#include <StepWisePoseAligner.hh>

Inheritance diagram for protocols::stepwise::modeler::align::StepWisePoseAligner:

Public Member Functions
	StepWisePoseAligner (core::pose::Pose const &reference_pose)

	~StepWisePoseAligner () override

void	apply (core::pose::Pose &pose)

core::Real	get_rmsd_over_all_poses (core::pose::Pose &pose)

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

core::Real	get_rmsd_no_superimpose (core::pose::Pose const &pose, bool const check_align=true)

core::Real	get_rmsd_no_superimpose (core::pose::Pose const &pose, core::pose::Pose const &pose_reference, bool const check_align=true)

void	create_coordinate_constraints (core::pose::Pose &pose, core::Real const rmsd_screen)

std::map< core::id::AtomID, core::id::AtomID >	create_coordinate_constraint_atom_id_map (core::pose::Pose const &pose)

void	set_superimpose_over_all_instantiated (bool const &setting)

bool	superimpose_over_all_instantiated () const

void	set_root_partition_res (utility::vector1< core::Size > const &setting)

void	set_user_defined_calc_rms_res (utility::vector1< core::Size > const &setting)

core::Real	rmsd () const

core::Size	natoms_rmsd () const

core::Real	superimpose_rmsd () const

core::Size	natoms_superimpose_rmsd () const

std::map< core::id::AtomID, core::id::AtomID > const &	superimpose_atom_id_map ()

core::Real	rmsd_over_alignment_atoms () const

bool	check_matching_atom_names (core::pose::Pose const &pose1, core::pose::Pose const &pose2, bool const verbose=true)

bool	check_matching_atom_names (core::pose::Pose const &pose1, core::pose::Pose const &pose2, std::map< core::id::AtomID, core::id::AtomID > const &atom_id_map, bool const verbose=true)

utility::vector1< core::Size > const &	rmsd_res_in_pose ()

utility::vector1< core::Size > const &	superimpose_res_in_pose ()

Private Member Functions
void	superimpose_recursively (core::pose::Pose &pose, core::Real &rmsd_over_all, core::Size &natoms_over_all)

core::Real	do_superimposition (core::pose::Pose &pose)

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

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

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

void	get_calc_rms_atom_id_map (std::map< core::id::AtomID, core::id::AtomID > &calc_rms_atom_id_map, core::pose::Pose const &pose, utility::vector1< core::Size > const &calc_rms_res) const

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

core::Size	get_rmsd_res_and_superimpose_res_in_pose (core::pose::Pose const &pose)

void	add_coordinate_constraints_from_map (core::pose::Pose &pose, core::pose::Pose const &reference_pose, std::map< core::id::AtomID, core::id::AtomID > const &atom_id_map, core::Real const &constraint_x0, core::Real const &constraint_tol) const

bool	do_checks (std::string const &atom_name, core::Size const n, core::pose::Pose const &pose) const

bool	add_to_atom_id_map_after_checks (std::map< core::id::AtomID, core::id::AtomID > &atom_id_map, std::string const &atom_name, core::Size const n1, core::Size const n2, core::pose::Pose const &pose1, core::pose::Pose const &pose2, bool const do_the_checks=true) const

std::map< core::id::AtomID, core::id::AtomID >	get_root_triad_atom_id_map (core::pose::Pose const &pose) const

void	output_atom_id_map (std::map< core::id::AtomID, core::id::AtomID > const &atom_id_map) const

void	output_atom_id_map (std::map< core::id::AtomID, core::id::AtomID > const &atom_id_map, core::pose::Pose const &pose1, core::pose::Pose const &pose2) const

std::map< core::id::AtomID, core::id::AtomID >	filter_virtual_atoms (std::map< core::id::AtomID, core::id::AtomID > const &atom_id_map, core::pose::Pose const &pose)

Private Attributes
core::pose::Pose const &	reference_pose_

core::pose::PoseCOP	reference_pose_local_

core::pose::PoseOP	mod_reference_pose_local_ = nullptr

utility::vector1< core::Size >	root_partition_res_

utility::vector1< core::Size >	user_defined_calc_rms_res_

utility::vector1< core::Size >	rmsd_res_in_pose_

utility::vector1< core::Size >	superimpose_res_in_pose_

std::map< core::id::AtomID, core::id::AtomID >	calc_rms_atom_id_map_

std::map< core::id::AtomID, core::id::AtomID >	complete_moving_atom_id_map_

std::map< core::id::AtomID, core::id::AtomID >	superimpose_atom_id_map_

std::string	annotated_sequence_used_for_atom_id_maps_

core::Real	rmsd_

core::Real	superimpose_rmsd_

core::Real const	check_alignment_tolerance_

bool	superimpose_over_all_instantiated_

Constructor & Destructor Documentation

◆ StepWisePoseAligner()

protocols::stepwise::modeler::align::StepWisePoseAligner::StepWisePoseAligner ( core::pose::Pose const & reference_pose )

◆ ~StepWisePoseAligner()

protocols::stepwise::modeler::align::StepWisePoseAligner::~StepWisePoseAligner ( )

overridedefault

Member Function Documentation

◆ add_coordinate_constraints_from_map()

void protocols::stepwise::modeler::align::StepWisePoseAligner::add_coordinate_constraints_from_map	(	core::pose::Pose &	pose,
		core::pose::Pose const &	reference_pose,
		std::map< core::id::AtomID, core::id::AtomID > const &	atom_id_map,
		core::Real const &	constraint_x0,
		core::Real const &	constraint_tol
	)		const

private

References core::id::AtomID::atomno(), core::pose::Pose::constraint_set(), core::pose::Pose::fold_tree(), core::pose::Pose::residue(), core::kinematics::FoldTree::root(), core::id::AtomID::rsd(), and core::conformation::Residue::xyz().

Referenced by create_coordinate_constraints().

◆ add_to_atom_id_map_after_checks()

bool protocols::stepwise::modeler::align::StepWisePoseAligner::add_to_atom_id_map_after_checks	(	std::map< core::id::AtomID, core::id::AtomID > &	atom_id_map,
		std::string const &	atom_name,
		core::Size const	n1,
		core::Size const	n2,
		core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		bool const	do_the_checks = `true`
	)		const

private

References core::chemical::ResidueTypeBase::aa(), core::chemical::ResidueType::atom_index(), do_checks(), core::chemical::ResidueTypeBase::na_analogue(), core::pose::Pose::residue_type(), core::chemical::rna::rna_dna_match(), and core::pose::Pose::size().

Referenced by create_coordinate_constraint_atom_id_map(), get_calc_rms_atom_id_map(), get_root_triad_atom_id_map(), and update_superimpose_atom_id_map().

◆ apply()

void protocols::stepwise::modeler::align::StepWisePoseAligner::apply ( core::pose::Pose & pose )

References do_superimposition(), and initialize().

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

◆ check_matching_atom_names() [1/2]

bool protocols::stepwise::modeler::align::StepWisePoseAligner::check_matching_atom_names	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		bool const	verbose = `true`
	)

References calc_rms_atom_id_map_.

◆ check_matching_atom_names() [2/2]

bool protocols::stepwise::modeler::align::StepWisePoseAligner::check_matching_atom_names	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		std::map< core::id::AtomID, core::id::AtomID > const &	atom_id_map,
		bool const	verbose = `true`
	)

References core::chemical::ResidueType::atom_name(), core::id::AtomID::atomno(), core::pose::Pose::residue_type(), core::id::AtomID::rsd(), and protocols::TR().

◆ create_coordinate_constraint_atom_id_map()

std::map< id::AtomID, id::AtomID > protocols::stepwise::modeler::align::StepWisePoseAligner::create_coordinate_constraint_atom_id_map ( core::pose::Pose const & pose )

References add_to_atom_id_map_after_checks(), core::chemical::ResidueType::atom_name(), get_res_list_in_reference(), mod_reference_pose_local_, core::chemical::rings::q, reference_pose_local_, core::pose::Pose::residue_type(), and core::pose::Pose::size().

Referenced by create_coordinate_constraints().

◆ create_coordinate_constraints()

void protocols::stepwise::modeler::align::StepWisePoseAligner::create_coordinate_constraints	(	core::pose::Pose &	pose,
		core::Real const	rmsd_screen
	)

References add_coordinate_constraints_from_map(), create_coordinate_constraint_atom_id_map(), and reference_pose_local_.

Referenced by protocols::stepwise::modeler::align::align_pose_and_add_rmsd_constraints().

◆ do_checks()

bool protocols::stepwise::modeler::align::StepWisePoseAligner::do_checks	(	std::string const &	atom_name,
		core::Size const	n,
		core::pose::Pose const &	pose
	)		const

private

Referenced by add_to_atom_id_map_after_checks().

◆ do_superimposition()

Real protocols::stepwise::modeler::align::StepWisePoseAligner::do_superimposition ( core::pose::Pose & pose )

private

References calc_rms_atom_id_map_, core::chemical::element::F, mod_reference_pose_local_, natoms_rmsd(), reference_pose_local_, core::scoring::rms_at_corresponding_atoms_no_super(), rmsd_, rmsd_res_in_pose_, core::pose::full_model_info::sub_to_full(), superimpose_atom_id_map_, core::scoring::superimpose_pose(), superimpose_res_in_pose_, superimpose_rmsd_, and protocols::TR().

Referenced by apply().

◆ filter_virtual_atoms()

std::map< core::id::AtomID, core::id::AtomID > protocols::stepwise::modeler::align::StepWisePoseAligner::filter_virtual_atoms	(	std::map< core::id::AtomID, core::id::AtomID > const &	atom_id_map,
		core::pose::Pose const &	pose
	)

private

◆ get_calc_rms_atom_id_map()

void protocols::stepwise::modeler::align::StepWisePoseAligner::get_calc_rms_atom_id_map	(	std::map< core::id::AtomID, core::id::AtomID > &	calc_rms_atom_id_map,
		core::pose::Pose const &	pose,
		utility::vector1< core::Size > const &	calc_rms_res
	)		const

private

References add_to_atom_id_map_after_checks(), core::chemical::ResidueType::atom_name(), core::pose::full_model_info::const_full_model_info(), core::chemical::CUTPOINT_LOWER, protocols::stepwise::modeler::align::extra_suite_atoms_lower(), protocols::stepwise::modeler::align::extra_suite_atoms_upper(), core::pose::full_model_info::FullModelInfo::fixed_domain_map(), core::pose::Pose::fold_tree(), get_res_list_in_reference(), core::chemical::ResidueTypeBase::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), core::chemical::ResidueTypeBase::is_polymer(), core::chemical::ResidueTypeBase::is_protein(), core::chemical::ResidueTypeBase::is_RNA(), mod_reference_pose_local_, core::chemical::rings::q, reference_pose_local_, core::pose::full_model_info::FullModelInfo::res_list(), core::pose::Pose::residue_type(), and core::pose::Pose::size().

Referenced by update_calc_rms_atom_id_map(), and update_superimpose_atom_id_map().

◆ get_res_list_in_reference()

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

private

References core::pose::full_model_info::const_full_model_info(), core::pose::full_model_info::FullModelParameters::conventional_to_full(), core::pose::full_model_info::FullModelInfo::full_model_parameters(), core::pose::full_model_info::FullModelParameters::full_to_conventional_resnum_and_chain_and_segid(), core::pose::full_model_info::get_res_list_const(), core::pose::full_model_info::get_res_list_from_full_model_info_const(), core::pose::full_model_info::FullModelParameters::has_conventional_residue(), reference_pose_, and core::pose::Pose::size().

Referenced by create_coordinate_constraint_atom_id_map(), get_calc_rms_atom_id_map(), get_root_triad_atom_id_map(), update_reference_pose_local(), and update_superimpose_atom_id_map().

◆ get_rmsd_no_superimpose() [1/2]

Real protocols::stepwise::modeler::align::StepWisePoseAligner::get_rmsd_no_superimpose	(	core::pose::Pose const &	pose,
		bool const	check_align = `true`
	)

References reference_pose_local_.

Referenced by protocols::stepwise::modeler::align::get_rmsd().

◆ get_rmsd_no_superimpose() [2/2]

Real protocols::stepwise::modeler::align::StepWisePoseAligner::get_rmsd_no_superimpose	(	core::pose::Pose const &	pose,
		core::pose::Pose const &	pose_reference,
		bool const	check_align = `true`
	)

References core::pose::Pose::annotated_sequence(), annotated_sequence_used_for_atom_id_maps_, calc_rms_atom_id_map_, check_alignment_tolerance_, core::pose::Pose::dump_pdb(), output_atom_id_map(), reference_pose_local_, core::scoring::rms_at_corresponding_atoms_no_super(), rmsd_, rmsd_res_in_pose_, superimpose_atom_id_map_, superimpose_res_in_pose_, superimpose_rmsd_, and protocols::TR().

◆ get_rmsd_over_all_poses()

Real protocols::stepwise::modeler::align::StepWisePoseAligner::get_rmsd_over_all_poses ( core::pose::Pose & pose )

References superimpose_recursively().

Referenced by protocols::stepwise::modeler::align::superimpose_with_stepwise_aligner().

◆ get_rmsd_res_and_superimpose_res_in_pose()

Size protocols::stepwise::modeler::align::StepWisePoseAligner::get_rmsd_res_and_superimpose_res_in_pose ( core::pose::Pose const & pose )

private

References core::pose::full_model_info::FullModelInfo::alignment_anchor_res(), core::pose::full_model_info::const_full_model_info(), core::pose::Pose::fold_tree(), core::pose::full_model_info::get_fixed_domain_from_full_model_info_const(), core::chemical::ResidueTypeBase::is_polymer(), core::pose::Pose::residue_type(), rmsd_res_in_pose_, core::kinematics::FoldTree::root(), root_partition_res_, core::pose::Pose::size(), superimpose_over_all_instantiated_, superimpose_res_in_pose_, and user_defined_calc_rms_res_.

Referenced by initialize().

◆ get_root_triad_atom_id_map()

std::map< id::AtomID, id::AtomID > protocols::stepwise::modeler::align::StepWisePoseAligner::get_root_triad_atom_id_map ( core::pose::Pose const & pose ) const

private

References add_to_atom_id_map_after_checks(), core::kinematics::AtomTree::atom_dont_do_update(), core::chemical::ResidueType::atom_name(), core::pose::Pose::atom_tree(), core::pose::Pose::fold_tree(), get_res_list_in_reference(), core::conformation::get_root_residue_root_atomno(), core::kinematics::tree::Atom::get_self_ptr(), mod_reference_pose_local_, core::chemical::rings::q, reference_pose_local_, core::pose::Pose::residue(), core::pose::Pose::residue_type(), and core::kinematics::FoldTree::root().

Referenced by update_superimpose_atom_id_map().

◆ initialize()

void protocols::stepwise::modeler::align::StepWisePoseAligner::initialize ( core::pose::Pose const & pose )

References core::pose::Pose::annotated_sequence(), annotated_sequence_used_for_atom_id_maps_, get_rmsd_res_and_superimpose_res_in_pose(), update_calc_rms_atom_id_map(), update_reference_pose_local(), and update_superimpose_atom_id_map().

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

◆ natoms_rmsd()

core::Size protocols::stepwise::modeler::align::StepWisePoseAligner::natoms_rmsd ( ) const

inline

References calc_rms_atom_id_map_.

Referenced by do_superimposition(), and superimpose_recursively().

◆ natoms_superimpose_rmsd()

core::Size protocols::stepwise::modeler::align::StepWisePoseAligner::natoms_superimpose_rmsd ( ) const

inline

References superimpose_atom_id_map_.

Referenced by superimpose_recursively().

◆ output_atom_id_map() [1/2]

void protocols::stepwise::modeler::align::StepWisePoseAligner::output_atom_id_map ( std::map< core::id::AtomID, core::id::AtomID > const & atom_id_map ) const

private

References protocols::TR().

Referenced by get_rmsd_no_superimpose().

◆ output_atom_id_map() [2/2]

void protocols::stepwise::modeler::align::StepWisePoseAligner::output_atom_id_map	(	std::map< core::id::AtomID, core::id::AtomID > const &	atom_id_map,
		core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2
	)		const

private

References core::chemical::ResidueType::atom_name(), core::pose::Pose::residue_type(), protocols::TR(), and core::pose::Pose::xyz().

◆ rmsd()

core::Real protocols::stepwise::modeler::align::StepWisePoseAligner::rmsd ( ) const

inline

References rmsd_.

Referenced by superimpose_recursively().

◆ rmsd_over_alignment_atoms()

core::Real protocols::stepwise::modeler::align::StepWisePoseAligner::rmsd_over_alignment_atoms ( ) const

inline

References superimpose_rmsd_.

◆ rmsd_res_in_pose()

utility::vector1< core::Size > const& protocols::stepwise::modeler::align::StepWisePoseAligner::rmsd_res_in_pose ( )

inline

References rmsd_res_in_pose_.

◆ set_root_partition_res()

void protocols::stepwise::modeler::align::StepWisePoseAligner::set_root_partition_res ( utility::vector1< core::Size > const & setting )

inline

References root_partition_res_.

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

◆ set_superimpose_over_all_instantiated()

void protocols::stepwise::modeler::align::StepWisePoseAligner::set_superimpose_over_all_instantiated ( bool const & setting )

inline

References superimpose_over_all_instantiated_.

Referenced by protocols::stepwise::modeler::align::superimpose_with_stepwise_aligner().

◆ set_user_defined_calc_rms_res()

void protocols::stepwise::modeler::align::StepWisePoseAligner::set_user_defined_calc_rms_res ( utility::vector1< core::Size > const & setting )

inline

References user_defined_calc_rms_res_.

Referenced by protocols::stepwise::modeler::align::get_rmsd().

◆ superimpose_atom_id_map()

std::map< core::id::AtomID, core::id::AtomID > const& protocols::stepwise::modeler::align::StepWisePoseAligner::superimpose_atom_id_map ( )

inline

References superimpose_atom_id_map_.

Referenced by protocols::stepwise::modeler::align::align_pose_and_add_rmsd_constraints().

◆ superimpose_over_all_instantiated()

bool protocols::stepwise::modeler::align::StepWisePoseAligner::superimpose_over_all_instantiated ( ) const

inline

References superimpose_over_all_instantiated_.

◆ superimpose_recursively()

void protocols::stepwise::modeler::align::StepWisePoseAligner::superimpose_recursively	(	core::pose::Pose &	pose,
		core::Real &	rmsd_over_all,
		core::Size &	natoms_over_all
	)

private

References apply(), natoms_rmsd(), natoms_superimpose_rmsd(), core::pose::full_model_info::nonconst_full_model_info(), core::scoring::other_pose, core::pose::full_model_info::FullModelInfo::other_pose_list(), rmsd(), and superimpose_rmsd().

Referenced by get_rmsd_over_all_poses().

◆ superimpose_res_in_pose()

utility::vector1< core::Size > const& protocols::stepwise::modeler::align::StepWisePoseAligner::superimpose_res_in_pose ( )

inline

References superimpose_res_in_pose_.

◆ superimpose_rmsd()

core::Real protocols::stepwise::modeler::align::StepWisePoseAligner::superimpose_rmsd ( ) const

inline

References superimpose_rmsd_.

Referenced by superimpose_recursively().

◆ update_calc_rms_atom_id_map()

void protocols::stepwise::modeler::align::StepWisePoseAligner::update_calc_rms_atom_id_map ( core::pose::Pose const & pose )

private

References calc_rms_atom_id_map_, core::pose::full_model_info::const_full_model_info(), get_calc_rms_atom_id_map(), core::pose::full_model_info::FullModelInfo::res_list(), rmsd_res_in_pose_, core::pose::Pose::size(), and user_defined_calc_rms_res_.

Referenced by initialize().

◆ update_reference_pose_local()

void protocols::stepwise::modeler::align::StepWisePoseAligner::update_reference_pose_local ( core::pose::Pose const & pose )

private

References core::pose::Pose::clone(), core::pose::full_model_info::const_full_model_info(), core::pose::full_model_info::FullModelInfo::full_sequence(), core::pose::full_model_info::get_res_list_from_full_model_info_const(), get_res_list_in_reference(), protocols::stepwise::modeler::align::match_up_to_rna_dna(), mod_reference_pose_local_, core::pose::rna::mutate_position(), reference_pose_, reference_pose_local_, core::pose::rna::remove_bracketed(), core::pose::Pose::sequence(), and core::pose::Pose::size().

Referenced by initialize().

◆ update_superimpose_atom_id_map()

void protocols::stepwise::modeler::align::StepWisePoseAligner::update_superimpose_atom_id_map ( core::pose::Pose const & pose )

private

Member Data Documentation

◆ annotated_sequence_used_for_atom_id_maps_

std::string protocols::stepwise::modeler::align::StepWisePoseAligner::annotated_sequence_used_for_atom_id_maps_

private

Referenced by get_rmsd_no_superimpose(), and initialize().

◆ calc_rms_atom_id_map_

std::map< core::id::AtomID, core::id::AtomID > protocols::stepwise::modeler::align::StepWisePoseAligner::calc_rms_atom_id_map_

private

Referenced by check_matching_atom_names(), do_superimposition(), get_rmsd_no_superimpose(), natoms_rmsd(), and update_calc_rms_atom_id_map().

◆ check_alignment_tolerance_

core::Real const protocols::stepwise::modeler::align::StepWisePoseAligner::check_alignment_tolerance_

private

Referenced by get_rmsd_no_superimpose().

◆ complete_moving_atom_id_map_

std::map< core::id::AtomID, core::id::AtomID > protocols::stepwise::modeler::align::StepWisePoseAligner::complete_moving_atom_id_map_

private

Referenced by update_superimpose_atom_id_map().

◆ mod_reference_pose_local_

core::pose::PoseOP protocols::stepwise::modeler::align::StepWisePoseAligner::mod_reference_pose_local_ = nullptr

private

Referenced by create_coordinate_constraint_atom_id_map(), do_superimposition(), get_calc_rms_atom_id_map(), get_root_triad_atom_id_map(), update_reference_pose_local(), and update_superimpose_atom_id_map().

◆ reference_pose_

core::pose::Pose const& protocols::stepwise::modeler::align::StepWisePoseAligner::reference_pose_

private

Referenced by get_res_list_in_reference(), and update_reference_pose_local().

◆ reference_pose_local_

core::pose::PoseCOP protocols::stepwise::modeler::align::StepWisePoseAligner::reference_pose_local_

private

Referenced by create_coordinate_constraint_atom_id_map(), create_coordinate_constraints(), do_superimposition(), get_calc_rms_atom_id_map(), get_rmsd_no_superimpose(), get_root_triad_atom_id_map(), update_reference_pose_local(), and update_superimpose_atom_id_map().

◆ rmsd_

core::Real protocols::stepwise::modeler::align::StepWisePoseAligner::rmsd_

private

Referenced by do_superimposition(), get_rmsd_no_superimpose(), and rmsd().

◆ rmsd_res_in_pose_

utility::vector1< core::Size > protocols::stepwise::modeler::align::StepWisePoseAligner::rmsd_res_in_pose_

private

Referenced by do_superimposition(), get_rmsd_no_superimpose(), get_rmsd_res_and_superimpose_res_in_pose(), rmsd_res_in_pose(), update_calc_rms_atom_id_map(), and update_superimpose_atom_id_map().

◆ root_partition_res_

utility::vector1< core::Size > protocols::stepwise::modeler::align::StepWisePoseAligner::root_partition_res_

private

Referenced by get_rmsd_res_and_superimpose_res_in_pose(), and set_root_partition_res().

◆ superimpose_atom_id_map_

std::map< core::id::AtomID, core::id::AtomID > protocols::stepwise::modeler::align::StepWisePoseAligner::superimpose_atom_id_map_

private

Referenced by do_superimposition(), get_rmsd_no_superimpose(), natoms_superimpose_rmsd(), superimpose_atom_id_map(), and update_superimpose_atom_id_map().

◆ superimpose_over_all_instantiated_

bool protocols::stepwise::modeler::align::StepWisePoseAligner::superimpose_over_all_instantiated_

private

Referenced by get_rmsd_res_and_superimpose_res_in_pose(), set_superimpose_over_all_instantiated(), superimpose_over_all_instantiated(), and update_superimpose_atom_id_map().

◆ superimpose_res_in_pose_

utility::vector1< core::Size > protocols::stepwise::modeler::align::StepWisePoseAligner::superimpose_res_in_pose_

private

Referenced by do_superimposition(), get_rmsd_no_superimpose(), get_rmsd_res_and_superimpose_res_in_pose(), superimpose_res_in_pose(), and update_superimpose_atom_id_map().

◆ superimpose_rmsd_

core::Real protocols::stepwise::modeler::align::StepWisePoseAligner::superimpose_rmsd_

private

Referenced by do_superimposition(), get_rmsd_no_superimpose(), rmsd_over_alignment_atoms(), and superimpose_rmsd().

◆ user_defined_calc_rms_res_

utility::vector1< core::Size > protocols::stepwise::modeler::align::StepWisePoseAligner::user_defined_calc_rms_res_

private

Referenced by get_rmsd_res_and_superimpose_res_in_pose(), set_user_defined_calc_rms_res(), and update_calc_rms_atom_id_map().

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

src/protocols/stepwise/modeler/align/StepWisePoseAligner.hh
src/protocols/stepwise/modeler/align/StepWisePoseAligner.cc

Public Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ StepWisePoseAligner()

◆ ~StepWisePoseAligner()

Member Function Documentation

◆ add_coordinate_constraints_from_map()

◆ add_to_atom_id_map_after_checks()

◆ apply()

◆ check_matching_atom_names() [1/2]

◆ check_matching_atom_names() [2/2]

◆ create_coordinate_constraint_atom_id_map()

◆ create_coordinate_constraints()

◆ do_checks()

◆ do_superimposition()

◆ filter_virtual_atoms()

◆ get_calc_rms_atom_id_map()

◆ get_res_list_in_reference()

◆ get_rmsd_no_superimpose() [1/2]

◆ get_rmsd_no_superimpose() [2/2]

◆ get_rmsd_over_all_poses()

◆ get_rmsd_res_and_superimpose_res_in_pose()

◆ get_root_triad_atom_id_map()

◆ initialize()

◆ natoms_rmsd()

◆ natoms_superimpose_rmsd()

◆ output_atom_id_map() [1/2]

◆ output_atom_id_map() [2/2]

◆ rmsd()

◆ rmsd_over_alignment_atoms()

◆ rmsd_res_in_pose()

◆ set_root_partition_res()

◆ set_superimpose_over_all_instantiated()

◆ set_user_defined_calc_rms_res()

◆ superimpose_atom_id_map()

◆ superimpose_over_all_instantiated()

◆ superimpose_recursively()

◆ superimpose_res_in_pose()

◆ superimpose_rmsd()

◆ update_calc_rms_atom_id_map()

◆ update_reference_pose_local()

◆ update_superimpose_atom_id_map()

Member Data Documentation

◆ annotated_sequence_used_for_atom_id_maps_

◆ calc_rms_atom_id_map_

◆ check_alignment_tolerance_

◆ complete_moving_atom_id_map_

◆ mod_reference_pose_local_

◆ reference_pose_

◆ reference_pose_local_

◆ rmsd_

◆ rmsd_res_in_pose_

◆ root_partition_res_

◆ superimpose_atom_id_map_

◆ superimpose_over_all_instantiated_

◆ superimpose_res_in_pose_

◆ superimpose_rmsd_

◆ user_defined_calc_rms_res_