Module which computes a pairwise structural alignment of two protein structures. More...

#include "Pairwise_structural_alignment_module.hpp"

Public Types
enum	run_type
	The run type for the module. More...

typedef Alignment_engine::Aligner_algorithm	Aligner_algorithm
	Core algorithm performing the alignment. More...

typedef Alignment_engine::Alignment_unit	Structure_unit
	Type for a unit (e.g residue or nucleotid) More...

Public Member Functions
virtual std::string	get_output_prefix (void) const
	Returns a prefix that concatains the input line options used when running the module. More...

Mandatory Requirements
void	run (unsigned verbose, std::ostream &out)
	Runs the module following the input options. More...

Optional Requirements
const boost::program_options::options_description *	get_options (void) const
	Access to the options' description of the module. More...

boost::program_options::options_description *&	get_options (void)
	Access to the options' description of the module. More...

boost::program_options::options_description	add_options () const
	Virtual method for adding options to the module. More...

bool	check_options (std::string &message) const
	Checks that the input options' values are coherent. More...

void	report (const std::string &prefix)
	Reports the output and statistics in output files. More...

Printers
void	print_alignment (const std::string &filename)
	Print the alignment (as a pairing of residue sequence numbers) More...

void	write_pymol_script (const std::string &filename)
	Write a PyMol script. More...

template<class Archive >
void	serialize (Archive &ar, const unsigned BOOST_PFTO int version)
	Serialize. More...

Accessors
Structure *&	get_aligned_structure_1 ()
	Return the aligned residues belonging to the first chain. More...

Structure *&	get_aligned_structure_2 ()
	Return the aligned residues belonging to the second chain. More...

double	get_alignment_lRMSD () const
	Return the least RMSD. More...

double	get_distance_RMSD () const
	Return the distance RMSD. More...

unsigned	get_size () const
	Return the alignment size. More...

double	get_similarity_percentage () const
	Return the sequence similarity percentage. More...

double	get_identity_percentage () const
	Return the sequence identity percentage. More...

Residue_set	get_first_chain_motif_as_residue_set (void)
	Return the first motif as a residue set (as defined in the traits class). More...

Residue_set	get_second_chain_motif_as_residue_set (void)
	Return the second motif as a residue set (as defined in the traits class). More...

double	get_lrmsd_ratio (void)

bool	is_structural_motif (void) const

template<class OutputIterator >
void	get_first_structure_score_ordering (OutputIterator out)

template<class OutputIterator >
void	get_second_structure_score_ordering (OutputIterator out)

static unsigned	get_size_threshold (void)

static Shelf *&	get_shelf ()
	Return the shelf. More...

Modifiers
void	set_persistence_one (std::pair< double, double > persistence)
	Set the persistence values for the blocks. More...

void	set_persistence_two (std::pair< double, double > persistence)

void	set_run_type (run_type new_type)
	Set the run type of the module. More...

static void	set_reference_lrmsd (double lrmsd)
	Set the reference lRMSD (used to determine if a motif is interesting) More...

Input Accessors and modifiers
Structure *&	get_first_structure (void)

Structure *&	get_second_structure (void)

const Alignment_type &	get_alignment (void) const

Aligner_algorithm &	get_aligner_algorithm (void)

const Aligner_algorithm &	get_aligner_algorithm (void) const

Alignment_engine *&	get_alignment_engine (void)

const Alignment_engine *	get_alignment_engine (void) const

void	initialize_engine (void)

static SBL::CSB::Alignment_substitution_matrix_type &	get_substition_matrix_type (void)

static string &	get_alignment_viewer_name (void)

static Sequence_length_type &	get_percentage_length_type (void)

Mandatory Requirements
bool	is_runnable (void) const
	Checks that all the input options were set. More...

void	statistics (std::ostream &out)
	Reports high-level statistics on the module. More...

std::string	get_name (void) const
	Returns the name of the package. More...

Modules Management
void	set_module_instance_name (const std::string &module_instance_name)
	Sets a name for this instance of this module. In particular, it will be used in the prefix of output files generated by a collection of modules. More...

const std::string &	get_module_instance_name (void) const
	Get the name of this instance of this module. More...

void	set_report_mode (std::ios_base::openmode report_mode)
	Set a report mode, that is open or append modes. More...

void	set_report_mode (std::ios_base::openmode &report_mode)
	Set a report mode, that is open or append modes. More...

const std::ios_base::openmode	get_report_mode (void) const
	Get the report mode to be used when reporting. More...

Others
template<class Self_ >
Self_ *	clone (const Self_ *s) const
	Clones the object using the copy constructor. More...

virtual bool	is_logical_module (void) const
	Checks that this module defines a logical operator. More...

virtual bool	is_condition_module (void) const
	Checks that this module defines a condition operator. More...

virtual bool	operator() (void)
	Only for condition modules, for returning the predicate value. More...

virtual bool	is_modules_collection (void) const
	Checks that this module defines a collection of modules. More...

Detailed Description

template<class ModuleTraits, class AlignmentEngine>
class SBL::Modules::T_Pairwise_structural_alignment_module< ModuleTraits, AlignmentEngine >

Module which computes a pairwise structural alignment of two protein structures.

It is designed such that the input can be either a collection of 3D spheres representing the particles, or a collection of particles with the type derived from ParticleTraits, depending on the type of the output $\alpha$ -complex:

Template Parameters

ModuleTraits Traits class defining the types T_Alpha_complex_of_molecular_model_module::Alpha_complex and T_Alpha_complex_of_molecular_model_module::Particles_container.

Member Typedef Documentation

◆ Aligner_algorithm

typedef Alignment_engine::Aligner_algorithm Aligner_algorithm

inherited

Core algorithm performing the alignment.

◆ Structure_unit

typedef Alignment_engine::Alignment_unit Structure_unit

inherited

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

Member Enumeration Documentation

◆ run_type

enum run_type

The run type for the module.

SCORE type dictates that the module should run the initial alignment and compute calpha ranks. LRMSD dictates that the module should only compute the alignment and return the lRMSD (used for the module collection).

Member Function Documentation

◆ add_options()

boost::program_options::options_description add_options ( ) const

inlinevirtual

Virtual method for adding options to the module.

Reimplemented from T_Module_option_description<>.

◆ check_options()

bool check_options ( std::string & message ) const

inlinevirtual

Checks that the input options' values are coherent.

Reimplemented from T_Module_option_description<>.

◆ clone()

Self_* clone ( const Self_ * s ) const

inlineinherited

Clones the object using the copy constructor.

◆ get_aligned_structure_1()

Structure*& get_aligned_structure_1 ( )

inline

Return the aligned residues belonging to the first chain.

◆ get_aligned_structure_2()

Structure*& get_aligned_structure_2 ( )

inline

Return the aligned residues belonging to the second chain.

◆ get_alignment_lRMSD()

double get_alignment_lRMSD ( ) const

inline

Return the least RMSD.

◆ get_distance_RMSD()

double get_distance_RMSD ( ) const

inline

Return the distance RMSD.

◆ get_first_chain_motif_as_residue_set()

Residue_set get_first_chain_motif_as_residue_set ( void )

inline

Return the first motif as a residue set (as defined in the traits class).

◆ get_identity_percentage()

double get_identity_percentage ( ) const

inline

Return the sequence identity percentage.

◆ get_module_instance_name()

const std::string& get_module_instance_name ( void ) const

inlineinherited

Get the name of this instance of this module.

◆ get_name()

std::string get_name ( void ) const

inlinevirtualinherited

Returns the name of the package.

Reimplemented from Module_base.

◆ get_options() [1/2]

const boost::program_options::options_description* get_options ( void ) const

inline

Access to the options' description of the module.

◆ get_options() [2/2]

boost::program_options::options_description*& get_options ( void )

inline

Access to the options' description of the module.

◆ get_output_prefix()

virtual std::string get_output_prefix ( void ) const

inlinevirtualinherited

Returns a prefix that concatains the input line options used when running the module.

◆ get_report_mode()

const std::ios_base::openmode get_report_mode ( void ) const

inlineinherited

Get the report mode to be used when reporting.

◆ get_second_chain_motif_as_residue_set()

Residue_set get_second_chain_motif_as_residue_set ( void )

inline

Return the second motif as a residue set (as defined in the traits class).

◆ get_shelf()

static Shelf*& get_shelf ( )

inlinestatic

Return the shelf.

◆ get_similarity_percentage()

double get_similarity_percentage ( ) const

inline

Return the sequence similarity percentage.

◆ get_size()

unsigned get_size ( ) const

inline

Return the alignment size.

◆ is_condition_module()

virtual bool is_condition_module ( void ) const

inlineprotectedvirtualinherited

Checks that this module defines a condition operator.

◆ is_logical_module()

virtual bool is_logical_module ( void ) const

inlineprotectedvirtualinherited

Checks that this module defines a logical operator.

◆ is_modules_collection()

virtual bool is_modules_collection ( void ) const

inlineprotectedvirtualinherited

Checks that this module defines a collection of modules.

◆ is_runnable()

bool is_runnable ( void ) const

inlinevirtualinherited

Checks that all the input options were set.

Reimplemented from Module_base.

◆ operator()()

virtual bool operator() ( void )

inlineprotectedvirtualinherited

Only for condition modules, for returning the predicate value.

◆ print_alignment()

void print_alignment ( const std::string & filename )

inline

Print the alignment (as a pairing of residue sequence numbers)

◆ report()

void report ( const std::string & prefix )

inlinevirtual

Reports the output and statistics in output files.

Reimplemented from Module_base.

◆ run()

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

inlinevirtual

Runs the module following the input options.

Implements Module_base.

◆ serialize()

void serialize	(	Archive &	ar,
		const unsigned BOOST_PFTO int	version
	)

inline

Serialize.

◆ set_module_instance_name()

void set_module_instance_name ( const std::string & module_instance_name )

inlineinherited

Sets a name for this instance of this module. In particular, it will be used in the prefix of output files generated by a collection of modules.

◆ set_persistence_one()

void set_persistence_one ( std::pair< double, double > persistence )

inline

Set the persistence values for the blocks.

◆ set_reference_lrmsd()

static void set_reference_lrmsd ( double lrmsd )

inlinestatic

Set the reference lRMSD (used to determine if a motif is interesting)

◆ set_report_mode() [1/2]

void set_report_mode ( std::ios_base::openmode report_mode )

inlineinherited

Set a report mode, that is open or append modes.

◆ set_report_mode() [2/2]

void set_report_mode ( std::ios_base::openmode & report_mode )

inlineinherited

Set a report mode, that is open or append modes.

◆ set_run_type()

void set_run_type ( run_type new_type )

inline

Set the run type of the module.

◆ statistics()

void statistics ( std::ostream & out )

inlinevirtualinherited

Reports high-level statistics on the module.

Reimplemented from Module_base.

◆ write_pymol_script()

void write_pymol_script ( const std::string & filename )

inline

Write a PyMol script.

Public Types

Public Member Functions

Mandatory Requirements

Optional Requirements

Printers

Accessors

Modifiers

Input Accessors and modifiers

Mandatory Requirements

Modules Management

Others

Detailed Description

template<class ModuleTraits, class AlignmentEngine> class SBL::Modules::T_Pairwise_structural_alignment_module< ModuleTraits, AlignmentEngine >

Member Typedef Documentation

◆ Aligner_algorithm

◆ Structure_unit

Member Enumeration Documentation

◆ run_type

Member Function Documentation

◆ add_options()

◆ check_options()

◆ clone()

◆ get_aligned_structure_1()

◆ get_aligned_structure_2()

◆ get_alignment_lRMSD()

◆ get_distance_RMSD()

◆ get_first_chain_motif_as_residue_set()

◆ get_identity_percentage()

◆ get_module_instance_name()

◆ get_name()

◆ get_options() [1/2]

◆ get_options() [2/2]

◆ get_output_prefix()

◆ get_report_mode()

◆ get_second_chain_motif_as_residue_set()

◆ get_shelf()

◆ get_similarity_percentage()

◆ get_size()

◆ is_condition_module()

◆ is_logical_module()

◆ is_modules_collection()

◆ is_runnable()

◆ operator()()

◆ print_alignment()

◆ report()

◆ run()

◆ serialize()

◆ set_module_instance_name()

◆ set_persistence_one()

◆ set_reference_lrmsd()

◆ set_report_mode() [1/2]

◆ set_report_mode() [2/2]

◆ set_run_type()

◆ statistics()

◆ write_pymol_script()

template<class ModuleTraits, class AlignmentEngine>
class SBL::Modules::T_Pairwise_structural_alignment_module< ModuleTraits, AlignmentEngine >