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core::scoring::hbonds::HBondSet Class Reference

#include <HBondSet.hh>

Inheritance diagram for core::scoring::hbonds::HBondSet:
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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< HBondOPhbonds_
 
utility::vector1< boolbackbone_backbone_donor_
 
utility::vector1< boolbackbone_backbone_acceptor_
 
utility::vector1< intnbrs_
 
HBondAtomMap atom_map_
 
bool atom_map_init_
 

Static Private Attributes

static utility::vector1< HBondCOPempty_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...
 

Member Typedef Documentation

Constructor & Destructor Documentation

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

Referenced by clone().

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

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.

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

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

Member Function Documentation

bool core::scoring::hbonds::HBondSet::acc_bbg_in_bb_bb_hbond ( Size const  residue) const
bool core::scoring::hbonds::HBondSet::allow_hbond ( Size const  index) const
bool core::scoring::hbonds::HBondSet::allow_hbond ( HBond const &  hbond) const
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 
)
utility::vector1< HBondCOP > const & core::scoring::hbonds::HBondSet::atom_hbonds ( AtomID const &  atom) const

Get a vector of all the hbonds involving this atom.

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 ( )
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)
bool core::scoring::hbonds::HBondSet::don_bbg_in_bb_bb_hbond ( Size const  residue) const
HBond const & core::scoring::hbonds::HBondSet::hbond ( Size const  number) const
HBondOptions const & core::scoring::hbonds::HBondSet::hbond_options ( ) const
int core::scoring::hbonds::HBondSet::nbrs ( Size const  seqpos) const
Size core::scoring::hbonds::HBondSet::nhbonds ( ) const
void core::scoring::hbonds::HBondSet::resize_bb_donor_acceptor_arrays ( Size const  new_dimension)
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.

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.

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 
)

References nbrs_.

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

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

References show().

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

Friends And Related Function Documentation

std::ostream& operator<< ( std::ostream &  out,
const HBondSet hbond_set 
)
friend
bool operator== ( HBondSet const &  a,
HBondSet const &  b 
)
friend

equality operator

Member Data Documentation

HBondAtomMap core::scoring::hbonds::HBondSet::atom_map_
mutableprivate
bool core::scoring::hbonds::HBondSet::atom_map_init_
mutableprivate
utility::vector1< bool > core::scoring::hbonds::HBondSet::backbone_backbone_acceptor_
private
utility::vector1< bool > core::scoring::hbonds::HBondSet::backbone_backbone_donor_
private
utility::vector1< HBondCOP > core::scoring::hbonds::HBondSet::empty_list_of_hbonds_
staticprivate

Referenced by atom_hbonds().

utility::vector1< HBondOP > core::scoring::hbonds::HBondSet::hbonds_
private
utility::vector1< int > core::scoring::hbonds::HBondSet::nbrs_
private
HBondOptionsCOP core::scoring::hbonds::HBondSet::options_
private

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