protocols::stepwise::sampling::general::StepWisePoseAligner Class Reference

#include <StepWisePoseAligner.hh>

Public Member Functions
	StepWisePoseAligner (pose::Pose const &reference_pose)
	~StepWisePoseAligner ()
void	apply (pose::Pose &pose)
void	create_coordinate_constraints (pose::Pose &pose, Real const rmsd_screen)
void	set_skip_bulges (bool const &setting)
bool	skip_bulges () const
void	set_root_partition_res (utility::vector1< Size > const &setting)
Real	rmsd () const
Size	natoms_rmsd () const

Private Member Functions
void	superimpose_at_fixed_res (pose::Pose &pose)
Size	get_rmsd_res_and_superimpose_res_in_pose (pose::Pose const &pose, utility::vector1< Size > &rmsd_res_in_pose, utility::vector1< Size > &superimpose_res_in_pose) const
void	add_coordinate_constraints_from_map (pose::Pose &pose, pose::Pose const &reference_pose, std::map< id::AtomID, id::AtomID > const &superimpose_atom_id_map, core::Real const &constraint_x0, core::Real const &constraint_tol) const
void	add_to_atom_id_map_after_checks (std::map< id::AtomID, id::AtomID > &atom_id_map, std::string const &atom_name, Size const &n1, Size const &n2, pose::Pose const &pose1, pose::Pose const &pose2)
bool	residue_is_bulged (pose::Pose const &pose, Size const &resid)
void	output_atom_id_map (std::map< id::AtomID, id::AtomID > const &atom_id_map)

Private Attributes
pose::Pose const &	reference_pose_
pose::PoseOP	reference_pose_local_
bool	skip_bulges_
utility::vector1< Size >	root_partition_res_
std::map< id::AtomID, id::AtomID >	calc_rms_atom_id_map_
std::map< id::AtomID, id::AtomID >	superimpose_atom_id_map_
Real	rmsd_

Constructor & Destructor Documentation

protocols::stepwise::sampling::general::StepWisePoseAligner::StepWisePoseAligner

(

pose::Pose const &

reference_pose

)

protocols::stepwise::sampling::general::StepWisePoseAligner::~StepWisePoseAligner

(

)

Member Function Documentation

void protocols::stepwise::sampling::general::StepWisePoseAligner::add_coordinate_constraints_from_map ( pose::Pose &  pose, pose::Pose const &  reference_pose, std::map< id::AtomID, id::AtomID > const &  superimpose_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 protocols::kinmatch::xyz().

Referenced by create_coordinate_constraints().

void protocols::stepwise::sampling::general::StepWisePoseAligner::add_to_atom_id_map_after_checks ( std::map< id::AtomID, id::AtomID > &  atom_id_map, std::string const &  atom_name, Size const &  n1, Size const &  n2, pose::Pose const &  pose1, pose::Pose const &  pose2  )

private

References core::chemical::ResidueType::aa(), core::chemical::ResidueType::atom_index(), core::chemical::ResidueType::first_sidechain_atom(), core::chemical::ResidueType::has(), core::chemical::ResidueType::is_protein(), core::chemical::ResidueType::is_virtual(), core::pose::Pose::residue_type(), runtime_assert, and core::pose::Pose::total_residue().

Referenced by create_coordinate_constraints(), and superimpose_at_fixed_res().

void protocols::stepwise::sampling::general::StepWisePoseAligner::apply

(

pose::Pose &

pose

)

References superimpose_at_fixed_res().

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

void protocols::stepwise::sampling::general::StepWisePoseAligner::create_coordinate_constraints	(	pose::Pose &	pose,
		Real const	rmsd_screen
	)

References add_coordinate_constraints_from_map(), add_to_atom_id_map_after_checks(), core::chemical::ResidueType::atom_name(), core::chemical::ResidueType::nheavyatoms(), nonconst_full_model_info(), q, reference_pose_local_, core::pose::Pose::remove_constraints(), core::pose::Pose::residue_type(), runtime_assert, and core::pose::Pose::total_residue().

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

Size protocols::stepwise::sampling::general::StepWisePoseAligner::get_rmsd_res_and_superimpose_res_in_pose ( pose::Pose const &  pose, utility::vector1< Size > &  rmsd_res_in_pose, utility::vector1< Size > &  superimpose_res_in_pose  ) const

private

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

Referenced by superimpose_at_fixed_res().

Size protocols::stepwise::sampling::general::StepWisePoseAligner::natoms_rmsd ( ) const

inline

Referenced by superimpose_at_fixed_res(), and protocols::stepwise::superimpose_at_fixed_res().

void protocols::stepwise::sampling::general::StepWisePoseAligner::output_atom_id_map ( std::map< id::AtomID, id::AtomID > const &  atom_id_map )

private

References protocols::TR.

bool protocols::stepwise::sampling::general::StepWisePoseAligner::residue_is_bulged ( pose::Pose const &  pose, Size const &  resid  )

private

References core::pose::Pose::get_stacking_map(), and num_stacks.

Referenced by superimpose_at_fixed_res().

Real protocols::stepwise::sampling::general::StepWisePoseAligner::rmsd ( ) const

inline

Referenced by protocols::stepwise::superimpose_at_fixed_res().

void protocols::stepwise::sampling::general::StepWisePoseAligner::set_root_partition_res ( utility::vector1< Size > const &  setting )

inline

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

void protocols::stepwise::sampling::general::StepWisePoseAligner::set_skip_bulges ( bool const &  setting )

inline

Referenced by protocols::stepwise::superimpose_at_fixed_res().

bool protocols::stepwise::sampling::general::StepWisePoseAligner::skip_bulges ( ) const

inline

void protocols::stepwise::sampling::general::StepWisePoseAligner::superimpose_at_fixed_res ( pose::Pose &  pose )

private

References add_to_atom_id_map_after_checks(), core::chemical::ResidueType::atom_name(), calc_rms_atom_id_map_, calc_rms_res, core::pose::Pose::clone(), CUTPOINT_LOWER, core::pose::Pose::fold_tree(), get_rmsd_res_and_superimpose_res_in_pose(), core::chemical::ResidueType::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), core::chemical::ResidueType::is_protein(), core::chemical::ResidueType::is_RNA(), make_tag_with_dashes(), utility::tools::make_vector1(), natoms_rmsd(), core::chemical::ResidueType::nheavyatoms(), nonconst_full_model_info(), q, reference_pose_, reference_pose_local_, residue_is_bulged(), core::pose::Pose::residue_type(), rms_at_corresponding_atoms_no_super(), rmsd_, runtime_assert, core::pose::Pose::sequence(), skip_bulges_, sub_to_full(), superimpose_atom_id_map_, protocols::stepwise::superimpose_pose(), core::pose::Pose::total_residue(), and protocols::TR.

Referenced by apply().

Member Data Documentation

std::map< id::AtomID, id::AtomID > protocols::stepwise::sampling::general::StepWisePoseAligner::calc_rms_atom_id_map_

private

Referenced by superimpose_at_fixed_res().

pose::Pose const& protocols::stepwise::sampling::general::StepWisePoseAligner::reference_pose_

private

Referenced by superimpose_at_fixed_res().

pose::PoseOP protocols::stepwise::sampling::general::StepWisePoseAligner::reference_pose_local_

private

Referenced by create_coordinate_constraints(), and superimpose_at_fixed_res().

Real protocols::stepwise::sampling::general::StepWisePoseAligner::rmsd_

private

Referenced by superimpose_at_fixed_res().

utility::vector1< Size > protocols::stepwise::sampling::general::StepWisePoseAligner::root_partition_res_

private

Referenced by get_rmsd_res_and_superimpose_res_in_pose().

bool protocols::stepwise::sampling::general::StepWisePoseAligner::skip_bulges_

private

Referenced by superimpose_at_fixed_res().

std::map< id::AtomID, id::AtomID > protocols::stepwise::sampling::general::StepWisePoseAligner::superimpose_atom_id_map_

private

Referenced by superimpose_at_fixed_res().

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

• symlinks/rosetta/src/protocols/stepwise/sampling/general/StepWisePoseAligner.hh
• symlinks/rosetta/src/protocols/stepwise/sampling/general/StepWisePoseAligner.cc