#include <HBondSet.hh>

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

Collaboration diagram for core::scoring::hbonds::HBondSet:

Public Types
typedef id::AtomID	AtomID

Public Member Functions
	HBondSet ()

	~HBondSet ()

	HBondSet (Size const nres)

	HBondSet (HBondOptions const &options)

	HBondSet (HBondOptions const &options, Size const nres)

	HBondSet (pose::Pose &pose)
	convenience constructor: Find all the hbonds in the pose. More...

	HBondSet (HBondOptions const &options, pose::Pose &pose)
	convenience constructor: Find all the hbonds in the pose. 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...

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

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

int	nbrs (Size const seqpos) const

void	set_nbrs (Size const seqpos, Size value)

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

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

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

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

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

void	clear ()
	Delete all the data. 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	setup_for_residue_pair_energies (pose::Pose const &pose, bool const calculate_derivative=false, bool const backbone_only=true)

void	sort_by_weighted_energy ()

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

void	set_hbond_options (HBondOptions const &options)
	set the hbond options for this hbond set; clears all hbonds already stored 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 std::map< AtomID, utility::vector1< HBondCOP > >	HBondAtomMap

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_

Static Private Attributes
static utility::vector1< HBondCOP >	empty_list_of_hbonds_

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

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

Detailed Description

Definition at line 216 of file HBondSet.hh.

Member Typedef Documentation

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

Definition at line 245 of file HBondSet.hh.

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

private

Definition at line 393 of file HBondSet.hh.

Constructor & Destructor Documentation

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

Definition at line 374 of file HBondSet.cc.

Referenced by clone().

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

Definition at line 379 of file HBondSet.cc.

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

Definition at line 381 of file HBondSet.cc.

References resize_bb_donor_acceptor_arrays().

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

Definition at line 393 of file HBondSet.cc.

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

Definition at line 398 of file HBondSet.cc.

References resize_bb_donor_acceptor_arrays().

core::scoring::hbonds::HBondSet::HBondSet ( pose::Pose & pose)

convenience constructor: Find all the hbonds in the pose.

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.

Definition at line 410 of file HBondSet.cc.

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

core::scoring::hbonds::HBondSet::HBondSet	(	HBondOptions const &	opts,
		pose::Pose &	pose
	)

convenience constructor: Find all the hbonds in the pose.

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.

Definition at line 424 of file HBondSet.cc.

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

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

copy ctor

Definition at line 436 of file HBondSet.cc.

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

Definition at line 451 of file HBondSet.cc.

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

Definition at line 478 of file HBondSet.cc.

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

Definition at line 500 of file HBondSet.cc.

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?

Definition at line 638 of file HBondSet.cc.

References backbone_backbone_acceptor_.

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

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

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

Definition at line 615 of file HBondSet.cc.

References hbonds_.

Referenced by core::optimization::AtomTreeMultifunc::dump(), core::optimization::CartesianMultifunc::dump(), core::optimization::symmetry::SymAtomTreeMultifunc::dump(), core::scoring::hbonds::get_hbond_energies(), and setup_atom_map().

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

Definition at line 621 of file HBondSet.cc.

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.

Definition at line 561 of file HBondSet.cc.

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::hbonds::fill_hbond_set_by_AHdist_threshold(), core::scoring::WaterAdductHBondPotential::get_residue_residue_h2o_hbonds_1way(), core::scoring::hbonds::identify_hbonds_1way(), 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) const

Get a vector of all the hbonds involving this atom.

Definition at line 652 of file HBondSet.cc.

References atom_map_, empty_list_of_hbonds_, and setup_atom_map().

Referenced by core::scoring::methods::WaterAdductHBondEnergy::get_atom_h2o_hbond_derivative().

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

Delete all the data.

Definition at line 663 of file HBondSet.cc.

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

Referenced by 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

Definition at line 523 of file HBondSet.cc.

References HBondSet().

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

Definition at line 691 of file HBondSet.cc.

References backbone_backbone_acceptor_, and backbone_backbone_donor_.

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?

Definition at line 645 of file HBondSet.cc.

References backbone_backbone_donor_.

Referenced by core::scoring::hbonds::HBondEnergy::backbone_sidechain_energy(), core::scoring::hbonds::create_rotamer_descriptor(), core::scoring::geometric_solvation::GeometricSolEnergy::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.

Definition at line 552 of file HBondSet.cc.

References hbonds_.

Referenced by core::optimization::AtomTreeMultifunc::dump(), core::optimization::CartesianMultifunc::dump(), core::optimization::symmetry::SymAtomTreeMultifunc::dump(), core::scoring::hbonds::get_hbond_energies(), hbonded(), HBondSet(), core::scoring::symmetry::SymmetricScoreFunction::intersubunit_hbond_energy(), core::scoring::hbonds::operator==(), protocols::features::HBondFeatures::report_features(), setup_atom_map(), and show().

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

Read access to the stored hbond options.

Definition at line 791 of file HBondSet.cc.

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_membrane(), core::scoring::hbonds::identify_intra_res_hbonds(), and protocols::features::HBondFeatures::report_features().

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

Definition at line 538 of file HBondSet.cc.

References nbrs_.

Referenced by core::scoring::hbonds::HBondEnergy::backbone_backbone_energy(), core::scoring::hbonds::HBondEnergy::backbone_sidechain_energy(), core::scoring::hbonds::HBondEnergy::evaluate_rotamer_background_energies(), core::scoring::hbonds::HBondEnergy::evaluate_rotamer_pair_energies(), core::scoring::hbonds::HBondEnergy::residue_pair_energy(), and core::scoring::hbonds::HBondEnergy::setup_for_minimizing_for_residue().

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

Number of hbonds.

Definition at line 530 of file HBondSet.cc.

References hbonds_.

Referenced by protocols::toolbox::pose_metric_calculators::NumberHBondsCalculator::compute_Hbonds_for_residue(), core::optimization::AtomTreeMultifunc::dump(), core::optimization::CartesianMultifunc::dump(), core::optimization::symmetry::SymAtomTreeMultifunc::dump(), core::scoring::hbonds::get_hbond_energies(), hbonded(), HBondSet(), core::scoring::symmetry::SymmetricScoreFunction::intersubunit_hbond_energy(), core::scoring::hbonds::operator==(), protocols::features::HBondFeatures::report_features(), and show().

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

Resize bb info arrays.

Definition at line 684 of file HBondSet.cc.

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

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

Definition at line 299 of file HBondSet.hh.

References backbone_backbone_acceptor_.

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

inline

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

Definition at line 306 of file HBondSet.hh.

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

Definition at line 796 of file HBondSet.cc.

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
	)

Definition at line 544 of file HBondSet.cc.

References nbrs_.

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

Setup the mapping from atoms to hbonds.

Definition at line 705 of file HBondSet.cc.

References core::scoring::hbonds::HBond::acc_atm(), core::scoring::hbonds::HBond::acc_res(), allow_hbond(), atom_map_, atom_map_init_, core::scoring::hbonds::HBond::don_hatm(), core::scoring::hbonds::HBond::don_res(), hbond(), 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`
	)

Definition at line 729 of file HBondSet.cc.

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(), nbrs_, core::pose::Pose::residue(), core::pose::Pose::residue_type(), resize_bb_donor_acceptor_arrays(), core::scoring::Energies::tenA_neighbor_graph(), and core::pose::Pose::total_residue().

Referenced by protocols::toolbox::pose_metric_calculators::find_res_unsat_polars(), hbonded(), 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.

Definition at line 809 of file HBondSet.cc.

References hbond(), and nhbonds().

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

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

inline

Definition at line 357 of file HBondSet.hh.

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.

Definition at line 851 of file HBondSet.cc.

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

Definition at line 367 of file HBondSet.hh.

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.

Definition at line 868 of file HBondSet.cc.

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