Namespaces
	monte_carlo

	sampling

	screener

Classes
class	StepWiseSampleAndScreen

Typedefs
typedef utility::pointer::owning_ptr < StepWiseSampleAndScreen >	StepWiseSampleAndScreenOP

typedef utility::pointer::owning_ptr < StepWiseSampleAndScreen const >	StepWiseSampleAndScreenCOP

typedef std::map< std::string, pose::PoseOP >	PoseList

Functions
Size	make_cut_at_moving_suite (core::kinematics::FoldTree &fold_tree, Size const &moving_suite)

Size	make_cut_at_moving_suite (pose::Pose &pose, Size const &moving_suite)

Size	find_jump_number_at_suite (kinematics::FoldTree const &fold_tree, Size const &moving_suite)

Size	look_for_unique_jump_to_moving_res (kinematics::FoldTree const &fold_tree, Size const &i)

bool	is_cutpoint_closed (pose::Pose const &pose, Size const seq_num)

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

bool	is_close_chain_break (pose::Pose const &pose)

void	output_boolean (std::string const &tag, bool boolean, std::ostream &TR)

void	output_boolean (bool boolean, std::ostream &TR)

void	output_movemap (kinematics::MoveMap const &mm, Size const total_residue, std::ostream &TR)

void	figure_out_moving_residues (core::kinematics::MoveMap &mm, core::pose::Pose const &pose, utility::vector1< core::Size > const &fixed_res, bool const move_takeoff_torsions, bool const move_jumps_between_chains)

void	pdbslice (core::pose::Pose &new_pose, core::pose::Pose const &pose, utility::vector1< core::Size > const &slice_res)

void	pdbslice (core::pose::Pose &pose, utility::vector1< core::Size > const &slice_res)

Real	superimpose_pose (pose::Pose &mod_pose, pose::Pose const &ref_pose, std::map< Size, Size > const &res_map)
	Superimpose mod_pose onto ref_pose using the mapping of residues from mod_pose to ref_pose given by res_map. Simple wrapper around superimpose_pose using IDs. More...

id::AtomID_Map< id::AtomID >	create_alignment_id_map (pose::Pose const &mod_pose, pose::Pose const &ref_pose, utility::vector1< core::Size > const &superimpose_res)

id::AtomID_Map< id::AtomID >	create_alignment_id_map (pose::Pose const &mod_pose, pose::Pose const &ref_pose, std::map< core::Size, core::Size > res_map)

utility::vector1< Size > const	convert_to_working_res (utility::vector1< Size > const &res_vector, utility::vector1< Size > const &working_res)

core::scoring::constraints::ConstraintSetOP	constraint_set_slice (core::scoring::constraints::ConstraintSetOP &cst_set, utility::vector1< core::Size > const &slice_res, pose::Pose const &pose, pose::Pose const &full_pose)

utility::vector1< std::string >	load_s_and_l ()

std::string	get_file_name (std::string const &silent_file, std::string const &tag)

void	check_scorefxn_has_constraint_terms_if_pose_has_constraints (pose::Pose const &pose, core::scoring::ScoreFunctionOP &scorefxn)

utility::vector1< Size >	merge_vectors (utility::vector1< Size > const &vec1, utility::vector1< Size > const &vec2)

void	create_euler_rotation (Matrix &M, Real const &alpha, Real const &beta, Real const &gamma, Vector const &, Vector const &axis2, Vector const &axis3)

void	create_euler_rotation (Matrix &M, Real const &alpha, Real const &beta, Real const &gamma)

void	get_euler_angles (Real &alpha, Real &beta, Real &gamma, Matrix M1, Matrix M2, bool const verbose)

void	translate (pose::Pose &pose, Vector const shift, pose::Pose const &ref_pose, utility::vector1< Size > const &moving_res)

void	rotate (pose::Pose &pose, Matrix const M, pose::Pose const &ref_pose, utility::vector1< Size > const &moving_res, Vector const &centroid)

void	rotate (pose::Pose &pose, Matrix const M, pose::Pose const &ref_pose, utility::vector1< Size > const &moving_res)

void	get_base_centroid_and_rotation_matrix (pose::Pose const &pose, Size const i, Vector &centroid, Matrix &M)

void	translate_and_rotate_residue_to_origin (pose::Pose &pose, Size const i, utility::vector1< Size > const moving_res, bool const do_not_rotate)

void	translate_and_rotate_residue_to_origin (pose::Pose &pose, Size const i)

void	superimpose_at_fixed_res (pose::Pose &pose, pose::Pose const &native_pose, Real &rmsd, Size &natoms_rmsd, bool skip_bulges)

Real	superimpose_at_fixed_res_and_get_all_atom_rmsd (pose::Pose &pose, pose::Pose const &native_pose, bool skip_bulges)

void	superimpose_recursively (pose::Pose &pose, pose::Pose const &native_pose, Real &rmsd, Size &natoms, bool skip_bulges=false)

Real	superimpose_recursively (pose::Pose &pose, pose::Pose const &native_pose)

Size	get_number_missing_residue_connections (pose::Pose &pose)

bool	is_at_terminus (core::pose::Pose const &pose, Size const i)

void	get_jump_partners_from_pose (utility::vector1< Size > &jump_partners1, utility::vector1< Size > &jump_partners2, utility::vector1< std::string > &jump_atoms1, utility::vector1< std::string > &jump_atoms2, pose::Pose const &pose, utility::vector1< Size > const &working_res)

void	get_endpoints_from_pose (utility::vector1< Size > &endpoints, pose::Pose const &pose, utility::vector1< Size > const &working_res)

utility::vector1< Size >	map_to_local_numbering (utility::vector1< Size > const &vec, utility::vector1< Size > const &working_res)

std::map< Size, Size >	get_res_map (utility::vector1< Size > const &working_res, utility::vector1< Size > const &source_res)

utility::vector1< Size >	merge_disjoint_vectors (utility::vector1< Size > const &res_vector1, utility::vector1< Size > const &res_vector2)

void	remove_upper_terminus (core::conformation::ResidueOP &rsd)

void	remove_lower_terminus (core::conformation::ResidueOP &rsd)

bool	find_root_without_virtual_ribose (kinematics::FoldTree const &f, pose::Pose const &pose)

bool	definite_terminal_root (pose::Pose const &pose, Size const i)

void	try_reroot_at_fixed_domain (pose::Pose &pose)

Size	find_first_root_residue (kinematics::FoldTree const &f, utility::vector1< Size > const &working_res_subset, utility::vector1< Size > const &working_res)

void	reroot_based_on_full_model_info (pose::Pose &pose, utility::vector1< Size > const &root_partition_res)

void	merge_in_other_pose_by_jump (pose::Pose &pose, pose::Pose const &pose2, Size const lower_merge_res, Size const upper_merge_res)

void	merge_in_other_pose_by_bond (pose::Pose &pose, pose::Pose const &pose2, Size const merge_res)

void	merge_in_other_pose (pose::Pose &pose, pose::Pose const &pose2, Size const lower_merge_res, Size const upper_merge_res, bool const connect_residues_by_bond)

utility::vector1< Size >	merge_two_poses_using_full_model_info (pose::Pose &pose, pose::Pose const &pose1, pose::Pose const &pose2, Size const lower_merge_res, Size const upper_merge_res, bool const connect_residues_by_bond)

utility::vector1< Size >	merge_two_poses (pose::Pose &pose, pose::Pose const &pose1, pose::Pose const &pose2, utility::vector1< Size > const &working_res1, utility::vector1< Size > const &working_res2, Size const lower_merge_res, Size const upper_merge_res, bool const connect_residues_by_bond, bool const fix_first_pose)

utility::vector1< Size >	apply_numbering (utility::vector1< Size > const &res, utility::vector1< Size > const &numbering)

utility::vector1< Size >	get_other_residues (utility::vector1< Size > const &res, Size const &nres)

void	slice_out_pose (pose::Pose &pose, pose::Pose &sliced_out_pose, utility::vector1< Size > const &residues_to_delete)

void	slice (pose::Pose &sliced_out_pose, pose::Pose const &pose, utility::vector1< Size > const &slice_res)

Size	check_jump_to_previous_residue_in_chain (pose::Pose const &pose, Size const i, utility::vector1< Size > const &current_element, FullModelInfo const &full_model_info)

Size	check_jump_to_previous_residue_in_chain (pose::Pose const &pose, Size const i, utility::vector1< Size > const &current_element)

Size	check_jump_to_previous_residue_in_chain (pose::Pose const &pose, Size const i, utility::vector1< Size > const &current_element, utility::vector1< Size > const &res_list, utility::vector1< Size > const &chains_in_full_model)

Size	check_jump_to_next_residue_in_chain (pose::Pose const &pose, Size const i, utility::vector1< Size > const &current_element, FullModelInfo const &full_model_info)

Size	check_jump_to_next_residue_in_chain (pose::Pose const &pose, Size const i, utility::vector1< Size > const &current_element)

Size	check_jump_to_next_residue_in_chain (pose::Pose const &pose, Size const i, utility::vector1< Size > const &current_element, utility::vector1< Size > const &res_list, utility::vector1< Size > const &chains_in_full_model)

void	fix_up_residue_type_variants_at_strand_end (pose::Pose &pose, Size const res)

void	fix_up_residue_type_variants_at_strand_beginning (pose::Pose &pose, Size const res)

void	fix_up_residue_type_variants_at_floating_base (pose::Pose &pose, Size const res)

void	fix_up_residue_type_variants (pose::Pose &pose_to_fix)

void	fix_up_jump_atoms (pose::Pose &pose)

void	fix_up_jump_atoms_and_residue_type_variants (pose::Pose &pose_to_fix)

void	switch_focus_to_other_pose (pose::Pose &pose, Size const &focus_pose_idx)

bool	switch_focus_among_poses_randomly (pose::Pose &pose, scoring::ScoreFunctionOP scorefxn, bool force_switch)

void	test_merge_and_slice_with_two_helix_test_case (utility::vector1< core::pose::PoseOP > const &input_poses, core::scoring::ScoreFunctionOP scorefxn)

utility::vector1< Size >	figure_out_moving_chain_break_res (pose::Pose const &pose, kinematics::MoveMap const &mm)

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

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

bool	check_for_fixed_domain (pose::Pose const &pose)

void	make_variants_match (pose::Pose &pose, pose::Pose const &reference_pose, Size const &n, chemical::VariantType const variant_type)

utility::vector1< Size >	figure_out_moving_cutpoints_closed_from_moving_res (pose::Pose const &pose, Size const moving_res)

utility::vector1< Size >	figure_out_moving_cutpoints_closed (pose::Pose const &pose, utility::vector1< Size > moving_partition_pos)

void	figure_out_moving_chain_breaks (pose::Pose const &pose, utility::vector1< Size > moving_partition_pos, utility::vector1< Size > &cutpoints_closed, utility::vector1< Size > &five_prime_chain_breaks, utility::vector1< Size > &three_prime_chain_breaks, utility::vector1< Size > &chain_break_gap_sizes)

utility::vector1< bool >	get_partition_definition_by_jump (pose::Pose const &pose, Size const &jump_nr)

utility::vector1< bool >	get_partition_definition (pose::Pose const &pose, Size const &moving_suite)

Size	figure_out_reference_res_for_suite (pose::Pose const &pose, Size const moving_res)

utility::vector1< Size >	figure_out_moving_partition_res_for_suite (pose::Pose const &pose, Size const moving_res, Size const reference_res)

utility::vector1< Size >	figure_out_moving_partition_res_for_jump (pose::Pose const &pose, Size const jump_nr)

utility::vector1< Size >	figure_out_moving_partition_res (pose::Pose const &pose, Size const moving_res)

utility::vector1< Size >	figure_out_moving_partition_res (pose::Pose const &pose, utility::vector1< Size > const &moving_res_list)

utility::vector1< Size >	figure_out_root_partition_res (pose::Pose const &pose, utility::vector1< Size > const &moving_res_list)

void	figure_out_root_and_moving_partition_res (pose::Pose const &pose, Size const moving_res, utility::vector1< Size > &root_partition_res, utility::vector1< Size > &moving_partition_res)

bool	revise_root_and_moving_res (pose::Pose &pose, Size &moving_res)

bool	revise_root_and_moving_res_list (pose::Pose &pose, utility::vector1< Size > &moving_res_list)

Size	split_pose (pose::Pose &pose, Size const moving_res, Size const reference_res)

void	split_pose (pose::Pose &pose, utility::vector1< Size > const &moving_res_list)

void	fix_protein_jump_atom (pose::Pose &pose, Size const res, std::string const atom_name)

Typedef Documentation

typedef std::map< std::string, pose::PoseOP > protocols::stepwise::PoseList

typedef utility::pointer::owning_ptr< StepWiseSampleAndScreen const > protocols::stepwise::StepWiseSampleAndScreenCOP

typedef utility::pointer::owning_ptr< StepWiseSampleAndScreen > protocols::stepwise::StepWiseSampleAndScreenOP

Function Documentation

utility::vector1< Size > protocols::stepwise::apply_numbering	(	utility::vector1< Size > const &	res,
		utility::vector1< Size > const &	numbering
	)

References runtime_assert.

Referenced by slice_out_pose().

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

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

Referenced by protocols::stepwise::monte_carlo::SWA_MoveSelector::check_for_fixed_domain_or_from_scratch(), and protocols::stepwise::monte_carlo::rna::DeleteMover::decide_to_keep_pose().

bool protocols::stepwise::check_for_fixed_domain ( pose::Pose const & pose )

References core::pose::Pose::total_residue().

Size protocols::stepwise::check_jump_to_next_residue_in_chain	(	pose::Pose const &	pose,
		Size const	i,
		utility::vector1< Size > const &	current_element,
		FullModelInfo const &	full_model_info
	)

References core::pose::full_model_info::FullModelInfo::chains_in_full_model(), check_jump_to_next_residue_in_chain(), and get_res_list_from_full_model_info_const().

Referenced by protocols::stepwise::monte_carlo::SWA_MoveSelector::get_attachments(), and protocols::stepwise::sampling::rna::setup_job_parameters_legacy().

Size protocols::stepwise::check_jump_to_next_residue_in_chain	(	pose::Pose const &	pose,
		Size const	i,
		utility::vector1< Size > const &	current_element
	)

References check_jump_to_next_residue_in_chain(), and core::pose::Pose::total_residue().

Size protocols::stepwise::check_jump_to_next_residue_in_chain	(	pose::Pose const &	pose,
		Size const	i,
		utility::vector1< Size > const &	current_element,
		utility::vector1< Size > const &	res_list,
		utility::vector1< Size > const &	chains_in_full_model
	)

References core::pose::Pose::fold_tree(), utility::vector1< T, class >::has_value(), core::kinematics::FoldTree::jump_nr(), and core::pose::Pose::total_residue().

Referenced by check_jump_to_next_residue_in_chain(), and slice().

Size protocols::stepwise::check_jump_to_previous_residue_in_chain	(	pose::Pose const &	pose,
		Size const	i,
		utility::vector1< Size > const &	current_element,
		FullModelInfo const &	full_model_info
	)

References core::pose::full_model_info::FullModelInfo::chains_in_full_model(), check_jump_to_previous_residue_in_chain(), and get_res_list_from_full_model_info_const().

Referenced by protocols::stepwise::monte_carlo::SWA_MoveSelector::get_attachments(), and protocols::stepwise::sampling::rna::setup_job_parameters_legacy().

Size protocols::stepwise::check_jump_to_previous_residue_in_chain	(	pose::Pose const &	pose,
		Size const	i,
		utility::vector1< Size > const &	current_element
	)

References check_jump_to_previous_residue_in_chain(), and core::pose::Pose::total_residue().

Size protocols::stepwise::check_jump_to_previous_residue_in_chain	(	pose::Pose const &	pose,
		Size const	i,
		utility::vector1< Size > const &	current_element,
		utility::vector1< Size > const &	res_list,
		utility::vector1< Size > const &	chains_in_full_model
	)

References core::pose::Pose::fold_tree(), utility::vector1< T, class >::has_value(), and core::kinematics::FoldTree::jump_nr().

Referenced by check_jump_to_previous_residue_in_chain(), and slice().

void protocols::stepwise::check_scorefxn_has_constraint_terms_if_pose_has_constraints	(	pose::Pose const &	pose,
		core::scoring::ScoreFunctionOP &	scorefxn
	)

References atom_pair_constraint, core::pose::Pose::constraint_set(), coordinate_constraint, and utility_exit_with_message.

Referenced by protocols::stepwise::sampling::protein::StepWiseProteinModeler::do_minimizing(), and protocols::stepwise::sampling::protein::StepWiseProteinResidueSampler::get_packer().

scoring::constraints::ConstraintSetOP protocols::stepwise::constraint_set_slice	(	core::scoring::constraints::ConstraintSetOP &	cst_set,
		utility::vector1< core::Size > const &	slice_res,
		pose::Pose const &	pose,
		pose::Pose const &	full_pose
	)

References core::scoring::constraints::ConstraintSet::add_constraint(), cst, core::scoring::constraints::ConstraintSet::get_all_constraints(), and core::pose::Pose::total_residue().

Referenced by protocols::stepwise::sampling::protein::StepWisePoseSetup::setup_constraints().

utility::vector1< Size > const protocols::stepwise::convert_to_working_res	(	utility::vector1< Size > const &	res_vector,
		utility::vector1< Size > const &	working_res
	)

References full_to_sub().

id::AtomID_Map< id::AtomID > protocols::stepwise::create_alignment_id_map	(	pose::Pose const &	mod_pose,
		pose::Pose const &	ref_pose,
		utility::vector1< core::Size > const &	superimpose_res
	)

References create_alignment_id_map(), utility::vector1< T, class >::has_value(), and core::pose::Pose::total_residue().

Referenced by protocols::farna::RNA_DeNovoProtocol::align_and_output_to_silent_file(), protocols::stepwise::sampling::protein::StepWisePoseSetup::align_poses(), protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker::align_VDW_rep_screen_pose(), and protocols::stepwise::sampling::protein::InputStreamWithResidueInfo::apply_current_pose_segment().

id::AtomID_Map< id::AtomID > protocols::stepwise::create_alignment_id_map	(	pose::Pose const &	mod_pose,
		pose::Pose const &	ref_pose,
		std::map< core::Size, core::Size >	res_map
	)

References BOGUS_ATOM_ID, chemical, core::pose::initialize_atomid_map(), core::conformation::Residue::is_protein(), core::conformation::Residue::is_RNA(), core::pose::Pose::residue(), protocols::stepwise::sampling::protein::setup_protein_backbone_atom_id_map(), protocols::stepwise::sampling::rna::setup_suite_atom_id_map(), and core::pose::Pose::total_residue().

Referenced by create_alignment_id_map(), and superimpose_pose().

void protocols::stepwise::create_euler_rotation	(	Matrix &	M,
		Real const &	alpha,
		Real const &	beta,
		Real const &	gamma,
		Vector const &	,
		Vector const &	axis2,
		Vector const &	axis3
	)

References radians(), and numeric::rotation_matrix().

Referenced by protocols::stepwise::sampling::legacy::RigidBodySampler::apply_rigid_body_settings(), and protocols::stepwise::sampling::legacy::RigidBodySampler::search_rotations_and_translations().

void protocols::stepwise::create_euler_rotation	(	Matrix &	M,
		Real const &	alpha,
		Real const &	beta,
		Real const &	gamma
	)

Referenced by get_euler_angles().

bool protocols::stepwise::definite_terminal_root	(	pose::Pose const &	pose,
		Size const	i
	)

References const_full_model_info().

Referenced by reroot_based_on_full_model_info(), and try_reroot_at_fixed_domain().

utility::vector1< Size > protocols::stepwise::figure_out_moving_chain_break_res	(	pose::Pose const &	pose,
		kinematics::MoveMap const &	mm
	)

References core::id::BB, cutpoint_closed, core::pose::Pose::fold_tree(), core::kinematics::MoveMap::get(), get_cutpoint_closed(), utility::vector1< T, class >::has_value(), core::kinematics::FoldTree::is_cutpoint(), core::kinematics::FoldTree::partition_by_residue(), and core::pose::Pose::total_residue().

Referenced by protocols::farna::RNA_Minimizer::apply(), and protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::apply().

void protocols::stepwise::figure_out_moving_chain_breaks	(	pose::Pose const &	pose,
		utility::vector1< Size >	moving_partition_pos,
		utility::vector1< Size > &	cutpoints_closed,
		utility::vector1< Size > &	five_prime_chain_breaks,
		utility::vector1< Size > &	three_prime_chain_breaks,
		utility::vector1< Size > &	chain_break_gap_sizes
	)

References core::conformation::Residue::aa(), core::chemical::aa_vrt, figure_out_chains_from_full_model_info_const(), core::pose::Pose::fold_tree(), get_res_list_from_full_model_info_const(), utility::vector1< T, class >::has_value(), core::chemical::ResidueType::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), runtime_assert, and core::pose::Pose::total_residue().

Referenced by figure_out_moving_cutpoints_closed(), protocols::stepwise::sampling::rna::connection::StepWiseRNA_ConnectionSampler::initialize_poses_and_checkers(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodyConnectionSampler::initialize_poses_and_stubs_and_checkers(), and protocols::stepwise::sampling::rna::setup_job_parameters_explicit().

utility::vector1< Size > protocols::stepwise::figure_out_moving_cutpoints_closed	(	pose::Pose const &	pose,
		utility::vector1< Size >	moving_partition_pos
	)

References figure_out_moving_chain_breaks().

Referenced by protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::do_the_sampling(), and figure_out_moving_cutpoints_closed_from_moving_res().

utility::vector1< Size > protocols::stepwise::figure_out_moving_cutpoints_closed_from_moving_res	(	pose::Pose const &	pose,
		Size const	moving_res
	)

References figure_out_moving_cutpoints_closed(), and figure_out_moving_partition_res().

Referenced by protocols::stepwise::sampling::protein::StepWiseProteinModeler::figure_out_protein_moving_res_list_from_most_distal_res().

utility::vector1< Size > protocols::stepwise::figure_out_moving_partition_res	(	pose::Pose const &	pose,
		Size const	moving_res
	)

References figure_out_root_and_moving_partition_res().

Referenced by protocols::stepwise::sampling::protein::StepWiseProteinResidueSampler::initialize_screeners().

utility::vector1< Size > protocols::stepwise::figure_out_moving_partition_res	(	pose::Pose const &	pose,
		utility::vector1< Size > const &	moving_res_list
	)

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

Referenced by figure_out_moving_cutpoints_closed_from_moving_res(), and figure_out_root_partition_res().

utility::vector1< Size > protocols::stepwise::figure_out_moving_partition_res_for_jump	(	pose::Pose const &	pose,
		Size const	jump_nr
	)

References core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), get_partition_definition_by_jump(), and core::pose::Pose::total_residue().

Referenced by protocols::stepwise::sampling::rna::phosphate::MultiPhosphateSampler::initialize_by_prepack().

utility::vector1< Size > protocols::stepwise::figure_out_moving_partition_res_for_suite	(	pose::Pose const &	pose,
		Size const	moving_res,
		Size const	reference_res
	)

References get_partition_definition(), and core::pose::Pose::total_residue().

Referenced by protocols::stepwise::sampling::rna::connection::StepWiseRNA_ConnectionSampler::figure_out_reference_res().

void protocols::stepwise::figure_out_moving_residues	(	core::kinematics::MoveMap &	mm,
		core::pose::Pose const &	pose,
		utility::vector1< core::Size > const &	fixed_res,
		bool const	move_takeoff_torsions,
		bool const	move_jumps_between_chains
	)

References core::id::BB, core::id::CHI, core::pose::Pose::conformation(), core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), core::conformation::Conformation::get_torsion_angle_atom_ids(), core::chemical::ResidueType::has_variant_type(), core::conformation::Residue::has_variant_type(), core::chemical::ResidueType::is_lower_terminus(), core::conformation::Residue::mainchain_torsions(), core::chemical::N_ACETYLATION, core::conformation::Residue::nchi(), nres, core::kinematics::FoldTree::num_jump(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::id::AtomID::rsd(), core::kinematics::MoveMap::set(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), core::kinematics::MoveMap::set_jump(), core::pose::Pose::total_residue(), TR, and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by protocols::stepwise::sampling::protein::StepWiseProteinPoseMinimizer::apply().

Size protocols::stepwise::figure_out_reference_res_for_suite	(	pose::Pose const &	pose,
		Size const	moving_res
	)

References core::pose::Pose::fold_tree(), core::kinematics::FoldTree::get_parent_residue(), and runtime_assert.

Referenced by protocols::stepwise::sampling::rna::connection::StepWiseRNA_ConnectionSampler::figure_out_reference_res().

void protocols::stepwise::figure_out_root_and_moving_partition_res	(	pose::Pose const &	pose,
		Size const	moving_res,
		utility::vector1< Size > &	root_partition_res,
		utility::vector1< Size > &	moving_partition_res
	)

References core::pose::Pose::fold_tree(), core::kinematics::FoldTree::get_parent_residue(), get_partition_definition(), get_partition_definition_by_jump(), core::kinematics::FoldTree::jump_nr(), jump_nr, runtime_assert, and core::pose::Pose::total_residue().

Referenced by figure_out_moving_partition_res(), revise_root_and_moving_res(), and protocols::stepwise::monte_carlo::rna::ResampleMover::slide_jump_randomly().

utility::vector1< Size > protocols::stepwise::figure_out_root_partition_res	(	pose::Pose const &	pose,
		utility::vector1< Size > const &	moving_res_list
	)

References figure_out_moving_partition_res(), utility::vector1< T, class >::has_value(), and core::pose::Pose::total_residue().

Referenced by protocols::stepwise::sampling::protein::StepWiseProteinModeler::align_pose_and_add_rmsd_constraints().

Size protocols::stepwise::find_first_root_residue	(	kinematics::FoldTree const &	f,
		utility::vector1< Size > const &	working_res_subset,
		utility::vector1< Size > const &	working_res
	)

References utility::vector1< T, class >::has_value(), core::kinematics::FoldTree::nres(), core::kinematics::FoldTree::possible_root(), and runtime_assert.

Referenced by merge_two_poses().

Size protocols::stepwise::find_jump_number_at_suite	(	kinematics::FoldTree const &	fold_tree,
		Size const &	moving_suite
	)

References core::kinematics::FoldTree::downstream_jump_residue(), j, core::kinematics::FoldTree::num_jump(), core::kinematics::FoldTree::upstream_jump_residue(), and utility_exit_with_message.

Referenced by make_cut_at_moving_suite().

bool protocols::stepwise::find_root_without_virtual_ribose	(	kinematics::FoldTree const &	f,
		pose::Pose const &	pose
	)

References core::chemical::ResidueType::has_variant_type(), core::kinematics::FoldTree::nres(), core::kinematics::FoldTree::possible_root(), core::pose::Pose::residue_type(), and utility_exit_with_message.

void protocols::stepwise::fix_protein_jump_atom	(	pose::Pose &	pose,
		Size const	res,
		std::string const	atom_name
	)

References core::pose::Pose::fold_tree(), core::chemical::ResidueType::is_protein(), core::pose::Pose::residue_type(), and core::kinematics::FoldTree::set_jump_atoms().

Referenced by protocols::stepwise::sampling::protein::StepWiseProteinCCD_Closer::fix_jump_atoms_at_loop_boundaries().

void protocols::stepwise::fix_up_jump_atoms ( pose::Pose & pose )

References core::pose::Pose::fold_tree(), and core::kinematics::FoldTree::reassign_atoms_for_intra_residue_stubs().

Referenced by fix_up_jump_atoms_and_residue_type_variants().

void protocols::stepwise::fix_up_jump_atoms_and_residue_type_variants ( pose::Pose & pose_to_fix )

References fix_up_jump_atoms(), and fix_up_residue_type_variants().

Referenced by protocols::stepwise::monte_carlo::rna::FromScratchMover::apply(), protocols::stepwise::monte_carlo::rna::DeleteMover::apply(), and protocols::stepwise::monte_carlo::rna::AddMover::apply().

void protocols::stepwise::fix_up_residue_type_variants ( pose::Pose & pose_to_fix )

References core::pose::Pose::conformation(), CUTPOINT_LOWER, CUTPOINT_UPPER, fix_up_residue_type_variants_at_floating_base(), fix_up_residue_type_variants_at_strand_beginning(), fix_up_residue_type_variants_at_strand_end(), LOWER_TERMINUS, core::pose::Pose::pdb_info(), remove_variant_type_from_pose_residue(), runtime_assert, UPPER_TERMINUS, and VIRTUAL_PHOSPHATE.

Referenced by fix_up_jump_atoms_and_residue_type_variants(), and protocols::stepwise::monte_carlo::rna::StepWiseMonteCarlo::preminimize_pose().

void protocols::stepwise::fix_up_residue_type_variants_at_floating_base	(	pose::Pose &	pose,
		Size const	res
	)

References add_variant_type_to_pose_residue(), const_full_model_info(), core::pose::full_model_info::FullModelInfo::cutpoint_open_in_full_model(), core::pose::full_model_info::FullModelInfo::fixed_domain_map(), get_res_list_from_full_model_info(), utility::vector1< T, class >::has_value(), core::chemical::ResidueType::has_variant_type(), core::conformation::Residue::is_RNA(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), and core::pose::Pose::total_residue().

Referenced by fix_up_residue_type_variants().

void protocols::stepwise::fix_up_residue_type_variants_at_strand_beginning	(	pose::Pose &	pose,
		Size const	res
	)

References add_variant_type_to_pose_residue(), const_full_model_info(), core::pose::rna::correctly_add_cutpoint_variants(), CUTPOINT_UPPER, get_chains_full(), get_res_list_from_full_model_info(), core::chemical::ResidueType::has_variant_type(), core::chemical::ResidueType::is_protein(), core::chemical::ResidueType::is_RNA(), LOWER_TERMINUS, remove_variant_type_from_pose_residue(), core::pose::Pose::residue_type(), and TR.

Referenced by fix_up_residue_type_variants().

void protocols::stepwise::fix_up_residue_type_variants_at_strand_end	(	pose::Pose &	pose,
		Size const	res
	)

References add_variant_type_to_pose_residue(), const_full_model_info(), core::pose::rna::correctly_add_cutpoint_variants(), CUTPOINT_LOWER, get_chains_full(), get_res_list_from_full_model_info(), core::chemical::ResidueType::is_protein(), remove_variant_type_from_pose_residue(), core::pose::Pose::residue_type(), core::pose::Pose::total_residue(), TR, and UPPER_TERMINUS.

Referenced by fix_up_residue_type_variants().

void protocols::stepwise::get_base_centroid_and_rotation_matrix	(	pose::Pose const &	pose,
		Size const	i,
		Vector &	centroid,
		Matrix &	M
	)

References core::pose::Pose::residue(), and s.

Referenced by translate_and_rotate_residue_to_origin().

utility::vector1< Size > protocols::stepwise::get_cutpoint_closed ( pose::Pose const & pose )

References cutpoint_closed, is_cutpoint_closed(), and core::pose::Pose::total_residue().

Referenced by figure_out_moving_chain_break_res().

void protocols::stepwise::get_endpoints_from_pose	(	utility::vector1< Size > &	endpoints,
		pose::Pose const &	pose,
		utility::vector1< Size > const &	working_res
	)

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

Referenced by merge_two_poses().

void protocols::stepwise::get_euler_angles	(	Real &	alpha,
		Real &	beta,
		Real &	gamma,
		Matrix	M1,
		Matrix	M2,
		bool const	verbose
	)

References numeric::xyzMatrix< class >::col_x(), numeric::xyzMatrix< class >::col_y(), numeric::xyzMatrix< class >::col_z(), create_euler_rotation(), degrees(), rotation_matrix(), and numeric::xyzMatrix< class >::transposed().

std::string protocols::stepwise::get_file_name	(	std::string const &	silent_file,
		std::string const &	tag
	)

References runtime_assert.

Referenced by protocols::stepwise::sampling::protein::StepWiseProteinModeler::do_minimizing(), protocols::rotamer_sampler::protein::generate_beta_database_test(), and protocols::stepwise::sampling::protein::StepWiseProteinResidueSampler::get_basic_sampler().

void protocols::stepwise::get_jump_partners_from_pose	(	utility::vector1< Size > &	jump_partners1,
		utility::vector1< Size > &	jump_partners2,
		utility::vector1< std::string > &	jump_atoms1,
		utility::vector1< std::string > &	jump_atoms2,
		pose::Pose const &	pose,
		utility::vector1< Size > const &	working_res
	)

References core::pose::Pose::fold_tree(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by merge_two_poses().

Size protocols::stepwise::get_number_missing_residue_connections ( pose::Pose & pose )

References const_full_model_info(), cutpoint_open, core::pose::full_model_info::FullModelInfo::cutpoint_open_in_full_model(), figure_out_pose_domain_map(), core::pose::full_model_info::FullModelInfo::fixed_domain_map(), and nres.

Referenced by protocols::stepwise::monte_carlo::output_to_silent_file().

utility::vector1< Size > protocols::stepwise::get_other_residues	(	utility::vector1< Size > const &	res,
		Size const &	nres
	)

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

Referenced by revise_root_and_moving_res_list(), and slice_out_pose().

utility::vector1< bool > protocols::stepwise::get_partition_definition	(	pose::Pose const &	pose,
		Size const &	moving_suite
	)

References core::pose::Pose::fold_tree(), core::kinematics::FoldTree::partition_by_residue(), and core::pose::Pose::total_residue().

Referenced by figure_out_moving_partition_res_for_suite(), figure_out_root_and_moving_partition_res(), protocols::stepwise::monte_carlo::SWA_MoveSelector::get_intramolecular_split_move_elements(), protocols::stepwise::sampling::rna::setup_job_parameters_explicit(), and protocols::stepwise::sampling::rna::setup_job_parameters_legacy().

utility::vector1< bool > protocols::stepwise::get_partition_definition_by_jump	(	pose::Pose const &	pose,
		Size const &	jump_nr
	)

References core::pose::Pose::fold_tree(), core::kinematics::FoldTree::partition_by_jump(), and core::pose::Pose::total_residue().

Referenced by figure_out_moving_partition_res_for_jump(), figure_out_root_and_moving_partition_res(), protocols::stepwise::monte_carlo::SWA_MoveSelector::get_intermolecular_split_move_elements(), protocols::stepwise::monte_carlo::SWA_MoveSelector::get_intramolecular_split_move_elements(), and protocols::stepwise::sampling::rna::get_partition_definition_floating_base().

std::map< Size, Size > protocols::stepwise::get_res_map	(	utility::vector1< Size > const &	working_res,
		utility::vector1< Size > const &	source_res
	)

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

Referenced by protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::initialize_rigid_body_sampler(), and merge_two_poses().

bool protocols::stepwise::is_at_terminus	(	core::pose::Pose const &	pose,
		Size const	i
	)

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

bool protocols::stepwise::is_close_chain_break ( pose::Pose const & pose )

References is_cutpoint_closed(), and core::pose::Pose::total_residue().

Referenced by protocols::stepwise::sampling::protein::StepWisePoseSetup::check_close_chain_break().

bool protocols::stepwise::is_cutpoint_closed	(	pose::Pose const &	pose,
		Size const	seq_num
	)

References core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::conformation::Residue::has_variant_type(), core::pose::Pose::residue(), runtime_assert, and core::pose::Pose::total_residue().

Referenced by protocols::stepwise::sampling::rna::apply_virtual_rna_residue_variant_type(), protocols::stepwise::sampling::rna::figure_out_rebuild_bulge_mode(), get_cutpoint_closed(), is_close_chain_break(), and protocols::stepwise::sampling::rna::remove_chain_break_variants().

utility::vector1< std::string > protocols::stepwise::load_s_and_l ( )

References filename(), getline(), in::file::l, in::file::list, basic::options::option, option, in::file::s, and utility_exit_with_message.

Referenced by protocols::rotamer_sampler::protein::generate_beta_database_test().

Size protocols::stepwise::look_for_unique_jump_to_moving_res	(	kinematics::FoldTree const &	fold_tree,
		Size const &	i
	)

References core::kinematics::FoldTree::downstream_jump_residue(), core::kinematics::FoldTree::num_jump(), runtime_assert, and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by protocols::rotamer_sampler::rigid_body::RigidBodyRotamer::calculate_jump(), protocols::stepwise::sampling::rna::get_anchor_res(), and protocols::stepwise::sampling::rna::get_partition_definition_floating_base().

Size protocols::stepwise::make_cut_at_moving_suite	(	core::kinematics::FoldTree &	fold_tree,
		Size const &	moving_suite
	)

References find_jump_number_at_suite(), and core::kinematics::FoldTree::new_jump().

Size protocols::stepwise::make_cut_at_moving_suite	(	pose::Pose &	pose,
		Size const &	moving_suite
	)

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

Referenced by split_pose().

void protocols::stepwise::make_variants_match	(	pose::Pose &	pose,
		pose::Pose const &	reference_pose,
		Size const &	n,
		chemical::VariantType const	variant_type
	)

References add_variant_type_to_pose_residue(), core::conformation::Residue::has_variant_type(), remove_variant_type_from_pose_residue(), and core::pose::Pose::residue().

Referenced by protocols::stepwise::sampling::rna::phosphate::copy_over_phosphate_variants(), protocols::stepwise::sampling::protein::StepWiseProteinPacker::do_prepack(), and protocols::stepwise::sampling::protein::StepWiseProteinPacker::reinstate_side_chain_angles().

utility::vector1< Size > protocols::stepwise::map_to_local_numbering	(	utility::vector1< Size > const &	vec,
		utility::vector1< Size > const &	working_res
	)

References utility::vector1< T, class >::index().

Referenced by merge_two_poses().

utility::vector1< Size > protocols::stepwise::merge_disjoint_vectors	(	utility::vector1< Size > const &	res_vector1,
		utility::vector1< Size > const &	res_vector2
	)

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

Referenced by merge_two_poses().

void protocols::stepwise::merge_in_other_pose	(	pose::Pose &	pose,
		pose::Pose const &	pose2,
		Size const	lower_merge_res,
		Size const	upper_merge_res,
		bool const	connect_residues_by_bond
	)

References core::pose::Pose::conformation(), merge_two_poses_using_full_model_info(), nonconst_full_model_info(), runtime_assert, and update_pdb_info_from_full_model_info().

Referenced by merge_in_other_pose_by_bond(), and merge_in_other_pose_by_jump().

void protocols::stepwise::merge_in_other_pose_by_bond	(	pose::Pose &	pose,
		pose::Pose const &	pose2,
		Size const	merge_res
	)

References merge_in_other_pose().

Referenced by protocols::stepwise::monte_carlo::rna::AddMover::append_other_pose(), and protocols::stepwise::monte_carlo::rna::AddMover::prepend_other_pose().

void protocols::stepwise::merge_in_other_pose_by_jump	(	pose::Pose &	pose,
		pose::Pose const &	pose2,
		Size const	lower_merge_res,
		Size const	upper_merge_res
	)

References merge_in_other_pose(), and runtime_assert.

Referenced by protocols::stepwise::monte_carlo::rna::AddMover::append_other_pose(), and protocols::stepwise::monte_carlo::rna::AddMover::prepend_other_pose().

utility::vector1< Size > protocols::stepwise::merge_two_poses	(	pose::Pose &	pose,
		pose::Pose const &	pose1,
		pose::Pose const &	pose2,
		utility::vector1< Size > const &	working_res1,
		utility::vector1< Size > const &	working_res2,
		Size const	lower_merge_res,
		Size const	upper_merge_res,
		bool const	connect_residues_by_bond,
		bool const	fix_first_pose
	)

utility::vector1< Size > protocols::stepwise::merge_two_poses_using_full_model_info	(	pose::Pose &	pose,
		pose::Pose const &	pose1,
		pose::Pose const &	pose2,
		Size const	lower_merge_res,
		Size const	upper_merge_res,
		bool const	connect_residues_by_bond
	)

References get_res_list_from_full_model_info_const(), merge_two_poses(), and runtime_assert.

Referenced by merge_in_other_pose(), and test_merge_and_slice_with_two_helix_test_case().

utility::vector1< Size > protocols::stepwise::merge_vectors	(	utility::vector1< Size > const &	vec1,
		utility::vector1< Size > const &	vec2
	)

Referenced by protocols::stepwise::sampling::protein::StepWiseProteinResidueSampler::close_loops_in_samples().

void protocols::stepwise::output_boolean	(	std::string const &	tag,
		bool	boolean,
		std::ostream &	TR
	)

void protocols::stepwise::output_boolean	(	bool	boolean,
		std::ostream &	TR
	)

Referenced by output_movemap().

void protocols::stepwise::output_movemap	(	kinematics::MoveMap const &	mm,
		Size const	total_residue,
		std::ostream &	TR
	)

References core::id::BB, core::id::CHI, core::kinematics::MoveMap::get(), protocols::abinitio::abscript::I, output_boolean(), and TR.

void protocols::stepwise::pdbslice	(	core::pose::Pose &	new_pose,
		core::pose::Pose const &	pose,
		utility::vector1< core::Size > const &	slice_res
	)

References core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), chi1_torsion_atom(), core::pose::Pose::clear(), core::conformation::Residue::clone(), core::pose::Pose::fold_tree(), core::conformation::Residue::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_RNA(), core::chemical::ResidueType::is_RNA(), core::pose::Pose::residue(), and core::pose::Pose::residue_type().

Referenced by protocols::stepwise::sampling::general::StepWiseClusterer::do_some_clustering(), protocols::stepwise::sampling::general::StepWiseClustererSilentBased::do_some_clustering(), protocols::stepwise::sampling::protein::StepWisePoseSetup::make_pose(), and protocols::stepwise::sampling::protein::setup_job_parameters_for_protein_swa().

void protocols::stepwise::pdbslice	(	core::pose::Pose &	pose,
		utility::vector1< core::Size > const &	slice_res
	)

Size protocols::stepwise::primary_fixed_domain	(	pose::Pose const &	pose,
		utility::vector1< Size > const &	partition_res
	)

References d_min, and core::pose::full_model_info::get_fixed_domain_from_full_model_info_const().

Referenced by revise_root_and_moving_res().

void protocols::stepwise::remove_lower_terminus ( core::conformation::ResidueOP & rsd )

References chemical, core::conformation::Residue::has_variant_type(), LOWER_TERMINUS, core::conformation::Residue::residue_type_set(), and core::conformation::Residue::type().

Referenced by merge_two_poses(), and slice().

void protocols::stepwise::remove_upper_terminus ( core::conformation::ResidueOP & rsd )

References chemical, core::conformation::Residue::has_variant_type(), core::conformation::Residue::residue_type_set(), core::conformation::Residue::type(), and UPPER_TERMINUS.

Referenced by merge_two_poses(), and slice().

void protocols::stepwise::reroot_based_on_full_model_info	(	pose::Pose &	pose,
		utility::vector1< Size > const &	root_partition_res
	)

References definite_terminal_root(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::possible_root(), protocols::farna::possible_root(), core::kinematics::FoldTree::reorder(), and runtime_assert.

Referenced by revise_root_and_moving_res(), and revise_root_and_moving_res_list().

bool protocols::stepwise::revise_root_and_moving_res	(	pose::Pose &	pose,
		Size &	moving_res
	)

References figure_out_root_and_moving_partition_res(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::get_parent_residue(), primary_fixed_domain(), reroot_based_on_full_model_info(), and runtime_assert.

Referenced by protocols::stepwise::sampling::rna::StepWiseRNA_Modeler::initialize_job_parameters_and_root(), and revise_root_and_moving_res_list().

bool protocols::stepwise::revise_root_and_moving_res_list	(	pose::Pose &	pose,
		utility::vector1< Size > &	moving_res_list
	)

References core::pose::Pose::fold_tree(), get_other_residues(), core::kinematics::FoldTree::get_parent_residue(), utility::vector1< T, class >::has_value(), core::kinematics::FoldTree::jump_nr(), utility::tools::make_vector1(), reroot_based_on_full_model_info(), revise_root_and_moving_res(), core::kinematics::FoldTree::root(), runtime_assert, and core::pose::Pose::total_residue().

Referenced by protocols::stepwise::sampling::protein::StepWiseProteinModeler::initialize_job_parameters_and_root().

void protocols::stepwise::rotate	(	pose::Pose &	pose,
		Matrix const	M,
		pose::Pose const &	ref_pose,
		utility::vector1< Size > const &	moving_res,
		Vector const &	centroid
	)

References core::chemical::ResidueType::natoms(), core::pose::Pose::residue_type(), core::pose::Pose::set_xyz(), and core::pose::Pose::xyz().

Referenced by protocols::ligand_docking::Rotates::apply(), protocols::stepwise::sampling::legacy::RigidBodySampler::apply_rigid_body_settings(), and protocols::stepwise::sampling::legacy::RigidBodySampler::search_rotations_and_translations().

void protocols::stepwise::rotate	(	pose::Pose &	pose,
		Matrix const	M,
		pose::Pose const &	ref_pose,
		utility::vector1< Size > const &	moving_res
	)

References centroid.

Referenced by translate_and_rotate_residue_to_origin().

void protocols::stepwise::slice	(	pose::Pose &	sliced_out_pose,
		pose::Pose const &	pose,
		utility::vector1< Size > const &	slice_res
	)

void protocols::stepwise::slice_out_pose	(	pose::Pose &	pose,
		pose::Pose &	sliced_out_pose,
		utility::vector1< Size > const &	residues_to_delete
	)

References apply_numbering(), core::pose::Pose::conformation(), core::pose::Pose::data(), core::pose::datacache::CacheableDataType::FULL_MODEL_INFO, get_other_residues(), nonconst_full_model_info(), basic::datacache::BasicDataCache::set(), slice(), core::pose::Pose::total_residue(), and update_pdb_info_from_full_model_info().

Referenced by protocols::stepwise::monte_carlo::rna::DeleteMover::apply(), and test_merge_and_slice_with_two_helix_test_case().

Size protocols::stepwise::split_pose	(	pose::Pose &	pose,
		Size const	moving_res,
		Size const	reference_res
	)

References add_variant_type_to_pose_residue(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::is_cutpoint(), core::chemical::ResidueType::is_RNA(), j, core::pose::Pose::jump(), core::kinematics::FoldTree::jump_nr(), make_cut_at_moving_suite(), core::pose::Pose::residue_type(), runtime_assert, core::pose::Pose::set_jump(), core::kinematics::Jump::set_translation(), and core::chemical::VIRTUAL_PHOSPHATE.

Referenced by protocols::simple_filters::InterfaceSasaFilter::compute(), protocols::simple_filters::DdgFilter::compute(), protocols::stepwise::sampling::protein::StepWiseProteinPacker::do_prepack(), protocols::stepwise::sampling::protein::checker::ProteinAtrRepChecker::get_base_atr_rep_score(), protocols::stepwise::sampling::rna::checker::AtrRepChecker::get_base_atr_rep_score(), protocols::stepwise::sampling::rna::phosphate::MultiPhosphateSampler::initialize_by_prepack(), and protocols::optimize_weights::IterativeOptEDriver::score_ligand_interface().

void protocols::stepwise::split_pose	(	pose::Pose &	pose,
		utility::vector1< Size > const &	moving_res_list
	)

References core::pose::Pose::fold_tree(), and core::kinematics::FoldTree::get_parent_residue().

void protocols::stepwise::superimpose_at_fixed_res	(	pose::Pose &	pose,
		pose::Pose const &	native_pose,
		Real &	rmsd,
		Size &	natoms_rmsd,
		bool	skip_bulges
	)

References protocols::stepwise::sampling::general::StepWisePoseAligner::apply(), protocols::stepwise::sampling::general::StepWisePoseAligner::natoms_rmsd(), protocols::stepwise::sampling::general::StepWisePoseAligner::rmsd(), and protocols::stepwise::sampling::general::StepWisePoseAligner::set_skip_bulges().

Referenced by superimpose_at_fixed_res_and_get_all_atom_rmsd(), and superimpose_recursively().

Real protocols::stepwise::superimpose_at_fixed_res_and_get_all_atom_rmsd	(	pose::Pose &	pose,
		pose::Pose const &	native_pose,
		bool	skip_bulges
	)

References rmsd, and superimpose_at_fixed_res().

Real protocols::stepwise::superimpose_pose	(	pose::Pose &	mod_pose,
		pose::Pose const &	ref_pose,
		std::map< Size, Size > const &	res_map
	)

Superimpose mod_pose onto ref_pose using the mapping of residues from mod_pose to ref_pose given by res_map. Simple wrapper around superimpose_pose using IDs.

Superimpose mod_pose onto ref_pose using the mapping of residues from mod_pose to ref_pose given by res_map.

References create_alignment_id_map(), and core::scoring::superimpose_pose().

Referenced by protocols::antibody::GraftOneCDRLoop::apply(), protocols::comparative_modeling::ExtraThreadingMover::apply(), protocols::antibody_legacy::GraftOneMover::apply(), protocols::stepwise::sampling::protein::InputStreamWithResidueInfo::apply_current_pose_segment(), merge_two_poses(), slice(), protocols::stepwise::sampling::general::StepWisePoseAligner::superimpose_at_fixed_res(), protocols::grafting::GraftMoverBase::superimpose_overhangs_heavy(), and protocols::fibril::superimpose_pose_on_subset_bb().

void protocols::stepwise::superimpose_recursively	(	pose::Pose &	pose,
		pose::Pose const &	native_pose,
		Real &	rmsd,
		Size &	natoms,
		bool	skip_bulges = `false`
	)

References nonconst_full_model_info(), core::pose::full_model_info::FullModelInfo::other_pose_list(), runtime_assert, superimpose_at_fixed_res(), and superimpose_recursively().

Referenced by protocols::stepwise::monte_carlo::output_to_silent_file().

Real protocols::stepwise::superimpose_recursively	(	pose::Pose &	pose,
		pose::Pose const &	native_pose
	)

References rmsd.

Referenced by superimpose_recursively().

bool protocols::stepwise::switch_focus_among_poses_randomly	(	pose::Pose &	pose,
		scoring::ScoreFunctionOP	scorefxn,
		bool	force_switch
	)

References const_full_model_info(), core::pose::full_model_info::FullModelInfo::other_pose_list(), numeric::random::RandomGenerator::random_range(), RG, runtime_assert, switch_focus_to_other_pose(), TR, and utility_exit_with_message.

Referenced by protocols::stepwise::monte_carlo::rna::StepWiseMonteCarlo::do_main_loop(), and protocols::stepwise::monte_carlo::rna::DeleteMover::remove_singletons_and_update_pose_focus().

void protocols::stepwise::switch_focus_to_other_pose	(	pose::Pose &	pose,
		Size const &	focus_pose_idx
	)

References core::pose::Pose::clone(), clone(), core::pose::full_model_info::FullModelInfo::clone_info(), const_full_model_info(), core::pose::Pose::data(), core::pose::datacache::CacheableDataType::FULL_MODEL_INFO, nonconst_full_model_info(), other_pose, core::pose::full_model_info::FullModelInfo::other_pose_list(), runtime_assert, basic::datacache::BasicDataCache::set(), and core::pose::full_model_info::FullModelInfo::set_other_pose_list().

Referenced by protocols::stepwise::monte_carlo::rna::DeleteMover::apply(), protocols::stepwise::monte_carlo::rna::DeleteMover::remove_singletons_and_update_pose_focus(), and switch_focus_among_poses_randomly().

void protocols::stepwise::test_merge_and_slice_with_two_helix_test_case	(	utility::vector1< core::pose::PoseOP > const &	input_poses,
		core::scoring::ScoreFunctionOP	scorefxn
	)

References const_full_model_info(), merge_two_poses_using_full_model_info(), core::pose::full_model_info::FullModelInfo::res_list(), and slice_out_pose().

void protocols::stepwise::translate	(	pose::Pose &	pose,
		Vector const	shift,
		pose::Pose const &	ref_pose,
		utility::vector1< Size > const &	moving_res
	)

References core::chemical::ResidueType::natoms(), core::pose::Pose::residue_type(), core::pose::Pose::set_xyz(), and core::pose::Pose::xyz().

Referenced by protocols::protein_interface_design::movers::PrepackMover::apply(), protocols::toolbox::task_operations::SelectBySASAOperation::apply(), protocols::ligand_docking::CompoundTranslate::apply(), protocols::ncbb::NcbbDockDesignProtocol::apply(), protocols::ncbb::oop::OopDockDesignProtocol::apply(), protocols::stepwise::sampling::legacy::RigidBodySampler::apply_rigid_body_settings(), protocols::simple_filters::InterfaceSasaFilter::compute(), protocols::simple_filters::RotamerBoltzmannWeight::compute(), protocols::protein_interface_design::filters::InterfaceHolesFilter::compute(), protocols::simple_filters::DdgFilter::compute(), protocols::stepwise::sampling::legacy::RigidBodySampler::figure_out_reference_energy(), protocols::analysis::InterfaceAnalyzerMover::make_separated_pose(), protocols::ligand_docking::CompoundTranslate::parse_my_tag(), protocols::protein_interface_design::movers::part_complex(), protocols::hybridization::DomainAssembly::run(), protocols::stepwise::sampling::legacy::RigidBodySampler::search_translations(), translate_and_rotate_residue_to_origin(), and protocols::simple_moves::ddG::unbind().

void protocols::stepwise::translate_and_rotate_residue_to_origin	(	pose::Pose &	pose,
		Size const	i,
		utility::vector1< Size > const	moving_res,
		bool const	do_not_rotate
	)

References centroid, get_base_centroid_and_rotation_matrix(), rotate(), and translate().

void protocols::stepwise::translate_and_rotate_residue_to_origin	(	pose::Pose &	pose,
		Size const	i
	)

References utility::tools::make_vector1().

void protocols::stepwise::try_reroot_at_fixed_domain ( pose::Pose & pose )

References definite_terminal_root(), and core::pose::Pose::fold_tree().

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