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protocols::stepwise::modeler::align::StepWisePoseAligner Class Reference

#include <StepWisePoseAligner.hh>

Inheritance diagram for protocols::stepwise::modeler::align::StepWisePoseAligner:
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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::Sizeget_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::Sizeroot_partition_res_
 
utility::vector1< core::Sizeuser_defined_calc_rms_res_
 
utility::vector1< core::Sizermsd_res_in_pose_
 
utility::vector1< core::Sizesuperimpose_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

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

Member Function Documentation

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

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 
)
std::map< id::AtomID, id::AtomID > protocols::stepwise::modeler::align::StepWisePoseAligner::create_coordinate_constraint_atom_id_map ( core::pose::Pose const &  pose)
void protocols::stepwise::modeler::align::StepWisePoseAligner::create_coordinate_constraints ( core::pose::Pose pose,
core::Real const  rmsd_screen 
)
bool protocols::stepwise::modeler::align::StepWisePoseAligner::do_checks ( std::string const &  atom_name,
core::Size const  n,
core::pose::Pose const &  pose 
) const
private
Real protocols::stepwise::modeler::align::StepWisePoseAligner::do_superimposition ( core::pose::Pose pose)
private
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
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
utility::vector1< core::Size > protocols::stepwise::modeler::align::StepWisePoseAligner::get_res_list_in_reference ( core::pose::Pose const &  pose) const
private
Real protocols::stepwise::modeler::align::StepWisePoseAligner::get_rmsd_no_superimpose ( core::pose::Pose const &  pose,
bool const  check_align = true 
)
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 
)
Real protocols::stepwise::modeler::align::StepWisePoseAligner::get_rmsd_over_all_poses ( core::pose::Pose pose)
Size protocols::stepwise::modeler::align::StepWisePoseAligner::get_rmsd_res_and_superimpose_res_in_pose ( core::pose::Pose const &  pose)
private
std::map< id::AtomID, id::AtomID > protocols::stepwise::modeler::align::StepWisePoseAligner::get_root_triad_atom_id_map ( core::pose::Pose const &  pose) const
private
void protocols::stepwise::modeler::align::StepWisePoseAligner::initialize ( core::pose::Pose const &  pose)
core::Size protocols::stepwise::modeler::align::StepWisePoseAligner::natoms_rmsd ( ) const
inline
core::Size protocols::stepwise::modeler::align::StepWisePoseAligner::natoms_superimpose_rmsd ( ) const
inline
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().

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

References rmsd_.

Referenced by superimpose_recursively().

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

References superimpose_rmsd_.

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

References rmsd_res_in_pose_.

void protocols::stepwise::modeler::align::StepWisePoseAligner::set_root_partition_res ( utility::vector1< core::Size > const &  setting)
inline
void protocols::stepwise::modeler::align::StepWisePoseAligner::set_superimpose_over_all_instantiated ( bool const &  setting)
inline
void protocols::stepwise::modeler::align::StepWisePoseAligner::set_user_defined_calc_rms_res ( utility::vector1< core::Size > const &  setting)
inline
std::map< core::id::AtomID, core::id::AtomID > const& protocols::stepwise::modeler::align::StepWisePoseAligner::superimpose_atom_id_map ( )
inline
bool protocols::stepwise::modeler::align::StepWisePoseAligner::superimpose_over_all_instantiated ( ) const
inline
void protocols::stepwise::modeler::align::StepWisePoseAligner::superimpose_recursively ( core::pose::Pose pose,
core::Real rmsd_over_all,
core::Size natoms_over_all 
)
private
utility::vector1< core::Size > const& protocols::stepwise::modeler::align::StepWisePoseAligner::superimpose_res_in_pose ( )
inline
core::Real protocols::stepwise::modeler::align::StepWisePoseAligner::superimpose_rmsd ( ) const
inline

References superimpose_rmsd_.

Referenced by superimpose_recursively().

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

Member Data Documentation

std::string protocols::stepwise::modeler::align::StepWisePoseAligner::annotated_sequence_used_for_atom_id_maps_
private
std::map< core::id::AtomID, core::id::AtomID > protocols::stepwise::modeler::align::StepWisePoseAligner::calc_rms_atom_id_map_
private
core::Real const protocols::stepwise::modeler::align::StepWisePoseAligner::check_alignment_tolerance_
private

Referenced by get_rmsd_no_superimpose().

std::map< core::id::AtomID, core::id::AtomID > protocols::stepwise::modeler::align::StepWisePoseAligner::complete_moving_atom_id_map_
private
core::pose::PoseOP protocols::stepwise::modeler::align::StepWisePoseAligner::mod_reference_pose_local_ = nullptr
private
core::pose::Pose const& protocols::stepwise::modeler::align::StepWisePoseAligner::reference_pose_
private
core::pose::PoseCOP protocols::stepwise::modeler::align::StepWisePoseAligner::reference_pose_local_
private
core::Real protocols::stepwise::modeler::align::StepWisePoseAligner::rmsd_
private
utility::vector1< core::Size > protocols::stepwise::modeler::align::StepWisePoseAligner::rmsd_res_in_pose_
private
utility::vector1< core::Size > protocols::stepwise::modeler::align::StepWisePoseAligner::root_partition_res_
private
std::map< core::id::AtomID, core::id::AtomID > protocols::stepwise::modeler::align::StepWisePoseAligner::superimpose_atom_id_map_
private
bool protocols::stepwise::modeler::align::StepWisePoseAligner::superimpose_over_all_instantiated_
private
utility::vector1< core::Size > protocols::stepwise::modeler::align::StepWisePoseAligner::superimpose_res_in_pose_
private
core::Real protocols::stepwise::modeler::align::StepWisePoseAligner::superimpose_rmsd_
private
utility::vector1< core::Size > protocols::stepwise::modeler::align::StepWisePoseAligner::user_defined_calc_rms_res_
private

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