#include <SWA_MoveSelector.hh>

Public Member Functions
	SWA_MoveSelector ()

	~SWA_MoveSelector ()

void	get_random_add_or_delete_element (pose::Pose const &pose, SWA_Move &swa_move)

void	get_random_add_or_delete_element (pose::Pose const &pose, SWA_Move &swa_move, utility::vector1< Size > const &sample_res)

void	get_resample_move_elements (pose::Pose const &pose, utility::vector1< SWA_Move > &swa_moves)

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

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

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

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

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

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

void	set_allow_delete (bool const &setting)

bool	allow_delete () const

void	set_allow_skip_bulge (bool const &setting)

bool	allow_skip_bulge () const

void	set_allow_internal_hinge (bool const &setting)

bool	allow_internal_hinge () const

void	set_allow_internal_local (bool const &setting)

bool	allow_internal_local () const

void	set_from_scratch_frequency (Real const &setting)

Real	from_scratch_frequency () const

void	set_intermolecular_frequency (Real const &setting)

Real	intermolecular_frequency () const

void	set_allow_shared_chains_in_dock_poses (bool const &setting)

bool	allow_shared_chains_in_dock_poses () const

Private Member Functions
void	get_intramolecular_add_and_delete_elements (pose::Pose const &pose, utility::vector1< SWA_Move > &swa_moves, utility::vector1< Size > const &sample_res)

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

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

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

void	filter_by_sample_res (utility::vector1< SWA_Move > &swa_moves, utility::vector1< Size > const &sample_res)

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

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

void	get_intermolecular_add_and_delete_elements (pose::Pose const &pose, utility::vector1< SWA_Move > &swa_moves, utility::vector1< Size > const &sample_res)

void	get_intermolecular_add_move_elements (pose::Pose const &pose, utility::vector1< SWA_Move > &swa_moves)

void	get_intermolecular_delete_move_elements (pose::Pose const &pose, utility::vector1< SWA_Move > &swa_moves)

void	get_intermolecular_split_move_elements (pose::Pose const &pose, utility::vector1< SWA_Move > &swa_moves, MoveType const move_type)

void	get_from_scratch_add_and_delete_elements (pose::Pose const &pose, utility::vector1< SWA_Move > &swa_moves, utility::vector1< Size > const &sample_res)

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

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

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

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

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

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

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

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

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

Private Attributes
bool	allow_delete_

bool	allow_skip_bulge_

bool	allow_internal_hinge_

bool	allow_internal_local_

Real	from_scratch_frequency_

Real	intermolecular_frequency_

bool	only_dock_preexisting_chunks_

bool	allow_shared_chains_in_dock_poses_

bool	resampling_

Constructor & Destructor Documentation

protocols::stepwise::monte_carlo::SWA_MoveSelector::SWA_MoveSelector ( )

protocols::stepwise::monte_carlo::SWA_MoveSelector::~SWA_MoveSelector ( )

Member Function Documentation

bool protocols::stepwise::monte_carlo::SWA_MoveSelector::allow_delete ( ) const

inline

bool protocols::stepwise::monte_carlo::SWA_MoveSelector::allow_internal_hinge ( ) const

inline

bool protocols::stepwise::monte_carlo::SWA_MoveSelector::allow_internal_local ( ) const

inline

bool protocols::stepwise::monte_carlo::SWA_MoveSelector::allow_shared_chains_in_dock_poses ( ) const

inline

bool protocols::stepwise::monte_carlo::SWA_MoveSelector::allow_skip_bulge ( ) const

inline

bool protocols::stepwise::monte_carlo::SWA_MoveSelector::already_instantiated_in_pose	(	pose::Pose const &	pose,
		Size const &	resnum_in_full_model_numbering
	)		const

private

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

Referenced by get_from_scratch_add_move_elements().

bool protocols::stepwise::monte_carlo::SWA_MoveSelector::check_for_fixed_domain_or_from_scratch	(	pose::Pose const &	pose,
		utility::vector1< Size > const &	partition_res
	)		const

private

References protocols::stepwise::check_for_fixed_domain(), from_scratch_frequency_, and resampling_.

Referenced by get_intramolecular_split_move_elements().

void protocols::stepwise::monte_carlo::SWA_MoveSelector::figure_out_from_scratch_delete_move_elements	(	pose::Pose const &	pose,
		utility::vector1< SWA_Move > &	swa_moves
	)		const

private

References protocols::stepwise::monte_carlo::BOND_TO_NEXT, protocols::stepwise::monte_carlo::BOND_TO_PREVIOUS, const_full_model_info(), protocols::stepwise::monte_carlo::DELETE, core::pose::full_model_info::get_fixed_domain_from_full_model_info_const(), utility::tools::make_vector1(), core::pose::full_model_info::FullModelInfo::other_pose_list(), partition_splits_a_fixed_domain(), sub_to_full(), and core::pose::Pose::total_residue().

Referenced by get_from_scratch_delete_move_elements().

void protocols::stepwise::monte_carlo::SWA_MoveSelector::filter_by_sample_res	(	utility::vector1< SWA_Move > &	swa_moves,
		utility::vector1< Size > const &	sample_res
	)

private

References protocols::stepwise::monte_carlo::ADD, protocols::stepwise::monte_carlo::FROM_SCRATCH, utility::vector1< T, class >::has_value(), protocols::stepwise::monte_carlo::SWA_Move::move_element(), and protocols::stepwise::monte_carlo::SWA_Move::move_type().

Referenced by get_from_scratch_add_and_delete_elements(), get_intermolecular_add_and_delete_elements(), and get_intramolecular_add_and_delete_elements().

Real protocols::stepwise::monte_carlo::SWA_MoveSelector::from_scratch_frequency ( ) const

inline

Attachments protocols::stepwise::monte_carlo::SWA_MoveSelector::get_attachments	(	pose::Pose const &	pose,
		Size const &	moving_res
	)

References utility::tools::make_vector1().

Referenced by get_internal_move_elements(), and get_terminal_move_elements().

Attachments protocols::stepwise::monte_carlo::SWA_MoveSelector::get_attachments	(	pose::Pose const &	pose,
		MoveElement const &	move_element
	)

References protocols::stepwise::monte_carlo::BOND_TO_NEXT, protocols::stepwise::monte_carlo::BOND_TO_PREVIOUS, protocols::stepwise::check_jump_to_next_residue_in_chain(), protocols::stepwise::check_jump_to_previous_residue_in_chain(), const_full_model_info(), fold_tree, core::pose::Pose::fold_tree(), get_res_list_from_full_model_info_const(), utility::vector1< T, class >::has_value(), utility::vector1< T, class >::index(), protocols::stepwise::monte_carlo::JUMP_TO_NEXT_IN_CHAIN, protocols::stepwise::monte_carlo::JUMP_TO_PREV_IN_CHAIN, nres, and core::pose::Pose::total_residue().

void protocols::stepwise::monte_carlo::SWA_MoveSelector::get_from_scratch_add_and_delete_elements	(	pose::Pose const &	pose,
		utility::vector1< SWA_Move > &	swa_moves,
		utility::vector1< Size > const &	sample_res
	)

private

References filter_by_sample_res(), get_from_scratch_add_move_elements(), and get_from_scratch_delete_move_elements().

Referenced by get_random_add_or_delete_element().

void protocols::stepwise::monte_carlo::SWA_MoveSelector::get_from_scratch_add_move_elements	(	pose::Pose const &	pose,
		utility::vector1< SWA_Move > &	swa_moves
	)

private

References already_instantiated_in_pose(), const_full_model_info(), core::pose::full_model_info::FullModelInfo::cutpoint_open_in_full_model(), protocols::stepwise::monte_carlo::FROM_SCRATCH, core::pose::full_model_info::FullModelInfo::full_sequence(), utility::vector1< T, class >::has_value(), and utility::tools::make_vector1().

Referenced by get_from_scratch_add_and_delete_elements().

void protocols::stepwise::monte_carlo::SWA_MoveSelector::get_from_scratch_delete_move_elements	(	pose::Pose const &	pose,
		utility::vector1< SWA_Move > &	swa_moves
	)

private

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

Referenced by get_from_scratch_add_and_delete_elements().

void protocols::stepwise::monte_carlo::SWA_MoveSelector::get_intermolecular_add_and_delete_elements	(	pose::Pose const &	pose,
		utility::vector1< SWA_Move > &	swa_moves,
		utility::vector1< Size > const &	sample_res
	)

private

References filter_by_sample_res(), get_intermolecular_add_move_elements(), and get_intermolecular_delete_move_elements().

Referenced by get_random_add_or_delete_element().

void protocols::stepwise::monte_carlo::SWA_MoveSelector::get_intermolecular_add_move_elements	(	pose::Pose const &	pose,
		utility::vector1< SWA_Move > &	swa_moves
	)

private

References protocols::stepwise::monte_carlo::ADD, allow_shared_chains_in_dock_poses_, const_full_model_info(), figure_out_chains_from_full_model_info_const(), get_chains_full(), get_res_list_from_full_model_info_const(), get_unique_chains(), j, protocols::stepwise::monte_carlo::JUMP_INTERCHAIN, nres, only_dock_preexisting_chunks_, other_pose, core::pose::full_model_info::FullModelInfo::other_pose_list(), q, share_chains(), and core::pose::Pose::total_residue().

Referenced by get_intermolecular_add_and_delete_elements().

void protocols::stepwise::monte_carlo::SWA_MoveSelector::get_intermolecular_delete_move_elements	(	pose::Pose const &	pose,
		utility::vector1< SWA_Move > &	swa_moves
	)

private

References protocols::stepwise::monte_carlo::DELETE, and get_intermolecular_split_move_elements().

Referenced by get_intermolecular_add_and_delete_elements().

void protocols::stepwise::monte_carlo::SWA_MoveSelector::get_intermolecular_split_move_elements	(	pose::Pose const &	pose,
		utility::vector1< SWA_Move > &	swa_moves,
		MoveType const	move_type
	)

private

References const_full_model_info(), core::kinematics::FoldTree::downstream_jump_residue(), figure_out_chains_from_full_model_info_const(), core::pose::Pose::fold_tree(), core::pose::full_model_info::get_fixed_domain_from_full_model_info_const(), protocols::stepwise::get_partition_definition_by_jump(), get_partition_res(), protocols::stepwise::monte_carlo::JUMP_INTERCHAIN, core::kinematics::FoldTree::num_jump(), partition_splits_a_fixed_domain(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by get_intermolecular_delete_move_elements(), and get_resample_internal_move_elements().

void protocols::stepwise::monte_carlo::SWA_MoveSelector::get_internal_move_elements	(	pose::Pose const &	pose,
		utility::vector1< SWA_Move > &	swa_moves,
		MoveType const &	move_type
	)

private

References protocols::stepwise::monte_carlo::BOND_TO_NEXT, protocols::stepwise::monte_carlo::BOND_TO_PREVIOUS, get_attachments(), and get_move_elements_from_full_model_info_const().

Referenced by get_resample_internal_local_move_elements().

void protocols::stepwise::monte_carlo::SWA_MoveSelector::get_intramolecular_add_and_delete_elements	(	pose::Pose const &	pose,
		utility::vector1< SWA_Move > &	swa_moves,
		utility::vector1< Size > const &	sample_res
	)

private

References allow_delete_, filter_by_sample_res(), get_intramolecular_add_move_elements(), and get_intramolecular_delete_move_elements().

Referenced by get_random_add_or_delete_element().

void protocols::stepwise::monte_carlo::SWA_MoveSelector::get_intramolecular_add_move_elements	(	pose::Pose const &	pose,
		utility::vector1< SWA_Move > &	swa_moves
	)

private

References protocols::stepwise::monte_carlo::ADD, allow_skip_bulge_, protocols::stepwise::monte_carlo::BOND_TO_NEXT, protocols::stepwise::monte_carlo::BOND_TO_PREVIOUS, const_full_model_info(), fold_tree, core::pose::Pose::fold_tree(), get_res_list_from_full_model_info_const(), protocols::stepwise::monte_carlo::JUMP_TO_NEXT_IN_CHAIN, protocols::stepwise::monte_carlo::JUMP_TO_PREV_IN_CHAIN, nres, and core::pose::Pose::total_residue().

Referenced by get_intramolecular_add_and_delete_elements().

void protocols::stepwise::monte_carlo::SWA_MoveSelector::get_intramolecular_delete_move_elements	(	pose::Pose const &	pose,
		utility::vector1< SWA_Move > &	swa_moves
	)

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

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

void protocols::stepwise::monte_carlo::SWA_MoveSelector::get_intramolecular_split_move_elements	(	pose::Pose const &	pose,
		utility::vector1< SWA_Move > &	swa_moves,
		MoveType const	move_type
	)

private

References protocols::stepwise::monte_carlo::BOND_TO_NEXT, protocols::stepwise::monte_carlo::BOND_TO_PREVIOUS, check_for_fixed_domain_or_from_scratch(), const_full_model_info(), core::kinematics::FoldTree::downstream_jump_residue(), figure_out_chains_from_full_model_info_const(), core::pose::Pose::fold_tree(), protocols::stepwise::sampling::rna::get_anchor_res(), core::pose::full_model_info::get_fixed_domain_from_full_model_info_const(), protocols::stepwise::get_partition_definition(), protocols::stepwise::get_partition_definition_by_jump(), get_partition_res(), core::kinematics::FoldTree::is_cutpoint(), protocols::stepwise::monte_carlo::JUMP_TO_NEXT_IN_CHAIN, protocols::stepwise::monte_carlo::JUMP_TO_PREV_IN_CHAIN, core::kinematics::FoldTree::num_jump(), partition_splits_a_fixed_domain(), core::pose::Pose::total_residue(), type, and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by get_intramolecular_delete_move_elements(), and get_resample_internal_move_elements().

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

private

Referenced by get_intermolecular_split_move_elements(), and get_intramolecular_split_move_elements().

void protocols::stepwise::monte_carlo::SWA_MoveSelector::get_random_add_or_delete_element	(	pose::Pose const &	pose,
		SWA_Move &	swa_move
	)

References sample_res.

void protocols::stepwise::monte_carlo::SWA_MoveSelector::get_random_add_or_delete_element	(	pose::Pose const &	pose,
		SWA_Move &	swa_move,
		utility::vector1< Size > const &	sample_res
	)

References from_scratch_frequency_, get_from_scratch_add_and_delete_elements(), get_intermolecular_add_and_delete_elements(), get_intramolecular_add_and_delete_elements(), intermolecular_frequency_, numeric::random::RandomGenerator::random_element(), protocols::RG, protocols::TR, and numeric::random::RandomGenerator::uniform().

void protocols::stepwise::monte_carlo::SWA_MoveSelector::get_resample_internal_local_move_elements	(	pose::Pose const &	pose,
		utility::vector1< SWA_Move > &	swa_moves
	)

References get_internal_move_elements(), remove_from_consideration_first_multi_residue_move_element(), and protocols::stepwise::monte_carlo::RESAMPLE_INTERNAL_LOCAL.

Referenced by get_resample_move_elements().

void protocols::stepwise::monte_carlo::SWA_MoveSelector::get_resample_internal_move_elements	(	pose::Pose const &	pose,
		utility::vector1< SWA_Move > &	swa_moves
	)

References get_intermolecular_split_move_elements(), get_intramolecular_split_move_elements(), intermolecular_frequency_, and protocols::stepwise::monte_carlo::RESAMPLE.

Referenced by get_resample_move_elements().

void protocols::stepwise::monte_carlo::SWA_MoveSelector::get_resample_move_elements	(	pose::Pose const &	pose,
		utility::vector1< SWA_Move > &	swa_moves
	)

References allow_internal_hinge_, allow_internal_local_, get_resample_internal_local_move_elements(), get_resample_internal_move_elements(), get_resample_terminal_move_elements(), resampling_, and protocols::TR.

void protocols::stepwise::monte_carlo::SWA_MoveSelector::get_resample_terminal_move_elements	(	pose::Pose const &	pose,
		utility::vector1< SWA_Move > &	swa_moves
	)

References get_terminal_move_elements(), remove_from_consideration_first_multi_residue_move_element(), and protocols::stepwise::monte_carlo::RESAMPLE.

Referenced by get_resample_move_elements().

void protocols::stepwise::monte_carlo::SWA_MoveSelector::get_terminal_move_elements	(	pose::Pose const &	pose,
		utility::vector1< SWA_Move > &	swa_moves,
		MoveType const &	move_type
	)

private

References get_attachments(), get_move_elements_from_full_model_info_const(), get_res_list_from_full_model_info_const(), protocols::stepwise::monte_carlo::JUMP_TO_NEXT_IN_CHAIN, protocols::stepwise::monte_carlo::JUMP_TO_PREV_IN_CHAIN, runtime_assert, and size().

Referenced by get_resample_terminal_move_elements().

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

private

References figure_out_chains_from_full_model_info_const(), and utility::vector1< T, class >::has_value().

Referenced by get_intermolecular_add_move_elements(), and share_chains().

Real protocols::stepwise::monte_carlo::SWA_MoveSelector::intermolecular_frequency ( ) const

inline

bool protocols::stepwise::monte_carlo::SWA_MoveSelector::partition_splits_a_fixed_domain	(	utility::vector1< Size > const &	partition_definition,
		utility::vector1< Size > const &	domain_map
	)		const

private

Referenced by figure_out_from_scratch_delete_move_elements(), get_intermolecular_split_move_elements(), and get_intramolecular_split_move_elements().

void protocols::stepwise::monte_carlo::SWA_MoveSelector::remove_from_consideration_first_multi_residue_move_element	(	utility::vector1< SWA_Move > &	swa_moves,
		bool	remove_even_if_not_singlet
	)

private

References runtime_assert.

Referenced by get_resample_internal_local_move_elements(), and get_resample_terminal_move_elements().

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

inline

void protocols::stepwise::monte_carlo::SWA_MoveSelector::set_allow_internal_hinge ( bool const & setting )

inline

void protocols::stepwise::monte_carlo::SWA_MoveSelector::set_allow_internal_local ( bool const & setting )

inline

void protocols::stepwise::monte_carlo::SWA_MoveSelector::set_allow_shared_chains_in_dock_poses ( bool const & setting )

inline

void protocols::stepwise::monte_carlo::SWA_MoveSelector::set_allow_skip_bulge ( bool const & setting )

inline

void protocols::stepwise::monte_carlo::SWA_MoveSelector::set_from_scratch_frequency ( Real const & setting )

inline

void protocols::stepwise::monte_carlo::SWA_MoveSelector::set_intermolecular_frequency ( Real const & setting )

inline

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