protocols::sewing::data_storage::SmartAssembly Class Reference

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

protocols::sewing::data_storage::SmartAssembly::SmartAssembly

(

)

References all_basis_pairs_.

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_.

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_.

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

override

References ligand_conformers_, local_ligands_, local_segments_, core::scoring::pair, pdb_segments_, and protocols::sewing::data_storage::SmartSegment::set_n_terminal_neighbor().

Member Function Documentation

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().

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

Reimplemented in protocols::sewing::data_storage::HashedSmartAssembly.

References add_segment_and_neighbors_to_local_segments(), all_basis_pairs_, c_terminal_segment_, chimerize(), first_segment_, get_length(), get_random_segment_id(), iterate_over_basis_pairs(), last_change_, last_change_was_n_terminal_, last_chimaera_, length_, local_segments_, protocols::mean_field::max(), n_terminal_segment_, pdb_segments_, resID_1_, resID_2_, core::scoring::rg, segID_1_, segID_2_, segment_vector_, size_, protocols::TR(), and window_width_.

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::LigandSegment::clone(), 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 protocols::sewing::data_storage::HashedSmartAssembly::add_segment(), add_segment(), chimerize(), pdb_segments(), pick_random_starting_segment(), and set_starting_segment().

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_.

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

SmartAssemblyOP protocols::sewing::data_storage::SmartAssembly::clone

(

)

const

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

(

)

const

References pdb_segments_.

Referenced by SmartAssembly().

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().

void protocols::sewing::data_storage::SmartAssembly::dump_side_chains

(

)

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().

std::string protocols::sewing::data_storage::SmartAssembly::get_comprehensive_assembly_string

(

)

const

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

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().

std::string protocols::sewing::data_storage::SmartAssembly::get_comprehensive_reverse_assembly

(

)

const

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

std::string protocols::sewing::data_storage::SmartAssembly::get_forward_assembly

(

)

const

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

char protocols::sewing::data_storage::SmartAssembly::get_last_change

(

)

const

References last_change_.

bool protocols::sewing::data_storage::SmartAssembly::get_last_change_was_n_terminal

(

)

const

References last_change_was_n_terminal_.

SmartSegmentOP protocols::sewing::data_storage::SmartAssembly::get_last_chimaera

(

)

const

References last_chimaera_.

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

BasisPair protocols::sewing::data_storage::SmartAssembly::get_last_chimaera_deleted

(

)

const

References last_chimaera_deleted_.

core::Size protocols::sewing::data_storage::SmartAssembly::get_length

(

)

const

References length_.

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

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

(

)

References local_ligands_.

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

(

)

const

References local_ligands_.

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.

char protocols::sewing::data_storage::SmartAssembly::get_modifiable_terminus

(

)

References modifiable_terminus_.

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().

bool protocols::sewing::data_storage::SmartAssembly::get_output_partner

(

)

const

References output_partner_.

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

(

)

const

References partner_.

Referenced by SmartAssembly().

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

(

)

const

References partner_ligands_.

Referenced by SmartAssembly().

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

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

protected

References resID_1_.

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

protected

References resID_2_.

std::string protocols::sewing::data_storage::SmartAssembly::get_reverse_assembly

(

)

const

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

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

protected

References segID_1_.

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

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

protected

References segID_2_.

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

SmartSegmentOP protocols::sewing::data_storage::SmartAssembly::get_segment

(

core::Size

seg_id

)

References n_terminal_segment_.

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().

core::Size protocols::sewing::data_storage::SmartAssembly::get_size

(

)

const

References size_.

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

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

(

)

References start_node_vital_segments_.

Referenced by pick_random_starting_segment(), and reconstitute_assembly_from_string().

core::Size protocols::sewing::data_storage::SmartAssembly::get_window_width

(

)

const

References window_width_.

bool protocols::sewing::data_storage::SmartAssembly::has_segment

(

core::Size

seg_id

)

References n_terminal_segment_.

bool protocols::sewing::data_storage::SmartAssembly::is_continuous

(

)

const

References get_n_terminal_segment().

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().

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.

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().

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_.

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().

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(), get_start_node_vital_segments(), local_segments_, pdb_segments_, core::scoring::rg, segment_vector_, set_starting_segment(), and protocols::TR().

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().

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().

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().

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

Referenced by unchimerize_ligand_segment().

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().

bool protocols::sewing::data_storage::SmartAssembly::sample_ligand

(

)

References protocols::sewing::data_storage::LigandSegment::get_owned_ligand_residues(), last_change_, last_sampled_ligand_, ligand_conformers_, local_ligands_, and core::scoring::rg.

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().

void protocols::sewing::data_storage::SmartAssembly::set_last_change

(

char

last_change

)

References last_change_.

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

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().

void protocols::sewing::data_storage::SmartAssembly::set_last_chimaera

(

SmartSegmentOP

last_chimaera

)

References last_chimaera_.

void protocols::sewing::data_storage::SmartAssembly::set_last_chimaera_deleted

(

BasisPair

last_chimaera_deleted

)

References last_chimaera_deleted_.

void protocols::sewing::data_storage::SmartAssembly::set_length

(

core::Size

new_length

)

References length_.

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

void protocols::sewing::data_storage::SmartAssembly::set_modifiable_terminus

(

char

modifiable_terminus

)

References modifiable_terminus_.

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().

void protocols::sewing::data_storage::SmartAssembly::set_output_partner

(

bool

output_partner

)

References output_partner_.

void protocols::sewing::data_storage::SmartAssembly::set_partner

(

core::pose::PoseOP

partner_pose

)

References partner_.

Referenced by SmartAssembly().

void protocols::sewing::data_storage::SmartAssembly::set_partner_ligands

(

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

ligs

)

References local_ligands_, and partner_ligands_.

Referenced by SmartAssembly().

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().

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().

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().

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().

void protocols::sewing::data_storage::SmartAssembly::set_segment_vector

(

hashing::SegmentVectorCOP

segment_vector

)

References segment_vector_.

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

void protocols::sewing::data_storage::SmartAssembly::set_size

(

core::Size

new_size

)

References size_.

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

void protocols::sewing::data_storage::SmartAssembly::set_start_node_vital_segments

(

std::string

start_node_vital_segments

)

References start_node_vital_segments_.

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().

void protocols::sewing::data_storage::SmartAssembly::set_window_width

(

core::Size

width

)

References window_width_.

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().

core::pose::Pose protocols::sewing::data_storage::SmartAssembly::to_pose

(

std::string

residue_type_set

)

References core::pose::append_pose_to_pose(), core::pose::Pose::append_residue_by_jump(), core::conformation::Residue::clone(), core::conformation::ResidueFactory::create_residue(), protocols::sewing::data_storage::SmartSegment::get_c_terminal_neighbor(), get_n_terminal_segment(), core::chemical::has(), core::chemical::ResidueType::is_lower_terminus(), core::chemical::ResidueType::is_upper_terminus(), protocols::sewing::data_storage::ligand, core::chemical::LOWER_TERMINUS_VARIANT, core::pose::make_pose_from_sequence(), output_partner_, partner_, core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::chemical::string_from_type_set_mode(), core::util::switch_to_residue_type_set(), core::pose::Pose::total_residue(), protocols::TR(), core::conformation::Residue::type(), and core::chemical::UPPER_TERMINUS_VARIANT.

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(), core::pose::full_model_info::get_residue(), protocols::sewing::data_storage::ligand, local_segments_, protocols::TR(), window_width_, and protocols::kinmatch::xyz().

Referenced by chimerize(), and reconstitute_assembly_from_string().

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().

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().

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().

void protocols::sewing::data_storage::SmartAssembly::unsample_ligand

(

)

References protocols::sewing::data_storage::LigandSegment::get_owned_ligand_residues(), last_sampled_ligand_, and local_ligands_.

Referenced by revert().

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

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().

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().

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

private

Referenced by get_random_segment_id(), and SmartAssembly().

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

private

Referenced by load_initial_conformers(), and pdb_segments().

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

private

Referenced by set_starting_segment().

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

private

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

private

Referenced by add_segment().

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().

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().

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

private

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

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().

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().

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

private

Referenced by sample_ligand(), and unsample_ligand().

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().

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().

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().

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().

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

private

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

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().

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

private

Referenced by get_random_segment_id(), and SmartAssembly().

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

private

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

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

private

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

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

private

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

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().

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

private

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

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

private

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

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

private

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

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

private

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

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().

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().

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().

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