protocols::sewing::data_storage::SmartSegment Class Reference

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

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_.

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_.

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_.

protocols::sewing::data_storage::SmartSegment::SmartSegment

(

SmartSegment const &

src

)

References basis_pair_, c_terminal_neighbor_, c_terminal_parent_, const_reference_segment_, dssp_code_, get_basis_pair(), get_c_terminal_parent(), get_const_reference_segment(), get_const_residue_vector(), get_dssp_code(), get_length(), get_n_terminal_parent(), get_segment_id(), is_a_chimaera_, is_chimaeric(), is_in_Assembly_, is_vital(), is_vital_, length_, n_terminal_neighbor_, n_terminal_parent_, residues_, segment_id_, and vital_residues_.

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

override

Member Function Documentation

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().

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().

SmartSegmentOP protocols::sewing::data_storage::SmartSegment::clone

(

)

const

BasisPair protocols::sewing::data_storage::SmartSegment::get_basis_pair

(

)

const

References basis_pair_.

Referenced by SmartSegment().

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().

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

static

References get_c_most_segment().

SmartSegmentOP protocols::sewing::data_storage::SmartSegment::get_c_terminal_neighbor

(

)

const

References c_terminal_neighbor_.

Referenced by isolate(), and protocols::sewing::data_storage::SmartAssembly::to_pose().

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().

SmartSegmentCOP protocols::sewing::data_storage::SmartSegment::get_const_reference_segment

(

)

const

References const_reference_segment_.

Referenced by SmartSegment().

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

(

)

const

References residues_.

Referenced by SmartSegment().

char protocols::sewing::data_storage::SmartSegment::get_dssp_code

(

)

const

References dssp_code_.

Referenced by SmartSegment().

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().

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().

core::Size protocols::sewing::data_storage::SmartSegment::get_length

(

)

const

References residues_.

Referenced by become(), and SmartSegment().

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::hashing::Hasher::transform_segments(), and protocols::sewing::data_storage::SmartAssembly::transform_segments().

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

static

References get_n_most_segment().

SmartSegmentOP protocols::sewing::data_storage::SmartSegment::get_n_terminal_neighbor

(

)

const

References n_terminal_neighbor_.

Referenced by isolate().

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().

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

inlinevirtual

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

SmartSewingResidueOP protocols::sewing::data_storage::SmartSegment::get_residue

(

core::Size

resnum

)

References residues_, and protocols::TR().

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

(

)

References residues_.

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().

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

(

)

const

References vital_residues_.

bool protocols::sewing::data_storage::SmartSegment::is_c_terminus_fixed

(

)

const

References c_terminal_neighbor_.

Referenced by is_hashable(), and isolate().

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().

bool protocols::sewing::data_storage::SmartSegment::is_hashable

(

)

const

References is_c_terminus_fixed(), and is_n_terminus_fixed().

bool protocols::sewing::data_storage::SmartSegment::is_in_Assembly

(

)

const

References is_in_Assembly_.

bool protocols::sewing::data_storage::SmartSegment::is_n_terminus_fixed

(

)

const

References n_terminal_neighbor_.

Referenced by is_hashable(), and isolate().

bool protocols::sewing::data_storage::SmartSegment::is_vital

(

)

const

References is_vital_.

Referenced by set_is_vital(), and SmartSegment().

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().

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

static

Referenced by protocols::sewing::hashing::AlignmentFileGeneratorMover::add_pose_segments_to_segment_vector(), protocols::sewing::data_storage::SmartAssembly::add_segment_and_neighbors_to_local_segments(), protocols::sewing::data_storage::SmartAssembly::chimerize(), protocols::sewing::hashing::LigandBindingResPlacer::choose_best_metal_coordinator(), protocols::sewing::data_storage::SmartAssembly::delete_segment(), protocols::sewing::hashing::ModelFileReader::read_model_file(), protocols::sewing::data_storage::SmartAssembly::reconstitute_assembly_from_string(), protocols::sewing::data_storage::SmartAssembly::recurse_revert_far_c_terminal_parent(), protocols::sewing::data_storage::SmartAssembly::recurse_revert_far_n_terminal_parent(), and protocols::sewing::hashing::Hasher::transform_segments().

bool protocols::sewing::data_storage::SmartSegment::residue_is_vital

(

core::Size

resnum

)

References vital_residues_.

void protocols::sewing::data_storage::SmartSegment::set_basis_pair

(

BasisPair

basis_pair

)

References basis_pair_.

void protocols::sewing::data_storage::SmartSegment::set_c_terminal_neighbor

(

SmartSegmentOP

new_c_terminal_neighbor

)

References c_terminal_neighbor_.

Referenced by isolate().

void protocols::sewing::data_storage::SmartSegment::set_c_terminal_parent

(

SmartSegmentOP

new_c_terminal_parent

)

References c_terminal_parent_.

void protocols::sewing::data_storage::SmartSegment::set_chimaeric_status

(

bool

is_chimaera

)

References is_a_chimaera_.

void protocols::sewing::data_storage::SmartSegment::set_const_reference_segment

(

SmartSegmentCOP

ref

)

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

void protocols::sewing::data_storage::SmartSegment::set_dssp_code

(

char

new_dssp_code

)

References dssp_code_.

void protocols::sewing::data_storage::SmartSegment::set_is_in_Assembly

(

bool

is_in_assembly

)

References is_in_Assembly_.

void protocols::sewing::data_storage::SmartSegment::set_is_vital

(

bool

is_vital

)

References is_vital(), and is_vital_.

Referenced by protocols::sewing::hashing::LigandBindingResPlacer::choose_best_metal_coordinator(), and protocols::sewing::data_storage::LigandSegment::LigandSegment().

void protocols::sewing::data_storage::SmartSegment::set_length

(

core::Size

new_length

)

References length_.

void protocols::sewing::data_storage::SmartSegment::set_n_terminal_neighbor

(

SmartSegmentOP

new_n_terminal_neighbor

)

References n_terminal_neighbor_.

Referenced by isolate(), and protocols::sewing::data_storage::SmartAssembly::~SmartAssembly().

void protocols::sewing::data_storage::SmartSegment::set_n_terminal_parent

(

SmartSegmentOP

new_n_terminal_parent

)

References n_terminal_parent_.

void protocols::sewing::data_storage::SmartSegment::set_residue_vector

(

utility::vector1< SmartSewingResidueOP >

new_residue_vector

)

References length_, and residues_.

void protocols::sewing::data_storage::SmartSegment::set_segment_id

(

core::Size

new_segment_id

)

References segment_id_.

void protocols::sewing::data_storage::SmartSegment::set_vital_residues

(

std::set< core::Size >

vital

)

References vital_residues_.

Member Data Documentation

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().

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().

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

private

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

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

private

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

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

private

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

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

private

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

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

private

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

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

private

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

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

private

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

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().

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

private

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

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().

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

private

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

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