protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator Class Reference

#include <SemiExplicitWaterUnsatisfiedPolarsCalculator.hh>

Inheritance diagram for protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator:

Public Member Functions
	SemiExplicitWaterUnsatisfiedPolarsCalculator (std::string const &hbond_calc, core::scoring::ScoreFunctionOP scorefxn)
	SemiExplicitWaterUnsatisfiedPolarsCalculator (std::string const &hbond_calc, core::scoring::ScoreFunctionOP scorefxn, core::Real semiexpl_water_cutoff)
	SemiExplicitWaterUnsatisfiedPolarsCalculator (std::string const &hbond_calc, core::scoring::ScoreFunctionOP scorefxn, std::set< core::Size > const &special_region)
	SemiExplicitWaterUnsatisfiedPolarsCalculator (std::string const &hbond_calc, core::scoring::ScoreFunctionOP scorefxn, std::set< core::Size > const &special_region, core::Real semiexpl_water_cutoff)
core::Real	semiexpl_water_hbgeom_score (core::pose::Pose pose, core::scoring::ScoreFunctionOP scorefxn, core::Size seqpos, core::Size atomno, core::conformation::Residue new_rsd, core::Size new_atomno)
core::pose::metrics::PoseMetricCalculatorOP	clone () const override
std::string const &	name_of_hbond_calc () const
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 should just be caled "compute" More...

Private Member Functions
void	assert_calculators ()

Static Private Member Functions
static core::Size	satisfaction_cutoff (std::string atom_type)

Private Attributes
core::scoring::hbonds::HBondDatabaseCOP	hb_database_
core::Size	all_unsat_polars_ = 0
core::Size	special_region_unsat_polars_ = 0
core::id::AtomID_Map< bool >	atom_unsat_
utility::vector1< core::Size >	residue_unsat_polars_
utility::vector1< core::Real >	residue_semiexpl_score_
core::id::AtomID_Map< core::Real >	atom_semiexpl_score_
core::Real	semiexpl_water_cutoff_
std::string	name_of_hbond_calc_
core::scoring::ScoreFunctionOP	scorefxn_
std::set< core::Size >	special_region_

Constructor & Destructor Documentation

SemiExplicitWaterUnsatisfiedPolarsCalculator() [1/4]

protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::SemiExplicitWaterUnsatisfiedPolarsCalculator	(	std::string const &	hbond_calc,
		core::scoring::ScoreFunctionOP	scorefxn
	)

SemiExplicitWaterUnsatisfiedPolarsCalculator() [2/4]

protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::SemiExplicitWaterUnsatisfiedPolarsCalculator	(	std::string const &	hbond_calc,
		core::scoring::ScoreFunctionOP	scorefxn,
		core::Real	semiexpl_water_cutoff
	)

SemiExplicitWaterUnsatisfiedPolarsCalculator() [3/4]

protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::SemiExplicitWaterUnsatisfiedPolarsCalculator	(	std::string const &	hbond_calc,
		core::scoring::ScoreFunctionOP	scorefxn,
		std::set< core::Size > const &	special_region
	)

SemiExplicitWaterUnsatisfiedPolarsCalculator() [4/4]

protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::SemiExplicitWaterUnsatisfiedPolarsCalculator	(	std::string const &	hbond_calc,
		core::scoring::ScoreFunctionOP	scorefxn,
		std::set< core::Size > const &	special_region,
		core::Real	semiexpl_water_cutoff
	)

References assert_calculators().

Member Function Documentation

assert_calculators()

void protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::assert_calculators ( )

private

References name_of_hbond_calc_, and protocols::pose_metric_calculators::TR().

Referenced by SemiExplicitWaterUnsatisfiedPolarsCalculator().

clone()

core::pose::metrics::PoseMetricCalculatorOP protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::clone ( ) const

inlineoverridevirtual

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

References name_of_hbond_calc_, scorefxn_, and semiexpl_water_cutoff_.

lookup()

void protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::lookup ( std::string const &  key, basic::MetricValueBase *  valptr  ) const

overrideprotectedvirtual

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

References all_unsat_polars_, atom_semiexpl_score_, atom_unsat_, residue_semiexpl_score_, residue_unsat_polars_, and special_region_unsat_polars_.

name_of_hbond_calc()

std::string const& protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::name_of_hbond_calc ( ) const

inline

References name_of_hbond_calc_.

print()

std::string protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::print ( std::string const &  key ) const

overrideprotectedvirtual

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

References all_unsat_polars_, residue_unsat_polars_, special_region_unsat_polars_, and core::id::to_string().

recompute()

void protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute ( core::pose::Pose const &  this_pose )

overrideprotectedvirtual

this should just be caled "compute"

for non-hbonded polar atoms, attempt docking single water residues, then count number still unsatisfied

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

References all_unsat_polars_, core::conformation::Residue::atom_name(), atom_semiexpl_score_, core::chemical::ResidueType::atom_type(), core::conformation::Residue::atom_type(), atom_unsat_, core::chemical::ResidueType::attached_H_begin(), core::chemical::ResidueType::attached_H_end(), core::scoring::fa_sol, core::pose::get_restype_for_pose(), core::chemical::AtomType::is_acceptor(), core::chemical::AtomType::is_donor(), core::pose::Pose::metric(), core::conformation::Residue::n_bonded_neighbor_all_res(), core::chemical::AtomType::name(), core::conformation::Residue::name3(), name_of_hbond_calc_, core::conformation::Residue::natoms(), core::chemical::ResidueType::number_bonded_hydrogens(), core::pose::Pose::residue(), residue_semiexpl_score_, residue_unsat_polars_, core::id::AtomID_Map< T >::resize(), satisfaction_cutoff(), scorefxn_, semiexpl_water_cutoff_, semiexpl_water_hbgeom_score(), core::id::AtomID_Map< T >::set(), core::pose::Pose::size(), special_region_, special_region_unsat_polars_, core::id::to_string(), protocols::pose_metric_calculators::TR(), and core::conformation::Residue::type().

satisfaction_cutoff()

core::Size protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::satisfaction_cutoff ( std::string  atom_type )

staticprivate

Referenced by recompute().

semiexpl_water_hbgeom_score()

Real protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score	(	core::pose::Pose	pose,
		core::scoring::ScoreFunctionOP	scorefxn,
		core::Size	seqpos,
		core::Size	atomno,
		core::conformation::Residue	new_rsd,
		core::Size	new_atomno
	)

References core::conformation::Residue::abase2(), core::pose::Pose::append_residue_by_jump(), core::conformation::Residue::atom_base(), core::conformation::Residue::atom_name(), core::conformation::Residue::atom_type(), core::pose::Pose::conformation(), core::scoring::EMapVector::dot(), core::pose::Pose::energies(), protocols::pose_metric_calculators::fast_clash_check(), core::pose::Pose::fold_tree(), core::pose::get_restype_for_pose(), hb_database_, core::scoring::hbonds::hb_energy(), core::scoring::hbonds::hbond_compute_energy(), core::chemical::AtomType::is_acceptor(), core::chemical::AtomType::is_polar_hydrogen(), core::pose::Pose::jump(), core::scoring::hbonds::MAX_R, core::scoring::hbonds::MAX_xD, core::scoring::hbonds::MAX_xH, core::scoring::hbonds::MIN_R, core::scoring::hbonds::MIN_xD, core::scoring::hbonds::MIN_xH, core::chemical::ResidueTypeBase::mode(), core::conformation::Residue::natoms(), core::kinematics::FoldTree::new_chemical_bond(), core::kinematics::FoldTree::num_jump(), core::pose::Pose::residue(), core::scoring::Energies::residue_total_energies(), core::conformation::Conformation::set_bond_angle(), core::conformation::Conformation::set_bond_length(), core::conformation::Conformation::set_torsion_angle(), core::pose::Pose::size(), core::id::to_string(), and core::conformation::Residue::type().

Referenced by recompute().

Member Data Documentation

all_unsat_polars_

core::Size protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::all_unsat_polars_ = 0

private

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

atom_semiexpl_score_

core::id::AtomID_Map< core::Real > protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::atom_semiexpl_score_

private

Referenced by lookup(), and recompute().

atom_unsat_

core::id::AtomID_Map< bool > protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::atom_unsat_

private

Referenced by lookup(), and recompute().

hb_database_

core::scoring::hbonds::HBondDatabaseCOP protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::hb_database_

private

Referenced by semiexpl_water_hbgeom_score().

name_of_hbond_calc_

std::string protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::name_of_hbond_calc_

private

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

residue_semiexpl_score_

utility::vector1< core::Real > protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::residue_semiexpl_score_

private

Referenced by lookup(), and recompute().

residue_unsat_polars_

utility::vector1< core::Size > protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::residue_unsat_polars_

private

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

scorefxn_

core::scoring::ScoreFunctionOP protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::scorefxn_

private

Referenced by clone(), and recompute().

semiexpl_water_cutoff_

core::Real protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_cutoff_

private

Referenced by clone(), and recompute().

special_region_

std::set< core::Size > protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::special_region_

private

Referenced by recompute().

special_region_unsat_polars_

core::Size protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::special_region_unsat_polars_ = 0

private

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

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

• src/protocols/pose_metric_calculators/SemiExplicitWaterUnsatisfiedPolarsCalculator.hh
• src/protocols/pose_metric_calculators/SemiExplicitWaterUnsatisfiedPolarsCalculator.cc