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protocols::buns::BuriedUnsatisfiedPolarsCalculator2 Class Reference

#include <BuriedUnsatisfiedPolarsCalculator2.hh>

Inheritance diagram for protocols::buns::BuriedUnsatisfiedPolarsCalculator2:
Inheritance graph
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Public Member Functions

 BuriedUnsatisfiedPolarsCalculator2 (std::string const &weak_bunsat_calc_)
 
 BuriedUnsatisfiedPolarsCalculator2 (std::string const &weak_bunsat_calc, std::set< core::Size > const &special_region)
 
core::pose::metrics::PoseMetricCalculatorOP clone () const override
 
std::string const & name_of_weak_bunsat_calc () const
 
void set_layered_sasa (bool val)
 
void set_generous_hbonds (bool val)
 
void set_sasa_burial_cutoff (core::Real const &val)
 
void set_AHD_cutoff (core::Real const &val)
 
void set_dist_cutoff (core::Real const &val)
 
void set_hxl_dist_cutoff (core::Real const &val)
 
void set_sulph_dist_cutoff (core::Real const &val)
 
void set_metal_dist_cutoff (core::Real const &val)
 
- Public Member Functions inherited from core::pose::metrics::EnergyDependentCalculator
 EnergyDependentCalculator ()
 
void notify_energy_change () override
 
void get (std::string const &key, basic::MetricValueBase &val, Pose const &this_pose) override
 
std::string get (std::string const &key, Pose const &this_pose) override
 
- Public Member Functions inherited from core::pose::metrics::PoseMetricCalculator
 PoseMetricCalculator ()
 
virtual void notify_structure_change ()
 

Protected Member Functions

void lookup (std::string const &key, basic::MetricValueBase *valptr) const override
 
std::string print (std::string const &key) const override
 
void recompute (core::pose::Pose const &this_pose) override
 

Private Member Functions

virtual void generous_hbond () const
 
virtual void bunsats_thorough_check (core::pose::Pose const &pose, core::id::AtomID_Map< bool > &bunsat_thorough_atomid_map)
 
virtual bool single_bunsat_thorough_check (core::pose::Pose const &pose, core::id::AtomID const &bunsat_candidate_atom_id)
 
virtual void bunsat_donor_nbr_residue_check (core::pose::Pose const &pose, core::id::AtomID const &bunsat_candidate_atom_id, core::conformation::Residue const &bunsat_rsd, numeric::xyzVector< core::Real > const &bunsat_xyz, core::Size const test_resi, core::Size &num_hbonds)
 
virtual void bunsat_acc_nbr_residue_check (core::pose::Pose const &pose, core::id::AtomID const &bunsat_candidate_atom_id, core::conformation::Residue const &bunsat_rsd, numeric::xyzVector< core::Real > const &bunsat_xyz, core::Size const &test_resi, core::Size &num_hbonds)
 
bool metal_check (core::conformation::Residue const &test_rsd, numeric::xyzVector< core::Real > const &bunsat_xyz, numeric::xyzVector< core::Real > const &test_xyz) const
 
bool adjacent_bbbb_check (core::Size const &bunsat_resi, std::string const &bunsat_atom_name, core::Size const &test_resi, std::string const &test_atom_name) const
 
bool self_scsc (core::conformation::Residue const &bunsat_rsd, core::Size const &bunsat_resi, core::Size const &bunsat_atom_num, core::conformation::Residue const &test_rsd, core::Size const &test_resi, core::Size const &test_atom_num) const
 
bool sulphur_bond_check (core::conformation::Residue const &test_rsd, core::Size const &test_atom_num, numeric::xyzVector< core::Real > const &bunsat_xyz, numeric::xyzVector< core::Real > const &test_xyz) const
 
bool don_geom_check (core::pose::Pose const &pose, core::conformation::Residue const &bunsat_rsd, core::Size const &bunsat_atom_num, numeric::xyzVector< core::Real > const &bunsat_xyz, numeric::xyzVector< core::Real > const &test_xyz) const
 
bool acc_geom_check (core::pose::Pose const &pose, numeric::xyzVector< core::Real > const &bunsat_xyz, core::conformation::Residue const &test_rsd, core::Size const &test_atom_num, numeric::xyzVector< core::Real > const &test_xyz) const
 return true if bunsat_atom_num in bunsat_rsd as an hbond acceptor to a donor at test_xyz has acceptable hbond geometry, otherwise return false More...
 
void assert_calculators ()
 
void show ()
 

Static Private Member Functions

static core::Size satisfaction_cutoff (std::string atom_type)
 

Private Attributes

core::Size all_bur_unsat_polars_
 
core::Size special_region_bur_unsat_polars_
 
core::id::AtomID_Map< boolatom_bur_unsat_
 
utility::vector1< core::Sizeresidue_bur_unsat_polars_
 
std::string name_of_weak_bunsat_calc_
 
std::set< core::Sizespecial_region_
 
bool layered_sasa_
 
bool generous_hbonds_
 
core::Real sasa_burial_cutoff_
 
core::Real AHD_cutoff_
 
core::Real dist_cutoff_
 
core::Real hxl_dist_cutoff_
 
core::Real sulph_dist_cutoff_
 
core::Real metal_dist_cutoff_
 

Constructor & Destructor Documentation

protocols::buns::BuriedUnsatisfiedPolarsCalculator2::BuriedUnsatisfiedPolarsCalculator2 ( std::string const &  weak_bunsat_calc_)
protocols::buns::BuriedUnsatisfiedPolarsCalculator2::BuriedUnsatisfiedPolarsCalculator2 ( std::string const &  weak_bunsat_calc,
std::set< core::Size > const &  special_region 
)

Member Function Documentation

bool protocols::buns::BuriedUnsatisfiedPolarsCalculator2::acc_geom_check ( core::pose::Pose const &  pose,
numeric::xyzVector< core::Real > const &  bunsat_xyz,
core::conformation::Residue const &  test_rsd,
core::Size const &  test_atom_num,
numeric::xyzVector< core::Real > const &  test_xyz 
) const
private
bool protocols::buns::BuriedUnsatisfiedPolarsCalculator2::adjacent_bbbb_check ( core::Size const &  bunsat_resi,
std::string const &  bunsat_atom_name,
core::Size const &  test_resi,
std::string const &  test_atom_name 
) const
private
void protocols::buns::BuriedUnsatisfiedPolarsCalculator2::assert_calculators ( )
private
void protocols::buns::BuriedUnsatisfiedPolarsCalculator2::bunsat_acc_nbr_residue_check ( core::pose::Pose const &  pose,
core::id::AtomID const &  bunsat_candidate_atom_id,
core::conformation::Residue const &  bunsat_rsd,
numeric::xyzVector< core::Real > const &  bunsat_xyz,
core::Size const &  test_resi,
core::Size num_hbonds 
)
privatevirtual
void protocols::buns::BuriedUnsatisfiedPolarsCalculator2::bunsat_donor_nbr_residue_check ( core::pose::Pose const &  pose,
core::id::AtomID const &  bunsat_candidate_atom_id,
core::conformation::Residue const &  bunsat_rsd,
numeric::xyzVector< core::Real > const &  bunsat_xyz,
core::Size const  test_resi,
core::Size num_hbonds 
)
privatevirtual
void protocols::buns::BuriedUnsatisfiedPolarsCalculator2::bunsats_thorough_check ( core::pose::Pose const &  pose,
core::id::AtomID_Map< bool > &  bunsat_thorough_atomid_map 
)
privatevirtual
core::pose::metrics::PoseMetricCalculatorOP protocols::buns::BuriedUnsatisfiedPolarsCalculator2::clone ( ) const
inlineoverridevirtual
bool protocols::buns::BuriedUnsatisfiedPolarsCalculator2::don_geom_check ( core::pose::Pose const &  pose,
core::conformation::Residue const &  bunsat_rsd,
core::Size const &  bunsat_atom_num,
numeric::xyzVector< core::Real > const &  bunsat_xyz,
numeric::xyzVector< core::Real > const &  test_xyz 
) const
private
void protocols::buns::BuriedUnsatisfiedPolarsCalculator2::generous_hbond ( ) const
privatevirtual
void protocols::buns::BuriedUnsatisfiedPolarsCalculator2::lookup ( std::string const &  key,
basic::MetricValueBase *  valptr 
) const
overrideprotectedvirtual
bool protocols::buns::BuriedUnsatisfiedPolarsCalculator2::metal_check ( core::conformation::Residue const &  test_rsd,
numeric::xyzVector< core::Real > const &  bunsat_xyz,
numeric::xyzVector< core::Real > const &  test_xyz 
) const
private
std::string const& protocols::buns::BuriedUnsatisfiedPolarsCalculator2::name_of_weak_bunsat_calc ( ) const
inline
std::string protocols::buns::BuriedUnsatisfiedPolarsCalculator2::print ( std::string const &  key) const
overrideprotectedvirtual
void protocols::buns::BuriedUnsatisfiedPolarsCalculator2::recompute ( core::pose::Pose const &  this_pose)
overrideprotectedvirtual
core::Size protocols::buns::BuriedUnsatisfiedPolarsCalculator2::satisfaction_cutoff ( std::string  atom_type)
staticprivate
bool protocols::buns::BuriedUnsatisfiedPolarsCalculator2::self_scsc ( core::conformation::Residue const &  bunsat_rsd,
core::Size const &  bunsat_resi,
core::Size const &  bunsat_atom_num,
core::conformation::Residue const &  test_rsd,
core::Size const &  test_resi,
core::Size const &  test_atom_num 
) const
private
void protocols::buns::BuriedUnsatisfiedPolarsCalculator2::set_AHD_cutoff ( core::Real const &  val)
inline
void protocols::buns::BuriedUnsatisfiedPolarsCalculator2::set_dist_cutoff ( core::Real const &  val)
inline
void protocols::buns::BuriedUnsatisfiedPolarsCalculator2::set_generous_hbonds ( bool  val)
inline
void protocols::buns::BuriedUnsatisfiedPolarsCalculator2::set_hxl_dist_cutoff ( core::Real const &  val)
inline
void protocols::buns::BuriedUnsatisfiedPolarsCalculator2::set_layered_sasa ( bool  val)
inline
void protocols::buns::BuriedUnsatisfiedPolarsCalculator2::set_metal_dist_cutoff ( core::Real const &  val)
inline
void protocols::buns::BuriedUnsatisfiedPolarsCalculator2::set_sasa_burial_cutoff ( core::Real const &  val)
inline
void protocols::buns::BuriedUnsatisfiedPolarsCalculator2::set_sulph_dist_cutoff ( core::Real const &  val)
inline
void protocols::buns::BuriedUnsatisfiedPolarsCalculator2::show ( )
private
bool protocols::buns::BuriedUnsatisfiedPolarsCalculator2::single_bunsat_thorough_check ( core::pose::Pose const &  pose,
core::id::AtomID const &  bunsat_candidate_atom_id 
)
privatevirtual
bool protocols::buns::BuriedUnsatisfiedPolarsCalculator2::sulphur_bond_check ( core::conformation::Residue const &  test_rsd,
core::Size const &  test_atom_num,
numeric::xyzVector< core::Real > const &  bunsat_xyz,
numeric::xyzVector< core::Real > const &  test_xyz 
) const
private

Member Data Documentation

core::Real protocols::buns::BuriedUnsatisfiedPolarsCalculator2::AHD_cutoff_
private
core::Size protocols::buns::BuriedUnsatisfiedPolarsCalculator2::all_bur_unsat_polars_
private
core::id::AtomID_Map< bool > protocols::buns::BuriedUnsatisfiedPolarsCalculator2::atom_bur_unsat_
private
core::Real protocols::buns::BuriedUnsatisfiedPolarsCalculator2::dist_cutoff_
private
bool protocols::buns::BuriedUnsatisfiedPolarsCalculator2::generous_hbonds_
private
core::Real protocols::buns::BuriedUnsatisfiedPolarsCalculator2::hxl_dist_cutoff_
private
bool protocols::buns::BuriedUnsatisfiedPolarsCalculator2::layered_sasa_
private
core::Real protocols::buns::BuriedUnsatisfiedPolarsCalculator2::metal_dist_cutoff_
private
std::string protocols::buns::BuriedUnsatisfiedPolarsCalculator2::name_of_weak_bunsat_calc_
private
utility::vector1< core::Size > protocols::buns::BuriedUnsatisfiedPolarsCalculator2::residue_bur_unsat_polars_
private
core::Real protocols::buns::BuriedUnsatisfiedPolarsCalculator2::sasa_burial_cutoff_
private
std::set< core::Size > protocols::buns::BuriedUnsatisfiedPolarsCalculator2::special_region_
private
core::Size protocols::buns::BuriedUnsatisfiedPolarsCalculator2::special_region_bur_unsat_polars_
private
core::Real protocols::buns::BuriedUnsatisfiedPolarsCalculator2::sulph_dist_cutoff_
private

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