core::pose::full_model_info::FullModelInfo Class Reference

Keep track of all information related to how a subpose 'fits in' to global modeling scheme. More...

#include <FullModelInfo.hh>

Inheritance diagram for core::pose::full_model_info::FullModelInfo:

Public Member Functions
	FullModelInfo (std::string const &full_sequence, utility::vector1< Size > const &cutpoint_open_in_full_model, utility::vector1< Size > const &res_numbers_in_pose)
	FullModelInfo (FullModelParametersCOP full_model_parameters)
	FullModelInfo (pose::Pose &pose)
	FullModelInfo (FullModelInfo const &src)
	~FullModelInfo () override
basic::datacache::CacheableDataOP	clone () const override
FullModelInfoOP	clone_info () const
FullModelParametersCOP	full_model_parameters () const
void	set_full_model_parameters (FullModelParametersCOP setting)
std::string const &	full_sequence () const
std::string const &	global_sequence () const
utility::vector1< Size > const &	global_mapping () const
utility::vector1< int > const &	conventional_numbering () const
utility::vector1< char > const &	conventional_chains () const
utility::vector1< std::string > const &	conventional_segids () const
utility::vector1< Size > const &	cutpoint_open_in_full_model () const
utility::vector1< Size > const &	dock_domain_map () const
utility::vector1< Size > const &	fixed_domain_map () const
utility::vector1< Size > const &	input_domain_map () const
utility::vector1< Size > const &	extra_minimize_res () const
utility::vector1< Size > const &	preferred_root_res () const
utility::vector1< Size > const &	sample_res () const
utility::vector1< Size > const &	working_res () const
utility::vector1< Size > const &	calc_rms_res () const
utility::vector1< Size > const &	rna_syn_chi_res () const
utility::vector1< Size > const &	rna_anti_chi_res () const
utility::vector1< Size > const &	rna_terminal_res () const
utility::vector1< Size > const &	rna_block_stack_above_res () const
utility::vector1< Size > const &	rna_block_stack_below_res () const
utility::vector1< Size > const &	rna_bulge_res () const
utility::vector1< Size > const &	alignment_anchor_res () const
utility::vector1< Size > const &	rna_sample_sugar_res () const
utility::vector1< std::pair< Size, Size > >	fiveprime_cap () const
utility::vector1< std::pair< Size, Size > >	jump_pairs () const
utility::vector1< std::pair< Size, Size > >	disulfide_pairs () const
utility::vector1< std::pair< Size, Size > >	cyclize_res () const
utility::vector1< std::pair< Size, Size > >	twoprime_res () const
utility::vector1< Size > const &	jump_res_map () const
void	clear_res_list ()
void	clear_other_pose_list ()
utility::vector1< core::pose::PoseOP > const &	other_pose_list () const
utility::vector1< Size > const &	res_list () const
utility::vector1< Size >	full_to_sub (utility::vector1< Size > const &res_in_full_model_numbering) const
Size	full_to_sub (Size const res_in_full_model_numbering) const
utility::vector1< Size >	sub_to_full (utility::vector1< Size > const &res) const
std::map< Size, Size >	full_to_sub () const
Size	sub_to_full (Size const &res) const
void	add_other_pose (core::pose::PoseOP pose)
void	set_other_pose_list (utility::vector1< pose::PoseOP > const &setting)
void	set_res_list (utility::vector1< Size > const &res_list)
void	remove_other_pose_at_idx (Size const idx)
Size	find_index_in_other_pose_list (pose::Pose const &pose) const
Size	get_idx_for_other_pose_with_residues (utility::vector1< Size > const &input_res) const
	return index of pose in other_pose_list More...
Size	get_idx_for_other_pose_with_residue (Size const input_res) const
Size	get_idx_for_other_pose (pose::Pose const &pose) const
utility::vector1< Size >	chains_in_full_model () const
Size	size () const
utility::vector1< SubMotifInfoOP > &	submotif_info_list () const
bool	is_a_submotif () const
	Return true if res_list_ matches a submotif exactly. More...
bool	is_a_submotif_seed () const
	Return true if res_list_ matches a submotif_seed exactly. More...
bool	is_a_submotif (utility::vector1< Size > const &res_list, bool const &check_other_poses=false) const
	Return true if residues match a submotif exactly. More...
bool	is_a_submotif_seed (utility::vector1< Size > const &res_list, bool const &check_other_poses=false) const
	Return true if residues match a submotif_seed exactly. More...
SubMotifInfoOP	submotif_info (utility::vector1< Size > const &res_list, bool const &check_other_poses=false) const
	Return a submotif_info_op with matching residues (in full model numbering). More...
bool	in_a_submotif (utility::vector1< Size > const &res_list, bool const &check_other_poses=false) const
	Return true if residues are found in a submotif. More...
bool	in_a_submotif_seed (utility::vector1< Size > const &res_list, bool const &check_other_poses=false) const
	Return true if residues are found in a submotif_seed. More...
SubMotifInfoOP	submotif_info_containing_residues (utility::vector1< Size > const &res_list, bool const &check_other_poses=false) const
	Return the submotif_info_op that contains (but not limited to) input residues. More...
void	update_submotif_info_list ()
	Delete submotif_infos with residues that are not found in res_list_. More...
void	add_submotif_info (utility::vector1< Size > const &res_list, std::string const &tag, bool const &seed=false)
	Create new SubMotifInfoOP and add it to the submotif_info_list_. More...
void	add_submotif_info (utility::vector1< SubMotifInfoOP > submotif_info_list)
	Add a list of SubMotifInfoOPs to the submotif_info_list_. More...
void	add_submotif_info (SubMotifInfoOP submotif_info_op)
	Add a SubMotifInfoOP to the submotif_info_list_. More...
void	delete_submotif_info (utility::vector1< Size > const &res_list, std::string const &tag, bool const &seed=false)
	Delete SubMotifInfoOP (with equal values) from submotif_info_list_. More...
void	delete_submotif_info (utility::vector1< SubMotifInfoOP > submotif_info_list)
	Delete a list of SubMotifInfoOPs from submotif_info_list_. More...
void	delete_submotif_info (SubMotifInfoOP submotif_info_op)
	Delete SubMotifInfoOP in submotif_info_list_ if values are equal to submotif_info. Should submotif_info deleted if seed() == true? More...
void	show_submotif_info_list (bool const &for_all_poses=false) const
	Delete SubMotifInfoOP in submotif_info_list_ if values are equal to submotif_info. Should submotif_info deleted if seed() == true? More...

Private Member Functions
utility::vector1< Size >	get_cutpoint_open_from_pdb_info (pose::Pose const &pose) const
void	get_sequence_with_gaps_filled_with_n (pose::Pose const &pose, std::string &sequence, utility::vector1< Size > &full_numbering) const

Private Attributes
utility::vector1< Size >	res_list_
utility::vector1< core::pose::PoseOP >	other_pose_list_
FullModelParametersCOP	full_model_parameters_
utility::vector1< SubMotifInfoOP >	submotif_info_list_

Detailed Description

Keep track of all information related to how a subpose 'fits in' to global modeling scheme.

See FullModelParameters for more information on the global modeling scheme, including full_sequence, etc.

Constructor & Destructor Documentation

FullModelInfo() [1/4]

core::pose::full_model_info::FullModelInfo::FullModelInfo	(	std::string const &	full_sequence,
		utility::vector1< Size > const &	cutpoint_open_in_full_model,
		utility::vector1< Size > const &	res_numbers_in_pose
	)

FullModelInfo() [2/4]

core::pose::full_model_info::FullModelInfo::FullModelInfo

(

FullModelParametersCOP

full_model_parameters

)

FullModelInfo() [3/4]

core::pose::full_model_info::FullModelInfo::FullModelInfo

(

pose::Pose &

pose

)

References full_model_parameters_, and res_list_.

FullModelInfo() [4/4]

core::pose::full_model_info::FullModelInfo::FullModelInfo

(

FullModelInfo const &

src

)

Copy constructors must copy all data, not just some...

References other_pose_list_.

~FullModelInfo()

core::pose::full_model_info::FullModelInfo::~FullModelInfo ( )

overridedefault

Member Function Documentation

add_other_pose()

void core::pose::full_model_info::FullModelInfo::add_other_pose

(

core::pose::PoseOP

pose

)

References other_pose_list_.

Referenced by protocols::stepwise::monte_carlo::mover::AddOrDeleteMover::apply(), protocols::stepwise::monte_carlo::mover::DeleteMover::remove_singletons_and_update_pose_focus(), and core::io::silent::BinarySilentStruct::setup_other_poses().

add_submotif_info() [1/3]

void core::pose::full_model_info::FullModelInfo::add_submotif_info

(

SubMotifInfoOP

submotif_info_op

)

Add a SubMotifInfoOP to the submotif_info_list_.

References submotif_info_list_.

add_submotif_info() [2/3]

void core::pose::full_model_info::FullModelInfo::add_submotif_info	(	utility::vector1< Size > const &	res_list,
		std::string const &	tag,
		bool const &	seed = false
	)

Create new SubMotifInfoOP and add it to the submotif_info_list_.

References res_list().

Referenced by add_submotif_info(), and protocols::stepwise::modeler::merge_in_other_pose().

add_submotif_info() [3/3]

void core::pose::full_model_info::FullModelInfo::add_submotif_info

(

utility::vector1< SubMotifInfoOP >

submotif_info_list

)

Add a list of SubMotifInfoOPs to the submotif_info_list_.

References add_submotif_info(), and submotif_info_list().

alignment_anchor_res()

utility::vector1< Size > const & core::pose::full_model_info::FullModelInfo::alignment_anchor_res

(

)

const

References core::pose::full_model_info::ALIGNMENT_ANCHOR_RES, and full_model_parameters_.

Referenced by protocols::stepwise::modeler::align::StepWisePoseAligner::get_rmsd_res_and_superimpose_res_in_pose().

calc_rms_res()

utility::vector1< Size > const & core::pose::full_model_info::FullModelInfo::calc_rms_res

(

)

const

References core::pose::full_model_info::CALC_RMS, and full_model_parameters_.

Referenced by protocols::stepwise::modeler::working_parameters::setup_working_parameters_explicit().

chains_in_full_model()

utility::vector1< Size > core::pose::full_model_info::FullModelInfo::chains_in_full_model

(

)

const

References full_model_parameters_.

clear_other_pose_list()

void core::pose::full_model_info::FullModelInfo::clear_other_pose_list

(

)

References other_pose_list_.

clear_res_list()

void core::pose::full_model_info::FullModelInfo::clear_res_list

(

)

References res_list_.

clone()

basic::datacache::CacheableDataOP core::pose::full_model_info::FullModelInfo::clone ( ) const

inlineoverride

clone_info()

FullModelInfoOP core::pose::full_model_info::FullModelInfo::clone_info ( ) const

inline

Referenced by protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::apply(), protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_reference_xyz_average(), core::pose::pdbslice(), protocols::stepwise::monte_carlo::mover::DeleteMover::remove_singletons_and_update_pose_focus(), protocols::stepwise::modeler::slice_out_pose(), protocols::stepwise::modeler::switch_focus_to_other_pose(), protocols::stepwise::monte_carlo::mover::FromScratchMover::update_full_model_info_and_switch_focus_to_new_pose(), protocols::magnesium::MgHydrater::update_full_model_info_with_new_waters(), protocols::stepwise::monte_carlo::mover::VaryLoopLengthMover::update_full_model_parameters(), and core::pose::full_model_info::update_res_list_in_full_model_info_and_pdb_info().

conventional_chains()

utility::vector1< char > const & core::pose::full_model_info::FullModelInfo::conventional_chains

(

)

const

References full_model_parameters_.

Referenced by core::pose::full_model_info::figure_out_conventional_chains_from_full_model_info().

conventional_numbering()

utility::vector1< int > const & core::pose::full_model_info::FullModelInfo::conventional_numbering

(

)

const

References full_model_parameters_.

Referenced by core::pose::full_model_info::check_full_model_info_OK().

conventional_segids()

utility::vector1< std::string > const & core::pose::full_model_info::FullModelInfo::conventional_segids

(

)

const

References full_model_parameters_.

Referenced by core::pose::full_model_info::figure_out_conventional_segids_from_full_model_info().

cutpoint_open_in_full_model()

utility::vector1< Size > const & core::pose::full_model_info::FullModelInfo::cutpoint_open_in_full_model

(

)

const

References core::pose::full_model_info::CUTPOINT_OPEN, and full_model_parameters_.

Referenced by core::pose::definite_terminal_root(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::figure_out_attachment(), core::pose::fix_up_residue_type_variants_at_floating_base(), core::pose::fix_up_residue_type_variants_at_strand_beginning(), core::pose::fix_up_residue_type_variants_at_strand_end(), protocols::stepwise::monte_carlo::mover::AddMover::get_add_res(), core::pose::full_model_info::get_chains_full(), core::pose::get_definite_terminal_root(), protocols::stepwise::modeler::get_domain_boundary_suites(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_from_scratch_add_move_elements(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_intramolecular_add_move_elements(), protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::get_matches_for_one_submotif_sequence_set(), core::energy_methods::IntermolEnergy::get_num_chains_frozen(), core::pose::full_model_info::get_number_missing_residues_and_connections(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_vary_loop_length_moves(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::just_simple_cycles(), protocols::stepwise::modeler::reroot_based_on_full_model_info(), core::energy_methods::FreeDOF_Energy::residue_energy(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_through_build_full_model_info(), core::scoring::loop_graph::LoopGraph::update(), and core::scoring::loop_graph::LoopGraph::update_loops().

cyclize_res()

utility::vector1< std::pair< Size, Size > > core::pose::full_model_info::FullModelInfo::cyclize_res

(

)

const

References core::pose::full_model_info::CYCLIZE_RES, and full_model_parameters_.

delete_submotif_info() [1/3]

void core::pose::full_model_info::FullModelInfo::delete_submotif_info

(

SubMotifInfoOP

submotif_info_op

)

Delete SubMotifInfoOP in submotif_info_list_ if values are equal to submotif_info. Should submotif_info deleted if seed() == true?

References submotif_info_list_.

delete_submotif_info() [2/3]

void core::pose::full_model_info::FullModelInfo::delete_submotif_info	(	utility::vector1< Size > const &	res_list,
		std::string const &	tag,
		bool const &	seed = false
	)

Delete SubMotifInfoOP (with equal values) from submotif_info_list_.

References res_list().

Referenced by delete_submotif_info(), and update_submotif_info_list().

delete_submotif_info() [3/3]

void core::pose::full_model_info::FullModelInfo::delete_submotif_info

(

utility::vector1< SubMotifInfoOP >

submotif_info_list

)

Delete a list of SubMotifInfoOPs from submotif_info_list_.

References delete_submotif_info(), and submotif_info_list().

disulfide_pairs()

utility::vector1< std::pair< Size, Size > > core::pose::full_model_info::FullModelInfo::disulfide_pairs

(

)

const

References core::pose::full_model_info::DISULFIDE, and full_model_parameters_.

Referenced by core::pose::fix_up_residue_type_variants().

dock_domain_map()

utility::vector1< Size > const & core::pose::full_model_info::FullModelInfo::dock_domain_map

(

)

const

References core::pose::full_model_info::DOCK_DOMAIN, and full_model_parameters_.

Referenced by protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::figure_out_attachment(), core::pose::full_model_info::figure_out_dock_domain_map_from_full_model_info_const(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_dock_domains(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_docking_add_move_elements(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_docking_split_move_elements(), and core::pose::full_model_info::get_preferred_jump_pair_for_docking_domains().

extra_minimize_res()

utility::vector1< Size > const & core::pose::full_model_info::FullModelInfo::extra_minimize_res

(

)

const

References core::pose::full_model_info::EXTRA_MINIMIZE, and full_model_parameters_.

Referenced by protocols::stepwise::modeler::StepWiseMinimizer::figure_out_working_minimize_res(), and protocols::stepwise::modeler::working_parameters::setup_working_parameters_for_swa().

find_index_in_other_pose_list()

Size core::pose::full_model_info::FullModelInfo::find_index_in_other_pose_list

(

pose::Pose const &

pose

)

const

References other_pose_list_.

fiveprime_cap()

utility::vector1< std::pair< Size, Size > > core::pose::full_model_info::FullModelInfo::fiveprime_cap

(

)

const

References core::pose::full_model_info::FIVEPRIME_CAP, and full_model_parameters_.

fixed_domain_map()

utility::vector1< Size > const & core::pose::full_model_info::FullModelInfo::fixed_domain_map

(

)

const

References core::pose::full_model_info::FIXED_DOMAIN, and full_model_parameters_.

Referenced by protocols::stepwise::modeler::align::StepWisePoseAligner::get_calc_rms_atom_id_map(), core::pose::get_definite_terminal_root(), protocols::stepwise::modeler::get_domain_boundary_suites(), core::pose::full_model_info::get_fixed_domain_from_full_model_info_const(), core::pose::full_model_info::get_moving_res_from_full_model_info(), core::pose::full_model_info::get_moving_res_from_full_model_info_const(), protocols::stepwise::modeler::reroot_based_on_full_model_info(), and protocols::stepwise::modeler::working_parameters::setup_working_parameters_for_swa().

full_model_parameters()

FullModelParametersCOP core::pose::full_model_info::FullModelInfo::full_model_parameters

(

)

const

References full_model_parameters_.

Referenced by core::pose::full_model_info::add_new_sequence_into_global_sequence(), protocols::stepwise::monte_carlo::mover::FromScratchMover::apply(), protocols::stepwise::monte_carlo::mover::AddMover::create_residue_to_add(), core::io::rna::RNA_DataReader::fill_backbone_array(), core::io::rna::RNA_DataReader::fill_rna_data_info(), core::pose::full_model_info::get_current_global_sequence(), core::pose::full_model_info::get_preferred_jump_pair_for_docking_domains(), protocols::stepwise::modeler::align::StepWisePoseAligner::get_res_list_in_reference(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_vary_loop_length_moves(), core::pose::operator<<(), protocols::rna::movers::ErraserMinimizerMover::pose_preliminaries(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_through_build_full_model_info(), core::energy_methods::RNA_StubCoordinateEnergy::setup_for_scoring(), protocols::stepwise::modeler::working_parameters::setup_working_parameters_explicit(), protocols::stepwise::modeler::working_parameters::setup_working_parameters_for_swa(), core::pose::full_model_info::update_constraint_set_from_full_model_info(), core::pose::full_model_info::update_disulfides_from_full_model_info(), and protocols::magnesium::MgHydrater::update_full_model_info_with_new_waters().

full_sequence()

std::string const & core::pose::full_model_info::FullModelInfo::full_sequence

(

)

const

References full_model_parameters_.

Referenced by protocols::stepwise::monte_carlo::mover::FromScratchMover::apply(), core::pose::full_model_info::check_full_model_info_OK(), protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::create_new_submotif(), protocols::stepwise::monte_carlo::mover::AddMover::create_residue_to_add(), protocols::stepwise::monte_carlo::mover::AddMover::do_append(), core::scoring::rna::data::RNA_DMS_LowResolutionPotential::evaluate(), core::scoring::rna::data::RNA_DMS_Potential::evaluate(), protocols::stepwise::monte_carlo::mover::AddMover::get_add_res(), core::pose::full_model_info::get_chains_full(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_from_scratch_add_move_elements(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_intramolecular_add_move_elements(), protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::get_matches_for_one_submotif_sequence_set(), core::pose::full_model_info::get_number_missing_residues_and_connections(), core::scoring::loop_graph::LoopGraph::missing_residues(), protocols::stepwise::modeler::rna::mutate_res_if_allowed(), protocols::stepwise::modeler::working_parameters::setup_working_parameters_explicit(), protocols::stepwise::modeler::working_parameters::setup_working_parameters_for_swa(), and protocols::stepwise::modeler::align::StepWisePoseAligner::update_reference_pose_local().

full_to_sub() [1/3]

std::map< Size, Size > core::pose::full_model_info::FullModelInfo::full_to_sub

(

)

const

References res_list_, and size().

full_to_sub() [2/3]

Size core::pose::full_model_info::FullModelInfo::full_to_sub

(

Size const

res_in_full_model_numbering

)

const

References res_list_.

full_to_sub() [3/3]

utility::vector1< Size > core::pose::full_model_info::FullModelInfo::full_to_sub

(

utility::vector1< Size > const &

res_in_full_model_numbering

)

const

References res_list_.

Referenced by protocols::stepwise::monte_carlo::mover::DeleteMover::apply(), core::scoring::rna::data::RNA_DMS_LowResolutionPotential::evaluate(), core::scoring::rna::data::RNA_DMS_Potential::evaluate(), protocols::stepwise::modeler::StepWiseMinimizer::figure_out_working_minimize_res(), core::pose::full_model_info::full_to_sub(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_actual_moving_res(), core::pose::full_model_info::get_sample_res_for_pose(), core::scoring::constraints::ConstraintIO::parse_residue(), protocols::stepwise::monte_carlo::mover::AddMover::setup_initial_jump(), protocols::stepwise::modeler::working_parameters::setup_working_parameters_explicit(), protocols::stepwise::modeler::working_parameters::setup_working_parameters_for_swa(), and core::pose::full_model_info::update_disulfides_from_full_model_info().

get_cutpoint_open_from_pdb_info()

utility::vector1< Size > core::pose::full_model_info::FullModelInfo::get_cutpoint_open_from_pdb_info ( pose::Pose const &  pose ) const

private

get_idx_for_other_pose()

Size core::pose::full_model_info::FullModelInfo::get_idx_for_other_pose

(

pose::Pose const &

pose

)

const

References get_idx_for_other_pose_with_residue(), core::pose::full_model_info::get_res_list_from_full_model_info_const(), other_pose_list_, size(), and core::pose::Pose::size().

Referenced by protocols::stepwise::monte_carlo::mover::DeleteMover::remove_singletons_and_update_pose_focus().

get_idx_for_other_pose_with_residue()

Size core::pose::full_model_info::FullModelInfo::get_idx_for_other_pose_with_residue

(

Size const

input_res

)

const

References core::pose::full_model_info::const_full_model_info(), other_pose_list_, and res_list().

Referenced by protocols::stepwise::monte_carlo::mover::DeleteMover::apply(), protocols::stepwise::monte_carlo::mover::AddMover::do_append(), protocols::stepwise::monte_carlo::mover::AddMover::do_prepend(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::fill_moves_for_other_poses(), get_idx_for_other_pose(), get_idx_for_other_pose_with_residues(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_intramolecular_add_move_elements(), protocols::stepwise::monte_carlo::mover::DeleteMover::remove_singletons_and_update_pose_focus(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::reverse_delete_move(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::share_chains(), submotif_info(), and submotif_info_containing_residues().

get_idx_for_other_pose_with_residues()

Size core::pose::full_model_info::FullModelInfo::get_idx_for_other_pose_with_residues

(

utility::vector1< Size > const &

input_res

)

const

return index of pose in other_pose_list

References get_idx_for_other_pose_with_residue().

get_sequence_with_gaps_filled_with_n()

void core::pose::full_model_info::FullModelInfo::get_sequence_with_gaps_filled_with_n ( pose::Pose const &  pose, std::string &  sequence, utility::vector1< Size > &  full_numbering  ) const

private

global_mapping()

utility::vector1< Size > const & core::pose::full_model_info::FullModelInfo::global_mapping

(

)

const

References full_model_parameters_.

Referenced by core::energy_methods::RNA_PartitionEnergy::set_up_residuearrayannealableenergy_for_packing().

global_sequence()

std::string const & core::pose::full_model_info::FullModelInfo::global_sequence

(

)

const

References full_model_parameters_.

Referenced by core::energy_methods::RNA_PartitionEnergy::finalize_total_energy(), and core::energy_methods::RNA_PartitionEnergy::set_up_residuearrayannealableenergy_for_packing().

in_a_submotif()

bool core::pose::full_model_info::FullModelInfo::in_a_submotif	(	utility::vector1< Size > const &	res_list,
		bool const &	check_other_poses = false
	)		const

Return true if residues are found in a submotif.

References res_list(), and submotif_info_containing_residues().

Referenced by protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::check_for_intramolecular_submotif_jump(), and in_a_submotif_seed().

in_a_submotif_seed()

bool core::pose::full_model_info::FullModelInfo::in_a_submotif_seed	(	utility::vector1< Size > const &	res_list,
		bool const &	check_other_poses = false
	)		const

Return true if residues are found in a submotif_seed.

References in_a_submotif(), res_list(), and submotif_info_containing_residues().

input_domain_map()

utility::vector1< Size > const & core::pose::full_model_info::FullModelInfo::input_domain_map

(

)

const

References full_model_parameters_, and core::pose::full_model_info::INPUT_DOMAIN.

Referenced by core::pose::full_model_info::check_all_residues_sampled(), core::pose::full_model_info::get_input_domain_from_full_model_info_const(), core::pose::full_model_info::get_move_elements_from_full_model_info_const(), core::pose::full_model_info::get_number_missing_residues_and_connections(), core::scoring::loop_graph::LoopGraph::missing_residues(), and core::scoring::loop_graph::LoopGraph::nmissing().

is_a_submotif() [1/2]

bool core::pose::full_model_info::FullModelInfo::is_a_submotif

(

)

const

Return true if res_list_ matches a submotif exactly.

References res_list_, and submotif_info_list_.

Referenced by is_a_submotif_seed().

is_a_submotif() [2/2]

bool core::pose::full_model_info::FullModelInfo::is_a_submotif	(	utility::vector1< Size > const &	res_list,
		bool const &	check_other_poses = false
	)		const

Return true if residues match a submotif exactly.

References res_list(), and submotif_info().

is_a_submotif_seed() [1/2]

bool core::pose::full_model_info::FullModelInfo::is_a_submotif_seed

(

)

const

Return true if res_list_ matches a submotif_seed exactly.

References res_list_, and submotif_info_list_.

Referenced by protocols::stepwise::monte_carlo::mover::DeleteMover::decide_to_keep_pose().

is_a_submotif_seed() [2/2]

bool core::pose::full_model_info::FullModelInfo::is_a_submotif_seed	(	utility::vector1< Size > const &	res_list,
		bool const &	check_other_poses = false
	)		const

Return true if residues match a submotif_seed exactly.

References is_a_submotif(), res_list(), and submotif_info().

jump_pairs()

utility::vector1< std::pair< Size, Size > > core::pose::full_model_info::FullModelInfo::jump_pairs

(

)

const

References full_model_parameters_, and core::pose::full_model_info::JUMP.

jump_res_map()

utility::vector1< Size > const & core::pose::full_model_info::FullModelInfo::jump_res_map

(

)

const

References full_model_parameters_, and core::pose::full_model_info::JUMP.

Referenced by protocols::stepwise::monte_carlo::mover::ResampleMover::slide_jump_randomly().

other_pose_list()

utility::vector1< core::pose::PoseOP > const& core::pose::full_model_info::FullModelInfo::other_pose_list ( ) const

inline

References other_pose_list_.

Referenced by protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::already_instantiated_in_pose(), protocols::stepwise::monte_carlo::mover::AddMover::append_other_pose(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::figure_out_already_docked(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::figure_out_from_scratch_delete_move_elements(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::fill_moves_for_other_poses(), core::io::silent::SilentStruct::fill_other_struct_list(), protocols::stepwise::monte_carlo::get_all_res_list(), core::pose::full_model_info::get_current_global_sequence(), core::pose::full_model_info::get_residue(), core::io::rna::get_rna_data_info(), protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::preminimize_pose(), protocols::stepwise::monte_carlo::mover::AddMover::prepend_other_pose(), protocols::stepwise::monte_carlo::mover::DeleteMover::remove_singletons_and_update_pose_focus(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::reverse_delete_move(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::share_chains(), protocols::stepwise::modeler::align::StepWisePoseAligner::superimpose_recursively(), protocols::stepwise::modeler::switch_focus_among_poses_randomly(), protocols::stepwise::modeler::switch_focus_to_other_pose(), protocols::stepwise::monte_carlo::mover::VaryLoopLengthMover::update_full_model_parameters(), and core::pose::full_model_info::update_pose_domain_map_const().

preferred_root_res()

utility::vector1< Size > const & core::pose::full_model_info::FullModelInfo::preferred_root_res

(

)

const

References full_model_parameters_, and core::pose::full_model_info::PREFERRED_ROOT.

Referenced by protocols::stepwise::modeler::reroot_based_on_full_model_info().

remove_other_pose_at_idx()

void core::pose::full_model_info::FullModelInfo::remove_other_pose_at_idx

(

Size const

idx

)

References other_pose_list_.

Referenced by protocols::stepwise::monte_carlo::mover::AddMover::append_other_pose(), protocols::stepwise::monte_carlo::mover::AddMover::prepend_other_pose(), and protocols::stepwise::monte_carlo::mover::DeleteMover::remove_singletons_and_update_pose_focus().

res_list()

utility::vector1< Size > const& core::pose::full_model_info::FullModelInfo::res_list ( ) const

inline

References res_list_.

Referenced by core::pose::rna::add_chi_constraints(), core::pose::full_model_info::add_new_sequence_into_global_sequence(), add_submotif_info(), core::pose::full_model_info::append_virtual_residue_to_full_model_info(), protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::build_full_model(), core::pose::full_model_info::check_all_residues_sampled(), protocols::stepwise::modeler::check_jump_to_next_residue_in_chain(), protocols::stepwise::modeler::check_jump_to_previous_residue_in_chain(), core::pose::full_model_info::check_sample_sugar_in_full_model_info(), core::pose::definite_terminal_root(), delete_submotif_info(), core::scoring::rna::data::RNA_DMS_LowResolutionPotential::evaluate(), core::scoring::rna::data::RNA_DMS_Potential::evaluate(), core::pose::full_model_info::full_to_sub(), protocols::stepwise::monte_carlo::mover::AddMover::get_add_res(), protocols::stepwise::modeler::align::StepWisePoseAligner::get_calc_rms_atom_id_map(), core::pose::get_definite_terminal_root(), protocols::stepwise::modeler::get_domain_boundary_suites(), core::pose::full_model_info::get_fixed_domain_from_full_model_info_const(), get_idx_for_other_pose_with_residue(), core::pose::full_model_info::get_input_domain_from_full_model_info_const(), core::pose::full_model_info::get_move_elements_from_full_model_info_const(), core::pose::full_model_info::get_moving_res_from_full_model_info(), core::pose::full_model_info::get_moving_res_from_full_model_info_const(), core::pose::full_model_info::get_res_list_from_full_model_info(), core::pose::full_model_info::get_res_list_from_full_model_info_const(), core::pose::full_model_info::get_residue(), in_a_submotif(), in_a_submotif_seed(), is_a_submotif(), is_a_submotif_seed(), protocols::stepwise::sampler::rna::modeler_sugar_at_five_prime(), protocols::stepwise::sampler::rna::modeler_sugar_at_three_prime(), protocols::magnesium::remove_mg_bound_waters(), protocols::stepwise::monte_carlo::mover::DeleteMover::remove_singletons_and_update_pose_focus(), protocols::stepwise::modeler::reroot_based_on_full_model_info(), core::energy_methods::FreeDOF_Energy::residue_energy(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::reverse_add_move(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::reverse_delete_move(), set_res_list(), core::energy_methods::RNA_PartitionEnergy::set_up_residuearrayannealableenergy_for_packing(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_through_build_full_model_info(), protocols::stepwise::modeler::working_parameters::setup_working_parameters_explicit(), protocols::stepwise::modeler::working_parameters::setup_working_parameters_for_swa(), protocols::stepwise::modeler::slice_out_pose(), core::pose::stepwise_addable_pose_residue(), core::pose::full_model_info::sub_to_full(), submotif_info(), submotif_info_containing_residues(), protocols::stepwise::modeler::test_merge_and_slice_with_two_helix_test_case(), core::pose::update_block_stack_variants(), protocols::stepwise::modeler::align::StepWisePoseAligner::update_calc_rms_atom_id_map(), core::pose::full_model_info::update_constraint_set_from_full_model_info(), core::pose::full_model_info::update_disulfides_from_full_model_info(), protocols::magnesium::MgHydrater::update_full_model_info_with_new_waters(), protocols::stepwise::monte_carlo::mover::VaryLoopLengthMover::update_full_model_parameters(), and core::pose::full_model_info::update_pose_domain_map_const().

rna_anti_chi_res()

utility::vector1< Size > const & core::pose::full_model_info::FullModelInfo::rna_anti_chi_res

(

)

const

References full_model_parameters_, and core::pose::full_model_info::RNA_ANTI_CHI.

Referenced by protocols::stepwise::modeler::working_parameters::setup_working_parameters_explicit().

rna_block_stack_above_res()

utility::vector1< Size > const & core::pose::full_model_info::FullModelInfo::rna_block_stack_above_res

(

)

const

References full_model_parameters_, and core::pose::full_model_info::RNA_BLOCK_STACK_ABOVE.

Referenced by protocols::stepwise::modeler::working_parameters::setup_working_parameters_explicit(), and core::pose::update_block_stack_variants().

rna_block_stack_below_res()

utility::vector1< Size > const & core::pose::full_model_info::FullModelInfo::rna_block_stack_below_res

(

)

const

References full_model_parameters_, and core::pose::full_model_info::RNA_BLOCK_STACK_BELOW.

Referenced by protocols::stepwise::modeler::working_parameters::setup_working_parameters_explicit(), and core::pose::update_block_stack_variants().

rna_bulge_res()

utility::vector1< Size > const & core::pose::full_model_info::FullModelInfo::rna_bulge_res

(

)

const

References full_model_parameters_, and core::pose::full_model_info::RNA_BULGE.

Referenced by protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::build_full_model(), protocols::stepwise::monte_carlo::StepWiseMonteCarlo::do_main_loop(), and protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::is_addable_res().

rna_sample_sugar_res()

utility::vector1< Size > const & core::pose::full_model_info::FullModelInfo::rna_sample_sugar_res

(

)

const

References full_model_parameters_, and core::pose::full_model_info::RNA_SAMPLE_SUGAR.

Referenced by core::pose::full_model_info::check_sample_sugar_in_full_model_info(), core::pose::fix_up_residue_type_variants_at_floating_base(), protocols::stepwise::sampler::rna::modeler_sugar_at_five_prime(), and protocols::stepwise::sampler::rna::modeler_sugar_at_three_prime().

rna_syn_chi_res()

utility::vector1< Size > const & core::pose::full_model_info::FullModelInfo::rna_syn_chi_res

(

)

const

References full_model_parameters_, and core::pose::full_model_info::RNA_SYN_CHI.

Referenced by protocols::stepwise::modeler::working_parameters::setup_working_parameters_explicit().

rna_terminal_res()

utility::vector1< Size > const & core::pose::full_model_info::FullModelInfo::rna_terminal_res

(

)

const

References full_model_parameters_, and core::pose::full_model_info::RNA_TERMINAL.

Referenced by protocols::stepwise::modeler::working_parameters::setup_working_parameters_explicit().

sample_res()

utility::vector1< Size > const & core::pose::full_model_info::FullModelInfo::sample_res

(

)

const

References full_model_parameters_, and core::pose::full_model_info::SAMPLE.

Referenced by protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::filter_pose_order(), core::pose::fix_up_residue_type_variants_at_floating_base(), core::pose::full_model_info::get_sample_res_for_pose(), protocols::stepwise::modeler::precomputed::PrecomputedLibraryMover::has_precomputed_move(), protocols::stepwise::sampler::rna::modeler_sugar_at_five_prime(), protocols::stepwise::sampler::rna::modeler_sugar_at_three_prime(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::reverse_delete_move(), and protocols::stepwise::modeler::working_parameters::setup_working_parameters_for_swa().

set_full_model_parameters()

void core::pose::full_model_info::FullModelInfo::set_full_model_parameters

(

FullModelParametersCOP

setting

)

References full_model_parameters_.

Referenced by protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_through_build_full_model_info().

set_other_pose_list()

void core::pose::full_model_info::FullModelInfo::set_other_pose_list

(

utility::vector1< pose::PoseOP > const &

setting

)

References other_pose_list_.

Referenced by protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_through_build_full_model_info(), and protocols::stepwise::modeler::switch_focus_to_other_pose().

set_res_list()

void core::pose::full_model_info::FullModelInfo::set_res_list ( utility::vector1< Size > const &  res_list )

inline

References res_list(), and res_list_.

Referenced by protocols::stepwise::modeler::merge_in_other_pose(), and protocols::stepwise::modeler::slice_out_pose().

show_submotif_info_list()

void core::pose::full_model_info::FullModelInfo::show_submotif_info_list

(

bool const &

for_all_poses = false

)

const

Delete SubMotifInfoOP in submotif_info_list_ if values are equal to submotif_info. Should submotif_info deleted if seed() == true?

References core::pose::full_model_info::const_full_model_info(), other_pose_list_, show_submotif_info_list(), and submotif_info_list_.

Referenced by protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::reverse_delete_move(), and show_submotif_info_list().

size()

Size core::pose::full_model_info::FullModelInfo::size

(

)

const

References full_model_parameters_.

Referenced by core::pose::definite_terminal_root(), core::pose::fix_up_residue_type_variants_at_strand_end(), core::pose::full_model_info::full_model_size(), full_to_sub(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_docking_add_move_elements(), get_idx_for_other_pose(), and update_submotif_info_list().

sub_to_full() [1/2]

Size core::pose::full_model_info::FullModelInfo::sub_to_full

(

Size const &

res

)

const

References res_list_.

sub_to_full() [2/2]

utility::vector1< Size > core::pose::full_model_info::FullModelInfo::sub_to_full

(

utility::vector1< Size > const &

res

)

const

References res_list_.

Referenced by protocols::stepwise::monte_carlo::mover::DeleteMover::apply(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_docking_split_move_elements(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_intramolecular_split_move_elements(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::ordered_move_from_partition(), protocols::stepwise::modeler::working_parameters::setup_working_parameters_explicit(), protocols::stepwise::modeler::working_parameters::setup_working_parameters_for_swa(), and core::pose::full_model_info::sub_to_full().

submotif_info()

SubMotifInfoOP core::pose::full_model_info::FullModelInfo::submotif_info	(	utility::vector1< Size > const &	res_list,
		bool const &	check_other_poses = false
	)		const

Return a submotif_info_op with matching residues (in full model numbering).

References core::pose::full_model_info::const_full_model_info(), get_idx_for_other_pose_with_residue(), other_pose_list_, res_list(), submotif_info(), and submotif_info_list_.

Referenced by is_a_submotif(), is_a_submotif_seed(), and submotif_info().

submotif_info_containing_residues()

SubMotifInfoOP core::pose::full_model_info::FullModelInfo::submotif_info_containing_residues	(	utility::vector1< Size > const &	res_list,
		bool const &	check_other_poses = false
	)		const

Return the submotif_info_op that contains (but not limited to) input residues.

References core::pose::full_model_info::const_full_model_info(), get_idx_for_other_pose_with_residue(), other_pose_list_, res_list(), submotif_info_containing_residues(), and submotif_info_list_.

Referenced by in_a_submotif(), in_a_submotif_seed(), and submotif_info_containing_residues().

submotif_info_list()

utility::vector1< SubMotifInfoOP >& core::pose::full_model_info::FullModelInfo::submotif_info_list ( ) const

inline

References submotif_info_list_.

Referenced by add_submotif_info(), delete_submotif_info(), core::io::silent::SilentStruct::fill_struct_with_submotif_info_list(), and protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::partitions_split_a_submotif().

twoprime_res()

utility::vector1< std::pair< Size, Size > > core::pose::full_model_info::FullModelInfo::twoprime_res

(

)

const

References full_model_parameters_, and core::pose::full_model_info::TWOPRIME_RES.

update_submotif_info_list()

void core::pose::full_model_info::FullModelInfo::update_submotif_info_list

(

)

Delete submotif_infos with residues that are not found in res_list_.

References delete_submotif_info(), res_list_, size(), and submotif_info_list_.

Referenced by protocols::stepwise::modeler::merge_in_other_pose(), and protocols::stepwise::modeler::slice_out_pose().

working_res()

utility::vector1< Size > const & core::pose::full_model_info::FullModelInfo::working_res

(

)

const

References full_model_parameters_, and core::pose::full_model_info::WORKING.

Referenced by protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::build_full_model(), core::pose::definite_terminal_root(), core::scoring::rna::data::RNA_DMS_LowResolutionPotential::evaluate(), core::scoring::rna::data::RNA_DMS_Potential::evaluate(), core::pose::get_definite_terminal_root(), core::pose::full_model_info::get_number_missing_residues_and_connections(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::is_addable_res(), core::scoring::loop_graph::LoopGraph::missing_residues(), core::scoring::loop_graph::LoopGraph::nmissing(), and protocols::stepwise::modeler::reroot_based_on_full_model_info().

Member Data Documentation

full_model_parameters_

FullModelParametersCOP core::pose::full_model_info::FullModelInfo::full_model_parameters_

private

Referenced by alignment_anchor_res(), calc_rms_res(), chains_in_full_model(), conventional_chains(), conventional_numbering(), conventional_segids(), cutpoint_open_in_full_model(), cyclize_res(), disulfide_pairs(), dock_domain_map(), extra_minimize_res(), fiveprime_cap(), fixed_domain_map(), full_model_parameters(), full_sequence(), FullModelInfo(), global_mapping(), global_sequence(), input_domain_map(), jump_pairs(), jump_res_map(), preferred_root_res(), rna_anti_chi_res(), rna_block_stack_above_res(), rna_block_stack_below_res(), rna_bulge_res(), rna_sample_sugar_res(), rna_syn_chi_res(), rna_terminal_res(), sample_res(), set_full_model_parameters(), size(), twoprime_res(), and working_res().

other_pose_list_

utility::vector1< core::pose::PoseOP > core::pose::full_model_info::FullModelInfo::other_pose_list_

private

Referenced by add_other_pose(), clear_other_pose_list(), find_index_in_other_pose_list(), FullModelInfo(), get_idx_for_other_pose(), get_idx_for_other_pose_with_residue(), other_pose_list(), remove_other_pose_at_idx(), set_other_pose_list(), show_submotif_info_list(), submotif_info(), and submotif_info_containing_residues().

res_list_

utility::vector1< Size > core::pose::full_model_info::FullModelInfo::res_list_

private

Referenced by clear_res_list(), full_to_sub(), FullModelInfo(), is_a_submotif(), is_a_submotif_seed(), res_list(), set_res_list(), sub_to_full(), and update_submotif_info_list().

submotif_info_list_

utility::vector1< SubMotifInfoOP > core::pose::full_model_info::FullModelInfo::submotif_info_list_

mutableprivate

Referenced by add_submotif_info(), delete_submotif_info(), is_a_submotif(), is_a_submotif_seed(), show_submotif_info_list(), submotif_info(), submotif_info_containing_residues(), submotif_info_list(), and update_submotif_info_list().

---

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

• src/core/pose/full_model_info/FullModelInfo.hh
• src/core/pose/full_model_info/FullModelInfo.cc