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Public Member Functions | Protected Member Functions | Private Member Functions | Static Private Member Functions | Private Attributes | List of all members
protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator Class Reference

#include <BuriedUnsatisfiedPolarsCalculator.hh>

Inheritance diagram for protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator:
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Public Member Functions

 BuriedUnsatisfiedPolarsCalculator (std::string const &sasa_calc, std::string const &hbond_calc, core::Real const burial_cutoff=-1.0, bool const generous=true, bool const legacy=false, bool const vsasa=true)
 default constructor ( keeping this for historical reasons and compatibility with other code that calls this ) More...
 
 BuriedUnsatisfiedPolarsCalculator (std::string const &sasa_calc, std::string const &hbond_calc, std::set< core::Size > const &special_region, core::Real const burial_cutoff=-1.0, bool const generous=true, bool const legacy=false, bool const vsasa=true)
 default constructor with special_region ( keeping this for historical reasons and compatibility with other code that calls this ) More...
 
 BuriedUnsatisfiedPolarsCalculator (std::string const &sasa_calc, std::string const &hbond_calc, core::id::AtomID_Map< bool > const &special_region, core::Real const burial_cutoff, core::Real const probe_r, core::Real const residue_surface_cutoff, core::Real const max_hbond_energy, bool const generous, bool const legacy, bool const vsasa, bool const use_sc_neighbors, bool const skip_surface_res, bool const include_donors=true, bool const include_acceptor_hs=false, bool const cumul_hbonds=true)
 constructor where all options must be defined, for calling from code More...
 
core::pose::metrics::PoseMetricCalculatorOP clone () const override
 copy constructor implicit in clone call More...
 
std::string const & name_of_hbond_calc () const
 
std::string const & name_of_sasa_calc () const
 
void set_special_region (std::set< core::Size > const &special_region)
 
void set_special_region (core::id::AtomID_Map< bool > const &special_region)
 
- 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
 this function doesn't actually recompute anything by itself, but calls the More...
 

Private Member Functions

void calculate_sasa (core::pose::Pose const &pose, core::id::AtomID_Map< core::Real > &atom_sasa, utility::vector1< core::Real > &residue_sasa) const
 
void assert_calculators ()
 

Static Private Member Functions

static core::Size satisfaction_cutoff (std::string atom_type)
 ONLY USED FOR LEGACY BEHAVIOR (legacy=true), cutoff to determine if unsat. More...
 

Private Attributes

core::Size all_bur_unsat_polars_
 
core::Size bb_heavy_unsats_
 
core::Size all_heavy_unsats_
 
core::Size countable_nonheavy_unsats_
 
core::id::AtomID_Map< bool > atom_bur_unsat_
 
utility::vector1< core::Size > residue_bur_unsat_polars_
 
std::string name_of_hbond_calc_
 
std::string name_of_sasa_calc_
 
core::id::AtomID_Map< bool > special_region_
 
bool special_region_entire_residue_
 
core::Real burial_cutoff_
 
core::Real probe_radius_
 
core::Real residue_surface_cutoff_
 
core::Real max_hbond_energy_
 
bool generous_hbonds_
 
bool legacy_counting_
 
bool vsasa_
 
bool use_sc_neighbors_
 
bool skip_surface_res_
 
bool include_donors_
 
bool include_acceptor_hs_
 
bool cumul_hbonds_
 

Constructor & Destructor Documentation

◆ BuriedUnsatisfiedPolarsCalculator() [1/3]

protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::BuriedUnsatisfiedPolarsCalculator ( std::string const &  sasa_calc,
std::string const &  hbond_calc,
core::Real const  burial_cutoff = -1.0,
bool const  generous = true,
bool const  legacy = false,
bool const  vsasa = true 
)

default constructor ( keeping this for historical reasons and compatibility with other code that calls this )

References assert_calculators(), atom_bur_unsat_, burial_cutoff_, core::id::AtomID_Map< T >::clear(), residue_bur_unsat_polars_, residue_surface_cutoff_, special_region_, and vsasa_.

◆ BuriedUnsatisfiedPolarsCalculator() [2/3]

protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::BuriedUnsatisfiedPolarsCalculator ( std::string const &  sasa_calc,
std::string const &  hbond_calc,
std::set< core::Size > const &  special_region,
core::Real const  burial_cutoff = -1.0,
bool const  generous = true,
bool const  legacy = false,
bool const  vsasa = true 
)

default constructor with special_region ( keeping this for historical reasons and compatibility with other code that calls this )

References assert_calculators(), atom_bur_unsat_, burial_cutoff_, core::id::AtomID_Map< T >::clear(), residue_bur_unsat_polars_, residue_surface_cutoff_, set_special_region(), and vsasa_.

◆ BuriedUnsatisfiedPolarsCalculator() [3/3]

protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::BuriedUnsatisfiedPolarsCalculator ( std::string const &  sasa_calc,
std::string const &  hbond_calc,
core::id::AtomID_Map< bool > const &  special_region,
core::Real const  burial_cutoff,
core::Real const  probe_r,
core::Real const  residue_surface_cutoff,
core::Real const  max_hbond_energy,
bool const  generous,
bool const  legacy,
bool const  vsasa,
bool const  use_sc_neighbors,
bool const  skip_surface_res,
bool const  include_donors = true,
bool const  include_acceptor_hs = false,
bool const  cumul_hbonds = true 
)

constructor where all options must be defined, for calling from code

References assert_calculators(), atom_bur_unsat_, core::id::AtomID_Map< T >::clear(), and residue_bur_unsat_polars_.

Member Function Documentation

◆ assert_calculators()

void protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::assert_calculators ( )
private

References cumul_hbonds_, generous_hbonds_, max_hbond_energy_, name_of_hbond_calc_, name_of_sasa_calc_, probe_radius_, protocols::kinmatch::str(), and vsasa_.

Referenced by BuriedUnsatisfiedPolarsCalculator().

◆ calculate_sasa()

void protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::calculate_sasa ( core::pose::Pose const &  pose,
core::id::AtomID_Map< core::Real > &  atom_sasa,
utility::vector1< core::Real > &  residue_sasa 
) const
private

References core::scoring::calc_per_atom_sasa(), core::id::AtomID_Map< T >::clear(), core::scoring::packing::get_surf_vol(), core::pose::initialize_atomid_map(), core::pose::Pose::metric(), core::id::AtomID_Map< T >::n_atom(), name_of_sasa_calc_, probe_radius_, core::id::AtomID_Map< T >::resize(), core::id::AtomID_Map< T >::size(), and core::scoring::packing::SurfVol::surf.

Referenced by recompute().

◆ clone()

core::pose::metrics::PoseMetricCalculatorOP protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::clone ( ) const
inlineoverridevirtual

copy constructor implicit in clone call

Implements core::pose::metrics::PoseMetricCalculator.

◆ lookup()

void protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::lookup ( std::string const &  key,
basic::MetricValueBase *  valptr 
) const
overrideprotectedvirtual

Implements core::pose::metrics::EnergyDependentCalculator.

References all_bur_unsat_polars_, all_heavy_unsats_, atom_bur_unsat_, bb_heavy_unsats_, countable_nonheavy_unsats_, and residue_bur_unsat_polars_.

◆ name_of_hbond_calc()

std::string const& protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::name_of_hbond_calc ( ) const
inline

References name_of_hbond_calc_.

Referenced by protocols::dna::PDBOutput::output_buried_unsatisfied_hbonds().

◆ name_of_sasa_calc()

std::string const& protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::name_of_sasa_calc ( ) const
inline

References name_of_sasa_calc_.

Referenced by protocols::dna::PDBOutput::output_buried_unsatisfied_hbonds().

◆ print()

std::string protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::print ( std::string const &  key) const
overrideprotectedvirtual

Implements core::pose::metrics::EnergyDependentCalculator.

References all_bur_unsat_polars_, all_heavy_unsats_, bb_heavy_unsats_, countable_nonheavy_unsats_, residue_bur_unsat_polars_, and core::id::to_string().

◆ recompute()

void protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::recompute ( core::pose::Pose const &  this_pose)
overrideprotectedvirtual

this function doesn't actually recompute anything by itself, but calls the

two member calculators and then processes the information out of the two of them

Implements core::pose::metrics::EnergyDependentCalculator.

References all_bur_unsat_polars_, all_heavy_unsats_, atom_bur_unsat_, core::conformation::Residue::atom_is_backbone(), core::chemical::ResidueType::atom_type(), core::conformation::Residue::atom_type(), core::chemical::AtomType::atom_type_name(), core::conformation::Residue::atomic_charge(), core::conformation::Residue::attached_H_begin(), core::conformation::Residue::attached_H_end(), bb_heavy_unsats_, burial_cutoff_, calculate_sasa(), core::pose::Pose::conformation(), countable_nonheavy_unsats_, core::id::AtomID_Map< T >::empty(), include_acceptor_hs_, include_donors_, core::pose::initialize_atomid_map(), core::chemical::AtomType::is_acceptor(), core::chemical::AtomType::is_donor(), legacy_counting_, core::pose::Pose::metric(), core::conformation::Residue::n_bonded_neighbor_all_res(), core::chemical::AtomType::name(), core::conformation::Residue::name1(), name_of_hbond_calc_, core::chemical::ResidueType::number_bonded_hydrogens(), core::pose::Pose::residue(), residue_bur_unsat_polars_, residue_surface_cutoff_, satisfaction_cutoff(), core::id::AtomID_Map< T >::set(), core::pose::Pose::size(), skip_surface_res_, special_region_, special_region_entire_residue_, core::conformation::Residue::type(), and use_sc_neighbors_.

◆ satisfaction_cutoff()

core::Size protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::satisfaction_cutoff ( std::string  atom_type)
staticprivate

ONLY USED FOR LEGACY BEHAVIOR (legacy=true), cutoff to determine if unsat.

ONLY USED FOR LEGACY BEHAVIOR (legacy=true)

Referenced by recompute().

◆ set_special_region() [1/2]

void protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::set_special_region ( core::id::AtomID_Map< bool > const &  special_region)
inline

References core::pose::metrics::EnergyDependentCalculator::notify_energy_change(), special_region_, and special_region_entire_residue_.

◆ set_special_region() [2/2]

void protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::set_special_region ( std::set< core::Size > const &  special_region)
inline

References core::id::AtomID_Map< T >::clear(), core::pose::metrics::EnergyDependentCalculator::notify_energy_change(), core::id::AtomID_Map< T >::set(), special_region_, and special_region_entire_residue_.

Referenced by BuriedUnsatisfiedPolarsCalculator().

Member Data Documentation

◆ all_bur_unsat_polars_

core::Size protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::all_bur_unsat_polars_
private

Referenced by lookup(), print(), and recompute().

◆ all_heavy_unsats_

core::Size protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::all_heavy_unsats_
private

Referenced by lookup(), print(), and recompute().

◆ atom_bur_unsat_

core::id::AtomID_Map< bool > protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::atom_bur_unsat_
private

Referenced by BuriedUnsatisfiedPolarsCalculator(), lookup(), and recompute().

◆ bb_heavy_unsats_

core::Size protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::bb_heavy_unsats_
private

Referenced by lookup(), print(), and recompute().

◆ burial_cutoff_

core::Real protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::burial_cutoff_
private

Referenced by BuriedUnsatisfiedPolarsCalculator(), and recompute().

◆ countable_nonheavy_unsats_

core::Size protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::countable_nonheavy_unsats_
private

Referenced by lookup(), print(), and recompute().

◆ cumul_hbonds_

bool protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::cumul_hbonds_
private

Referenced by assert_calculators().

◆ generous_hbonds_

bool protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::generous_hbonds_
private

Referenced by assert_calculators().

◆ include_acceptor_hs_

bool protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::include_acceptor_hs_
private

Referenced by recompute().

◆ include_donors_

bool protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::include_donors_
private

Referenced by recompute().

◆ legacy_counting_

bool protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::legacy_counting_
private

Referenced by recompute().

◆ max_hbond_energy_

core::Real protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::max_hbond_energy_
private

Referenced by assert_calculators().

◆ name_of_hbond_calc_

std::string protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::name_of_hbond_calc_
private

Referenced by assert_calculators(), name_of_hbond_calc(), and recompute().

◆ name_of_sasa_calc_

std::string protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::name_of_sasa_calc_
private

Referenced by assert_calculators(), calculate_sasa(), and name_of_sasa_calc().

◆ probe_radius_

core::Real protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::probe_radius_
private

Referenced by assert_calculators(), and calculate_sasa().

◆ residue_bur_unsat_polars_

utility::vector1< core::Size > protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::residue_bur_unsat_polars_
private

Referenced by BuriedUnsatisfiedPolarsCalculator(), lookup(), print(), and recompute().

◆ residue_surface_cutoff_

core::Real protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::residue_surface_cutoff_
private

Referenced by BuriedUnsatisfiedPolarsCalculator(), and recompute().

◆ skip_surface_res_

bool protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::skip_surface_res_
private

Referenced by recompute().

◆ special_region_

core::id::AtomID_Map< bool > protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::special_region_
private

Referenced by BuriedUnsatisfiedPolarsCalculator(), recompute(), and set_special_region().

◆ special_region_entire_residue_

bool protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::special_region_entire_residue_
private

Referenced by recompute(), and set_special_region().

◆ use_sc_neighbors_

bool protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::use_sc_neighbors_
private

Referenced by recompute().

◆ vsasa_

bool protocols::simple_pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::vsasa_
private

Referenced by assert_calculators(), and BuriedUnsatisfiedPolarsCalculator().

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