an Assembly that makes use of the Hasher More...

#include <HashedSmartAssembly.hh>

Inheritance diagram for protocols::sewing::data_storage::HashedSmartAssembly:

Public Member Functions
	HashedSmartAssembly ()

	HashedSmartAssembly (hashing::SegmentVectorCOP)

	HashedSmartAssembly (HashedSmartAssembly const &src)

	~HashedSmartAssembly () override

HashedSmartAssemblyOP	clone () const

void	set_basis_map_generator (hashing::BasisMapGeneratorOP new_bmg)

bool	add_segment (bool n_terminus, core::Size seg_ID_to_add, core::Size res_ID_1, core::Size res_ID_2) override

core::Size	get_window_width () const

Public Member Functions inherited from protocols::sewing::data_storage::SmartAssembly
	SmartAssembly ()

	SmartAssembly (hashing::SegmentVectorCOP segment_vector, core::Size window_width=1)

	SmartAssembly (SmartAssembly const &src)

	~SmartAssembly () override

SmartAssemblyOP	clone () const

void	set_starting_segment (SmartSegmentOP start_segment, std::string start_node_vital_segments)

SmartSegmentOP	get_n_terminal_segment () const

void	set_n_terminal_segment (SmartSegmentOP new_segment)

bool	has_segment (core::Size seg_id)

SmartSegmentOP	get_segment (core::Size seg_id)

SmartSegmentOP	get_c_terminal_segment () const

void	set_c_terminal_segment (SmartSegmentOP new_segment)

std::string	get_start_node_vital_segments ()

void	set_start_node_vital_segments (std::string start_node_vital_segments)

bool	get_last_change_was_n_terminal () const

void	set_last_change_was_n_terminal (bool)

char	get_last_change () const

SmartSegmentOP	get_last_chimaera () const

BasisPair	get_last_chimaera_deleted () const

void	set_partner (core::pose::PoseOP partner_pose)

core::pose::PoseOP	get_partner () const

void	set_last_change (char)

void	set_last_chimaera (SmartSegmentOP)

void	set_last_chimaera_deleted (BasisPair)

bool	can_delete ()

void	pdb_segments (std::map< core::Size, data_storage::SmartSegmentOP >)

std::map< core::Size, data_storage::SmartSegmentOP > &	pdb_segments ()

std::map< core::Size, data_storage::SmartSegmentOP > &	local_segments ()

std::map< core::Size, data_storage::SmartSegmentOP >	const_pdb_segments () const

core::Size	get_length () const

void	set_length (core::Size)

core::Size	get_size () const

void	set_size (core::Size)

hashing::SegmentVectorCOP	get_segment_vector () const

void	set_segment_vector (hashing::SegmentVectorCOP)

bool	get_modifiable_terminus (char op)

char	get_modifiable_terminus ()

void	set_modifiable_terminus (char modifiable_terminus)

bool	is_continuous () const

core::Size	get_random_segment_id (bool n_terminus)

std::string	get_forward_assembly () const

std::string	get_comprehensive_forward_assembly () const

std::string	get_reverse_assembly () const

std::string	get_comprehensive_reverse_assembly () const

std::string	get_comprehensive_assembly_string () const

std::map< core::Size, LigandResidueCOP >	get_partner_ligands () const

void	set_partner_ligands (std::map< core::Size, LigandResidueCOP >)

std::map< core::Size, LigandResidueOP >	get_local_ligands ()

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

bool	add_segment (bool n_terminus)

bool	delete_segment (bool n_terminus)

bool	switch_segment (bool n_terminus)

bool	undelete_segment ()

void	unswitch_segment ()

SmartSegmentOP	recurse_revert_far_n_terminal_parent (SmartSegmentOP current_segment)

SmartSegmentOP	recurse_revert_far_c_terminal_parent (SmartSegmentOP current_segment)

void	unchimerize_ligand_segment (LigandSegmentOP ligseg)

void	revert ()

void	dump_side_chains ()

void	pick_random_starting_segment ()

core::pose::Pose	to_pose (std::string)

bool	transform_segments (BasisPair basis_pair)
	Transforms the segments in the second basis to the coordinate frame of the first basis. Returns the transformed (second) basis segment. More...

bool	chimerize (BasisPair basis_pair, bool n_terminus)

std::pair< bool, core::Size >	iterate_over_basis_pairs (SmartSegmentCOP segment_1, SmartSegmentCOP segment_2, bool n_terminus)

void	reset_chimaera_contacts (LigandResidueOP ligand, LigandSegmentOP ligand_chimaera, Basis nterm_basis, Basis cterm_basis, bool nterm)

void	add_segment_and_neighbors_to_local_segments (SmartSegmentCOP ref_seg, core::Size new_id=0)

bool	sample_ligand ()

void	unsample_ligand ()

void	load_initial_conformers (data_storage::LigandDescription ligdes)
	NOTE This method MUST be called after pdb_segments() is set and before the starting segment is picked for this to work. More...

core::Size	get_window_width () const

void	set_window_width (core::Size)

bool	get_output_partner () const

void	set_output_partner (bool)

void	reconstitute_assembly_from_string (std::string)

void	trim_terminal_segments (char, core::Size)

Private Attributes
hashing::BasisMapGeneratorOP	existing_alignments_

SmartSegmentOP	first_segment_

Additional Inherited Members
Protected Member Functions inherited from protocols::sewing::data_storage::SmartAssembly
void	set_resID_1 (core::Size)

void	set_resID_2 (core::Size)

core::Size	get_resID_1 () const

core::Size	get_resID_2 () const

void	set_segID_1 (core::Size)

void	set_segID_2 (core::Size)

core::Size	get_segID_1 () const

core::Size	get_segID_2 () const

Detailed Description

an Assembly that makes use of the Hasher

Constructor & Destructor Documentation

protocols::sewing::data_storage::HashedSmartAssembly::HashedSmartAssembly ( )

protocols::sewing::data_storage::HashedSmartAssembly::HashedSmartAssembly ( hashing::SegmentVectorCOP segment_vector )

References protocols::sewing::data_storage::SmartAssembly::set_segment_vector().

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

protocols::sewing::data_storage::HashedSmartAssembly::~HashedSmartAssembly ( )

override

Member Function Documentation

bool protocols::sewing::data_storage::HashedSmartAssembly::add_segment	(	bool	n_terminus,
		core::Size	seg_ID_to_add,
		core::Size	res_ID_1,
		core::Size	res_ID_2
	)

overridevirtual

Reimplemented from protocols::sewing::data_storage::SmartAssembly.

HashedSmartAssemblyOP protocols::sewing::data_storage::HashedSmartAssembly::clone ( ) const

core::Size protocols::sewing::data_storage::HashedSmartAssembly::get_window_width ( ) const

References existing_alignments_.

Referenced by add_segment().

void protocols::sewing::data_storage::HashedSmartAssembly::set_basis_map_generator ( hashing::BasisMapGeneratorOP new_bmg )

References existing_alignments_.

Member Data Documentation

hashing::BasisMapGeneratorOP protocols::sewing::data_storage::HashedSmartAssembly::existing_alignments_

private

Referenced by add_segment(), get_window_width(), and set_basis_map_generator().

SmartSegmentOP protocols::sewing::data_storage::HashedSmartAssembly::first_segment_

private

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

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

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation