Base engine for making alignments between structures. Base engine for making alignments between structures. More...

#include <Alignment_engine_structures.hpp>

Public Types
typedef Base::Alignment_unit	Alignment_unit
	Type for a unit (e.g residue or nucleotid) More...

typedef Base::Alignment_unit_rep	Alignment_unit_rep
	Representation of a unit for index purposes. More...

typedef Base::Alignment_unit_name	Alignment_unit_name
	Representation of the name of a unit. More...

typedef Base::Score_type	Score_type
	Representation of the score of the algorithm. More...

typedef Base::Aligned_pair	Aligned_pair
	Representation of two aligned units. More...

typedef Base::Alignment_type	Alignment_type
	Representation of an alignment as a sequence of aligned units. More...

typedef Base::Substitution_matrix	Substitution_matrix
	Representation of the storage of values of the subtitution matrix. More...

typedef Base::Matrix_function	Matrix_function
	Functor for the substitution matrix. Is imposed the following properties: (i) symmetry, (ii) undefined values are 0. Thus, it is just enough to specify non null values on only one triangle of the matrix. More...

typedef Base::Sequence_length_type	Sequence_length_type
	Enum for selecting the length of the sequence to consider when computing the similarity / identity percentages. More...

typedef std::vector< std::vector< FT > >	Distance_difference_matrix
	DDM for computing the dRMSD. More...

typedef CGAL::Cartesian_d< FT >::Point_d	Conformation
	Data type representing a conformation used in the lRMSD computation (constructor takes (dimension, begin_coordinates, end_coordinates)). More...

typedef StructureType	Sequence_or_structure
	Type for representing the sequences or the structures to align. More...

typedef AlignerAlgorithm	Aligner_algorithm
	Core algorithm performing the alignment. More...

typedef std::pair< Alignment_unit_name, Alignment_unit_name >	Name_pair
	Representation of two unit names. More...

Constructors
	T_Alignment_engine_structures (const StructureType &struct_1, const StructureType &struct_2, const AlignerAlgorithm &aligner=AlignerAlgorithm())
	Constructor initializing the input structures and possibly the aligner algorithm. More...

Overloaded Algorithm
void	align (void)

void	align (unsigned verbose, std::ostream &out)

Structures Analysis
const Distance_difference_matrix &	get_distance_difference_matrix (void)

FT	get_dRMSD (void)

FT	get_lRMSD (void)

void	statistics (std::ostream &out, Sequence_length_type type)

Accessors
const AlignerAlgorithm &	get_aligner (void) const

AlignerAlgorithm &	get_aligner (void)

const StructureType &	get_first_sos (void) const
	Returns the first sequence or structure of the alignment. More...

const StructureType &	get_second_sos (void) const
	Returns the second sequence or structure of the alignment. More...

Outputs
const Score_type &	get_score (void) const

Score_type &	get_score (void)

Alignment_type &	get_alignment (void)

const Alignment_type &	get_alignment (void) const

Analysis
void	set_substitution_matrix (const Substitution_matrix &matrix)
	The input is a map from pairs of Alignment_unit_name to the associated score. Note that by construction, it is enough to specify non null values on a half of the matrix, diagonal excluded. More...

void	load_substitution_matrix (const std::string &matrix_filename, unsigned nb_units_names)
	Loads directly the substitution matrix from a file of the format : Alignment_unit_name Alignment_unit_name Value. If duplicated values, the last one is taken. More...

void	set_blosum_30 (void)
	Set the current matrix as the BLOSUM30 matrix as defined in Seqan 2.0. More...

void	set_blosum_45 (void)
	Set the current matrix as the BLOSUM45 matrix as defined in Seqan 2.0. More...

void	set_blosum_62 (void)
	Set the current matrix as the BLOSUM62 matrix as defined in Seqan 2.0. More...

void	set_blosum_80 (void)
	Set the current matrix as the BLOSUM80 matrix as defined in Seqan 2.0. More...

void	set_pam_40 (void)
	Set the current matrix as the PAM40 matrix as defined in Seqan 2.0. More...

void	set_pam_120 (void)
	Set the current matrix as the PAM120 matrix as defined in Seqan 2.0. More...

void	set_pam_200 (void)
	Set the current matrix as the PAM200 matrix as defined in Seqan 2.0. More...

void	set_pam_250 (void)
	Set the current matrix as the PAM250 matrix as defined in Seqan 2.0. More...

void	set_vtml_200 (void)
	Set the current matrix as the VTML200 matrix as defined in Seqan 2.0. More...

void	set_standard_substitution_matrix (SBL::CSB::Alignment_substitution_matrix_type matrix_type)
	Set the current matrix as one of the standard substitution matrices. More...

Substitution_matrix &	get_substitution_matrix (void)

double	get_substitution_score (const Alignment_unit_name &p, const Alignment_unit_name &q) const

double	get_identity_percentage (Sequence_length_type type=ALIGNMENT_SEQUENCE_LENGTH) const

double	get_similarity_percentage (Sequence_length_type type=ALIGNMENT_SEQUENCE_LENGTH) const

void	statistics (std::ostream &out, Sequence_length_type type) const

void	print_alignment_txt (std::ostream &out) const
	Print the alignment in txt format. More...

void	print_alignment_dot (std::ostream &out) const
	Print the alignment as a dot graph. More...

Detailed Description

template<class StructureType, class AlignerAlgorithm, class FT = double, class MolecularDistance = T_Least_RMSD_cartesian<typename CGAL::Cartesian_d<FT>::Point_d>>
class SBL::CSB::T_Alignment_engine_structures< StructureType, AlignerAlgorithm, FT, MolecularDistance >

Base engine for making alignments between structures. Base engine for making alignments between structures.

It inherits from the generic interface for all alignments and provide its base functionality. It also implements functionality specific to structural alignments, in particular for anaylzing and comparing alignments. The specific functionality concerns:

the molecular distance between the two aligned structures (e.g the lRMSD),
the Distance Difference Matrix (DDM),
the dRMSD of the alignment.

Due to geometric nature of the structural alignment, the structure type requires that its units define 3D coordinates, i.e the Alignment_unit defines methods x(), y() and z().

Template Parameters

StructureType	Representation of a structure : it requires in particular to define the type Alignment_unit for the geometric representation of a unit to align (e.g a residue or a nucleotid with associated 3D coordinates), the type Alignment_unit indexing the units in the structure, the method size() to return the length of the sequence, and the operator [Alignment_unit_rep] for accessing to the corresponding unit of the structure.
AlignerAlgorithm	Base functor for the algorithm that makes the alignment between the two input structures : it requires to define a type Score_type for the score (e.g a double, or a pair of doubles if two scores are required), to take two input structures and an output iterator over pairs of Alignment_unit_rep for the output alignment, and to return the score of the algorithm
FT	Number type representation used for all statistics except the algorithm score.
MolecularDistance	Distance functor between two molecular structures (default is lRMSD).

Member Typedef Documentation

◆ Aligned_pair

typedef Base::Aligned_pair Aligned_pair

Representation of two aligned units.

◆ Aligner_algorithm

typedef AlignerAlgorithm Aligner_algorithm

inherited

Core algorithm performing the alignment.

◆ Alignment_type

typedef Base::Alignment_type Alignment_type

Representation of an alignment as a sequence of aligned units.

◆ Alignment_unit

typedef Base::Alignment_unit Alignment_unit

Type for a unit (e.g residue or nucleotid)

◆ Alignment_unit_name

typedef Base::Alignment_unit_name Alignment_unit_name

Representation of the name of a unit.

◆ Alignment_unit_rep

typedef Base::Alignment_unit_rep Alignment_unit_rep

Representation of a unit for index purposes.

◆ Conformation

typedef CGAL::Cartesian_d<FT>::Point_d Conformation

Data type representing a conformation used in the lRMSD computation (constructor takes (dimension, begin_coordinates, end_coordinates)).

◆ Distance_difference_matrix

typedef std::vector<std::vector<FT> > Distance_difference_matrix

DDM for computing the dRMSD.

◆ Matrix_function

typedef Base::Matrix_function Matrix_function

Functor for the substitution matrix. Is imposed the following properties: (i) symmetry, (ii) undefined values are 0. Thus, it is just enough to specify non null values on only one triangle of the matrix.

◆ Name_pair

typedef std::pair<Alignment_unit_name, Alignment_unit_name> Name_pair

inherited

Representation of two unit names.

◆ Score_type

typedef Base::Score_type Score_type

Representation of the score of the algorithm.

◆ Sequence_length_type

typedef Base::Sequence_length_type Sequence_length_type

Enum for selecting the length of the sequence to consider when computing the similarity / identity percentages.

◆ Sequence_or_structure

typedef StructureType Sequence_or_structure

inherited

Type for representing the sequences or the structures to align.

◆ Substitution_matrix

typedef Base::Substitution_matrix Substitution_matrix

Representation of the storage of values of the subtitution matrix.

Constructor & Destructor Documentation

◆ T_Alignment_engine_structures()

T_Alignment_engine_structures	(	const StructureType &	struct_1,
		const StructureType &	struct_2,
		const AlignerAlgorithm &	aligner = `AlignerAlgorithm()`
	)

inline

Constructor initializing the input structures and possibly the aligner algorithm.

Member Function Documentation

◆ get_first_sos()

const StructureType & get_first_sos ( void ) const

inlineinherited

Returns the first sequence or structure of the alignment.

◆ get_second_sos()

const StructureType & get_second_sos ( void ) const

inlineinherited

Returns the second sequence or structure of the alignment.

◆ load_substitution_matrix()

void load_substitution_matrix	(	const std::string &	matrix_filename,
		unsigned	nb_units_names
	)

inlineinherited

Loads directly the substitution matrix from a file of the format : Alignment_unit_name Alignment_unit_name Value. If duplicated values, the last one is taken.

◆ print_alignment_dot()

void print_alignment_dot ( std::ostream & out ) const

inlineinherited

Print the alignment as a dot graph.

◆ print_alignment_txt()

void print_alignment_txt ( std::ostream & out ) const

inlineinherited

Print the alignment in txt format.

◆ set_blosum_30()

void set_blosum_30 ( void )

inlineinherited

Set the current matrix as the BLOSUM30 matrix as defined in Seqan 2.0.

◆ set_blosum_45()

void set_blosum_45 ( void )

inlineinherited

Set the current matrix as the BLOSUM45 matrix as defined in Seqan 2.0.

◆ set_blosum_62()

void set_blosum_62 ( void )

inlineinherited

Set the current matrix as the BLOSUM62 matrix as defined in Seqan 2.0.

◆ set_blosum_80()

void set_blosum_80 ( void )

inlineinherited

Set the current matrix as the BLOSUM80 matrix as defined in Seqan 2.0.

◆ set_pam_120()

void set_pam_120 ( void )

inlineinherited

Set the current matrix as the PAM120 matrix as defined in Seqan 2.0.

◆ set_pam_200()

void set_pam_200 ( void )

inlineinherited

Set the current matrix as the PAM200 matrix as defined in Seqan 2.0.

◆ set_pam_250()

void set_pam_250 ( void )

inlineinherited

Set the current matrix as the PAM250 matrix as defined in Seqan 2.0.

◆ set_pam_40()

void set_pam_40 ( void )

inlineinherited

Set the current matrix as the PAM40 matrix as defined in Seqan 2.0.

◆ set_standard_substitution_matrix()

void set_standard_substitution_matrix ( SBL::CSB::Alignment_substitution_matrix_type matrix_type )

inlineinherited

Set the current matrix as one of the standard substitution matrices.

◆ set_substitution_matrix()

void set_substitution_matrix ( const Substitution_matrix & matrix )

inlineinherited

The input is a map from pairs of Alignment_unit_name to the associated score. Note that by construction, it is enough to specify non null values on a half of the matrix, diagonal excluded.

◆ set_vtml_200()

void set_vtml_200 ( void )

inlineinherited

Set the current matrix as the VTML200 matrix as defined in Seqan 2.0.

Public Types

Constructors

Overloaded Algorithm

Structures Analysis

Accessors

Outputs

Analysis

Detailed Description

template<class StructureType, class AlignerAlgorithm, class FT = double, class MolecularDistance = T_Least_RMSD_cartesian<typename CGAL::Cartesian_d<FT>::Point_d>> class SBL::CSB::T_Alignment_engine_structures< StructureType, AlignerAlgorithm, FT, MolecularDistance >

Member Typedef Documentation

◆ Aligned_pair

◆ Aligner_algorithm

◆ Alignment_type

◆ Alignment_unit

◆ Alignment_unit_name

◆ Alignment_unit_rep

◆ Conformation

◆ Distance_difference_matrix

◆ Matrix_function

◆ Name_pair

◆ Score_type

◆ Sequence_length_type

◆ Sequence_or_structure

◆ Substitution_matrix

Constructor & Destructor Documentation

◆ T_Alignment_engine_structures()

Member Function Documentation

◆ get_first_sos()

◆ get_second_sos()

◆ load_substitution_matrix()

◆ print_alignment_dot()

◆ print_alignment_txt()

◆ set_blosum_30()

◆ set_blosum_45()

◆ set_blosum_62()

◆ set_blosum_80()

◆ set_pam_120()

◆ set_pam_200()

◆ set_pam_250()

◆ set_pam_40()

◆ set_standard_substitution_matrix()

◆ set_substitution_matrix()

◆ set_vtml_200()

template<class StructureType, class AlignerAlgorithm, class FT = double, class MolecularDistance = T_Least_RMSD_cartesian<typename CGAL::Cartesian_d<FT>::Point_d>>
class SBL::CSB::T_Alignment_engine_structures< StructureType, AlignerAlgorithm, FT, MolecularDistance >