a neighbor-aware SewSegment version More...

#include <SmartSegment.hh>

Inheritance diagram for protocols::sewing::data_storage::SmartSegment:

Public Member Functions
	SmartSegment ()

	SmartSegment (bool is_vital)

	SmartSegment (bool is_vital, core::Size max_segment_length)

	SmartSegment (SmartSegment const &src)

	~SmartSegment () override

SmartSegmentOP	clone () const

void	set_segment_id (core::Size new_segment_id)

core::Size	get_segment_id () const

void	set_n_terminal_neighbor (SmartSegmentOP new_n_terminal_neighbor)

SmartSegmentOP	get_n_terminal_neighbor () const

void	set_c_terminal_neighbor (SmartSegmentOP new_c_terminal_neighbor)

SmartSegmentOP	get_c_terminal_neighbor () const

void	set_dssp_code (char new_dssp_code)

char	get_dssp_code () const

void	set_chimaeric_status (bool is_chimaera)

bool	is_chimaeric () const

void	set_n_terminal_parent (SmartSegmentOP new_n_terminal_parent)

void	set_c_terminal_parent (SmartSegmentOP new_c_terminal_parent)

SmartSegmentOP	get_n_terminal_parent () const

SmartSegmentOP	get_c_terminal_parent () const

bool	is_vital () const

void	set_is_vital (bool)

bool	is_in_Assembly () const

void	set_is_in_Assembly (bool)

bool	is_n_terminus_fixed () const

bool	is_c_terminus_fixed () const

bool	is_hashable () const

void	set_residue_vector (utility::vector1< SmartSewingResidueOP > new_residue_vector)

utility::vector1< SmartSewingResidueOP > &	get_residue_vector ()

utility::vector1< SmartSewingResidueOP > const &	get_const_residue_vector () const

SmartSewingResidueOP	get_residue (core::Size resnum)

void	set_length (core::Size new_length)

core::Size	get_length () const

void	set_basis_pair (BasisPair basis_pair)

BasisPair	get_basis_pair () const

std::set< core::Size >	get_vital_residues () const

void	set_vital_residues (std::set< core::Size >)

void	add_vital_residue (core::Size)

void	set_const_reference_segment (SmartSegmentCOP ref)

SmartSegmentCOP	get_const_reference_segment () const

void	isolate ()

bool	residue_is_vital (core::Size)

virtual std::string	get_name () const

Static Public Member Functions
static SmartSegmentOP	get_far_n_terminal_parent (SmartSegmentOP current_segment)

static SmartSegmentOP	get_far_c_terminal_parent (SmartSegmentOP current_segment)

static SmartSegmentCOP	get_n_most_segment (SmartSegmentCOP, bool cross_chimaerae)

static SmartSegmentOP	get_n_most_segment (SmartSegmentOP, bool cross_chimaerae)

static SmartSegmentCOP	get_c_most_segment (SmartSegmentCOP, bool cross_chimaerae)

static SmartSegmentOP	get_c_most_segment (SmartSegmentOP, bool cross_chimaerae)

static void	link_to (SmartSegmentOP n_term, SmartSegmentOP c_term)

static void	become (SmartSegmentOP changing_segment, SmartSegmentCOP src_segment)

Private Attributes
core::Size	segment_id_

SmartSegmentOP	n_terminal_neighbor_

SmartSegmentOP	c_terminal_neighbor_

utility::vector1< SmartSewingResidueOP >	residues_

char	dssp_code_

bool	is_a_chimaera_

SmartSegmentOP	n_terminal_parent_

SmartSegmentOP	c_terminal_parent_

bool	is_vital_

bool	is_in_Assembly_

core::Size	length_

BasisPair	basis_pair_ = std::make_pair( Basis( 0, 0), Basis( 0, 0) )

std::set< core::Size >	vital_residues_

SmartSegmentCOP	const_reference_segment_ = nullptr

Detailed Description

a neighbor-aware SewSegment version

Constructor & Destructor Documentation

◆ SmartSegment() [1/4]

protocols::sewing::data_storage::SmartSegment::SmartSegment ( )

References c_terminal_neighbor_, c_terminal_parent_, dssp_code_, is_a_chimaera_, is_in_Assembly_, is_vital_, length_, n_terminal_neighbor_, n_terminal_parent_, and segment_id_.

◆ SmartSegment() [2/4]

protocols::sewing::data_storage::SmartSegment::SmartSegment ( bool is_vital )

References c_terminal_neighbor_, c_terminal_parent_, dssp_code_, is_a_chimaera_, is_in_Assembly_, is_vital(), is_vital_, length_, n_terminal_neighbor_, n_terminal_parent_, and segment_id_.

◆ SmartSegment() [3/4]

protocols::sewing::data_storage::SmartSegment::SmartSegment	(	bool	is_vital,
		core::Size	max_segment_length
	)

References c_terminal_neighbor_, c_terminal_parent_, dssp_code_, is_a_chimaera_, is_in_Assembly_, is_vital(), is_vital_, length_, n_terminal_neighbor_, n_terminal_parent_, residues_, and segment_id_.

◆ SmartSegment() [4/4]

protocols::sewing::data_storage::SmartSegment::SmartSegment ( SmartSegment const & src )

◆ ~SmartSegment()

protocols::sewing::data_storage::SmartSegment::~SmartSegment ( )

override

Member Function Documentation

◆ add_vital_residue()

void protocols::sewing::data_storage::SmartSegment::add_vital_residue ( core::Size resnum )

References vital_residues_.

Referenced by protocols::sewing::data_storage::LigandSegment::add_ligand_contact().

◆ become()

void protocols::sewing::data_storage::SmartSegment::become	(	SmartSegmentOP	changing_segment,
		SmartSegmentCOP	src_segment
	)

static

References get_length().

Referenced by protocols::sewing::hashing::Hasher::transform_segments().

◆ clone()

SmartSegmentOP protocols::sewing::data_storage::SmartSegment::clone ( ) const

◆ get_basis_pair()

BasisPair protocols::sewing::data_storage::SmartSegment::get_basis_pair ( ) const

References basis_pair_.

Referenced by SmartSegment().

◆ get_c_most_segment() [1/2]

SmartSegmentCOP protocols::sewing::data_storage::SmartSegment::get_c_most_segment	(	SmartSegmentCOP	start_segment,
		bool	cross_chimaerae
	)

static

Referenced by protocols::sewing::hashing::EdgeMapGenerator::append_to_edge_map(), protocols::sewing::hashing::AlignmentFileGeneratorMover::apply(), get_c_most_segment(), protocols::sewing::data_storage::SmartAssembly::reconstitute_assembly_from_string(), protocols::sewing::hashing::BasisMapGenerator::recurse_over_segments(), and protocols::sewing::data_storage::SmartAssembly::set_starting_segment().

◆ get_c_most_segment() [2/2]

SmartSegmentOP protocols::sewing::data_storage::SmartSegment::get_c_most_segment	(	SmartSegmentOP	start_segment,
		bool	cross_chimaerae
	)

static

References get_c_most_segment().

◆ get_c_terminal_neighbor()

SmartSegmentOP protocols::sewing::data_storage::SmartSegment::get_c_terminal_neighbor ( ) const

References c_terminal_neighbor_.

Referenced by isolate().

◆ get_c_terminal_parent()

SmartSegmentOP protocols::sewing::data_storage::SmartSegment::get_c_terminal_parent ( ) const

References c_terminal_parent_, get_segment_id(), is_chimaeric(), and protocols::TR().

Referenced by SmartSegment().

◆ get_const_reference_segment()

SmartSegmentCOP protocols::sewing::data_storage::SmartSegment::get_const_reference_segment ( ) const

References const_reference_segment_.

Referenced by SmartSegment().

◆ get_const_residue_vector()

utility::vector1< SmartSewingResidueOP > const & protocols::sewing::data_storage::SmartSegment::get_const_residue_vector ( ) const

References residues_.

Referenced by SmartSegment().

◆ get_dssp_code()

char protocols::sewing::data_storage::SmartSegment::get_dssp_code ( ) const

References dssp_code_.

Referenced by SmartSegment().

◆ get_far_c_terminal_parent()

SmartSegmentOP protocols::sewing::data_storage::SmartSegment::get_far_c_terminal_parent ( SmartSegmentOP current_segment )

static

Referenced by protocols::sewing::data_storage::SmartAssembly::can_delete(), and protocols::sewing::data_storage::SmartAssembly::delete_segment().

◆ get_far_n_terminal_parent()

SmartSegmentOP protocols::sewing::data_storage::SmartSegment::get_far_n_terminal_parent ( SmartSegmentOP current_segment )

static

Referenced by protocols::sewing::data_storage::SmartAssembly::can_delete(), and protocols::sewing::data_storage::SmartAssembly::delete_segment().

◆ get_length()

core::Size protocols::sewing::data_storage::SmartSegment::get_length ( ) const

References residues_.

Referenced by become(), and SmartSegment().

◆ get_n_most_segment() [1/2]

SmartSegmentCOP protocols::sewing::data_storage::SmartSegment::get_n_most_segment	(	SmartSegmentCOP	start_segment,
		bool	cross_chimaerae
	)

static

Referenced by protocols::sewing::data_storage::SmartAssembly::add_segment_and_neighbors_to_local_segments(), protocols::sewing::hashing::EdgeMapGenerator::append_to_edge_map(), protocols::sewing::hashing::AlignmentFileGeneratorMover::apply(), protocols::sewing::data_storage::SmartAssembly::chimerize(), protocols::sewing::scoring::InterModelMotifScorer::full_motif_score(), get_n_most_segment(), protocols::sewing::data_storage::SmartAssembly::pick_random_starting_segment(), protocols::sewing::data_storage::SmartAssembly::set_starting_segment(), protocols::sewing::data_storage::SmartAssembly::transform_segments(), and protocols::sewing::hashing::Hasher::transform_segments().

◆ get_n_most_segment() [2/2]

SmartSegmentOP protocols::sewing::data_storage::SmartSegment::get_n_most_segment	(	SmartSegmentOP	start_segment,
		bool	cross_chimaerae
	)

static

References get_n_most_segment().

◆ get_n_terminal_neighbor()

SmartSegmentOP protocols::sewing::data_storage::SmartSegment::get_n_terminal_neighbor ( ) const

References n_terminal_neighbor_.

Referenced by isolate().

◆ get_n_terminal_parent()

SmartSegmentOP protocols::sewing::data_storage::SmartSegment::get_n_terminal_parent ( ) const

References get_segment_id(), is_chimaeric(), n_terminal_parent_, and protocols::TR().

Referenced by SmartSegment().

◆ get_name()

virtual std::string protocols::sewing::data_storage::SmartSegment::get_name ( ) const

inlinevirtual

Reimplemented in protocols::sewing::data_storage::LigandSegment.

◆ get_residue()

SmartSewingResidueOP protocols::sewing::data_storage::SmartSegment::get_residue ( core::Size resnum )

References residues_, and protocols::TR().

◆ get_residue_vector()

utility::vector1< SmartSewingResidueOP > & protocols::sewing::data_storage::SmartSegment::get_residue_vector ( )

References residues_.

◆ get_segment_id()

core::Size protocols::sewing::data_storage::SmartSegment::get_segment_id ( ) const

References segment_id_.

Referenced by get_c_terminal_parent(), get_n_terminal_parent(), and SmartSegment().

◆ get_vital_residues()

std::set< core::Size > protocols::sewing::data_storage::SmartSegment::get_vital_residues ( ) const

References vital_residues_.

◆ is_c_terminus_fixed()

bool protocols::sewing::data_storage::SmartSegment::is_c_terminus_fixed ( ) const

References c_terminal_neighbor_.

Referenced by is_hashable(), and isolate().

◆ is_chimaeric()

bool protocols::sewing::data_storage::SmartSegment::is_chimaeric ( ) const

References is_a_chimaera_.

Referenced by get_c_terminal_parent(), get_n_terminal_parent(), and SmartSegment().

◆ is_hashable()

bool protocols::sewing::data_storage::SmartSegment::is_hashable ( ) const

References is_c_terminus_fixed(), and is_n_terminus_fixed().

◆ is_in_Assembly()

bool protocols::sewing::data_storage::SmartSegment::is_in_Assembly ( ) const

References is_in_Assembly_.

◆ is_n_terminus_fixed()

bool protocols::sewing::data_storage::SmartSegment::is_n_terminus_fixed ( ) const

References n_terminal_neighbor_.

Referenced by is_hashable(), and isolate().

◆ is_vital()

bool protocols::sewing::data_storage::SmartSegment::is_vital ( ) const

References is_vital_.

Referenced by set_is_vital(), and SmartSegment().

◆ isolate()

void protocols::sewing::data_storage::SmartSegment::isolate ( )

References get_c_terminal_neighbor(), get_n_terminal_neighbor(), is_c_terminus_fixed(), is_n_terminus_fixed(), set_c_terminal_neighbor(), and set_n_terminal_neighbor().

◆ link_to()

void protocols::sewing::data_storage::SmartSegment::link_to	(	SmartSegmentOP	n_term,
		SmartSegmentOP	c_term
	)

static

◆ residue_is_vital()

bool protocols::sewing::data_storage::SmartSegment::residue_is_vital ( core::Size resnum )

References vital_residues_.

◆ set_basis_pair()

void protocols::sewing::data_storage::SmartSegment::set_basis_pair ( BasisPair basis_pair )

References basis_pair_.

◆ set_c_terminal_neighbor()

void protocols::sewing::data_storage::SmartSegment::set_c_terminal_neighbor ( SmartSegmentOP new_c_terminal_neighbor )

References c_terminal_neighbor_.

Referenced by isolate().

◆ set_c_terminal_parent()

void protocols::sewing::data_storage::SmartSegment::set_c_terminal_parent ( SmartSegmentOP new_c_terminal_parent )

References c_terminal_parent_.

◆ set_chimaeric_status()

void protocols::sewing::data_storage::SmartSegment::set_chimaeric_status ( bool is_chimaera )

References is_a_chimaera_.

◆ set_const_reference_segment()

void protocols::sewing::data_storage::SmartSegment::set_const_reference_segment ( SmartSegmentCOP ref )

References const_reference_segment_, and core::scoring::ref.

◆ set_dssp_code()

void protocols::sewing::data_storage::SmartSegment::set_dssp_code ( char new_dssp_code )

References dssp_code_.

◆ set_is_in_Assembly()

void protocols::sewing::data_storage::SmartSegment::set_is_in_Assembly ( bool is_in_assembly )

References is_in_Assembly_.

◆ set_is_vital()

void protocols::sewing::data_storage::SmartSegment::set_is_vital ( bool is_vital )

References is_vital(), and is_vital_.

Referenced by protocols::sewing::data_storage::LigandSegment::LigandSegment().

◆ set_length()

void protocols::sewing::data_storage::SmartSegment::set_length ( core::Size new_length )

References length_.

◆ set_n_terminal_neighbor()

void protocols::sewing::data_storage::SmartSegment::set_n_terminal_neighbor ( SmartSegmentOP new_n_terminal_neighbor )

References n_terminal_neighbor_.

Referenced by isolate().

◆ set_n_terminal_parent()

void protocols::sewing::data_storage::SmartSegment::set_n_terminal_parent ( SmartSegmentOP new_n_terminal_parent )

References n_terminal_parent_.

◆ set_residue_vector()

void protocols::sewing::data_storage::SmartSegment::set_residue_vector ( utility::vector1< SmartSewingResidueOP > new_residue_vector )

References length_, and residues_.

◆ set_segment_id()

void protocols::sewing::data_storage::SmartSegment::set_segment_id ( core::Size new_segment_id )

References segment_id_.

◆ set_vital_residues()

void protocols::sewing::data_storage::SmartSegment::set_vital_residues ( std::set< core::Size > vital )

References vital_residues_.

Member Data Documentation

◆ basis_pair_

BasisPair protocols::sewing::data_storage::SmartSegment::basis_pair_ = std::make_pair( Basis( 0, 0), Basis( 0, 0) )

private

Referenced by get_basis_pair(), set_basis_pair(), and SmartSegment().

◆ c_terminal_neighbor_

SmartSegmentOP protocols::sewing::data_storage::SmartSegment::c_terminal_neighbor_

private

Referenced by get_c_terminal_neighbor(), is_c_terminus_fixed(), set_c_terminal_neighbor(), and SmartSegment().

◆ c_terminal_parent_

SmartSegmentOP protocols::sewing::data_storage::SmartSegment::c_terminal_parent_

private

Referenced by get_c_terminal_parent(), set_c_terminal_parent(), and SmartSegment().

◆ const_reference_segment_

SmartSegmentCOP protocols::sewing::data_storage::SmartSegment::const_reference_segment_ = nullptr

private

Referenced by get_const_reference_segment(), set_const_reference_segment(), and SmartSegment().

◆ dssp_code_

char protocols::sewing::data_storage::SmartSegment::dssp_code_

private

Referenced by get_dssp_code(), set_dssp_code(), and SmartSegment().

◆ is_a_chimaera_

bool protocols::sewing::data_storage::SmartSegment::is_a_chimaera_

private

Referenced by is_chimaeric(), set_chimaeric_status(), and SmartSegment().

◆ is_in_Assembly_

bool protocols::sewing::data_storage::SmartSegment::is_in_Assembly_

private

Referenced by is_in_Assembly(), set_is_in_Assembly(), and SmartSegment().

◆ is_vital_

bool protocols::sewing::data_storage::SmartSegment::is_vital_

private

Referenced by is_vital(), set_is_vital(), and SmartSegment().

◆ length_

core::Size protocols::sewing::data_storage::SmartSegment::length_

private

Referenced by set_length(), set_residue_vector(), and SmartSegment().

◆ n_terminal_neighbor_

SmartSegmentOP protocols::sewing::data_storage::SmartSegment::n_terminal_neighbor_

private

Referenced by get_n_terminal_neighbor(), is_n_terminus_fixed(), set_n_terminal_neighbor(), and SmartSegment().

◆ n_terminal_parent_

SmartSegmentOP protocols::sewing::data_storage::SmartSegment::n_terminal_parent_

private

Referenced by get_n_terminal_parent(), set_n_terminal_parent(), and SmartSegment().

◆ residues_

utility::vector1<SmartSewingResidueOP> protocols::sewing::data_storage::SmartSegment::residues_

private

Referenced by get_const_residue_vector(), get_length(), get_residue(), get_residue_vector(), set_residue_vector(), and SmartSegment().

◆ segment_id_

core::Size protocols::sewing::data_storage::SmartSegment::segment_id_

private

Referenced by get_segment_id(), set_segment_id(), and SmartSegment().

◆ vital_residues_

std::set< core::Size > protocols::sewing::data_storage::SmartSegment::vital_residues_

private

Referenced by add_vital_residue(), get_vital_residues(), residue_is_vital(), set_vital_residues(), and SmartSegment().

The documentation for this class was generated from the following files:

src/protocols/sewing/data_storage/SmartSegment.hh
src/protocols/sewing/data_storage/SmartSegment.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ SmartSegment() [1/4]

◆ SmartSegment() [2/4]

◆ SmartSegment() [3/4]

◆ SmartSegment() [4/4]

◆ ~SmartSegment()

Member Function Documentation

◆ add_vital_residue()

◆ become()

◆ clone()

◆ get_basis_pair()

◆ get_c_most_segment() [1/2]

◆ get_c_most_segment() [2/2]

◆ get_c_terminal_neighbor()

◆ get_c_terminal_parent()

◆ get_const_reference_segment()

◆ get_const_residue_vector()

◆ get_dssp_code()

◆ get_far_c_terminal_parent()

◆ get_far_n_terminal_parent()

◆ get_length()

◆ get_n_most_segment() [1/2]

◆ get_n_most_segment() [2/2]

◆ get_n_terminal_neighbor()

◆ get_n_terminal_parent()

◆ get_name()

◆ get_residue()

◆ get_residue_vector()

◆ get_segment_id()

◆ get_vital_residues()

◆ is_c_terminus_fixed()

◆ is_chimaeric()

◆ is_hashable()

◆ is_in_Assembly()

◆ is_n_terminus_fixed()

◆ is_vital()

◆ isolate()

◆ link_to()

◆ residue_is_vital()

◆ set_basis_pair()

◆ set_c_terminal_neighbor()

◆ set_c_terminal_parent()

◆ set_chimaeric_status()

◆ set_const_reference_segment()

◆ set_dssp_code()

◆ set_is_in_Assembly()

◆ set_is_vital()

◆ set_length()

◆ set_n_terminal_neighbor()

◆ set_n_terminal_parent()

◆ set_residue_vector()

◆ set_segment_id()

◆ set_vital_residues()

Member Data Documentation

◆ basis_pair_

◆ c_terminal_neighbor_

◆ c_terminal_parent_

◆ const_reference_segment_

◆ dssp_code_

◆ is_a_chimaera_

◆ is_in_Assembly_

◆ is_vital_

◆ length_

◆ n_terminal_neighbor_

◆ n_terminal_parent_

◆ residues_

◆ segment_id_

◆ vital_residues_