#include <SHOBuriedUnsatisfiedPolarsCalculator.hh>

Inheritance diagram for protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator:

Public Member Functions
	SHOBuriedUnsatisfiedPolarsCalculator (core::Real sho_cutoff, std::string const &tgt_amino, std::string const &tgt_atom, core::scoring::ScoreFunctionCOP sfxn)
	constructs the calculator for a target atom in residues of a target amino acid type More...

	SHOBuriedUnsatisfiedPolarsCalculator (core::Real sho_cutoff, utility::vector1< core::Size > const &tgt_res_idxs, core::scoring::ScoreFunctionCOP sfxn)
	constructs the calculator for a target residue More...

core::pose::metrics::PoseMetricCalculatorOP	clone () const override
	clones this calculator More...

utility::vector1 < core::id::AtomID > const &	burunsat_atoms ()
	returns the set of target atoms classified as "buried unsatisfied" More...

utility::vector1 < core::id::AtomID > const &	other_atoms ()
	returns the set of target atoms classified as "other" More...

void	print_all_info (core::pose::Pose const &ps) const
	prints all information in this calculator More...

core::Real	hbond_energy (core::id::AtomID aid, core::pose::Pose const &ps) const
	returns the total H-bond energy of an atom More...

void	recompute_and_print (core::pose::Pose const &ps)
	recomputes all data from scratch and prints it to screen More...

Public Member Functions inherited from core::pose::metrics::StructureDependentCalculator
	StructureDependentCalculator ()

void	notify_structure_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_energy_change ()

Protected Member Functions
void	lookup (std::string const &key, basic::MetricValueBase *valptr) const override
	outputs a quantity's value that is cached in the calculator More...

std::string	print (std::string const &key) const override
	returns the string representation of a quantity's value that is cached in the calculator More...

void	recompute (core::pose::Pose const &ps) override
	finds buried unsatisfied atoms by building all needed data structures from scratch More...

Private Types
enum	SearchTyp { ANY_AA__TGT_ATOM, TGT_AA__TGT_ATOM, ALL_ATOMS, TGT_RES }
	identifiers for the allowed types of search More...

Private Member Functions
void	partition (core::pose::Pose const &ps)
	partitions target atoms into "buried unsatisfied" and "other" More...

void	residue_partition (core::pose::Pose const &ps, core::Size tgtidx)
	partitions a target residue's atoms into "buried unsatisfied" and "other" More...

void	print_sho_energies (core::pose::Pose const &ps)
	prints on screen the SHO energies of all atoms in a pose More...

void	assign_atom (core::id::AtomID aid)
	assigns an atom to either the "buried unsatisfied" class or the "other" class More...

bool	is_buried (core::id::AtomID aid)
	is aid buried? More...

bool	is_unsat (core::id::AtomID aid) const
	is aid unsatisfied? More...

void	print_atom_subset (utility::vector1< core::id::AtomID > const &subset, core::pose::Pose const &ps) const
	prints info on a subset of atoms More...

core::Real	get_average_energy (utility::vector1< core::id::AtomID > const &subset, std::map< core::id::AtomID, core::Real > &sho_energies) const
	returns the average SHO energy of a subset of atoms More...

void	print_atom_info (core::id::AtomID aid, core::pose::Pose const &ps) const
	prints an atom's identifier on screen More...

Private Attributes
SearchTyp	search_typ_
	selected type of search More...

core::energy_methods::ExactOccludedHbondSolEnergyOP	sho_meth_
	SHO energy calculator. More...

core::Real	sho_cutoff_
	maximum SHO energy value for a polar group to be considered as exposed (i.e., not buried) More...

utility::vector1< core::Size >	tgt_res_idxs_
	target residue indexes More...

std::string	tgt_amino_
	target amino acid type More...

std::string	tgt_atom_
	target atom type More...

core::scoring::hbonds::HBondSetCOP	hbond_set_
	stores H-bond info for the entire pose More...

std::map< core::id::AtomID, core::Real >	sho_energies_
	stores the SHO energies of all polar atoms in the pose More...

utility::vector1 < core::id::AtomID >	burunsat_atoms_
	set of buried unsatisfied atoms More...

core::Size	num_burunsat_atoms_
	number of buried unsatisfied atoms More...

utility::vector1 < core::id::AtomID >	other_atoms_
	set of atoms that are NOT buried unsatisfied More...

core::Size	num_other_atoms_
	number of atoms that are NOT buried unsatisfied More...

core::scoring::ScoreFunctionCOP	sfxn_
	score function used to (previously) score the pose More...

Member Enumeration Documentation

enum protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::SearchTyp

private

identifiers for the allowed types of search

Enumerator
ANY_AA__TGT_ATOM
TGT_AA__TGT_ATOM
ALL_ATOMS
TGT_RES

Constructor & Destructor Documentation

protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::SHOBuriedUnsatisfiedPolarsCalculator	(	core::Real	sho_cutoff,
		std::string const &	tgt_amino,
		std::string const &	tgt_atom,
		core::scoring::ScoreFunctionCOP	sfxn
	)

constructs the calculator for a target atom in residues of a target amino acid type

constructs the calculator for a target atom in residues of a target amino acid type.

[in] sho_cutoff maximum SHO energy value for a polar group to be considered as exposed (i.e., not buried). It must be expressed in original SHO units. [in] tgt_amino target amino acid type [in] tgt_atom target atom name [in] sfxn score function used to (previously) score the pose

The SHO method is initialized as in ExactOccludedHbondSolEnergyCreator::create_energy_method() for consistency with any scoring functions using SHO.

References ANY_AA__TGT_ATOM, search_typ_, TGT_AA__TGT_ATOM, and tgt_amino_.

protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::SHOBuriedUnsatisfiedPolarsCalculator	(	core::Real	sho_cutoff,
		utility::vector1< core::Size > const &	tgt_res_idxs,
		core::scoring::ScoreFunctionCOP	sfxn
	)

constructs the calculator for a target residue

constructs the calculator for a target residue set.

[in] sho_cutoff maximum SHO energy value for a polar group to be considered as exposed (i.e., not buried). It must be expressed in original SHO units. [in] tgt_res_idxs set of target residue indexes. An empty set means "all residues". [in] sfxn score function used to (previously) score the pose

The SHO method is initialized as in ExactOccludedHbondSolEnergyCreator::create_energy_method() for consistency with any scoring functions using SHO.

References ALL_ATOMS, search_typ_, TGT_RES, and tgt_res_idxs_.

Member Function Documentation

void protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::assign_atom ( core::id::AtomID aid )

private

assigns an atom to either the "buried unsatisfied" class or the "other" class

Parameters

[in] aid the atom

References burunsat_atoms_, is_buried(), is_unsat(), and other_atoms_.

Referenced by partition(), and residue_partition().

utility::vector1<core::id::AtomID> const& protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::burunsat_atoms ( )

inline

returns the set of target atoms classified as "buried unsatisfied"

References burunsat_atoms_.

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

overridevirtual

clones this calculator

members sho_meth_ and sfxn_ of the clone will point, respectively, to the same objects as members sho_meth_ and sfxn_ of this calculator.

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

core::Real protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::get_average_energy	(	utility::vector1< core::id::AtomID > const &	subset,
		std::map< core::id::AtomID, core::Real > &	sho_energies
	)		const

private

returns the average SHO energy of a subset of atoms

Real protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::hbond_energy	(	core::id::AtomID	aid,
		core::pose::Pose const &	ps
	)		const

returns the total H-bond energy of an atom

returns the total H-bond energy of an atom.

Parameters

[in]	aid	AtomID of the atom
[in]	ps	pose to which the atom belongs

the total H-bond energy of the atom is defined as half the sum of the weighted energies of the H-bonds that it forms.

Referenced by print_atom_subset().

bool protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::is_buried ( core::id::AtomID aid )

private

is aid buried?

is atom aid buried?

Parameters

[in] aid

References sho_cutoff_, and sho_energies_.

Referenced by assign_atom().

bool protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::is_unsat ( core::id::AtomID aid ) const

private

is aid unsatisfied?

is atom aid unsatisfied?

Parameters

[in] aid

References hbond_set_.

Referenced by assign_atom().

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

overrideprotectedvirtual

outputs a quantity's value that is cached in the calculator

Parameters

[in]	key	identifier of the quantity
[out]	valptr	storage for the value

Implements core::pose::metrics::StructureDependentCalculator.

References num_burunsat_atoms_.

utility::vector1<core::id::AtomID> const& protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::other_atoms ( )

inline

returns the set of target atoms classified as "other"

References other_atoms_.

void protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::partition ( core::pose::Pose const & ps )

private

partitions target atoms into "buried unsatisfied" and "other"

partitions target atoms into "buried unsatisfied" and "other".

[in] ps the pose at issue

At the end of this function burunsat_atoms_[i] will contain the identifier of the ith target atom for which functions is_buried() and is_unsat() are both true (i=1,...N, where N is the number of such atoms).

At the end of this function other_atoms_[i] will contain the identifier of the ith target atom for which either function is_buried() or function is_unsat() are false (i=1,...,M, where M is the number of such atoms)

In the above description, target atoms are assumed to be ordered by pose residue number under options ALL_ATOMS, TGT_AA__TGT_ATOM, and ANY_AA__TGT_ATOM, and by index in tgt_res_idxs_ under option TGT_RES.

References core::conformation::Residue::aa(), core::chemical::aa_from_oneletter_code(), ALL_ATOMS, ANY_AA__TGT_ATOM, assign_atom(), core::conformation::Residue::atom_index(), core::conformation::Residue::has(), core::chemical::element::N, core::pose::Pose::residue(), residue_partition(), search_typ_, core::pose::Pose::size(), TGT_AA__TGT_ATOM, tgt_amino_, tgt_atom_, TGT_RES, and tgt_res_idxs_.

Referenced by recompute().

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

overrideprotectedvirtual

returns the string representation of a quantity's value that is cached in the calculator

Parameters

[in] key identifier of the quantity

Implements core::pose::metrics::StructureDependentCalculator.

References num_burunsat_atoms_, and core::id::to_string().

void protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::print_all_info ( core::pose::Pose const & ps ) const

prints all information in this calculator

[in] ps the pose at issue

References ALL_ATOMS, burunsat_atoms_, other_atoms_, print_atom_subset(), search_typ_, sho_cutoff_, tgt_amino_, tgt_atom_, and tgt_res_idxs_.

Referenced by recompute_and_print().

void protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::print_atom_info	(	core::id::AtomID	aid,
		core::pose::Pose const &	ps
	)		const

private

prints an atom's identifier on screen

Parameters

[in]	aid	AtomID of the atom
[in]	ps	pose containing the atom

References core::id::AtomID::atomno(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), and core::id::AtomID::rsd().

Referenced by print_atom_subset(), and print_sho_energies().

void protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::print_atom_subset	(	utility::vector1< core::id::AtomID > const &	subset,
		core::pose::Pose const &	ps
	)		const

private

prints info on a subset of atoms

prints on screen info about the SHO energy and the hydrogen bonds of each atom in a subset (i.e., either the "buried unsatisfied" atoms or the "other" atoms).

Parameters

[in]	subset	the subset of atoms
[in]	ps	the pose containing the subset of atoms

The ith output line contains the identifier of the ith atom in the subset followed by its SHO energy and hydrogen bond info (i=1,...,N, where N is the number of atoms in the subset).

References hbond_energy(), hbond_set_, core::chemical::element::N, core::scoring::occ_sol_exact, print_atom_info(), sfxn_, and sho_energies_.

Referenced by print_all_info().

void protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::print_sho_energies ( core::pose::Pose const & ps )

private

prints on screen the SHO energies of all atoms in a pose

Parameters

[in] ps the pose

The output can be seen as a sequence of N blocks, where N is the number of residues in the pose. Block i contains the energies of residue i (i=1,...N). Within block i, line j contains the energy of atom j (j=1,...,M(i), where M(i) is the number of atoms in residue i). Each energy is preceded by the atom's identifier.

References core::chemical::element::N, core::conformation::Residue::natoms(), print_atom_info(), core::pose::Pose::residue(), sho_energies_, and core::pose::Pose::size().

void protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::recompute ( core::pose::Pose const & ps )

overrideprotectedvirtual

finds buried unsatisfied atoms by building all needed data structures from scratch

finds buried unsatisfied atoms by building all needed data structures from scratch.

Parameters

[in] ps pose for which the data are to be computed

Implements core::pose::metrics::StructureDependentCalculator.

References core::conformation::Residue::accpt_pos(), burunsat_atoms_, core::conformation::Residue::Hpos_polar(), core::chemical::element::N, num_burunsat_atoms_, num_other_atoms_, other_atoms_, partition(), core::pose::Pose::residue(), sho_energies_, sho_meth_, and core::pose::Pose::size().

Referenced by recompute_and_print().

void protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::recompute_and_print ( core::pose::Pose const & ps )

recomputes all data from scratch and prints it to screen

Parameters

[in] ps pose for which the data are to be computed

the pose must already have been scored by the score function pointed to by sfxn_.

References hbond_set_, print_all_info(), recompute(), and sho_meth_.

void protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::residue_partition	(	core::pose::Pose const &	ps,
		core::Size	tgtidx
	)

private

partitions a target residue's atoms into "buried unsatisfied" and "other"

partitions a target residue's polar atoms into "buried unsatisfied" and "other"

[in] ps the pose at issue [in] tgtidx pose index of the target residue

At the end of this function, burunsat_atoms_[B+i] will contain the ith polar atom in the target residue for which functions is_buried() and is_unsat() are both true (i=1,...N, where N is the number of such atoms; B is the size of burunsat_atoms_ before this function is called).

At the end of this function, other_atoms_[P+i] will contain the ith polar atom in the target residue for which either function is_buried() or function is_unsat() are false (i=1,...M, where M is the number of such atoms; P is the size of other_atoms_ before this function is called).

As to the ordering of atoms, donors are assumed to precede acceptors, donors follow the order specified by Hpos_polar(), and acceptors follow the order specified by accpt_pos().

References core::conformation::Residue::accpt_pos(), assign_atom(), core::conformation::Residue::Hpos_polar(), and core::pose::Pose::residue().

Referenced by partition().

Member Data Documentation

utility::vector1<core::id::AtomID> protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::burunsat_atoms_

private

set of buried unsatisfied atoms

Referenced by assign_atom(), burunsat_atoms(), print_all_info(), and recompute().

core::scoring::hbonds::HBondSetCOP protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::hbond_set_

private

stores H-bond info for the entire pose

Referenced by hbond_energy(), is_unsat(), print_atom_subset(), and recompute_and_print().

core::Size protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::num_burunsat_atoms_

private

number of buried unsatisfied atoms

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

core::Size protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::num_other_atoms_

private

number of atoms that are NOT buried unsatisfied

Referenced by recompute().

utility::vector1<core::id::AtomID> protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::other_atoms_

private

set of atoms that are NOT buried unsatisfied

Referenced by assign_atom(), other_atoms(), print_all_info(), and recompute().

SearchTyp protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::search_typ_

private

selected type of search

Referenced by partition(), print_all_info(), and SHOBuriedUnsatisfiedPolarsCalculator().

core::scoring::ScoreFunctionCOP protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::sfxn_

private

score function used to (previously) score the pose

Referenced by hbond_energy(), and print_atom_subset().

core::Real protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::sho_cutoff_

private

maximum SHO energy value for a polar group to be considered as exposed (i.e., not buried)

Referenced by is_buried(), and print_all_info().

std::map<core::id::AtomID, core::Real> protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::sho_energies_

private

stores the SHO energies of all polar atoms in the pose

Referenced by is_buried(), print_atom_subset(), print_sho_energies(), and recompute().

core::energy_methods::ExactOccludedHbondSolEnergyOP protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::sho_meth_

private

SHO energy calculator.

Referenced by recompute(), and recompute_and_print().

std::string protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::tgt_amino_

private

target amino acid type

Referenced by partition(), print_all_info(), and SHOBuriedUnsatisfiedPolarsCalculator().

std::string protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::tgt_atom_

private

target atom type

Referenced by partition(), and print_all_info().

utility::vector1<core::Size> protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::tgt_res_idxs_

private

target residue indexes

Referenced by partition(), print_all_info(), and SHOBuriedUnsatisfiedPolarsCalculator().

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

src/protocols/pose_metric_calculators/SHOBuriedUnsatisfiedPolarsCalculator.hh
src/protocols/pose_metric_calculators/SHOBuriedUnsatisfiedPolarsCalculator.cc

Public Member Functions

Protected Member Functions

Private Types

Private Member Functions

Private Attributes

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation