Namespaces
	align

	movemap

	options

	packer

	polar_hydrogens

	precomputed

	protein

	rna

	working_parameters

Classes
class	StepWiseConnectionSampler

class	StepWiseMinimizer

class	StepWiseModeler

Typedefs
typedef utility::pointer::shared_ptr < StepWiseConnectionSampler >	StepWiseConnectionSamplerOP

typedef utility::pointer::shared_ptr < StepWiseConnectionSampler const >	StepWiseConnectionSamplerCOP

typedef utility::pointer::shared_ptr < StepWiseMinimizer >	StepWiseMinimizerOP

typedef utility::pointer::shared_ptr < StepWiseMinimizer const >	StepWiseMinimizerCOP

typedef utility::pointer::shared_ptr < StepWiseModeler >	StepWiseModelerOP

typedef utility::pointer::shared_ptr < StepWiseModeler const >	StepWiseModelerCOP

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

Functions
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)

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

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

void	remove_silent_file_if_it_exists (std::string const &silent_file)

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

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

void	output_rna_movemap_header (Size const &spacing, std::ostream &outstream)

void	output_protein_movemap_header (Size const &spacing, std::ostream &outstream)

void	output_movemap (kinematics::MoveMap const &mm, core::pose::Pose const &pose, std::ostream &outstream)

core::scoring::ScoreFunctionOP	get_minimize_scorefxn (core::pose::Pose const &pose, core::scoring::ScoreFunctionCOP scorefxn, options::StepWiseModelerOptionsCOP options)

core::scoring::ScoreFunctionCOP	initialize_sample_scorefxn (core::scoring::ScoreFunctionCOP scorefxn, pose::Pose const &pose, options::StepWiseModelerOptionsCOP options)

core::scoring::ScoreFunctionCOP	initialize_pack_scorefxn (core::scoring::ScoreFunctionCOP sample_scorefxn, pose::Pose const &)

core::scoring::ScoreFunctionCOP	initialize_o2prime_pack_scorefxn (core::scoring::ScoreFunctionCOP const &scorefxn)

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)

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

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)

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

bool	effective_lower_terminus_based_on_working_res (Size const i, utility::vector1< Size > const &working_res, utility::vector1< Size > const &res_list, utility::vector1< Size > const &cutpoint_open_in_full_model)

bool	effective_upper_terminus_based_on_working_res (Size const i, utility::vector1< Size > const &working_res, utility::vector1< Size > const &res_list, utility::vector1< Size > const &cutpoint_open_in_full_model, Size const nres_full)

bool	definite_terminal_root (utility::vector1< Size > const &cutpoint_open_in_full_model, utility::vector1< Size > const &working_res, utility::vector1< Size > const &res_list, Size const nres, Size const i)

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

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

utility::vector1< Size >	reorder_root_partition_res (utility::vector1< Size > const &root_partition_res, utility::vector1< Size > const &res_list, utility::vector1< Size > const &fixed_domain_map)

void	reroot_based_on_full_model_info (pose::Pose &pose)

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

void	reroot (pose::Pose &pose, utility::vector1< Size > const &root_partition_res, utility::vector1< Size > const &res_list, utility::vector1< Size > const &preferred_root_res, utility::vector1< Size > const &fixed_domain_map, utility::vector1< Size > const &cutpoint_open_in_full_model, utility::vector1< Size > const &working_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_input_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_input_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_from_moving_res (pose::Pose const &pose, utility::vector1< Size > const &moving_res_list)

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

void	figure_out_moving_chain_breaks (pose::Pose const &pose, utility::vector1< Size > const &moving_partition_res, 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)

void	add_to_pose_list (utility::vector1< core::pose::PoseOP > &pose_list, pose::Pose const &pose, std::string const pose_tag)

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

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

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

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

utility::vector1< Size >	get_all_working_moving_res (working_parameters::StepWiseWorkingParametersCOP working_parameters)

void	virtualize_side_chains (pose::Pose &pose)

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

Size	find_downstream_connection_res (pose::Pose const &pose, utility::vector1< Size > const &moving_partition_res)

Size	get_unique_connection_res (pose::Pose const &pose, utility::vector1< Size > const &moving_partition_res)

void	map_constraints_from_original_pose (pose::Pose const &original_pose, pose::Pose &pose)

Typedef Documentation

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

typedef utility::pointer::shared_ptr< StepWiseConnectionSampler const > protocols::stepwise::modeler::StepWiseConnectionSamplerCOP

typedef utility::pointer::shared_ptr< StepWiseConnectionSampler > protocols::stepwise::modeler::StepWiseConnectionSamplerOP

typedef utility::pointer::shared_ptr< StepWiseMinimizer const > protocols::stepwise::modeler::StepWiseMinimizerCOP

typedef utility::pointer::shared_ptr< StepWiseMinimizer > protocols::stepwise::modeler::StepWiseMinimizerOP

typedef utility::pointer::shared_ptr< StepWiseModeler const > protocols::stepwise::modeler::StepWiseModelerCOP

typedef utility::pointer::shared_ptr< StepWiseModeler > protocols::stepwise::modeler::StepWiseModelerOP

Function Documentation

void protocols::stepwise::modeler::add_to_pose_list	(	utility::vector1< core::pose::PoseOP > &	pose_list,
		pose::Pose const &	pose,
		std::string const	pose_tag
	)

References core::pose::Pose::clone(), and tag_into_pose().

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

References runtime_assert.

Referenced by slice_out_pose().

bool protocols::stepwise::modeler::check_for_input_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_input_domain_or_from_scratch(), and protocols::stepwise::monte_carlo::mover::DeleteMover::decide_to_keep_pose().

bool protocols::stepwise::modeler::check_for_input_domain ( pose::Pose const & pose )

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

Size protocols::stepwise::modeler::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().

Size protocols::stepwise::modeler::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::modeler::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::modeler::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().

Size protocols::stepwise::modeler::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::modeler::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::modeler::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 get_minimize_scorefxn(), and initialize_sample_scorefxn().

core::scoring::constraints::ConstraintSetOP protocols::stepwise::modeler::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::pose::Pose::total_residue().

Referenced by protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::setup_constraints().

bool protocols::stepwise::modeler::definite_terminal_root	(	utility::vector1< Size > const &	cutpoint_open_in_full_model,
		utility::vector1< Size > const &	working_res,
		utility::vector1< Size > const &	res_list,
		Size const	nres,
		Size const	i
	)

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

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

References const_full_model_info().

Referenced by reroot().

bool protocols::stepwise::modeler::effective_lower_terminus_based_on_working_res	(	Size const	i,
		utility::vector1< Size > const &	working_res,
		utility::vector1< Size > const &	res_list,
		utility::vector1< Size > const &	cutpoint_open_in_full_model
	)

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

Referenced by definite_terminal_root().

bool protocols::stepwise::modeler::effective_upper_terminus_based_on_working_res	(	Size const	i,
		utility::vector1< Size > const &	working_res,
		utility::vector1< Size > const &	res_list,
		utility::vector1< Size > const &	cutpoint_open_in_full_model,
		Size const	nres_full
	)

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

Referenced by definite_terminal_root().

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

References core::id::BB, 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::legacy::modeler::rna::StepWiseRNA_Minimizer::apply().

void protocols::stepwise::modeler::figure_out_moving_chain_breaks	(	pose::Pose const &	pose,
		utility::vector1< Size > const &	moving_partition_res,
		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_chain_numbers_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::modeler::rna::figure_out_moving_rna_chain_breaks(), and protocols::stepwise::modeler::working_parameters::setup_working_parameters_explicit().

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

References figure_out_moving_chain_breaks().

Referenced by protocols::stepwise::modeler::movemap::check_move_map_against_working_parameters(), protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::do_the_modeler(), and figure_out_moving_cutpoints_closed_from_moving_res().

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

References figure_out_moving_cutpoints_closed(), and protocols::toolbox::rigid_body::figure_out_moving_partition_res().

Referenced by protocols::stepwise::modeler::StepWiseMinimizer::close_chainbreaks(), protocols::stepwise::modeler::protein::get_bridge_res(), and protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_checkers().

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

References figure_out_moving_cutpoints_closed(), protocols::toolbox::rigid_body::figure_out_moving_partition_res(), and merge_vectors().

utility::vector1< Size > protocols::stepwise::modeler::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::modeler::rna::phosphate::MultiPhosphateSampler::do_prepack(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::figure_out_partition_definition(), protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::initialize_by_prepack(), and protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::RigidBodyStepWiseSampler().

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

References protocols::toolbox::rigid_body::figure_out_moving_partition_res(), utility::vector1< T, class >::has_value(), core::chemical::ResidueType::has_variant_type(), and core::pose::Pose::residue_type().

utility::vector1< Size > protocols::stepwise::modeler::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().

utility::vector1< Size > protocols::stepwise::modeler::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::modeler::StepWiseConnectionSampler::figure_out_reference_res().

Size protocols::stepwise::modeler::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::modeler::StepWiseConnectionSampler::figure_out_reference_res().

void protocols::stepwise::modeler::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(), runtime_assert, and core::pose::Pose::total_residue().

Referenced by protocols::stepwise::screener::PartitionContactScreener::check_screen(), figure_out_moving_partition_res(), revise_root_and_moving_res(), and protocols::stepwise::monte_carlo::mover::ResampleMover::slide_jump_randomly().

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

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

Referenced by protocols::stepwise::modeler::align::align_pose_and_add_rmsd_constraints(), and protocols::stepwise::modeler::align::get_rmsd().

Size protocols::stepwise::modeler::find_downstream_connection_res	(	pose::Pose const &	pose,
		utility::vector1< Size > const &	moving_partition_res
	)

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

Referenced by get_unique_connection_res().

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

References core::kinematics::FoldTree::downstream_jump_residue(), 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::modeler::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::modeler::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::modeler::protein::loop_close::StepWiseProteinCCD_Closer::fix_jump_atoms_at_loop_boundaries().

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

References fix_up_jump_atoms(), fix_up_residue_type_variants(), and update_constraint_set_from_full_model_info().

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

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

References core::pose::Pose::conformation(), protocols::stepwise::modeler::rna::phosphate::FIVE_PRIME_PHOSPHATE, fix_up_residue_type_variants_at_floating_base(), fix_up_residue_type_variants_at_strand_beginning(), fix_up_residue_type_variants_at_strand_end(), core::pose::Pose::pdb_info(), remove_variant_type_from_pose_residue(), runtime_assert, and protocols::stepwise::modeler::rna::phosphate::THREE_PRIME_PHOSPHATE.

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

void protocols::stepwise::modeler::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(), protocols::stepwise::modeler::rna::phosphate::FIVE_PRIME_PHOSPHATE, 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(), core::pose::full_model_info::FullModelInfo::sample_res(), protocols::stepwise::modeler::rna::phosphate::THREE_PRIME_PHOSPHATE, and core::pose::Pose::total_residue().

Referenced by fix_up_residue_type_variants().

void protocols::stepwise::modeler::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::correctly_add_cutpoint_variants(), protocols::stepwise::modeler::rna::phosphate::FIVE_PRIME_PHOSPHATE, 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(), remove_variant_type_from_pose_residue(), core::pose::Pose::residue_type(), and TR().

Referenced by fix_up_residue_type_variants().

void protocols::stepwise::modeler::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::correctly_add_cutpoint_variants(), 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(), and TR().

Referenced by fix_up_residue_type_variants().

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

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

Referenced by protocols::stepwise::modeler::packer::StepWisePacker::figure_out_neighbors(), protocols::stepwise::modeler::StepWiseMinimizer::let_neighboring_side_chains_minimize(), protocols::stepwise::monte_carlo::StepWiseMonteCarlo::preminimize_pose(), and protocols::stepwise::modeler::packer::StepWisePacker::reset().

utility::vector1< Size > protocols::stepwise::modeler::get_all_working_moving_res ( working_parameters::StepWiseWorkingParametersCOP working_parameters )

References merge_vectors().

Referenced by protocols::stepwise::modeler::packer::StepWiseMasterPacker::initialize_packer(), and protocols::stepwise::modeler::StepWiseModeler::initialize_working_parameters_and_root().

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

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

Referenced by figure_out_moving_chain_break_res().

utility::vector1< core::Size > protocols::stepwise::modeler::get_domain_boundary_res ( pose::Pose const & pose )

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

Referenced by get_moving_res_including_domain_boundaries().

utility::vector1< core::Size > protocols::stepwise::modeler::get_domain_boundary_suites ( pose::Pose const & pose )

References const_full_model_info(), core::pose::full_model_info::FullModelInfo::cutpoint_open_in_full_model(), core::pose::full_model_info::FullModelInfo::fixed_domain_map(), core::pose::Pose::fold_tree(), utility::vector1< T, class >::has_value(), core::kinematics::FoldTree::is_cutpoint(), core::pose::full_model_info::FullModelInfo::res_list(), core::pose::Pose::total_residue(), and TR().

Referenced by protocols::stepwise::modeler::movemap::check_move_map_against_working_parameters(), and get_domain_boundary_res().

void protocols::stepwise::modeler::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().

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

References runtime_assert.

Referenced by protocols::stepwise::sampler::protein::generate_beta_database_test(), and protocols::stepwise::sampler::protein::get_basic_protein_sampler().

void protocols::stepwise::modeler::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().

core::scoring::ScoreFunctionOP protocols::stepwise::modeler::get_minimize_scorefxn	(	core::pose::Pose const &	pose,
		core::scoring::ScoreFunctionCOP	scorefxn,
		options::StepWiseModelerOptionsCOP	options
	)

References atom_pair_constraint, cart_bonded, check_scorefxn_has_constraint_terms_if_pose_has_constraints(), coordinate_constraint, elec_dens_atomwise, linear_chainbreak, and rna_chem_map.

Referenced by protocols::stepwise::modeler::StepWiseMinimizer::setup_scorefxns().

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

References get_domain_boundary_res(), and merge_vectors().

Referenced by protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_checkers().

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

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

Referenced by get_unique_connection_res(), revise_root_and_moving_res_list(), and slice_out_pose().

utility::vector1< bool > protocols::stepwise::modeler::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(), and protocols::stepwise::modeler::working_parameters::setup_working_parameters_explicit().

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

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

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

std::map< Size, Size > protocols::stepwise::modeler::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 merge_two_poses().

Size protocols::stepwise::modeler::get_unique_connection_res	(	pose::Pose const &	pose,
		utility::vector1< Size > const &	moving_partition_res
	)

References find_downstream_connection_res(), core::pose::Pose::fold_tree(), get_other_residues(), core::kinematics::FoldTree::root(), runtime_assert, and core::pose::Pose::total_residue().

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

core::scoring::ScoreFunctionCOP protocols::stepwise::modeler::initialize_o2prime_pack_scorefxn ( core::scoring::ScoreFunctionCOP const & scorefxn )

References fa_atr, fa_rep, fa_sol, free_2HOprime, hbond_lr_bb_sc, hbond_sc, hbond_sr_bb_sc, lk_nonpolar, and runtime_assert.

Referenced by protocols::stepwise::modeler::rna::o2prime::O2PrimePacker::O2PrimePacker().

core::scoring::ScoreFunctionCOP protocols::stepwise::modeler::initialize_pack_scorefxn	(	core::scoring::ScoreFunctionCOP	sample_scorefxn,
		pose::Pose const &
	)

References ch_bond, fa_sol, fa_stack, free_2HOprime, free_base, free_dof, free_side_chain, free_suite, geom_sol, geom_sol_fast, lk_nonpolar, rna_chem_map, and runtime_assert.

Referenced by protocols::stepwise::modeler::StepWiseModeler::initialize_scorefunctions().

core::scoring::ScoreFunctionCOP protocols::stepwise::modeler::initialize_sample_scorefxn	(	core::scoring::ScoreFunctionCOP	scorefxn,
		pose::Pose const &	pose,
		options::StepWiseModelerOptionsCOP	options
	)

References chainbreak, check_scorefxn_has_constraint_terms_if_pose_has_constraints(), elec_dens_atomwise, fa_rep, linear_chainbreak, and rna_chem_map.

Referenced by protocols::stepwise::modeler::StepWiseModeler::initialize_scorefunctions().

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

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

Referenced by protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::check_for_unique_cutpoint(), protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::check_for_unique_cutpoint_flanked_by_bridge_res(), protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::figure_out_loop(), protocols::stepwise::modeler::working_parameters::figure_out_rebuild_bulge_mode(), get_cutpoint_closed(), protocols::stepwise::legacy::modeler::protein::is_close_chain_break(), and protocols::stepwise::modeler::rna::remove_chain_break_variants().

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

References core::chemical::ResidueType::is_protein(), core::chemical::ResidueType::is_RNA(), core::pose::Pose::residue_type(), and runtime_assert.

Referenced by protocols::metal_interface::ZincHeterodimerMover::apply(), protocols::match::MatcherTask::initialize_scaffold_active_site_residue_list_from_command_line(), protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_useful_info(), and output_movemap().

Size protocols::stepwise::modeler::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::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::calculate_jump(), protocols::stepwise::modeler::rna::get_anchor_res(), and protocols::stepwise::modeler::rna::get_partition_definition_floating_base().

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

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

Referenced by split_pose().

void protocols::stepwise::modeler::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::modeler::packer::SideChainCopier::apply(), and protocols::stepwise::modeler::rna::phosphate::copy_over_phosphate_variants().

void protocols::stepwise::modeler::map_constraints_from_original_pose	(	pose::Pose const &	original_pose,
		pose::Pose &	pose
	)

References core::pose::Pose::constraint_set(), runtime_assert, and core::pose::Pose::total_residue().

Referenced by protocols::stepwise::modeler::rna::bulge::BulgeApplyMover::apply(), protocols::stepwise::modeler::rna::bulge::BulgeUnApplyMover::apply(), protocols::stepwise::modeler::packer::SideChainCopier::apply(), and protocols::stepwise::modeler::rna::phosphate::copy_over_phosphate_variants().

utility::vector1< Size > protocols::stepwise::modeler::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::modeler::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::modeler::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_pose_objects_from_full_model_info().

Referenced by merge_in_other_pose_by_bond(), and merge_in_other_pose_by_jump().

void protocols::stepwise::modeler::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::mover::AddMover::append_other_pose(), and protocols::stepwise::monte_carlo::mover::AddMover::prepend_other_pose().

void protocols::stepwise::modeler::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::mover::AddMover::append_other_pose(), and protocols::stepwise::monte_carlo::mover::AddMover::prepend_other_pose().

utility::vector1< Size > protocols::stepwise::modeler::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
	)

References core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), core::conformation::Residue::clone(), copy_dofs_match_atom_names(), core::chemical::rna::default_jump_atom(), find_first_root_residue(), protocols::stepwise::modeler::rna::phosphate::FIVE_PRIME_PHOSPHATE, core::pose::Pose::fold_tree(), get_endpoints_from_pose(), get_jump_partners_from_pose(), get_res_map(), protocols::stepwise::setup::get_tree(), utility::vector1< T, class >::has_value(), utility::vector1< T, class >::index(), core::kinematics::FoldTree::is_cutpoint(), map_to_local_numbering(), merge_disjoint_vectors(), remove_variant_type_from_residue(), core::pose::Pose::residue(), runtime_assert, protocols::stepwise::modeler::align::superimpose_pose_legacy(), protocols::stepwise::modeler::rna::phosphate::THREE_PRIME_PHOSPHATE, core::pose::Pose::total_residue(), and TR().

Referenced by merge_two_poses_using_full_model_info().

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

Referenced by protocols::stepwise::modeler::movemap::check_move_map_against_working_parameters(), figure_out_moving_cutpoints_closed_from_moving_res(), get_all_working_moving_res(), protocols::stepwise::modeler::protein::get_bridge_res(), and get_moving_res_including_domain_boundaries().

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

References output_boolean().

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

References output_boolean().

void protocols::stepwise::modeler::output_movemap	(	kinematics::MoveMap const &	mm,
		core::pose::Pose const &	pose,
		std::ostream &	outstream
	)

void protocols::stepwise::modeler::output_protein_movemap_header	(	Size const &	spacing,
		std::ostream &	outstream
	)

Referenced by output_movemap().

void protocols::stepwise::modeler::output_rna_movemap_header	(	Size const &	spacing,
		std::ostream &	outstream
	)

Referenced by output_movemap().

Size protocols::stepwise::modeler::primary_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 revise_root_and_moving_res().

void protocols::stepwise::modeler::remove_silent_file_if_it_exists ( std::string const & silent_file )

References utility::file::file_exists(), runtime_assert, and protocols::TR().

Referenced by protocols::stepwise::legacy::modeler::protein::output_pose_list(), and protocols::stepwise::setup::StepWiseCSA_JobDistributor::write_out_silent_file().

utility::vector1< Size > protocols::stepwise::modeler::reorder_root_partition_res	(	utility::vector1< Size > const &	root_partition_res,
		utility::vector1< Size > const &	res_list,
		utility::vector1< Size > const &	fixed_domain_map
	)

References max(), and runtime_assert.

Referenced by reroot().

void protocols::stepwise::modeler::reroot	(	pose::Pose &	pose,
		utility::vector1< Size > const &	root_partition_res,
		utility::vector1< Size > const &	res_list,
		utility::vector1< Size > const &	preferred_root_res,
		utility::vector1< Size > const &	fixed_domain_map,
		utility::vector1< Size > const &	cutpoint_open_in_full_model,
		utility::vector1< Size > const &	working_res
	)

References definite_terminal_root(), core::pose::Pose::fold_tree(), utility::vector1< T, class >::has_value(), core::kinematics::FoldTree::possible_root(), core::kinematics::FoldTree::reorder(), reorder_root_partition_res(), runtime_assert, and TR().

Referenced by reroot_based_on_full_model_info(), and protocols::stepwise::setup::setup_fold_trees().

void protocols::stepwise::modeler::reroot_based_on_full_model_info ( pose::Pose & pose )

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

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

References const_full_model_info(), core::pose::full_model_info::FullModelInfo::cutpoint_open_in_full_model(), core::pose::full_model_info::FullModelInfo::fixed_domain_map(), core::pose::full_model_info::FullModelInfo::preferred_root_res(), reroot(), core::pose::full_model_info::FullModelInfo::res_list(), and core::pose::full_model_info::FullModelInfo::working_res().

Referenced by reroot_based_on_full_model_info(), revise_root_and_moving_res(), and revise_root_and_moving_res_list().

bool protocols::stepwise::modeler::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 revise_root_and_moving_res_list().

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

References core::chemical::aa_vrt, 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(), core::pose::Pose::residue_type(), revise_root_and_moving_res(), core::kinematics::FoldTree::root(), runtime_assert, and core::pose::Pose::total_residue().

Referenced by protocols::stepwise::modeler::StepWiseModeler::initialize_working_parameters_and_root().

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

void protocols::stepwise::modeler::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_pose_objects_from_full_model_info().

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

Size protocols::stepwise::modeler::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(), 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(), and core::kinematics::Jump::set_translation().

Referenced by protocols::simple_filters::InterfaceSasaFilter::compute(), protocols::simple_filters::DdgFilter::compute(), protocols::stepwise::modeler::packer::StepWisePacker::do_prepack(), protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::do_prepack(), protocols::stepwise::modeler::protein::checker::ProteinAtrRepChecker::get_base_atr_rep_score(), protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::get_base_atr_rep_score(), and protocols::optimize_weights::IterativeOptEDriver::score_ligand_interface().

void protocols::stepwise::modeler::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().

bool protocols::stepwise::modeler::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(), numeric::random::rg(), runtime_assert, switch_focus_to_other_pose(), TR(), and utility_exit_with_message.

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

void protocols::stepwise::modeler::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::mover::DeleteMover::apply(), protocols::stepwise::monte_carlo::mover::DeleteMover::remove_singletons_and_update_pose_focus(), and switch_focus_among_poses_randomly().

void protocols::stepwise::modeler::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::modeler::virtualize_side_chains ( pose::Pose & pose )

References add_variant_type_to_pose_residue(), core::chemical::ResidueType::is_protein(), core::chemical::ResidueType::is_RNA(), core::pose::Pose::residue_type(), and core::pose::Pose::total_residue().

Referenced by protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::setup_using_working_pose().

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