#include <StepWiseMoveSelector.hh>

Inheritance diagram for protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector:

Public Member Functions
	StepWiseMoveSelector ()

	StepWiseMoveSelector (options::StepWiseMoveSelectorOptionsCOP options)

StepWiseMoveSelectorOP	clone () const
	clone the options More...

bool	figure_out_all_possible_moves (core::pose::Pose const &pose, bool const verbose=false)

void	output_moves () const

StepWiseMove	select_random_move (core::pose::Pose const &pose) const

utility::vector1< StepWiseMove > const &	swa_moves () const

core::Real	proposal_probability (StepWiseMove const &swa_move) const

void	get_add_or_delete_element (core::pose::Pose const &pose, StepWiseMove &swa_move)

void	get_resample_move_elements (core::pose::Pose const &pose, utility::vector1< StepWiseMove > &swa_moves, bool const save_moves=true)

void	get_resample_terminal_move_elements (core::pose::Pose const &pose, utility::vector1< StepWiseMove > &swa_moves)

void	get_resample_internal_move_elements (core::pose::Pose const &pose, utility::vector1< StepWiseMove > &swa_moves)

void	get_resample_internal_local_move_elements (core::pose::Pose const &pose, utility::vector1< StepWiseMove > &swa_moves)

void	get_intramolecular_delete_move_elements (core::pose::Pose const &pose, utility::vector1< StepWiseMove > &swa_moves)

Attachments	get_attachments (core::pose::Pose const &pose, core::Size const &moving_res)

Attachments	get_attachments (core::pose::Pose const &pose, MoveElement const &move_element)

void	set_allow_delete (bool const &setting)

bool	allow_delete () const

void	set_choose_random (bool const &setting)

bool	choose_random () const

void	set_force_unique_moves (bool const &setting)

bool	force_unique_moves () const

monte_carlo::submotif::SubMotifLibraryCOP	submotif_library ()

void	set_submotif_library (monte_carlo::submotif::SubMotifLibraryCOP setting)

StepWiseMove	reverse_move (StepWiseMove const &swa_move, core::pose::Pose const &pose_before, core::pose::Pose const &pose_after) const

bool	just_simple_cycles (StepWiseMove const &swa_move, core::pose::Pose const &pose, bool const verbose=false) const

void	set_options (protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptionsCOP setting)

protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptionsCOP	options () const

Private Member Functions
void	fill_moves_for_pose (core::pose::Pose const &pose)

void	fill_moves_for_other_poses (core::pose::Pose const &pose)

void	fill_denovo_moves (core::pose::Pose const &pose)

void	fill_vary_loop_length_moves (core::pose::Pose const &pose)

void	save_moves (utility::vector1< StepWiseMove > const &moves, core::Real const total_weight=1, bool const clear_moves_before_saving=false)

core::Real	sum_probabilities (core::Size const start_idx=1, core::Size const final_idx=0) const

void	normalize_probabilities (core::Size const start_idx=1, core::Size const final_idx=0, core::Real const desired_weight=1)

void	get_intramolecular_add_and_delete_elements (core::pose::Pose const &pose, utility::vector1< StepWiseMove > &swa_moves)

void	get_intramolecular_add_move_elements (core::pose::Pose const &pose, utility::vector1< StepWiseMove > &swa_moves)

void	get_intramolecular_split_move_elements (core::pose::Pose const &pose, utility::vector1< StepWiseMove > &swa_moves, MoveType const move_type)

bool	check_from_scratch (core::pose::Pose const &pose, utility::vector1< bool > const &partition_definition) const

void	remove_from_consideration_first_multi_residue_move_element (utility::vector1< StepWiseMove > &swa_moves, bool remove_even_if_not_singlet)

bool	is_addable_res (core::Size const n, core::pose::Pose const &pose) const

bool	remnant_would_be_deleted (core::pose::Pose const &pose, utility::vector1< core::Size > const &partition) const

bool	both_remnants_would_be_deleted (core::pose::Pose const &pose, utility::vector1< core::Size > const &partition1, utility::vector1< core::Size > const &partition2) const

bool	partitions_split_a_submotif (core::pose::Pose const &pose, utility::vector1< core::Size > const &partition1, utility::vector1< core::Size > const &partition2) const

bool	check_for_intramolecular_submotif_jump (core::pose::Pose const &pose, core::Size const &moving_res, core::Size const &attached_res) const

bool	check_for_input_domain_or_from_scratch (core::pose::Pose const &pose, utility::vector1< core::Size > const &partition_res) const

bool	already_instantiated_in_pose (core::pose::Pose const &pose, core::Size const &resnum_in_full_model_numbering) const

void	get_docking_add_and_delete_elements (core::pose::Pose const &pose, utility::vector1< StepWiseMove > &swa_moves)

std::set< core::Size >	get_dock_domains (utility::vector1< core::Size > const &move_element, core::pose::Pose const &pose) const

void	figure_out_already_docked (core::pose::Pose const &pose, std::map< std::pair< core::Size, core::Size >, bool > &already_docked) const

void	get_docking_add_move_elements (core::pose::Pose const &pose, utility::vector1< StepWiseMove > &swa_moves)

void	get_docking_delete_move_elements (core::pose::Pose const &pose, utility::vector1< StepWiseMove > &swa_moves)

void	get_docking_split_move_elements (core::pose::Pose const &pose, utility::vector1< StepWiseMove > &swa_moves, MoveType const move_type)

void	get_submotif_add_moves (core::pose::Pose const &pose, utility::vector1< StepWiseMove > &swa_moves)

void	filter_add_submotif_moves_to_not_redock_domain (utility::vector1< StepWiseMove > &submotif_add_moves, core::pose::Pose const &pose) const

void	get_from_scratch_add_and_delete_elements (core::pose::Pose const &pose, utility::vector1< StepWiseMove > &swa_moves)

void	get_from_scratch_add_move_elements (core::pose::Pose const &pose, utility::vector1< StepWiseMove > &swa_moves)

void	figure_out_from_scratch_delete_move_elements (core::pose::Pose const &pose, utility::vector1< StepWiseMove > &swa_moves) const

void	get_from_scratch_delete_move_elements (core::pose::Pose const &pose, utility::vector1< StepWiseMove > &swa_moves)

void	get_vary_loop_length_moves (core::pose::Pose const &pose, utility::vector1< StepWiseMove > &vary_loop_length_moves) const

void	get_terminal_move_elements (core::pose::Pose const &pose, utility::vector1< StepWiseMove > &swa_moves, MoveType const &move_type)

void	get_internal_move_elements (core::pose::Pose const &pose, utility::vector1< StepWiseMove > &swa_moves, MoveType const &move_type)

bool	partition_splits_an_input_domain (utility::vector1< core::Size > const &partition_definition, utility::vector1< core::Size > const &domain_map) const

utility::vector1< core::Size >	get_partition_res (utility::vector1< bool > const &partition_definition, bool const setting) const

utility::vector1< core::Size >	get_unique_chains (core::pose::Pose const &pose)

bool	share_chains (utility::vector1< core::Size > const &current_unique_chains, core::pose::Pose const &pose, core::Size const j_full)

utility::vector1< core::Size >	figure_out_first_res_in_pose (utility::vector1< core::Size > const &pose_domain_map) const

void	filter_pose_order (utility::vector1< StepWiseMove > &swa_moves, core::pose::Pose const &pose) const

core::Size	get_actual_moving_res (StepWiseMove const &swa_move, core::pose::Pose const &pose) const

StepWiseMove	reverse_add_move (StepWiseMove const &swa_move, core::pose::Pose const &pose_after) const

StepWiseMove	reverse_add_submotif_move (StepWiseMove const &swa_move, core::pose::Pose const &pose_after) const

StepWiseMove	reverse_resample_move (StepWiseMove const &swa_move, core::pose::Pose const &pose_after) const

StepWiseMove	reverse_delete_move (StepWiseMove const &swa_move, core::pose::Pose const &pose_before, core::pose::Pose const &pose_after) const

Attachment	figure_out_attachment (core::Size const moving_res, core::Size const attached_res, core::pose::Pose const &pose) const

StepWiseMove	ordered_move_from_partition (core::Size const actual_moving_res, core::Size const actual_attached_res, core::pose::Pose const &pose, MoveType const &move_type) const

void	filter_complex_cycles (utility::vector1< StepWiseMove > &swa_moves, core::pose::Pose const &pose) const

Private Attributes
protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptionsCOP	options_

bool	allow_delete_

bool	force_unique_moves_

bool	choose_random_

monte_carlo::submotif::SubMotifLibraryCOP	submotif_library_

utility::vector1< StepWiseMove >	swa_moves_

utility::vector1< core::Real >	proposal_probabilities_

Constructor & Destructor Documentation

protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::StepWiseMoveSelector ( )

protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::StepWiseMoveSelector ( options::StepWiseMoveSelectorOptionsCOP options )

Member Function Documentation

bool protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::allow_delete ( ) const

inline

References allow_delete_.

bool protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::already_instantiated_in_pose	(	core::pose::Pose const &	pose,
		core::Size const &	resnum_in_full_model_numbering
	)		const

private

References core::pose::full_model_info::const_full_model_info(), core::pose::full_model_info::get_res_list_from_full_model_info_const(), core::pose::full_model_info::FullModelInfo::other_pose_list(), and core::pose::Pose::size().

Referenced by get_from_scratch_add_move_elements().

bool protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::both_remnants_would_be_deleted	(	core::pose::Pose const &	pose,
		utility::vector1< core::Size > const &	partition1,
		utility::vector1< core::Size > const &	partition2
	)		const

private

References remnant_would_be_deleted().

Referenced by get_docking_split_move_elements(), and get_intramolecular_split_move_elements().

bool protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::check_for_input_domain_or_from_scratch	(	core::pose::Pose const &	pose,
		utility::vector1< core::Size > const &	partition_res
	)		const

private

bool protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::check_for_intramolecular_submotif_jump	(	core::pose::Pose const &	pose,
		core::Size const &	moving_res,
		core::Size const &	attached_res
	)		const

private

References core::pose::full_model_info::const_full_model_info(), core::pose::Pose::fold_tree(), core::pose::full_model_info::FullModelInfo::in_a_submotif(), and core::kinematics::FoldTree::jump_exists().

Referenced by figure_out_attachment().

bool protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::check_from_scratch	(	core::pose::Pose const &	pose,
		utility::vector1< bool > const &	partition_definition
	)		const

private

References core::pose::Pose::fold_tree(), core::kinematics::FoldTree::is_cutpoint(), options_, and core::pose::Pose::size().

Referenced by figure_out_from_scratch_delete_move_elements().

bool protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::choose_random ( ) const

inline

References choose_random_.

StepWiseMoveSelectorOP protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::clone ( ) const

clone the options

bool protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::figure_out_all_possible_moves	(	core::pose::Pose const &	pose,
		bool const	verbose = `false`
	)

References fill_denovo_moves(), fill_moves_for_other_poses(), fill_moves_for_pose(), fill_vary_loop_length_moves(), normalize_probabilities(), output_moves(), proposal_probabilities_, and swa_moves_.

void protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::figure_out_already_docked	(	core::pose::Pose const &	pose,
		std::map< std::pair< core::Size, core::Size >, bool > &	already_docked
	)		const

private

References core::pose::full_model_info::const_full_model_info(), get_dock_domains(), core::pose::full_model_info::get_res_list_from_full_model_info_const(), and core::pose::full_model_info::FullModelInfo::other_pose_list().

Referenced by filter_add_submotif_moves_to_not_redock_domain(), and get_docking_add_move_elements().

Attachment protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::figure_out_attachment	(	core::Size const	moving_res,
		core::Size const	attached_res,
		core::pose::Pose const &	pose
	)		const

private

References protocols::stepwise::monte_carlo::mover::BOND_TO_NEXT, protocols::stepwise::monte_carlo::mover::BOND_TO_PREVIOUS, check_for_intramolecular_submotif_jump(), core::pose::full_model_info::const_full_model_info(), core::pose::full_model_info::FullModelInfo::cutpoint_open_in_full_model(), core::pose::full_model_info::FullModelInfo::dock_domain_map(), core::pose::full_model_info::get_chains_full(), protocols::stepwise::monte_carlo::mover::JUMP_DOCK, protocols::stepwise::monte_carlo::mover::JUMP_TO_NEXT_IN_CHAIN, and protocols::stepwise::monte_carlo::mover::JUMP_TO_PREV_IN_CHAIN.

Referenced by ordered_move_from_partition(), and reverse_delete_move().

utility::vector1< core::Size > protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::figure_out_first_res_in_pose ( utility::vector1< core::Size > const & pose_domain_map ) const

private

References protocols::mean_field::max().

Referenced by filter_pose_order(), and reverse_delete_move().

void protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::figure_out_from_scratch_delete_move_elements	(	core::pose::Pose const &	pose,
		utility::vector1< StepWiseMove > &	swa_moves
	)		const

private

References protocols::stepwise::monte_carlo::mover::BOND_TO_NEXT, protocols::stepwise::monte_carlo::mover::BOND_TO_PREVIOUS, check_from_scratch(), core::pose::full_model_info::const_full_model_info(), protocols::stepwise::monte_carlo::mover::DELETE, force_unique_moves_, core::pose::full_model_info::get_input_domain_from_full_model_info_const(), core::pose::full_model_info::FullModelInfo::other_pose_list(), partition_splits_an_input_domain(), and core::pose::full_model_info::sub_to_full().

Referenced by get_from_scratch_delete_move_elements().

void protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::fill_denovo_moves ( core::pose::Pose const & pose )

private

References get_from_scratch_add_and_delete_elements(), get_submotif_add_moves(), options_, and save_moves().

Referenced by figure_out_all_possible_moves().

void protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::fill_moves_for_other_poses ( core::pose::Pose const & pose )

private

References core::pose::full_model_info::const_full_model_info(), fill_moves_for_pose(), core::pose::full_model_info::FullModelInfo::get_idx_for_other_pose_with_residue(), normalize_probabilities(), options_, core::pose::full_model_info::FullModelInfo::other_pose_list(), sum_probabilities(), swa_moves_, and protocols::stepwise::modeler::switch_focus_to_other_pose().

Referenced by figure_out_all_possible_moves().

void protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::fill_moves_for_pose ( core::pose::Pose const & pose )

private

References get_docking_add_and_delete_elements(), get_intramolecular_add_and_delete_elements(), get_resample_move_elements(), options_, and save_moves().

Referenced by figure_out_all_possible_moves(), and fill_moves_for_other_poses().

void protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::fill_vary_loop_length_moves ( core::pose::Pose const & pose )

private

References get_vary_loop_length_moves(), options_, and save_moves().

Referenced by figure_out_all_possible_moves().

void protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::filter_add_submotif_moves_to_not_redock_domain	(	utility::vector1< StepWiseMove > &	submotif_add_moves,
		core::pose::Pose const &	pose
	)		const

private

References protocols::stepwise::monte_carlo::mover::ADD_SUBMOTIF, figure_out_already_docked(), and get_dock_domains().

Referenced by get_submotif_add_moves().

void protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::filter_complex_cycles	(	utility::vector1< StepWiseMove > &	swa_moves,
		core::pose::Pose const &	pose
	)		const

private

References just_simple_cycles().

Referenced by get_docking_add_and_delete_elements(), get_from_scratch_add_and_delete_elements(), get_intramolecular_add_and_delete_elements(), and get_submotif_add_moves().

void protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::filter_pose_order	(	utility::vector1< StepWiseMove > &	swa_moves,
		core::pose::Pose const &	pose
	)		const

private

References protocols::stepwise::monte_carlo::mover::ADD, protocols::stepwise::monte_carlo::mover::StepWiseMove::attached_res(), core::pose::full_model_info::const_full_model_info(), figure_out_first_res_in_pose(), core::pose::full_model_info::figure_out_pose_domain_map_const(), force_unique_moves_, protocols::stepwise::monte_carlo::mover::StepWiseMove::move_type(), protocols::stepwise::monte_carlo::mover::StepWiseMove::moving_res(), and core::pose::full_model_info::FullModelInfo::sample_res().

Referenced by get_docking_add_and_delete_elements(), get_intramolecular_add_and_delete_elements(), and get_submotif_add_moves().

bool protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::force_unique_moves ( ) const

inline

References force_unique_moves_.

Size protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_actual_moving_res	(	StepWiseMove const &	swa_move,
		core::pose::Pose const &	pose
	)		const

private

References core::pose::full_model_info::const_full_model_info(), protocols::stepwise::modeler::find_downstream_connection_res(), core::pose::full_model_info::FullModelInfo::full_to_sub(), protocols::stepwise::monte_carlo::mover::StepWiseMove::move_element(), and core::pose::Pose::size().

Referenced by reverse_add_submotif_move(), reverse_delete_move(), and reverse_resample_move().

void protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_add_or_delete_element	(	core::pose::Pose const &	pose,
		StepWiseMove &	swa_move
	)

References choose_random_, get_docking_add_and_delete_elements(), get_from_scratch_add_and_delete_elements(), get_intramolecular_add_and_delete_elements(), get_submotif_add_moves(), options_, core::scoring::rg, save_moves(), swa_moves(), and protocols::TR().

Attachments protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_attachments	(	core::pose::Pose const &	pose,
		core::Size const &	moving_res
	)

Referenced by get_internal_move_elements(), get_terminal_move_elements(), and protocols::stepwise::monte_carlo::rna::RNA_TorsionMover::random_torsion_move().

Attachments protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_attachments	(	core::pose::Pose const &	pose,
		MoveElement const &	move_element
	)

References protocols::stepwise::monte_carlo::mover::BOND_TO_NEXT, protocols::stepwise::monte_carlo::mover::BOND_TO_PREVIOUS, 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::const_full_model_info(), core::pose::Pose::fold_tree(), core::pose::full_model_info::get_res_list_from_full_model_info_const(), protocols::stepwise::monte_carlo::mover::JUMP_TO_NEXT_IN_CHAIN, protocols::stepwise::monte_carlo::mover::JUMP_TO_PREV_IN_CHAIN, and core::pose::Pose::size().

std::set< core::Size > protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_dock_domains	(	utility::vector1< core::Size > const &	move_element,
		core::pose::Pose const &	pose
	)		const

private

References core::pose::full_model_info::const_full_model_info(), and core::pose::full_model_info::FullModelInfo::dock_domain_map().

Referenced by figure_out_already_docked(), and filter_add_submotif_moves_to_not_redock_domain().

void protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_docking_add_and_delete_elements	(	core::pose::Pose const &	pose,
		utility::vector1< StepWiseMove > &	swa_moves
	)

private

References allow_delete_, filter_complex_cycles(), filter_pose_order(), force_unique_moves_, get_docking_add_move_elements(), get_docking_delete_move_elements(), and options_.

Referenced by fill_moves_for_pose(), and get_add_or_delete_element().

void protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_docking_add_move_elements	(	core::pose::Pose const &	pose,
		utility::vector1< StepWiseMove > &	swa_moves
	)

private

References protocols::stepwise::monte_carlo::mover::ADD, core::pose::full_model_info::const_full_model_info(), core::pose::full_model_info::FullModelInfo::dock_domain_map(), figure_out_already_docked(), core::pose::full_model_info::get_preferred_jump_pair_for_docking_domains(), core::pose::full_model_info::get_res_list_from_full_model_info_const(), is_addable_res(), protocols::stepwise::monte_carlo::mover::JUMP_DOCK, and core::pose::Pose::size().

Referenced by get_docking_add_and_delete_elements().

void protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_docking_delete_move_elements	(	core::pose::Pose const &	pose,
		utility::vector1< StepWiseMove > &	swa_moves
	)

private

References protocols::stepwise::monte_carlo::mover::DELETE, and get_docking_split_move_elements().

Referenced by get_docking_add_and_delete_elements().

void protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_docking_split_move_elements	(	core::pose::Pose const &	pose,
		utility::vector1< StepWiseMove > &	swa_moves,
		MoveType const	move_type
	)

private

References both_remnants_would_be_deleted(), core::pose::full_model_info::const_full_model_info(), protocols::stepwise::monte_carlo::mover::DELETE, core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), protocols::stepwise::modeler::get_partition_definition_by_jump(), get_partition_res(), core::pose::full_model_info::get_res_list_from_full_model_info_const(), protocols::stepwise::monte_carlo::mover::JUMP_DOCK, core::kinematics::FoldTree::num_jump(), options_, partitions_split_a_submotif(), core::pose::stepwise_addable_pose_residue(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by get_docking_delete_move_elements(), and get_resample_internal_move_elements().

void protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_from_scratch_add_and_delete_elements	(	core::pose::Pose const &	pose,
		utility::vector1< StepWiseMove > &	swa_moves
	)

private

References allow_delete_, filter_complex_cycles(), get_from_scratch_add_move_elements(), get_from_scratch_delete_move_elements(), and options_.

Referenced by fill_denovo_moves(), and get_add_or_delete_element().

void protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_from_scratch_add_move_elements	(	core::pose::Pose const &	pose,
		utility::vector1< StepWiseMove > &	swa_moves
	)

private

References already_instantiated_in_pose(), core::pose::full_model_info::const_full_model_info(), core::pose::full_model_info::FullModelInfo::cutpoint_open_in_full_model(), protocols::stepwise::monte_carlo::mover::FROM_SCRATCH, core::pose::full_model_info::FullModelInfo::full_sequence(), is_addable_res(), and options_.

Referenced by get_from_scratch_add_and_delete_elements().

void protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_from_scratch_delete_move_elements	(	core::pose::Pose const &	pose,
		utility::vector1< StepWiseMove > &	swa_moves
	)

private

References core::pose::full_model_info::const_full_model_info(), figure_out_from_scratch_delete_move_elements(), and core::pose::Pose::size().

Referenced by get_from_scratch_add_and_delete_elements().

void protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_internal_move_elements	(	core::pose::Pose const &	pose,
		utility::vector1< StepWiseMove > &	swa_moves,
		MoveType const &	move_type
	)

private

References protocols::stepwise::monte_carlo::mover::BOND_TO_NEXT, protocols::stepwise::monte_carlo::mover::BOND_TO_PREVIOUS, get_attachments(), and core::pose::full_model_info::get_move_elements_from_full_model_info_const().

Referenced by get_resample_internal_local_move_elements().

void protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_intramolecular_add_and_delete_elements	(	core::pose::Pose const &	pose,
		utility::vector1< StepWiseMove > &	swa_moves
	)

private

References allow_delete_, filter_complex_cycles(), filter_pose_order(), force_unique_moves_, get_intramolecular_add_move_elements(), get_intramolecular_delete_move_elements(), and options_.

Referenced by fill_moves_for_pose(), and get_add_or_delete_element().

void protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_intramolecular_add_move_elements	(	core::pose::Pose const &	pose,
		utility::vector1< StepWiseMove > &	swa_moves
	)

private

References protocols::stepwise::monte_carlo::mover::ADD, protocols::stepwise::monte_carlo::mover::BOND_TO_NEXT, protocols::stepwise::monte_carlo::mover::BOND_TO_PREVIOUS, core::pose::full_model_info::const_full_model_info(), core::pose::Pose::fold_tree(), core::pose::full_model_info::get_res_list_from_full_model_info_const(), is_addable_res(), protocols::stepwise::monte_carlo::mover::JUMP_TO_NEXT_IN_CHAIN, protocols::stepwise::monte_carlo::mover::JUMP_TO_PREV_IN_CHAIN, options_, and core::pose::Pose::size().

Referenced by get_intramolecular_add_and_delete_elements(), and get_submotif_add_moves().

void protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_intramolecular_delete_move_elements	(	core::pose::Pose const &	pose,
		utility::vector1< StepWiseMove > &	swa_moves
	)

References core::pose::full_model_info::const_full_model_info(), protocols::stepwise::monte_carlo::mover::DELETE, get_intramolecular_split_move_elements(), and core::pose::Pose::size().

Referenced by get_intramolecular_add_and_delete_elements(), and protocols::stepwise::monte_carlo::mover::DeleteMover::wipe_out_moving_residues().

void protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_intramolecular_split_move_elements	(	core::pose::Pose const &	pose,
		utility::vector1< StepWiseMove > &	swa_moves,
		MoveType const	move_type
	)

private

Referenced by get_intramolecular_delete_move_elements(), and get_resample_internal_move_elements().

utility::vector1< core::Size > protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_partition_res	(	utility::vector1< bool > const &	partition_definition,
		bool const	setting
	)		const

private

Referenced by get_docking_split_move_elements(), and get_intramolecular_split_move_elements().

void protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_resample_internal_local_move_elements	(	core::pose::Pose const &	pose,
		utility::vector1< StepWiseMove > &	swa_moves
	)

References core::sequence::end, get_internal_move_elements(), remove_from_consideration_first_multi_residue_move_element(), and protocols::stepwise::monte_carlo::mover::RESAMPLE_INTERNAL_LOCAL.

Referenced by get_resample_move_elements().

void protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_resample_internal_move_elements	(	core::pose::Pose const &	pose,
		utility::vector1< StepWiseMove > &	swa_moves
	)

References core::sequence::end, get_docking_split_move_elements(), get_intramolecular_split_move_elements(), options_, and protocols::stepwise::monte_carlo::mover::RESAMPLE.

Referenced by get_resample_move_elements().

void protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_resample_move_elements	(	core::pose::Pose const &	pose,
		utility::vector1< StepWiseMove > &	swa_moves,
		bool const	save_moves = `true`
	)

References get_resample_internal_local_move_elements(), get_resample_internal_move_elements(), get_resample_terminal_move_elements(), options_, save_moves(), and swa_moves_.

Referenced by fill_moves_for_pose().

void protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_resample_terminal_move_elements	(	core::pose::Pose const &	pose,
		utility::vector1< StepWiseMove > &	swa_moves
	)

References core::sequence::end, get_terminal_move_elements(), remove_from_consideration_first_multi_residue_move_element(), and protocols::stepwise::monte_carlo::mover::RESAMPLE.

Referenced by get_resample_move_elements().

void protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_submotif_add_moves	(	core::pose::Pose const &	pose,
		utility::vector1< StepWiseMove > &	swa_moves
	)

private

References protocols::stepwise::monte_carlo::mover::ADD_SUBMOTIF, protocols::stepwise::monte_carlo::mover::StepWiseMove::attachments(), protocols::stepwise::monte_carlo::mover::check_for_connections_for_all_submotif_residues(), filter_add_submotif_moves_to_not_redock_domain(), filter_complex_cycles(), filter_pose_order(), force_unique_moves_, get_intramolecular_add_move_elements(), protocols::stepwise::monte_carlo::mover::StepWiseMove::moving_res(), options_, and submotif_library_.

Referenced by fill_denovo_moves(), and get_add_or_delete_element().

void protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_terminal_move_elements	(	core::pose::Pose const &	pose,
		utility::vector1< StepWiseMove > &	swa_moves,
		MoveType const &	move_type
	)

private

References get_attachments(), core::pose::full_model_info::get_move_elements_from_full_model_info_const(), core::pose::full_model_info::get_res_list_from_full_model_info_const(), protocols::stepwise::monte_carlo::mover::JUMP_TO_NEXT_IN_CHAIN, and protocols::stepwise::monte_carlo::mover::JUMP_TO_PREV_IN_CHAIN.

Referenced by get_resample_terminal_move_elements().

utility::vector1< core::Size > protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_unique_chains ( core::pose::Pose const & pose )

private

References core::pose::full_model_info::figure_out_chain_numbers_from_full_model_info_const().

Referenced by share_chains().

void protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_vary_loop_length_moves	(	core::pose::Pose const &	pose,
		utility::vector1< StepWiseMove > &	vary_loop_length_moves
	)		const

private

References protocols::stepwise::monte_carlo::mover::ADD_LOOP_RES, protocols::stepwise::monte_carlo::mover::BOND_TO_NEXT, protocols::stepwise::monte_carlo::mover::BOND_TO_PREVIOUS, core::pose::full_model_info::const_full_model_info(), core::pose::full_model_info::FullModelInfo::cutpoint_open_in_full_model(), protocols::stepwise::monte_carlo::mover::DELETE_LOOP_RES, core::pose::full_model_info::FullModelInfo::full_model_parameters(), protocols::stepwise::monte_carlo::mover::get_design_loops(), and core::chemical::rings::q.

Referenced by fill_vary_loop_length_moves().

bool protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::is_addable_res	(	core::Size const	n,
		core::pose::Pose const &	pose
	)		const

private

References core::pose::full_model_info::const_full_model_info(), core::pose::full_model_info::FullModelInfo::rna_bulge_res(), core::pose::stepwise_addable_residue(), and core::pose::full_model_info::FullModelInfo::working_res().

Referenced by get_docking_add_move_elements(), get_from_scratch_add_move_elements(), and get_intramolecular_add_move_elements().

bool protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::just_simple_cycles	(	StepWiseMove const &	swa_move,
		core::pose::Pose const &	pose,
		bool const	verbose = `false`
	)		const

Referenced by filter_complex_cycles().

void protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::normalize_probabilities	(	core::Size const	start_idx = `1`,
		core::Size const	final_idx = `0`,
		core::Real const	desired_weight = `1`
	)

private

References proposal_probabilities_, and sum_probabilities().

Referenced by figure_out_all_possible_moves(), and fill_moves_for_other_poses().

protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptionsCOP protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::options ( ) const

inline

References options_.

StepWiseMove protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::ordered_move_from_partition	(	core::Size const	actual_moving_res,
		core::Size const	actual_attached_res,
		core::pose::Pose const &	pose,
		MoveType const &	move_type
	)		const

private

References core::pose::full_model_info::const_full_model_info(), figure_out_attachment(), protocols::stepwise::modeler::figure_out_root_and_moving_partition_res(), and core::pose::full_model_info::FullModelInfo::sub_to_full().

Referenced by reverse_add_move(), reverse_add_submotif_move(), and reverse_resample_move().

void protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::output_moves ( ) const

References core::chemical::element::F, proposal_probabilities_, swa_moves_, and protocols::TR().

Referenced by figure_out_all_possible_moves().

bool protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::partition_splits_an_input_domain	(	utility::vector1< core::Size > const &	partition_definition,
		utility::vector1< core::Size > const &	domain_map
	)		const

private

Referenced by figure_out_from_scratch_delete_move_elements(), and get_intramolecular_split_move_elements().

bool protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::partitions_split_a_submotif	(	core::pose::Pose const &	pose,
		utility::vector1< core::Size > const &	partition1,
		utility::vector1< core::Size > const &	partition2
	)		const

private

References core::pose::full_model_info::const_full_model_info(), core::pose::full_model_info::get_res_list_from_full_model_info_const(), and core::pose::full_model_info::FullModelInfo::submotif_info_list().

Referenced by get_docking_split_move_elements(), and get_intramolecular_split_move_elements().

Real protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::proposal_probability ( StepWiseMove const & swa_move ) const

References proposal_probabilities_, swa_moves_, and protocols::TR().

bool protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::remnant_would_be_deleted	(	core::pose::Pose const &	pose,
		utility::vector1< core::Size > const &	partition
	)		const

private

References core::pose::full_model_info::const_full_model_info(), and core::pose::full_model_info::sub_to_full().

Referenced by both_remnants_would_be_deleted().

void protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::remove_from_consideration_first_multi_residue_move_element	(	utility::vector1< StepWiseMove > &	swa_moves,
		bool	remove_even_if_not_singlet
	)

private

Referenced by get_resample_internal_local_move_elements(), and get_resample_terminal_move_elements().

StepWiseMove protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::reverse_add_move	(	StepWiseMove const &	swa_move,
		core::pose::Pose const &	pose_after
	)		const

private

References protocols::stepwise::monte_carlo::mover::StepWiseMove::attached_res(), core::pose::full_model_info::const_full_model_info(), protocols::stepwise::monte_carlo::mover::DELETE, core::pose::Pose::fold_tree(), core::kinematics::FoldTree::get_parent_residue(), protocols::stepwise::monte_carlo::mover::StepWiseMove::moving_res(), ordered_move_from_partition(), core::pose::full_model_info::FullModelInfo::res_list(), and protocols::TR().

Referenced by reverse_move().

StepWiseMove protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::reverse_add_submotif_move	(	StepWiseMove const &	swa_move,
		core::pose::Pose const &	pose_after
	)		const

private

References protocols::stepwise::monte_carlo::mover::DELETE, core::pose::Pose::fold_tree(), get_actual_moving_res(), core::kinematics::FoldTree::get_parent_residue(), and ordered_move_from_partition().

Referenced by reverse_move().

StepWiseMove protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::reverse_delete_move	(	StepWiseMove const &	swa_move,
		core::pose::Pose const &	pose_before,
		core::pose::Pose const &	pose_after
	)		const

private

References protocols::stepwise::monte_carlo::mover::ADD, core::pose::full_model_info::const_full_model_info(), figure_out_attachment(), figure_out_first_res_in_pose(), core::pose::full_model_info::figure_out_pose_domain_map_const(), core::pose::Pose::fold_tree(), protocols::stepwise::monte_carlo::mover::FROM_SCRATCH, get_actual_moving_res(), core::pose::full_model_info::FullModelInfo::get_idx_for_other_pose_with_residue(), core::kinematics::FoldTree::get_parent_residue(), core::kinematics::FoldTree::is_cutpoint(), protocols::mean_field::max(), protocols::mean_field::min(), protocols::stepwise::monte_carlo::mover::StepWiseMove::move_element(), core::pose::full_model_info::FullModelInfo::other_pose_list(), core::pose::full_model_info::FullModelInfo::res_list(), core::pose::full_model_info::FullModelInfo::sample_res(), core::pose::full_model_info::FullModelInfo::show_submotif_info_list(), core::pose::Pose::size(), core::pose::full_model_info::sub_to_full(), and protocols::TR().

Referenced by reverse_move().

StepWiseMove protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::reverse_move	(	StepWiseMove const &	swa_move,
		core::pose::Pose const &	pose_before,
		core::pose::Pose const &	pose_after
	)		const

StepWiseMove protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::reverse_resample_move	(	StepWiseMove const &	swa_move,
		core::pose::Pose const &	pose_after
	)		const

private

References core::pose::Pose::fold_tree(), get_actual_moving_res(), core::kinematics::FoldTree::get_parent_residue(), ordered_move_from_partition(), and protocols::stepwise::monte_carlo::mover::RESAMPLE.

Referenced by reverse_move().

void protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::save_moves	(	utility::vector1< StepWiseMove > const &	moves,
		core::Real const	total_weight = `1`,
		bool const	clear_moves_before_saving = `false`
	)

private

References protocols::stepwise::monte_carlo::mover::ADD, protocols::stepwise::monte_carlo::mover::ADD_SUBMOTIF, force_unique_moves_, protocols::stepwise::monte_carlo::mover::JUMP_TO_NEXT_IN_CHAIN, protocols::stepwise::monte_carlo::mover::JUMP_TO_PREV_IN_CHAIN, options_, proposal_probabilities_, swa_moves_, and protocols::TR().

Referenced by fill_denovo_moves(), fill_moves_for_pose(), fill_vary_loop_length_moves(), get_add_or_delete_element(), and get_resample_move_elements().

StepWiseMove protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::select_random_move ( core::pose::Pose const & pose ) const

References proposal_probabilities_, core::scoring::rg, and swa_moves_.

void protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::set_allow_delete ( bool const & setting )

inline

References allow_delete_.

void protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::set_choose_random ( bool const & setting )

inline

References choose_random_.

void protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::set_force_unique_moves ( bool const & setting )

inline

References force_unique_moves_.

void protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::set_options ( protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptionsCOP setting )

inline

References options_.

void protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::set_submotif_library ( monte_carlo::submotif::SubMotifLibraryCOP setting )

inline

References submotif_library_.

bool protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::share_chains	(	utility::vector1< core::Size > const &	current_unique_chains,
		core::pose::Pose const &	pose,
		core::Size const	j_full
	)

private

References core::pose::full_model_info::const_full_model_info(), core::pose::full_model_info::get_chains_full(), core::pose::full_model_info::FullModelInfo::get_idx_for_other_pose_with_residue(), get_unique_chains(), core::pose::full_model_info::FullModelInfo::other_pose_list(), and core::chemical::rings::q.

monte_carlo::submotif::SubMotifLibraryCOP protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::submotif_library ( )

inline

References submotif_library_.

Real protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::sum_probabilities	(	core::Size const	start_idx = `1`,
		core::Size const	final_idx = `0`
	)		const

private

References proposal_probabilities_.

Referenced by fill_moves_for_other_poses(), and normalize_probabilities().

utility::vector1< StepWiseMove > const& protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::swa_moves ( ) const

inline

References swa_moves_.

Referenced by get_add_or_delete_element().

Member Data Documentation

bool protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::allow_delete_

private

Referenced by allow_delete(), get_docking_add_and_delete_elements(), get_from_scratch_add_and_delete_elements(), get_intramolecular_add_and_delete_elements(), and set_allow_delete().

bool protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::choose_random_

private

Referenced by choose_random(), get_add_or_delete_element(), and set_choose_random().

bool protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::force_unique_moves_

private

Referenced by figure_out_from_scratch_delete_move_elements(), filter_pose_order(), force_unique_moves(), get_docking_add_and_delete_elements(), get_intramolecular_add_and_delete_elements(), get_intramolecular_split_move_elements(), get_submotif_add_moves(), save_moves(), and set_force_unique_moves().

protocols::stepwise::monte_carlo::mover::options::StepWiseMoveSelectorOptionsCOP protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::options_

private

Referenced by check_from_scratch(), fill_denovo_moves(), fill_moves_for_other_poses(), fill_moves_for_pose(), fill_vary_loop_length_moves(), get_add_or_delete_element(), get_docking_add_and_delete_elements(), get_docking_split_move_elements(), get_from_scratch_add_and_delete_elements(), get_from_scratch_add_move_elements(), get_intramolecular_add_and_delete_elements(), get_intramolecular_add_move_elements(), get_intramolecular_split_move_elements(), get_resample_internal_move_elements(), get_resample_move_elements(), get_submotif_add_moves(), options(), save_moves(), and set_options().

utility::vector1< core::Real > protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::proposal_probabilities_

private

Referenced by figure_out_all_possible_moves(), normalize_probabilities(), output_moves(), proposal_probability(), save_moves(), select_random_move(), and sum_probabilities().

monte_carlo::submotif::SubMotifLibraryCOP protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::submotif_library_

private

Referenced by get_submotif_add_moves(), set_submotif_library(), and submotif_library().

utility::vector1< StepWiseMove > protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::swa_moves_

private

Referenced by figure_out_all_possible_moves(), fill_moves_for_other_poses(), get_resample_move_elements(), output_moves(), proposal_probability(), save_moves(), select_random_move(), and swa_moves().

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

src/protocols/stepwise/monte_carlo/mover/StepWiseMoveSelector.hh
src/protocols/stepwise/monte_carlo/mover/StepWiseMoveSelector.cc

Public Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation