Default and copy constructors.

operator=

OESequenceAlignment &operator=(const OESequenceAlignment &rhs)

Default assignment operator

operator bool

operator bool() const

An OESequenceAlignment object is considered invalid until its implementation is set.

Clear

void Clear()

Resets the object to the state in which it is default constructed.

GetBackboneMatch

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.

GetCAlphaMatch

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.

GetChainID

char GetChainID(unsigned int idx) const;

Returns the chain id of the given sequence.

idx: The index of the sequence. In a simple pairwise alignment this should be either 0 or 1.

GetExtend

int GetExtend() const

Returns an integer that is the extension penalty used in creating the sequence alignment.

GetGap

int GetGap() const

Returns an integer that is the gap penalty used in creating the sequence alignment.

GetMaxSeqIdx

unsigned GetMaxSeqIdx() const

Returns a pointer that is the maximum index of any of the sequences used in the alignment.

GetMethod

unsigned GetMethod() const

Returns the unsigned integer that corresponds to one of the constants in the namespace OESeqAlignmentMethod. This is the method that was used to create the alignment.

GetScore

int GetScore() const

Returns an integer that is the score of the sequence alignment.

GetSequenceIdentity

double GetSequenceIdentity() const;

Returns the percentage identity between the two sequences.

GetSequenceSimilarity

double GetSequenceSimilarity() const;

Returns the percentage similarity between the two sequences based on the given method.