protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator Class Reference

#include <SemiExplicitWaterUnsatisfiedPolarsCalculator.hh>

Inheritance diagram for protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator:

Collaboration diagram for protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator:

Public Member Functions
	SemiExplicitWaterUnsatisfiedPolarsCalculator (std::string hbond_calc, core::scoring::ScoreFunctionOP scorefxn, core::Real semiexpl_water_cutoff=basic::options::option[basic::options::OptionKeys::pose_metrics::semiex_water_burial_cutoff])
	SemiExplicitWaterUnsatisfiedPolarsCalculator (std::string hbond_calc, core::scoring::ScoreFunctionOP scorefxn, std::set< core::Size > const &special_region, core::Real semiexpl_water_cutoff=basic::options::option[basic::options::OptionKeys::pose_metrics::semiex_water_burial_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
std::string const &	name_of_hbond_calc () const
Public Member Functions inherited from core::pose::metrics::EnergyDependentCalculator
	EnergyDependentCalculator ()
void	notify_energy_change ()
void	get (std::string const &key, basic::MetricValueBase &val, Pose const &this_pose)
std::string	get (std::string const &key, Pose const &this_pose)
Public Member Functions inherited from core::pose::metrics::PoseMetricCalculator
	PoseMetricCalculator ()
virtual void	notify_structure_change ()

Protected Member Functions
virtual void	lookup (std::string const &key, basic::MetricValueBase *valptr) const
virtual std::string	print (std::string const &key) const
virtual void	recompute (core::pose::Pose const &this_pose)
	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_
core::Size	special_region_unsat_polars_
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_

Detailed Description

Definition at line 41 of file SemiExplicitWaterUnsatisfiedPolarsCalculator.hh.

Constructor & Destructor Documentation

protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::SemiExplicitWaterUnsatisfiedPolarsCalculator	(	std::string	hbond_calc,
		core::scoring::ScoreFunctionOP	scorefxn,
		core::Real	semiexpl_water_cutoff = basic::options::option[basic::options::OptionKeys::pose_metrics::semiex_water_burial_cutoff]
	)

Definition at line 101 of file SemiExplicitWaterUnsatisfiedPolarsCalculator.cc.

References assert_calculators(), atom_semiexpl_score_, atom_unsat_, core::id::AtomID_Map< T >::clear(), residue_semiexpl_score_, residue_unsat_polars_, and special_region_.

Referenced by clone().

protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::SemiExplicitWaterUnsatisfiedPolarsCalculator	(	std::string	hbond_calc,
		core::scoring::ScoreFunctionOP	scorefxn,
		std::set< core::Size > const &	special_region,
		core::Real	semiexpl_water_cutoff = basic::options::option[basic::options::OptionKeys::pose_metrics::semiex_water_burial_cutoff]
	)

Definition at line 121 of file SemiExplicitWaterUnsatisfiedPolarsCalculator.cc.

References assert_calculators(), atom_semiexpl_score_, atom_unsat_, core::id::AtomID_Map< T >::clear(), residue_semiexpl_score_, and residue_unsat_polars_.

Member Function Documentation

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

private

Definition at line 143 of file SemiExplicitWaterUnsatisfiedPolarsCalculator.cc.

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

Referenced by SemiExplicitWaterUnsatisfiedPolarsCalculator().

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

inlinevirtual

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

Definition at line 70 of file SemiExplicitWaterUnsatisfiedPolarsCalculator.hh.

References name_of_hbond_calc_, scorefxn_, semiexpl_water_cutoff_, and SemiExplicitWaterUnsatisfiedPolarsCalculator().

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

protectedvirtual

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

Definition at line 156 of file SemiExplicitWaterUnsatisfiedPolarsCalculator.cc.

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

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

inline

Definition at line 73 of file SemiExplicitWaterUnsatisfiedPolarsCalculator.hh.

References name_of_hbond_calc_.

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

protectedvirtual

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

Definition at line 196 of file SemiExplicitWaterUnsatisfiedPolarsCalculator.cc.

References all_unsat_polars_, residue_unsat_polars_, and special_region_unsat_polars_.

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

protectedvirtual

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.

Definition at line 472 of file SemiExplicitWaterUnsatisfiedPolarsCalculator.cc.

References all_unsat_polars_, core::io::serialization::at(), core::conformation::Residue::atom_name(), atom_semiexpl_score_, core::conformation::Residue::atom_type(), core::chemical::ResidueType::atom_type(), atom_unsat_, core::chemical::ResidueType::attached_H_begin(), core::chemical::ResidueType::attached_H_end(), core::scoring::fa_sol, 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_, core::conformation::Residue::residue_type_set(), 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(), special_region_, special_region_unsat_polars_, core::pose::Pose::total_residue(), protocols::toolbox::pose_metric_calculators::TR(), and core::conformation::Residue::type().

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

staticprivate

Definition at line 588 of file SemiExplicitWaterUnsatisfiedPolarsCalculator.cc.

Referenced by recompute().

Real protocols::toolbox::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
	)

Definition at line 255 of file SemiExplicitWaterUnsatisfiedPolarsCalculator.cc.

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::toolbox::pose_metric_calculators::fast_clash_check(), core::pose::Pose::fold_tree(), hb_database_, 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::conformation::Residue::natoms(), 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(), and core::pose::Pose::total_residue().

Referenced by recompute().

Member Data Documentation

core::Size protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::all_unsat_polars_

private

Definition at line 91 of file SemiExplicitWaterUnsatisfiedPolarsCalculator.hh.

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

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

private

Definition at line 96 of file SemiExplicitWaterUnsatisfiedPolarsCalculator.hh.

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

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

private

Definition at line 93 of file SemiExplicitWaterUnsatisfiedPolarsCalculator.hh.

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

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

private

Definition at line 90 of file SemiExplicitWaterUnsatisfiedPolarsCalculator.hh.

Referenced by semiexpl_water_hbgeom_score().

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

private

Definition at line 100 of file SemiExplicitWaterUnsatisfiedPolarsCalculator.hh.

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

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

private

Definition at line 95 of file SemiExplicitWaterUnsatisfiedPolarsCalculator.hh.

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

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

private

Definition at line 94 of file SemiExplicitWaterUnsatisfiedPolarsCalculator.hh.

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

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

private

Definition at line 101 of file SemiExplicitWaterUnsatisfiedPolarsCalculator.hh.

Referenced by clone(), and recompute().

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

private

Definition at line 97 of file SemiExplicitWaterUnsatisfiedPolarsCalculator.hh.

Referenced by clone(), and recompute().

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

private

Definition at line 103 of file SemiExplicitWaterUnsatisfiedPolarsCalculator.hh.

Referenced by recompute(), and SemiExplicitWaterUnsatisfiedPolarsCalculator().

core::Size protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::special_region_unsat_polars_

private

Definition at line 92 of file SemiExplicitWaterUnsatisfiedPolarsCalculator.hh.

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

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

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