OESequenceAlignment

class 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 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
OESequenceAlignment(rhs: OESequenceAlignment) -> OESequenceAlignment

Default and copy constructors.

operator bool

IsValid() -> bool

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

Clear

Clear() -> None

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

GetBackboneMatch

GetBackboneMatch(idx1: int = 0, idx2: int = 1) -> OEMatchBase

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

GetCAlphaMatch(idx1: int = 0, idx2: int = 1) -> OEMatchBase

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

GetChainID(idx: int) -> str

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

GetExtend() -> int

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

GetGap

GetGap() -> int

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

GetMaxSeqIdx

GetMaxSeqIdx() -> int

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

GetMethod

GetMethod() -> int

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

GetScore() -> int

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

GetSequenceIdentity

GetSequenceIdentity() -> float

Returns the percentage identity between the two sequences.

GetSequenceSimilarity

GetSequenceSimilarity() -> float

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