a segment that contains a single ligand residue with given attachment point(s) More...

#include <LigandSegment.hh>

Inheritance diagram for protocols::sewing::data_storage::LigandSegment:

Public Member Functions
	LigandSegment ()
	a segment that contains a single ligand residue with given attachment point(s) More...

	LigandSegment (bool is_vital)

	LigandSegment (bool is_vital, core::Size max_segment_length)

	LigandSegment (LigandSegment const &src)

	LigandSegment (SmartSegment const &src, bool is_vital, std::set< core::Size > ligand_residues, core::Size ligand_to_attach)
	Make a LigandSegment from a non-LigandSegment. More...

	~LigandSegment () override

LigandSegmentOP	clone () const

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

std::set< core::Size > &	get_nonconst_ligand_residues ()

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

std::set< core::Size > &	get_nonconst_ligand_contact_indices ()

void	add_ligand_contact (core::Size)

void	attach_unowned_ligand (LigandResidueCOP ligand_res)

void	attach_ligand (LigandResidueOP, bool)

std::string	get_name () const override

std::map< core::Size, LigandResidueOP > &	get_owned_ligand_residues ()

std::map< core::Size, LigandResidueOP > const	get_const_owned_ligand_residues () const

Public Member Functions inherited from protocols::sewing::data_storage::SmartSegment
	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)

Private Attributes
std::set< core::Size >	ligand_contacts_

std::set< core::Size >	ligand_residues_

std::map< core::Size, LigandResidueOP >	owned_ligand_residues_

Additional Inherited Members
Static Public Member Functions inherited from protocols::sewing::data_storage::SmartSegment
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)

Detailed Description

a segment that contains a single ligand residue with given attachment point(s)

Constructor & Destructor Documentation

protocols::sewing::data_storage::LigandSegment::LigandSegment ( )

a segment that contains a single ligand residue with given attachment point(s)

References ligand_contacts_, ligand_residues_, and owned_ligand_residues_.

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

References ligand_contacts_, ligand_residues_, and owned_ligand_residues_.

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

References ligand_contacts_, ligand_residues_, and owned_ligand_residues_.

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

References add_ligand_contact(), attach_ligand(), get_const_owned_ligand_residues(), get_ligand_contact_indices(), get_ligand_residues(), and ligand_residues_.

protocols::sewing::data_storage::LigandSegment::LigandSegment	(	SmartSegment const &	src,
		bool	is_vital,
		std::set< core::Size >	ligand_binding_residues,
		core::Size	ligand_to_attach
	)

Make a LigandSegment from a non-LigandSegment.

This constructor is for use with LigandBindingResPlacer It knows: *pointer to ligand (and therefore the ligand ID) *ligand contact residue(because it just added it) *There won't be any owned ligands We only need to allow for one ligand since this will only be used when the first contact is added

References add_ligand_contact(), ligand_residues_, and protocols::sewing::data_storage::SmartSegment::set_is_vital().

protocols::sewing::data_storage::LigandSegment::~LigandSegment ( )

override

Member Function Documentation

void protocols::sewing::data_storage::LigandSegment::add_ligand_contact ( core::Size contact_index )

References protocols::sewing::data_storage::SmartSegment::add_vital_residue(), and ligand_contacts_.

Referenced by LigandSegment().

void protocols::sewing::data_storage::LigandSegment::attach_ligand	(	LigandResidueOP	ligand_res,
		bool	owner
	)

References ligand_residues_, and owned_ligand_residues_.

Referenced by LigandSegment().

void protocols::sewing::data_storage::LigandSegment::attach_unowned_ligand ( LigandResidueCOP ligand_res )

References ligand_residues_.

LigandSegmentOP protocols::sewing::data_storage::LigandSegment::clone ( ) const

Referenced by protocols::sewing::data_storage::SmartAssembly::add_segment_and_neighbors_to_local_segments().

std::map< core::Size, LigandResidueOP > const protocols::sewing::data_storage::LigandSegment::get_const_owned_ligand_residues ( ) const

References owned_ligand_residues_.

Referenced by LigandSegment().

std::set< core::Size > protocols::sewing::data_storage::LigandSegment::get_ligand_contact_indices ( ) const

References ligand_contacts_.

Referenced by LigandSegment().

std::set< core::Size > protocols::sewing::data_storage::LigandSegment::get_ligand_residues ( ) const

References ligand_residues_.

Referenced by LigandSegment().

std::string protocols::sewing::data_storage::LigandSegment::get_name ( ) const

inlineoverridevirtual

Reimplemented from protocols::sewing::data_storage::SmartSegment.

std::set< core::Size > & protocols::sewing::data_storage::LigandSegment::get_nonconst_ligand_contact_indices ( )

References ligand_contacts_.

Referenced by protocols::sewing::hashing::LigandBindingResPlacer::revert_last_added_contact().

std::set< core::Size > & protocols::sewing::data_storage::LigandSegment::get_nonconst_ligand_residues ( )

References ligand_residues_.

std::map< core::Size, LigandResidueOP > & protocols::sewing::data_storage::LigandSegment::get_owned_ligand_residues ( )

References owned_ligand_residues_.

Referenced by protocols::sewing::data_storage::SmartAssembly::sample_ligand(), and protocols::sewing::data_storage::SmartAssembly::unsample_ligand().

Member Data Documentation

std::set< core::Size > protocols::sewing::data_storage::LigandSegment::ligand_contacts_

private

Referenced by add_ligand_contact(), get_ligand_contact_indices(), get_nonconst_ligand_contact_indices(), and LigandSegment().

std::set< core::Size > protocols::sewing::data_storage::LigandSegment::ligand_residues_

private

Referenced by attach_ligand(), attach_unowned_ligand(), get_ligand_residues(), get_nonconst_ligand_residues(), and LigandSegment().

std::map< core::Size, LigandResidueOP > protocols::sewing::data_storage::LigandSegment::owned_ligand_residues_

private

Referenced by attach_ligand(), get_const_owned_ligand_residues(), get_owned_ligand_residues(), and LigandSegment().

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

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

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation