A class that holds Hbond objects and helps setup Hbonds for scoring. More...

#include <HBondSet.hh>

Inheritance diagram for core::scoring::hbonds::HBondSet:

Public Member Functions
	HBondSet ()

	~HBondSet ()

	HBondSet (Size const nres)

	HBondSet (HBondOptions const &options)

	HBondSet (HBondOptions const &options, Size const nres)

	HBondSet (pose::Pose &pose, bool const bb_only=true)
	convenience constructor: Find all the hbonds in the pose. BB only default. More...

	HBondSet (HBondOptions const &options, pose::Pose &pose, bool const bb_only=true)
	convenience constructor: Find all the hbonds in the pose. BB only default. More...

	HBondSet (HBondSet const &src)
	copy ctor More...

	HBondSet (HBondSet const &src, utility::vector1< core::Size > exclude_list)
	copy ctor More...

	HBondSet (HBondSet const &src, utility::vector1< bool > residue_mask)
	copy ctor More...

	HBondSet (HBondSet const &src, Size seqpos)
	copy ctor More...

void	setup_for_residue_pair_energies (pose::Pose const &pose, bool const calculate_derivative=false, bool const backbone_only=true)

HBond const &	hbond (Size const number) const
	Access hbond. More...

HBondCOP	hbond_cop (Size const number) const
	Access hbond. More...

utility::vector1< HBondCOP > const	atom_hbonds (AtomID const &atom, bool include_only_allowed=true) const
	Get a vector of all the hbonds involving this atom. More...

utility::vector1< HBondCOP > const	residue_hbonds (Size const seqpos, bool include_only_allowed=true) const
	Get a vector of all the hbonds involving this residue. More...

Size	nhbonds () const
	Number of hbonds. More...

Size	nhbonds (Size const seqpos, bool include_only_allowed=true) const
	Number of hbonds involving this residue. More...

Size	nhbonds (AtomID const &atom, bool include_only_allowed=true) const
	Number of hbonds involving this atom. More...

int	nbrs (Size const seqpos) const
	general function for accessing the number of 10A neighbors of a given position set by setup_for_residue_pair_energies. More...

HBondOptions const &	hbond_options () const
	Read access to the stored hbond options. More...

bool	allow_hbond (Size const index) const
	Is this hbond allowed under the bb-bb exclusion scheme? More...

bool	allow_hbond (HBond const &hbond) const

bool	acc_bbg_in_bb_bb_hbond (Size const residue) const
	is the backbone bone acceptor group in a bb/bb hydrogen bond? More...

bool	don_bbg_in_bb_bb_hbond (Size const residue) const
	is the backbone bone donor group in a bb/bb hydrogen bond? More...

void	append_hbond (Size const dhatm, conformation::Residue const &don_rsd, Size const aatm, conformation::Residue const &acc_rsd, HBEvalTuple const &hbe_tuple, Real const energy, Real const weight, HBondDerivs const &deriv)
	Add a new hbond to the list updates the "hbchk" array as necessary. More...

void	set_hbond_options (HBondOptions const &options)
	set the hbond options for this hbond set; clears all hbonds already stored More...

void	sort_by_weighted_energy ()

void	clear ()
	Delete all the data. More...

void	set_backbone_backbone_acceptor (Size const residue, bool state)
	Manually set the state of backbone-backbone acceptor. Used for symmetry. More...

void	set_backbone_backbone_donor (Size const residue, bool state)
	Manually set the state of backbone-backbone donor. Used for symmetry. More...

void	resize_bb_donor_acceptor_arrays (Size const new_dimension)
	Resize bb info arrays. More...

void	copy_bb_donor_acceptor_arrays (HBondSet const &src)

void	set_nbrs (Size const seqpos, Size value)
	Used by SymmetricScorFunction. Not sure why. Not for general use. More...

basic::datacache::CacheableDataOP	clone () const
	Clone this object. More...

void	show (std::ostream &out) const
	Print just the information stored in each individual hbond. More...

void	show () const

void	show (pose::Pose const &pose, bool const print_header, std::ostream &out) const
	Print nicely formated summary of the hbonds and their geometry in the pose. More...

void	show (pose::Pose const &pose, bool const print_header=true) const

void	show (pose::Pose const &pose, Size const residue, bool const print_header, std::ostream &out) const
	Print nicely formated summary of all the hbonds to a specific residue. More...

void	show (pose::Pose const &pose, Size const residue, bool const print_header=true) const

Private Types
typedef id::AtomID	AtomID

typedef std::map< AtomID, utility::vector1< HBondCOP > >	HBondAtomMap

Private Member Functions
void	setup_atom_map () const
	Setup the mapping from atoms to hbonds. More...

Private Attributes
HBondOptionsCOP	options_

utility::vector1< HBondOP >	hbonds_

utility::vector1< bool >	backbone_backbone_donor_

utility::vector1< bool >	backbone_backbone_acceptor_

utility::vector1< int >	nbrs_

HBondAtomMap	atom_map_

bool	atom_map_init_

Friends
std::ostream &	operator<< (std::ostream &out, const HBondSet &hbond_set)

bool	operator== (HBondSet const &a, HBondSet const &b)
	equality operator More...

Detailed Description

A class that holds Hbond objects and helps setup Hbonds for scoring.

For general hydrogen bond information, either use the default or option constructor, then use the fill methods in hbonds.hh OR use the convenience constructors to detect all Hbonds. Use the copy constructors to fill HBondSets with the Hydrogen bonds you are interested in.

Member Typedef Documentation

typedef id::AtomID core::scoring::hbonds::HBondSet::AtomID

private

typedef std::map< AtomID, utility::vector1< HBondCOP > > core::scoring::hbonds::HBondSet::HBondAtomMap

private

Constructor & Destructor Documentation

core::scoring::hbonds::HBondSet::HBondSet ( )

Referenced by clone().

core::scoring::hbonds::HBondSet::~HBondSet ( )

core::scoring::hbonds::HBondSet::HBondSet ( Size const nres )

References resize_bb_donor_acceptor_arrays().

core::scoring::hbonds::HBondSet::HBondSet ( HBondOptions const & options )

core::scoring::hbonds::HBondSet::HBondSet	(	HBondOptions const &	options,
		Size const	nres
	)

References resize_bb_donor_acceptor_arrays().

core::scoring::hbonds::HBondSet::HBondSet	(	pose::Pose &	pose,
		bool const	bb_only = `true`
	)

convenience constructor: Find all the hbonds in the pose. BB only default.

convenience constructor. If you need more controlled construction please use one of the other constructors

The pose must be non-const because the neighbor graph may need to be initialized.

References setup_for_residue_pair_energies(), and core::pose::Pose::update_residue_neighbors().

core::scoring::hbonds::HBondSet::HBondSet	(	HBondOptions const &	opts,
		pose::Pose &	pose,
		bool const	bb_only = `true`
	)

convenience constructor: Find all the hbonds in the pose. BB only default.

convenience constructor. If you need more controlled construction please use one of the other constructors

The pose must be non-const because the neighbor graph may need to be initialized.

References setup_for_residue_pair_energies(), and core::pose::Pose::update_residue_neighbors().

core::scoring::hbonds::HBondSet::HBondSet ( HBondSet const & src )

copy ctor

References atom_map_init_, backbone_backbone_acceptor_, backbone_backbone_donor_, hbonds_, and nbrs_.

core::scoring::hbonds::HBondSet::HBondSet	(	HBondSet const &	src,
		utility::vector1< core::Size >	exclude_list
	)

copy ctor

References core::scoring::hbonds::HBond::acc_res(), atom_map_init_, backbone_backbone_acceptor_, backbone_backbone_donor_, core::scoring::hbonds::HBond::don_res(), hbond(), hbonds_, nbrs_, and nhbonds().

core::scoring::hbonds::HBondSet::HBondSet	(	HBondSet const &	src,
		utility::vector1< bool >	residue_mask
	)

copy ctor

References core::scoring::hbonds::HBond::acc_res(), atom_map_init_, backbone_backbone_acceptor_, backbone_backbone_donor_, core::scoring::hbonds::HBond::don_res(), hbond(), hbonds_, nbrs_, and nhbonds().

core::scoring::hbonds::HBondSet::HBondSet	(	HBondSet const &	src,
		Size	seqpos
	)

copy ctor

References core::scoring::hbonds::HBond::acc_res(), atom_map_init_, backbone_backbone_acceptor_, backbone_backbone_donor_, core::scoring::hbonds::HBond::don_res(), hbond(), hbonds_, nbrs_, and nhbonds().

Member Function Documentation

bool core::scoring::hbonds::HBondSet::acc_bbg_in_bb_bb_hbond ( Size const residue ) const

is the backbone bone acceptor group in a bb/bb hydrogen bond?

References backbone_backbone_acceptor_.

Referenced by core::scoring::hbonds::HBondEnergy::backbone_sidechain_energy(), core::scoring::hbonds::create_rotamer_descriptor(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor(), core::scoring::hbonds::HBondEnergy::residue_pair_energy(), core::scoring::hbonds::HBondEnergy::setup_for_minimizing_for_residue(), and core::scoring::symmetry::SymmetricScoreFunction::symmetrical_allow_hbonds().

bool core::scoring::hbonds::HBondSet::allow_hbond ( Size const index ) const

Is this hbond allowed under the bb-bb exclusion scheme?

bb-bb exclusion scheme means that if the query hbond is a sc making a sc-bb hbond with a backbone already involved in a bb-bb hbond, return false This has been included by default when assessing pose Hbond energies due to Rosetta designing too many ser/thr bifricated hbonds in ss structures. Part of the reason is that Rosetta currently does NOT treat bifricated hbonds differently - so both hbonds are counted toward the score. Another reason is that the rotamer library itself favors local bb-sc hbonds. NOTE: This function is called while evaluating / setting up for energies (get_hbond_energies method in hbonds.hh).

References hbonds_.

Referenced by atom_hbonds(), core::optimization::AtomTreeMultifunc::dump(), core::optimization::CartesianMultifunc::dump(), protocols::normalmode::NormalModeMultifunc::dump(), core::optimization::symmetry::SymAtomTreeMultifunc::dump(), core::scoring::hbonds::get_hbond_energies(), and residue_hbonds().

bool core::scoring::hbonds::HBondSet::allow_hbond ( HBond const & hbond ) const

References core::scoring::hbonds::HBond::acc_atm_is_protein_backbone(), core::scoring::hbonds::HBond::acc_res(), backbone_backbone_acceptor_, backbone_backbone_donor_, core::scoring::hbonds::HBond::don_hatm_is_protein_backbone(), and core::scoring::hbonds::HBond::don_res().

void core::scoring::hbonds::HBondSet::append_hbond	(	Size const	dhatm,
		conformation::Residue const &	don_rsd,
		Size const	aatm,
		conformation::Residue const &	acc_rsd,
		HBEvalTuple const &	hbe_tuple,
		Real const	energy,
		Real const	weight,
		HBondDerivs const &	deriv
	)

Add a new hbond to the list updates the "hbchk" array as necessary.

References core::conformation::Residue::atom_is_backbone(), atom_map_init_, backbone_backbone_acceptor_, backbone_backbone_donor_, hbonds_, core::conformation::Residue::is_DNA(), core::conformation::Residue::is_protein(), options_, resize_bb_donor_acceptor_arrays(), and core::conformation::Residue::seqpos().

Referenced by core::scoring::WaterAdductHBondPotential::get_residue_residue_h2o_hbonds_1way(), core::scoring::hbonds::identify_hbonds_1way(), core::scoring::hbonds::identify_hbonds_1way_AHdist(), core::scoring::hbonds::identify_hbonds_1way_membrane(), and core::scoring::hbonds::identify_intra_res_hbonds().

utility::vector1< HBondCOP > const core::scoring::hbonds::HBondSet::atom_hbonds	(	AtomID const &	atom,
		bool	include_only_allowed = `true`
	)		const

Get a vector of all the hbonds involving this atom.

Excludes 'not allowed' bonds by default. See hbond_allowed function for more info)

References allow_hbond(), atom_map_, and setup_atom_map().

Referenced by core::scoring::methods::WaterAdductHBondEnergy::get_atom_h2o_hbond_derivative(), protocols::toolbox::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::hbond_energy(), and nhbonds().

void core::scoring::hbonds::HBondSet::clear ( )

Delete all the data.

References atom_map_init_, backbone_backbone_acceptor_, backbone_backbone_donor_, hbonds_, and nbrs_.

Referenced by protocols::pockets::GenPharmacophore::extract_Hbond_atoms_from_protein_rna_complex(), core::scoring::WaterAdductHBondPotential::fill_h2o_hbond_set(), core::scoring::hbonds::fill_hbond_set(), core::scoring::hbonds::fill_hbond_set_by_AHdist_threshold(), and set_hbond_options().

basic::datacache::CacheableDataOP core::scoring::hbonds::HBondSet::clone ( ) const

Clone this object.

clone this object

References HBondSet().

void core::scoring::hbonds::HBondSet::copy_bb_donor_acceptor_arrays ( HBondSet const & src )

References backbone_backbone_acceptor_, and backbone_backbone_donor_.

Referenced by core::scoring::hbonds::HBondEnergy::setup_for_scoring().

bool core::scoring::hbonds::HBondSet::don_bbg_in_bb_bb_hbond ( Size const residue ) const

is the backbone bone donor group in a bb/bb hydrogen bond?

References backbone_backbone_donor_.

Referenced by core::scoring::hbonds::HBondEnergy::backbone_sidechain_energy(), core::scoring::hbonds::create_rotamer_descriptor(), core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_donor(), core::scoring::hbonds::HBondEnergy::residue_pair_energy(), and core::scoring::hbonds::HBondEnergy::setup_for_minimizing_for_residue().

HBond const & core::scoring::hbonds::HBondSet::hbond ( Size const number ) const

Access hbond.

References hbonds_.

Referenced by protocols::toolbox::task_operations::SelectByDeltaScoreOperation::apply(), protocols::simple_filters::TaskAwareScoreTypeFilter::compute(), core::optimization::AtomTreeMultifunc::dump(), core::optimization::CartesianMultifunc::dump(), protocols::normalmode::NormalModeMultifunc::dump(), core::optimization::symmetry::SymAtomTreeMultifunc::dump(), protocols::pockets::GenPharmacophore::extract_Hbond_atoms_from_protein_rna_complex(), core::scoring::hbonds::get_hbond_energies(), hbonded(), hbonded_atom(), HBondSet(), core::scoring::hbonds::identify_intra_res_hbonds(), core::scoring::symmetry::SymmetricScoreFunction::intersubunit_hbond_energy(), core::scoring::hbonds::operator==(), protocols::features::HBondFeatures::report_features(), show(), and core::scoring::symmetry::SymmetricScoreFunction::symmetrical_allow_hbonds().

HBondCOP core::scoring::hbonds::HBondSet::hbond_cop ( Size const number ) const

Access hbond.

References hbonds_.

Referenced by residue_hbonds(), and setup_atom_map().

HBondOptions const & core::scoring::hbonds::HBondSet::hbond_options ( ) const

Read access to the stored hbond options.

References options_.

Referenced by core::scoring::hbonds::fill_hbond_set(), core::scoring::hbonds::fill_hbond_set_by_AHdist_threshold(), core::scoring::hbonds::fill_intra_res_hbond_set(), core::scoring::hbonds::HBondEnergy::hbond_derivs_1way(), core::scoring::hbonds::identify_hbonds_1way(), core::scoring::hbonds::identify_hbonds_1way_AHdist(), core::scoring::hbonds::identify_hbonds_1way_membrane(), core::scoring::hbonds::identify_intra_res_hbonds(), and protocols::features::HBondFeatures::report_features().

int core::scoring::hbonds::HBondSet::nbrs ( Size const seqpos ) const

general function for accessing the number of 10A neighbors of a given position set by setup_for_residue_pair_energies.

References nbrs_.

Size core::scoring::hbonds::HBondSet::nhbonds ( ) const

Number of hbonds.

References hbonds_.

Referenced by protocols::toolbox::task_operations::SelectByDeltaScoreOperation::apply(), protocols::simple_filters::TaskAwareScoreTypeFilter::compute(), protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator::compute_Hbonds_for_residue(), core::optimization::AtomTreeMultifunc::dump(), core::optimization::CartesianMultifunc::dump(), protocols::normalmode::NormalModeMultifunc::dump(), core::optimization::symmetry::SymAtomTreeMultifunc::dump(), protocols::pockets::GenPharmacophore::extract_Hbond_atoms_from_protein_rna_complex(), core::scoring::hbonds::get_hbond_energies(), hbonded(), hbonded_atom(), HBondSet(), core::scoring::hbonds::identify_intra_res_hbonds(), core::scoring::symmetry::SymmetricScoreFunction::intersubunit_hbond_energy(), protocols::toolbox::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::is_unsat(), core::scoring::hbonds::operator==(), protocols::toolbox::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculator::print_atom_subset(), protocols::features::HBondFeatures::report_features(), residue_hbonds(), show(), and core::scoring::symmetry::SymmetricScoreFunction::symmetrical_allow_hbonds().

Size core::scoring::hbonds::HBondSet::nhbonds	(	Size const	seqpos,
		bool	include_only_allowed = `true`
	)		const

Number of hbonds involving this residue.

Excludes 'not allowed' bonds by default. See hbond_allowed function for more info)

References residue_hbonds().

Size core::scoring::hbonds::HBondSet::nhbonds	(	AtomID const &	atom,
		bool	include_only_allowed = `true`
	)		const

Number of hbonds involving this atom.

Excludes 'not allowed' bonds by default. See hbond_allowed function for more info)

References atom_hbonds().

utility::vector1< HBondCOP > const core::scoring::hbonds::HBondSet::residue_hbonds	(	Size const	seqpos,
		bool	include_only_allowed = `true`
	)		const

Get a vector of all the hbonds involving this residue.

Excludes 'not allowed' bonds by default. See hbond_allowed function for more info)

References allow_hbond(), hbond_cop(), and nhbonds().

Referenced by nhbonds().

void core::scoring::hbonds::HBondSet::resize_bb_donor_acceptor_arrays ( Size const new_dimension )

Resize bb info arrays.

References backbone_backbone_acceptor_, and backbone_backbone_donor_.

Referenced by append_hbond(), HBondSet(), and setup_for_residue_pair_energies().

void core::scoring::hbonds::HBondSet::set_backbone_backbone_acceptor	(	Size const	residue,
		bool	state
	)

inline

Manually set the state of backbone-backbone acceptor. Used for symmetry.

References backbone_backbone_acceptor_.

Referenced by core::scoring::symmetry::SymmetricScoreFunction::symmetrical_allow_hbonds().

void core::scoring::hbonds::HBondSet::set_backbone_backbone_donor	(	Size const	residue,
		bool	state
	)

inline

Manually set the state of backbone-backbone donor. Used for symmetry.

References backbone_backbone_donor_.

void core::scoring::hbonds::HBondSet::set_hbond_options ( HBondOptions const & options )

set the hbond options for this hbond set; clears all hbonds already stored

References clear(), and options_.

Referenced by core::scoring::WaterAdductHBondPotential::fill_h2o_hbond_set().

void core::scoring::hbonds::HBondSet::set_nbrs	(	Size const	seqpos,
		Size	value
	)

Used by SymmetricScorFunction. Not sure why. Not for general use.

References nbrs_.

Referenced by core::scoring::symmetry::SymmetricScoreFunction::set_symmetric_residue_neighbors_hbonds().

void core::scoring::hbonds::HBondSet::setup_atom_map ( ) const

private

Setup the mapping from atoms to hbonds.

References atom_map_, atom_map_init_, hbond_cop(), and hbonds_.

Referenced by atom_hbonds().

void core::scoring::hbonds::HBondSet::setup_for_residue_pair_energies	(	pose::Pose const &	pose,
		bool const	calculate_derivative = `false`,
		bool const	backbone_only = `true`
	)

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::graph::Node::const_edge_list_end(), core::pose::Pose::energies(), core::scoring::hbonds::fill_hbond_set(), core::graph::Edge::get_node(), core::scoring::hbonds::SSWeightParameters::h_, core::scoring::hbonds::SSWeightParameters::l_, core::scoring::hbonds::SSWeightParameters::len_h_, core::scoring::hbonds::SSWeightParameters::len_l_, nbrs_, options_, core::pose::Pose::residue(), resize_bb_donor_acceptor_arrays(), core::scoring::hbonds::SSWeightParameters::ssdep_, core::scoring::Energies::tenA_neighbor_graph(), and core::pose::Pose::total_residue().

Referenced by protocols::toolbox::pose_metric_calculators::find_res_unsat_polars(), protocols::helix_capper::HelixNCapperMover::get_Ncap_scores(), hbonded(), hbonded_atom(), HBondSet(), and protocols::features::HBondFeatures::report_features().

void core::scoring::hbonds::HBondSet::show ( std::ostream & out ) const

Print just the information stored in each individual hbond.

References hbond(), and nhbonds().

Referenced by core::scoring::hbonds::operator<<().

void core::scoring::hbonds::HBondSet::show ( ) const

inline

References show().

Referenced by show().

void core::scoring::hbonds::HBondSet::show	(	pose::Pose const &	pose,
		bool const	print_header,
		std::ostream &	out
	)		const

Print nicely formated summary of the hbonds and their geometry in the pose.

Optionally print a header, and then a row for each hydrogen bond in the set using the iterprable version of the hbond show format formatted for easy parsing by R, Excel, etc.

References hbond(), nhbonds(), and core::scoring::hbonds::HBond::show().

void core::scoring::hbonds::HBondSet::show	(	pose::Pose const &	pose,
		bool const	print_header = `true`
	)		const

inline

References show().

void core::scoring::hbonds::HBondSet::show	(	pose::Pose const &	pose,
		Size const	residue_number,
		bool const	print_header,
		std::ostream &	out
	)		const

Print nicely formated summary of all the hbonds to a specific residue.

Optionally print a header, and then a row for each hydrogen bond in the set using the iterprable version of the hbond show format formatted for easy parsing by R, Excel, etc.

References core::scoring::hbonds::HBond::acc_res(), hbond(), nhbonds(), and core::scoring::hbonds::HBond::show().