a SEWING Assembly composed of SmartSegments More...

#include <SmartAssembly.hh>

Inheritance diagram for protocols::sewing::data_storage::SmartAssembly:

Public Member Functions
	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)

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

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)

Protected Member Functions
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

Private Attributes
hashing::SegmentVectorCOP	segment_vector_

std::map< core::Size, SmartSegmentOP >	local_segments_

std::map< core::Size, data_storage::SmartSegmentOP >	pdb_segments_

std::map< core::Size, LigandResidueCOP >	const_ligands_

std::map< core::Size, LigandResidueCOP >	partner_ligands_

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

std::map< core::Size, utility::vector1< LigandResidueOP > >	ligand_conformers_

std::pair< core::Size, LigandResidueOP >	last_sampled_ligand_

utility::vector1< core::Size >	c_terminal_segments_

utility::vector1< core::Size >	n_terminal_segments_

core::Size	window_width_

SmartSegmentOP	first_segment_

SmartSegmentOP	n_terminal_segment_

SmartSegmentOP	c_terminal_segment_

bool	last_change_was_n_terminal_

SmartSegmentOP	last_chimaera_

BasisPair	last_chimaera_deleted_

SmartSegmentOP	last_reverted_parent_chimaera_

char	last_change_

core::Size	size_

core::Size	length_

SmartSegmentOP	counter_segment_

core::Size	segID_1_

core::Size	segID_2_

core::Size	resID_1_

core::Size	resID_2_

BasisPair	current_basis_pair_

utility::vector1< std::pair< core::Size, core::Size > >	all_basis_pairs_

core::pose::PoseOP	partner_

bool	output_partner_

char	modifiable_terminus_

std::string	start_node_vital_segments_

Detailed Description

a SEWING Assembly composed of SmartSegments

Constructor & Destructor Documentation

◆ SmartAssembly() [1/3]

protocols::sewing::data_storage::SmartAssembly::SmartAssembly ( )

References all_basis_pairs_.

◆ SmartAssembly() [2/3]

protocols::sewing::data_storage::SmartAssembly::SmartAssembly	(	hashing::SegmentVectorCOP	segment_vector,
		core::Size	window_width = `1`
	)

References all_basis_pairs_, c_terminal_segments_, modifiable_terminus_, n_terminal_segments_, output_partner_, segment_vector_, start_node_vital_segments_, protocols::TR(), and window_width_.

◆ SmartAssembly() [3/3]

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

References all_basis_pairs_, c_terminal_segments_, const_pdb_segments(), get_partner(), get_partner_ligands(), get_segment_vector(), n_terminal_segments_, pdb_segments(), segment_vector_, set_partner(), set_partner_ligands(), and window_width_.

◆ ~SmartAssembly()

protocols::sewing::data_storage::SmartAssembly::~SmartAssembly ( )

override

References ligand_conformers_, local_ligands_, local_segments_, core::scoring::pair, and pdb_segments_.

Member Function Documentation

◆ add_segment() [1/2]

bool protocols::sewing::data_storage::SmartAssembly::add_segment ( bool n_terminus )

References protocols::TR().

Referenced by recurse_revert_far_c_terminal_parent(), recurse_revert_far_n_terminal_parent(), switch_segment(), undelete_segment(), and unswitch_segment().

◆ add_segment() [2/2]

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

virtual

◆ add_segment_and_neighbors_to_local_segments()

void protocols::sewing::data_storage::SmartAssembly::add_segment_and_neighbors_to_local_segments	(	SmartSegmentCOP	ref_seg,
		core::Size	new_id = `0`
	)

References protocols::sewing::data_storage::SmartSegment::get_n_most_segment(), protocols::sewing::data_storage::ligand, ligand_conformers_, protocols::sewing::data_storage::SmartSegment::link_to(), local_ligands_, local_segments_, protocols::denovo_design::movers::new_id(), and protocols::TR().

Referenced by add_segment(), protocols::sewing::data_storage::HashedSmartAssembly::add_segment(), chimerize(), pdb_segments(), pick_random_starting_segment(), and set_starting_segment().

◆ can_delete()

bool protocols::sewing::data_storage::SmartAssembly::can_delete ( )

References c_terminal_segment_, protocols::sewing::data_storage::SmartSegment::get_far_c_terminal_parent(), protocols::sewing::data_storage::SmartSegment::get_far_n_terminal_parent(), and n_terminal_segment_.

◆ chimerize()

bool protocols::sewing::data_storage::SmartAssembly::chimerize	(	BasisPair	basis_pair,
		bool	n_terminus
	)

References add_segment_and_neighbors_to_local_segments(), get_length(), protocols::sewing::data_storage::SmartSegment::get_n_most_segment(), last_chimaera_, protocols::sewing::data_storage::ligand, protocols::sewing::data_storage::SmartSegment::link_to(), local_ligands_, local_segments_, pdb_segments_, core::scoring::rg, segment_vector_, protocols::TR(), and transform_segments().

Referenced by add_segment(), and protocols::sewing::data_storage::HashedSmartAssembly::add_segment().

◆ clone()

SmartAssemblyOP protocols::sewing::data_storage::SmartAssembly::clone ( ) const

◆ const_pdb_segments()

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

References pdb_segments_.

Referenced by SmartAssembly().

◆ delete_segment()

bool protocols::sewing::data_storage::SmartAssembly::delete_segment ( bool n_terminus )

References c_terminal_segment_, protocols::sewing::data_storage::SmartSegment::get_far_c_terminal_parent(), protocols::sewing::data_storage::SmartSegment::get_far_n_terminal_parent(), last_change_, last_change_was_n_terminal_, last_chimaera_deleted_, last_reverted_parent_chimaera_, length_, protocols::sewing::data_storage::SmartSegment::link_to(), n_terminal_segment_, recurse_revert_far_c_terminal_parent(), recurse_revert_far_n_terminal_parent(), size_, protocols::TR(), and unchimerize_ligand_segment().

Referenced by reconstitute_assembly_from_string(), revert(), switch_segment(), and unswitch_segment().

◆ dump_side_chains()

void protocols::sewing::data_storage::SmartAssembly::dump_side_chains ( )

◆ get_c_terminal_segment()

SmartSegmentOP protocols::sewing::data_storage::SmartAssembly::get_c_terminal_segment ( ) const

References c_terminal_segment_.

Referenced by protocols::sewing::data_storage::HashedSmartAssembly::add_segment(), get_comprehensive_reverse_assembly(), get_modifiable_terminus(), get_reverse_assembly(), reconstitute_assembly_from_string(), and trim_terminal_segments().

◆ get_comprehensive_assembly_string()

std::string protocols::sewing::data_storage::SmartAssembly::get_comprehensive_assembly_string ( ) const

References get_n_terminal_segment(), and core::id::to_string().

◆ get_comprehensive_forward_assembly()

std::string protocols::sewing::data_storage::SmartAssembly::get_comprehensive_forward_assembly ( ) const

References get_n_terminal_segment(), and core::id::to_string().

Referenced by reconstitute_assembly_from_string().

◆ get_comprehensive_reverse_assembly()

std::string protocols::sewing::data_storage::SmartAssembly::get_comprehensive_reverse_assembly ( ) const

References get_c_terminal_segment(), and core::id::to_string().

◆ get_forward_assembly()

std::string protocols::sewing::data_storage::SmartAssembly::get_forward_assembly ( ) const

References get_n_terminal_segment(), and core::id::to_string().

◆ get_last_change()

char protocols::sewing::data_storage::SmartAssembly::get_last_change ( ) const

References last_change_.

◆ get_last_change_was_n_terminal()

bool protocols::sewing::data_storage::SmartAssembly::get_last_change_was_n_terminal ( ) const

References last_change_was_n_terminal_.

◆ get_last_chimaera()

SmartSegmentOP protocols::sewing::data_storage::SmartAssembly::get_last_chimaera ( ) const

References last_chimaera_.

Referenced by protocols::sewing::data_storage::HashedSmartAssembly::add_segment().

◆ get_last_chimaera_deleted()

BasisPair protocols::sewing::data_storage::SmartAssembly::get_last_chimaera_deleted ( ) const

References last_chimaera_deleted_.

◆ get_length()

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

References length_.

Referenced by add_segment(), protocols::sewing::data_storage::HashedSmartAssembly::add_segment(), and chimerize().

◆ get_local_ligands() [1/2]

std::map< core::Size, LigandResidueOP > protocols::sewing::data_storage::SmartAssembly::get_local_ligands ( )

References local_ligands_.

◆ get_local_ligands() [2/2]

std::map< core::Size, LigandResidueOP > protocols::sewing::data_storage::SmartAssembly::get_local_ligands ( ) const

References local_ligands_.

◆ get_modifiable_terminus() [1/2]

char protocols::sewing::data_storage::SmartAssembly::get_modifiable_terminus ( )

References modifiable_terminus_.

◆ get_modifiable_terminus() [2/2]

bool protocols::sewing::data_storage::SmartAssembly::get_modifiable_terminus ( char op )

References get_c_terminal_segment(), get_n_terminal_segment(), modifiable_terminus_, and core::scoring::rg.

◆ get_n_terminal_segment()

SmartSegmentOP protocols::sewing::data_storage::SmartAssembly::get_n_terminal_segment ( ) const

References n_terminal_segment_.

Referenced by protocols::sewing::data_storage::HashedSmartAssembly::add_segment(), get_comprehensive_assembly_string(), get_comprehensive_forward_assembly(), get_forward_assembly(), get_modifiable_terminus(), is_continuous(), reconstitute_assembly_from_string(), to_pose(), and trim_terminal_segments().

◆ get_output_partner()

bool protocols::sewing::data_storage::SmartAssembly::get_output_partner ( ) const

References output_partner_.

◆ get_partner()

core::pose::PoseOP protocols::sewing::data_storage::SmartAssembly::get_partner ( ) const

References partner_.

Referenced by SmartAssembly().

◆ get_partner_ligands()

std::map< core::Size, LigandResidueCOP > protocols::sewing::data_storage::SmartAssembly::get_partner_ligands ( ) const

References partner_ligands_.

Referenced by SmartAssembly().

◆ get_random_segment_id()

core::Size protocols::sewing::data_storage::SmartAssembly::get_random_segment_id ( bool n_terminus )

References c_terminal_segments_, n_terminal_segments_, and core::scoring::rg.

Referenced by add_segment(), and protocols::sewing::data_storage::HashedSmartAssembly::add_segment().

◆ get_resID_1()

core::Size protocols::sewing::data_storage::SmartAssembly::get_resID_1 ( ) const

protected

References resID_1_.

◆ get_resID_2()

core::Size protocols::sewing::data_storage::SmartAssembly::get_resID_2 ( ) const

protected

References resID_2_.

◆ get_reverse_assembly()

std::string protocols::sewing::data_storage::SmartAssembly::get_reverse_assembly ( ) const

References get_c_terminal_segment(), and core::id::to_string().

◆ get_segID_1()

core::Size protocols::sewing::data_storage::SmartAssembly::get_segID_1 ( ) const

protected

References segID_1_.

Referenced by protocols::sewing::data_storage::HashedSmartAssembly::add_segment().

◆ get_segID_2()

core::Size protocols::sewing::data_storage::SmartAssembly::get_segID_2 ( ) const

protected

References segID_2_.

Referenced by protocols::sewing::data_storage::HashedSmartAssembly::add_segment().

◆ get_segment()

SmartSegmentOP protocols::sewing::data_storage::SmartAssembly::get_segment ( core::Size seg_id )

References n_terminal_segment_.

◆ get_segment_vector()

hashing::SegmentVectorCOP protocols::sewing::data_storage::SmartAssembly::get_segment_vector ( ) const

References segment_vector_.

Referenced by protocols::sewing::data_storage::HashedSmartAssembly::add_segment(), and SmartAssembly().

◆ get_size()

core::Size protocols::sewing::data_storage::SmartAssembly::get_size ( ) const

References size_.

Referenced by protocols::sewing::data_storage::HashedSmartAssembly::add_segment().

◆ get_start_node_vital_segments()

std::string protocols::sewing::data_storage::SmartAssembly::get_start_node_vital_segments ( )

References start_node_vital_segments_.

Referenced by reconstitute_assembly_from_string().

◆ get_window_width()

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

References window_width_.

◆ has_segment()

bool protocols::sewing::data_storage::SmartAssembly::has_segment ( core::Size seg_id )

References n_terminal_segment_.

◆ is_continuous()

bool protocols::sewing::data_storage::SmartAssembly::is_continuous ( ) const

References get_n_terminal_segment().

◆ iterate_over_basis_pairs()

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

References all_basis_pairs_, protocols::mean_field::max(), protocols::mean_field::min(), core::id::to_string(), protocols::TR(), and window_width_.

Referenced by add_segment().

◆ load_initial_conformers()

void protocols::sewing::data_storage::SmartAssembly::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.

References const_ligands_, ligand_conformers_, protocols::sewing::data_storage::LigandDescription::ligand_id, local_ligands_, and protocols::sewing::data_storage::LigandDescription::pdb_conformers.

◆ local_segments()

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

References local_segments_.

Referenced by protocols::sewing::data_storage::HashedSmartAssembly::add_segment().

◆ pdb_segments() [1/2]

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

References pdb_segments_.

Referenced by protocols::sewing::data_storage::HashedSmartAssembly::add_segment(), and SmartAssembly().

◆ pdb_segments() [2/2]

void protocols::sewing::data_storage::SmartAssembly::pdb_segments ( std::map< core::Size, data_storage::SmartSegmentOP > pdbsegs )

References add_segment_and_neighbors_to_local_segments(), const_ligands_, protocols::sewing::data_storage::ligand, local_ligands_, partner_ligands_, and pdb_segments_.

◆ pick_random_starting_segment()

void protocols::sewing::data_storage::SmartAssembly::pick_random_starting_segment ( )

References add_segment_and_neighbors_to_local_segments(), protocols::sewing::data_storage::SmartSegment::get_n_most_segment(), local_segments_, pdb_segments_, core::scoring::rg, segment_vector_, set_starting_segment(), and protocols::TR().

◆ reconstitute_assembly_from_string()

void protocols::sewing::data_storage::SmartAssembly::reconstitute_assembly_from_string ( std::string assembly_string )

References delete_segment(), protocols::sewing::data_storage::SmartSegment::get_c_most_segment(), get_c_terminal_segment(), get_comprehensive_forward_assembly(), get_n_terminal_segment(), protocols::features::strand_assembly::get_segment_id(), get_start_node_vital_segments(), protocols::sewing::data_storage::SmartSegment::link_to(), local_segments_, set_c_terminal_segment(), set_n_terminal_segment(), set_starting_segment(), protocols::TR(), and transform_segments().

◆ recurse_revert_far_c_terminal_parent()

SmartSegmentOP protocols::sewing::data_storage::SmartAssembly::recurse_revert_far_c_terminal_parent ( SmartSegmentOP current_segment )

References add_segment(), c_terminal_segment_, last_reverted_parent_chimaera_, length_, protocols::sewing::data_storage::SmartSegment::link_to(), n_terminal_segment_, size_, protocols::TR(), and unchimerize_ligand_segment().

Referenced by delete_segment().

◆ recurse_revert_far_n_terminal_parent()

SmartSegmentOP protocols::sewing::data_storage::SmartAssembly::recurse_revert_far_n_terminal_parent ( SmartSegmentOP current_segment )

References add_segment(), c_terminal_segment_, last_reverted_parent_chimaera_, length_, protocols::sewing::data_storage::SmartSegment::link_to(), n_terminal_segment_, size_, protocols::TR(), and unchimerize_ligand_segment().

Referenced by delete_segment().

◆ reset_chimaera_contacts()

void protocols::sewing::data_storage::SmartAssembly::reset_chimaera_contacts	(	LigandResidueOP	ligand,
		LigandSegmentOP	ligand_chimaera,
		Basis	nterm_basis,
		Basis	cterm_basis,
		bool	nterm
	)

References protocols::sewing::data_storage::ligand, protocols::sewing::data_storage::Basis::resnum(), protocols::sewing::data_storage::Basis::segment_id(), and protocols::TR().

Referenced by unchimerize_ligand_segment().

◆ revert()

void protocols::sewing::data_storage::SmartAssembly::revert ( )

References delete_segment(), last_change_, last_change_was_n_terminal_, protocols::TR(), undelete_segment(), unsample_ligand(), and unswitch_segment().

◆ sample_ligand()

bool protocols::sewing::data_storage::SmartAssembly::sample_ligand ( )

References last_change_, last_sampled_ligand_, ligand_conformers_, local_ligands_, and core::scoring::rg.

◆ set_c_terminal_segment()

void protocols::sewing::data_storage::SmartAssembly::set_c_terminal_segment ( SmartSegmentOP new_segment )

References c_terminal_segment_.

Referenced by protocols::sewing::data_storage::HashedSmartAssembly::add_segment(), reconstitute_assembly_from_string(), and trim_terminal_segments().

◆ set_last_change()

void protocols::sewing::data_storage::SmartAssembly::set_last_change ( char last_change )

References last_change_.

Referenced by protocols::sewing::data_storage::HashedSmartAssembly::add_segment().

◆ set_last_change_was_n_terminal()

void protocols::sewing::data_storage::SmartAssembly::set_last_change_was_n_terminal ( bool last_change_n )

References last_change_was_n_terminal_.

Referenced by protocols::sewing::data_storage::HashedSmartAssembly::add_segment().

◆ set_last_chimaera()

void protocols::sewing::data_storage::SmartAssembly::set_last_chimaera ( SmartSegmentOP last_chimaera )

References last_chimaera_.

◆ set_last_chimaera_deleted()

void protocols::sewing::data_storage::SmartAssembly::set_last_chimaera_deleted ( BasisPair last_chimaera_deleted )

References last_chimaera_deleted_.

◆ set_length()

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

References length_.

Referenced by protocols::sewing::data_storage::HashedSmartAssembly::add_segment().

◆ set_modifiable_terminus()

void protocols::sewing::data_storage::SmartAssembly::set_modifiable_terminus ( char modifiable_terminus )

References modifiable_terminus_.

◆ set_n_terminal_segment()

void protocols::sewing::data_storage::SmartAssembly::set_n_terminal_segment ( SmartSegmentOP new_segment )

References n_terminal_segment_.

Referenced by protocols::sewing::data_storage::HashedSmartAssembly::add_segment(), reconstitute_assembly_from_string(), and trim_terminal_segments().

◆ set_output_partner()

void protocols::sewing::data_storage::SmartAssembly::set_output_partner ( bool output_partner )

References output_partner_.

◆ set_partner()

void protocols::sewing::data_storage::SmartAssembly::set_partner ( core::pose::PoseOP partner_pose )

References partner_.

Referenced by SmartAssembly().

◆ set_partner_ligands()

void protocols::sewing::data_storage::SmartAssembly::set_partner_ligands ( std::map< core::Size, LigandResidueCOP > ligs )

References local_ligands_, and partner_ligands_.

Referenced by SmartAssembly().

◆ set_resID_1()

void protocols::sewing::data_storage::SmartAssembly::set_resID_1 ( core::Size id )

protected

References resID_1_.

Referenced by protocols::sewing::data_storage::HashedSmartAssembly::add_segment().

◆ set_resID_2()

void protocols::sewing::data_storage::SmartAssembly::set_resID_2 ( core::Size id )

protected

References resID_2_.

Referenced by protocols::sewing::data_storage::HashedSmartAssembly::add_segment().

◆ set_segID_1()

void protocols::sewing::data_storage::SmartAssembly::set_segID_1 ( core::Size id )

protected

References segID_1_.

Referenced by protocols::sewing::data_storage::HashedSmartAssembly::add_segment().

◆ set_segID_2()

void protocols::sewing::data_storage::SmartAssembly::set_segID_2 ( core::Size id )

protected

References segID_2_.

Referenced by protocols::sewing::data_storage::HashedSmartAssembly::add_segment().

◆ set_segment_vector()

void protocols::sewing::data_storage::SmartAssembly::set_segment_vector ( hashing::SegmentVectorCOP segment_vector )

References segment_vector_.

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

◆ set_size()

void protocols::sewing::data_storage::SmartAssembly::set_size ( core::Size new_size )

References size_.

Referenced by protocols::sewing::data_storage::HashedSmartAssembly::add_segment().

◆ set_start_node_vital_segments()

void protocols::sewing::data_storage::SmartAssembly::set_start_node_vital_segments ( std::string start_node_vital_segments )

References start_node_vital_segments_.

◆ set_starting_segment()

void protocols::sewing::data_storage::SmartAssembly::set_starting_segment	(	SmartSegmentOP	start_segment,
		std::string	start_node_vital_segments
	)

References add_segment_and_neighbors_to_local_segments(), c_terminal_segment_, counter_segment_, protocols::sewing::data_storage::SmartSegment::get_c_most_segment(), protocols::sewing::data_storage::SmartSegment::get_n_most_segment(), length_, local_segments_, n_terminal_segment_, and size_.

Referenced by pick_random_starting_segment(), and reconstitute_assembly_from_string().

◆ set_window_width()

void protocols::sewing::data_storage::SmartAssembly::set_window_width ( core::Size width )

References window_width_.

◆ switch_segment()

bool protocols::sewing::data_storage::SmartAssembly::switch_segment ( bool n_terminus )

References add_segment(), delete_segment(), last_change_, last_change_was_n_terminal_, last_chimaera_deleted_, protocols::TR(), and undelete_segment().

◆ to_pose()

core::pose::Pose protocols::sewing::data_storage::SmartAssembly::to_pose ( std::string residue_type_set )

◆ transform_segments()

bool protocols::sewing::data_storage::SmartAssembly::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.

References protocols::sewing::data_storage::SmartSegment::get_n_most_segment(), protocols::sewing::data_storage::ligand, local_segments_, protocols::TR(), window_width_, and protocols::kinmatch::xyz().

Referenced by chimerize(), and reconstitute_assembly_from_string().

◆ trim_terminal_segments()

void protocols::sewing::data_storage::SmartAssembly::trim_terminal_segments	(	char	terminus,
		core::Size	number
	)

References get_c_terminal_segment(), get_n_terminal_segment(), set_c_terminal_segment(), and set_n_terminal_segment().

◆ unchimerize_ligand_segment()

void protocols::sewing::data_storage::SmartAssembly::unchimerize_ligand_segment ( LigandSegmentOP ligseg )

References protocols::sewing::data_storage::ligand, local_ligands_, reset_chimaera_contacts(), and protocols::TR().

Referenced by delete_segment(), recurse_revert_far_c_terminal_parent(), and recurse_revert_far_n_terminal_parent().

◆ undelete_segment()

bool protocols::sewing::data_storage::SmartAssembly::undelete_segment ( )

References add_segment(), last_change_was_n_terminal_, and last_chimaera_deleted_.

Referenced by revert(), switch_segment(), and unswitch_segment().

◆ unsample_ligand()

void protocols::sewing::data_storage::SmartAssembly::unsample_ligand ( )

References last_sampled_ligand_, and local_ligands_.

Referenced by revert().

◆ unswitch_segment()

void protocols::sewing::data_storage::SmartAssembly::unswitch_segment ( )

References add_segment(), delete_segment(), last_change_was_n_terminal_, last_chimaera_deleted_, and undelete_segment().

Referenced by revert().

Member Data Documentation

◆ all_basis_pairs_

utility::vector1< std::pair< core::Size, core::Size > > protocols::sewing::data_storage::SmartAssembly::all_basis_pairs_

private

Referenced by add_segment(), iterate_over_basis_pairs(), and SmartAssembly().

◆ c_terminal_segment_

SmartSegmentOP protocols::sewing::data_storage::SmartAssembly::c_terminal_segment_

private

Referenced by add_segment(), can_delete(), delete_segment(), get_c_terminal_segment(), recurse_revert_far_c_terminal_parent(), recurse_revert_far_n_terminal_parent(), set_c_terminal_segment(), and set_starting_segment().

◆ c_terminal_segments_

utility::vector1<core::Size> protocols::sewing::data_storage::SmartAssembly::c_terminal_segments_

private

Referenced by get_random_segment_id(), and SmartAssembly().

◆ const_ligands_

std::map< core::Size, LigandResidueCOP > protocols::sewing::data_storage::SmartAssembly::const_ligands_

private

Referenced by load_initial_conformers(), and pdb_segments().

◆ counter_segment_

SmartSegmentOP protocols::sewing::data_storage::SmartAssembly::counter_segment_

private

Referenced by set_starting_segment().

◆ current_basis_pair_

BasisPair protocols::sewing::data_storage::SmartAssembly::current_basis_pair_

private

◆ first_segment_

SmartSegmentOP protocols::sewing::data_storage::SmartAssembly::first_segment_

private

Referenced by add_segment().

◆ last_change_

char protocols::sewing::data_storage::SmartAssembly::last_change_

private

Referenced by add_segment(), delete_segment(), get_last_change(), revert(), sample_ligand(), set_last_change(), and switch_segment().

◆ last_change_was_n_terminal_

bool protocols::sewing::data_storage::SmartAssembly::last_change_was_n_terminal_

private

Referenced by add_segment(), delete_segment(), get_last_change_was_n_terminal(), revert(), set_last_change_was_n_terminal(), switch_segment(), undelete_segment(), and unswitch_segment().

◆ last_chimaera_

SmartSegmentOP protocols::sewing::data_storage::SmartAssembly::last_chimaera_

private

Referenced by add_segment(), chimerize(), get_last_chimaera(), and set_last_chimaera().

◆ last_chimaera_deleted_

BasisPair protocols::sewing::data_storage::SmartAssembly::last_chimaera_deleted_

private

Referenced by delete_segment(), get_last_chimaera_deleted(), set_last_chimaera_deleted(), switch_segment(), undelete_segment(), and unswitch_segment().

◆ last_reverted_parent_chimaera_

SmartSegmentOP protocols::sewing::data_storage::SmartAssembly::last_reverted_parent_chimaera_

private

Referenced by delete_segment(), recurse_revert_far_c_terminal_parent(), and recurse_revert_far_n_terminal_parent().

◆ last_sampled_ligand_

std::pair< core::Size, LigandResidueOP > protocols::sewing::data_storage::SmartAssembly::last_sampled_ligand_

private

Referenced by sample_ligand(), and unsample_ligand().

◆ length_

core::Size protocols::sewing::data_storage::SmartAssembly::length_

private

Referenced by add_segment(), delete_segment(), get_length(), recurse_revert_far_c_terminal_parent(), recurse_revert_far_n_terminal_parent(), set_length(), and set_starting_segment().

◆ ligand_conformers_

std::map< core::Size, utility::vector1< LigandResidueOP > > protocols::sewing::data_storage::SmartAssembly::ligand_conformers_

private

Referenced by add_segment_and_neighbors_to_local_segments(), load_initial_conformers(), sample_ligand(), and ~SmartAssembly().

◆ local_ligands_

std::map< core::Size, LigandResidueOP > protocols::sewing::data_storage::SmartAssembly::local_ligands_

private

Referenced by add_segment_and_neighbors_to_local_segments(), chimerize(), get_local_ligands(), load_initial_conformers(), pdb_segments(), sample_ligand(), set_partner_ligands(), unchimerize_ligand_segment(), unsample_ligand(), and ~SmartAssembly().

◆ local_segments_

std::map< core::Size, SmartSegmentOP > protocols::sewing::data_storage::SmartAssembly::local_segments_

private

Referenced by add_segment(), add_segment_and_neighbors_to_local_segments(), chimerize(), local_segments(), pick_random_starting_segment(), reconstitute_assembly_from_string(), set_starting_segment(), transform_segments(), and ~SmartAssembly().

◆ modifiable_terminus_

char protocols::sewing::data_storage::SmartAssembly::modifiable_terminus_

private

Referenced by get_modifiable_terminus(), set_modifiable_terminus(), and SmartAssembly().

◆ n_terminal_segment_

SmartSegmentOP protocols::sewing::data_storage::SmartAssembly::n_terminal_segment_

private

Referenced by add_segment(), can_delete(), delete_segment(), get_n_terminal_segment(), get_segment(), has_segment(), recurse_revert_far_c_terminal_parent(), recurse_revert_far_n_terminal_parent(), set_n_terminal_segment(), and set_starting_segment().

◆ n_terminal_segments_

utility::vector1<core::Size> protocols::sewing::data_storage::SmartAssembly::n_terminal_segments_

private

Referenced by get_random_segment_id(), and SmartAssembly().

◆ output_partner_

bool protocols::sewing::data_storage::SmartAssembly::output_partner_

private

Referenced by get_output_partner(), set_output_partner(), SmartAssembly(), and to_pose().

◆ partner_

core::pose::PoseOP protocols::sewing::data_storage::SmartAssembly::partner_

private

Referenced by get_partner(), set_partner(), and to_pose().

◆ partner_ligands_

std::map< core::Size, LigandResidueCOP > protocols::sewing::data_storage::SmartAssembly::partner_ligands_

private

Referenced by get_partner_ligands(), pdb_segments(), and set_partner_ligands().

◆ pdb_segments_

std::map< core::Size, data_storage::SmartSegmentOP > protocols::sewing::data_storage::SmartAssembly::pdb_segments_

private

Referenced by add_segment(), chimerize(), const_pdb_segments(), pdb_segments(), pick_random_starting_segment(), and ~SmartAssembly().

◆ resID_1_

core::Size protocols::sewing::data_storage::SmartAssembly::resID_1_

private

Referenced by add_segment(), get_resID_1(), and set_resID_1().

◆ resID_2_

core::Size protocols::sewing::data_storage::SmartAssembly::resID_2_

private

Referenced by add_segment(), get_resID_2(), and set_resID_2().

◆ segID_1_

core::Size protocols::sewing::data_storage::SmartAssembly::segID_1_

private

Referenced by add_segment(), get_segID_1(), and set_segID_1().

◆ segID_2_

core::Size protocols::sewing::data_storage::SmartAssembly::segID_2_

private

Referenced by add_segment(), get_segID_2(), and set_segID_2().

◆ segment_vector_

hashing::SegmentVectorCOP protocols::sewing::data_storage::SmartAssembly::segment_vector_

private

Referenced by add_segment(), chimerize(), get_segment_vector(), pick_random_starting_segment(), set_segment_vector(), and SmartAssembly().

◆ size_

core::Size protocols::sewing::data_storage::SmartAssembly::size_

private

Referenced by add_segment(), delete_segment(), get_size(), recurse_revert_far_c_terminal_parent(), recurse_revert_far_n_terminal_parent(), set_size(), and set_starting_segment().

◆ start_node_vital_segments_

std::string protocols::sewing::data_storage::SmartAssembly::start_node_vital_segments_

private

Referenced by get_start_node_vital_segments(), set_start_node_vital_segments(), and SmartAssembly().

◆ window_width_

core::Size protocols::sewing::data_storage::SmartAssembly::window_width_

private

Referenced by add_segment(), get_window_width(), iterate_over_basis_pairs(), set_window_width(), SmartAssembly(), and transform_segments().

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

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

Public Member Functions

Protected Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ SmartAssembly() [1/3]

◆ SmartAssembly() [2/3]

◆ SmartAssembly() [3/3]

◆ ~SmartAssembly()

Member Function Documentation

◆ add_segment() [1/2]

◆ add_segment() [2/2]

◆ add_segment_and_neighbors_to_local_segments()

◆ can_delete()

◆ chimerize()

◆ clone()

◆ const_pdb_segments()

◆ delete_segment()

◆ dump_side_chains()

◆ get_c_terminal_segment()

◆ get_comprehensive_assembly_string()

◆ get_comprehensive_forward_assembly()

◆ get_comprehensive_reverse_assembly()

◆ get_forward_assembly()

◆ get_last_change()

◆ get_last_change_was_n_terminal()

◆ get_last_chimaera()

◆ get_last_chimaera_deleted()

◆ get_length()

◆ get_local_ligands() [1/2]

◆ get_local_ligands() [2/2]

◆ get_modifiable_terminus() [1/2]

◆ get_modifiable_terminus() [2/2]

◆ get_n_terminal_segment()

◆ get_output_partner()

◆ get_partner()

◆ get_partner_ligands()

◆ get_random_segment_id()

◆ get_resID_1()

◆ get_resID_2()

◆ get_reverse_assembly()

◆ get_segID_1()

◆ get_segID_2()

◆ get_segment()

◆ get_segment_vector()

◆ get_size()

◆ get_start_node_vital_segments()

◆ get_window_width()

◆ has_segment()

◆ is_continuous()

◆ iterate_over_basis_pairs()

◆ load_initial_conformers()

◆ local_segments()

◆ pdb_segments() [1/2]

◆ pdb_segments() [2/2]

◆ pick_random_starting_segment()

◆ reconstitute_assembly_from_string()

◆ recurse_revert_far_c_terminal_parent()

◆ recurse_revert_far_n_terminal_parent()

◆ reset_chimaera_contacts()

◆ revert()

◆ sample_ligand()

◆ set_c_terminal_segment()

◆ set_last_change()

◆ set_last_change_was_n_terminal()

◆ set_last_chimaera()

◆ set_last_chimaera_deleted()

◆ set_length()

◆ set_modifiable_terminus()

◆ set_n_terminal_segment()

◆ set_output_partner()

◆ set_partner()

◆ set_partner_ligands()

◆ set_resID_1()

◆ set_resID_2()

◆ set_segID_1()

◆ set_segID_2()

◆ set_segment_vector()

◆ set_size()

◆ set_start_node_vital_segments()