core::scoring::lkball::LKB_ResidueInfo Class Reference

#include <LK_BallInfo.hh>

Inheritance diagram for core::scoring::lkball::LKB_ResidueInfo:

Public Types
typedef utility::vector1< Vector >	Vectors

Public Member Functions
virtual	~LKB_ResidueInfo ()
	LKB_ResidueInfo (conformation::Residue const &rsd)
	LKB_ResidueInfo (LKB_ResidueInfo const &src)
	LKB_ResidueInfo ()
void	initialize (chemical::ResidueType const &rsd)
virtual basic::datacache::CacheableDataOP	clone () const
void	build_waters (conformation::Residue const &rsd)
WaterBuilders const &	get_water_builder (conformation::Residue const &rsd, Size heavyatom) const
utility::vector1< Vectors > const &	waters () const
utility::vector1 < utility::vector1 < numeric::xyzMatrix< Real > > > const &	atom1_derivs () const
utility::vector1 < utility::vector1 < numeric::xyzMatrix< Real > > > const &	atom2_derivs () const
utility::vector1 < utility::vector1 < numeric::xyzMatrix< Real > > > const &	atom3_derivs () const
bool	has_waters () const
utility::vector1 < utility::vector1< Real > > const &	atom_weights () const
void	remove_irrelevant_waters (Size const atom, chemical::ResidueType const &rsd_type, utility::vector1< Vector > &waters) const
bool	matches_residue_type (chemical::ResidueType const &rsd_type) const
chemical::ResidueType const &	residue_type () const

Static Public Member Functions
static void	reset_arrays_danger_expert_only ()
	danger More...

Private Types
typedef std::map < chemical::ResidueType const *, utility::vector1 < WaterBuilders > >	WaterBuilderMap
typedef std::map < chemical::ResidueType const *, utility::vector1 < utility::vector1< Real > > >	AtomWeightsMap

Private Member Functions
void	initialize_residue_type (chemical::ResidueType const &rsd_type) const
	called the first time we encounter a given ResidueType More...
void	setup_atom_weights (chemical::ResidueType const &rsd_type, utility::vector1< WaterBuilders > const &rsd_water_builders, utility::vector1< utility::vector1< Real > > &atom_wts) const

Private Attributes
chemical::ResidueTypeCOP	rsd_type_
utility::vector1< Vectors >	waters_
utility::vector1 < utility::vector1 < numeric::xyzMatrix< Real > > >	dwater_datom1_
utility::vector1 < utility::vector1 < numeric::xyzMatrix< Real > > >	dwater_datom2_
utility::vector1 < utility::vector1 < numeric::xyzMatrix< Real > > >	dwater_datom3_
utility::vector1 < utility::vector1< Real > >	atom_weights_
bool	has_waters_

Static Private Attributes
static WaterBuilderMap	water_builder_map_
	note that this number is re-defined in hbonds.cc !! More...
static AtomWeightsMap	atom_weights_map_

Member Typedef Documentation

typedef std::map< chemical::ResidueType const *, utility::vector1< utility::vector1< Real > > > core::scoring::lkball::LKB_ResidueInfo::AtomWeightsMap

private

typedef utility::vector1< Vector > core::scoring::lkball::LKB_ResidueInfo::Vectors

typedef std::map< chemical::ResidueType const *, utility::vector1< WaterBuilders > > core::scoring::lkball::LKB_ResidueInfo::WaterBuilderMap

private

Constructor & Destructor Documentation

core::scoring::lkball::LKB_ResidueInfo::~LKB_ResidueInfo ( )

virtual

Auto-generated virtual destructor

core::scoring::lkball::LKB_ResidueInfo::LKB_ResidueInfo

(

conformation::Residue const &

rsd

)

References core::conformation::Residue::type().

core::scoring::lkball::LKB_ResidueInfo::LKB_ResidueInfo

(

LKB_ResidueInfo const &

src

)

core::scoring::lkball::LKB_ResidueInfo::LKB_ResidueInfo

(

)

Referenced by clone().

Member Function Documentation

utility::vector1< utility::vector1< numeric::xyzMatrix< Real > > > const& core::scoring::lkball::LKB_ResidueInfo::atom1_derivs ( ) const

inline

References dwater_datom1_.

Referenced by core::scoring::lkball::LK_BallEnergy::sum_deriv_contributions_for_heavyatom_pair_one_way().

utility::vector1< utility::vector1< numeric::xyzMatrix< Real > > > const& core::scoring::lkball::LKB_ResidueInfo::atom2_derivs ( ) const

inline

References dwater_datom2_.

Referenced by core::scoring::lkball::LK_BallEnergy::sum_deriv_contributions_for_heavyatom_pair_one_way().

utility::vector1< utility::vector1< numeric::xyzMatrix< Real > > > const& core::scoring::lkball::LKB_ResidueInfo::atom3_derivs ( ) const

inline

References dwater_datom3_.

Referenced by core::scoring::lkball::LK_BallEnergy::sum_deriv_contributions_for_heavyatom_pair_one_way().

utility::vector1< utility::vector1< Real > > const& core::scoring::lkball::LKB_ResidueInfo::atom_weights ( ) const

inline

References atom_weights_.

Referenced by core::scoring::lkball::create_rotamer_descriptor(), core::scoring::lkball::LK_BallEnergy::finalize_total_energy(), core::scoring::lkball::LK_BallEnergy::residue_pair_energy(), and core::scoring::lkball::LK_BallEnergy::sum_deriv_contributions_for_heavyatom_pair_one_way().

void core::scoring::lkball::LKB_ResidueInfo::build_waters

(

conformation::Residue const &

rsd

)

References core::chemical::ResidueType::name(), core::conformation::Residue::nheavyatoms(), and core::conformation::Residue::type().

Referenced by core::scoring::lkball::LK_BallEnergy::setup_for_minimizing_for_residue(), core::scoring::lkball::LK_BallEnergy::setup_for_scoring_for_residue(), and core::scoring::lkball::LK_BallEnergy::update_residue_for_packing().

basic::datacache::CacheableDataOP core::scoring::lkball::LKB_ResidueInfo::clone ( ) const

virtual

References LKB_ResidueInfo().

WaterBuilders const & core::scoring::lkball::LKB_ResidueInfo::get_water_builder	(	conformation::Residue const &	rsd,
		Size	heavyatom
	)		const

References core::chemical::ResidueType::name(), and core::conformation::Residue::type().

Referenced by core::scoring::lkball::LK_BallEnergy::eval_atom_derivative(), and core::scoring::lkball::LK_BallEnergy::sum_deriv_contributions_for_heavyatom_pair_one_way().

bool core::scoring::lkball::LKB_ResidueInfo::has_waters ( ) const

inline

References has_waters_.

void core::scoring::lkball::LKB_ResidueInfo::initialize

(

chemical::ResidueType const &

rsd

)

resize the waters_ array set has_waters_ setup atom_weights_ fpd setup dwater_datom*_

References core::chemical::ResidueType::get_self_ptr(), and core::chemical::ResidueType::nheavyatoms().

Referenced by core::scoring::lkball::LK_BallEnergy::setup_for_minimizing_for_residue(), core::scoring::lkball::LK_BallEnergy::setup_for_scoring_for_residue(), and core::scoring::lkball::LK_BallEnergy::update_residue_for_packing().

void core::scoring::lkball::LKB_ResidueInfo::initialize_residue_type ( chemical::ResidueType const &  rsd_type ) const

private

called the first time we encounter a given ResidueType

References core::chemical::ResidueType::name(), core::scoring::lkball::setup_water_builders_for_residue_type(), and core::scoring::lkball::TR().

bool core::scoring::lkball::LKB_ResidueInfo::matches_residue_type

(

chemical::ResidueType const &

rsd_type

)

const

References rsd_type_.

Referenced by core::scoring::lkball::LK_BallEnergy::setup_for_scoring_for_residue(), and core::scoring::lkball::LK_BallEnergy::update_residue_for_packing().

void core::scoring::lkball::LKB_ResidueInfo::remove_irrelevant_waters	(	Size const	atom,
		chemical::ResidueType const &	rsd_type,
		utility::vector1< Vector > &	waters
	)		const

References core::chemical::ResidueType::atom_base(), core::chemical::ResidueType::atom_is_hydrogen(), and water_builder_map_.

void core::scoring::lkball::LKB_ResidueInfo::reset_arrays_danger_expert_only ( )

static

danger

References atom_weights_map_, and water_builder_map_.

chemical::ResidueType const & core::scoring::lkball::LKB_ResidueInfo::residue_type

(

)

const

References rsd_type_.

Referenced by core::scoring::lkball::LK_BallEnergy::setup_for_scoring_for_residue(), and core::scoring::lkball::LK_BallEnergy::update_residue_for_packing().

void core::scoring::lkball::LKB_ResidueInfo::setup_atom_weights ( chemical::ResidueType const &  rsd_type, utility::vector1< WaterBuilders > const &  rsd_water_builders, utility::vector1< utility::vector1< Real > > &  atom_wts  ) const

private

References protocols::comparative_modeling::features::A, core::chemical::ResidueType::aa(), core::chemical::aa_from_oneletter_code(), core::chemical::aa_pro, core::chemical::ResidueType::atom_is_backbone(), core::chemical::ResidueType::atom_name(), core::chemical::ResidueType::atom_type(), core::chemical::ResidueType::atom_type_set(), core::chemical::AtomType::extra_parameter(), core::chemical::element::F, core::init::init(), core::chemical::AtomType::is_acceptor(), core::chemical::AtomType::is_donor(), core::chemical::ResidueType::is_lower_terminus(), core::chemical::ResidueType::is_upper_terminus(), core::chemical::AtomType::name(), core::chemical::ResidueType::name(), core::chemical::ResidueType::name1(), core::chemical::ResidueType::natoms(), core::chemical::ResidueType::nheavyatoms(), core::chemical::num_aa_types, and core::scoring::lkball::TR().

utility::vector1< Vectors > const& core::scoring::lkball::LKB_ResidueInfo::waters ( ) const

inline

References waters_.

Referenced by core::scoring::lkball::create_rotamer_descriptor(), core::scoring::lkball::LK_BallEnergy::eval_atom_derivative(), core::scoring::lkball::LK_BallEnergy::finalize_total_energy(), core::scoring::lkball::LK_BallEnergy::residue_pair_energy(), and core::scoring::lkball::LK_BallEnergy::sum_deriv_contributions_for_heavyatom_pair_one_way().

Member Data Documentation

utility::vector1< utility::vector1< Real > > core::scoring::lkball::LKB_ResidueInfo::atom_weights_

private

Referenced by atom_weights().

LKB_ResidueInfo::AtomWeightsMap core::scoring::lkball::LKB_ResidueInfo::atom_weights_map_

staticprivate

Referenced by reset_arrays_danger_expert_only().

utility::vector1< utility::vector1< numeric::xyzMatrix< Real > > > core::scoring::lkball::LKB_ResidueInfo::dwater_datom1_

private

Referenced by atom1_derivs().

utility::vector1< utility::vector1< numeric::xyzMatrix< Real > > > core::scoring::lkball::LKB_ResidueInfo::dwater_datom2_

private

Referenced by atom2_derivs().

utility::vector1< utility::vector1< numeric::xyzMatrix< Real > > > core::scoring::lkball::LKB_ResidueInfo::dwater_datom3_

private

Referenced by atom3_derivs().

bool core::scoring::lkball::LKB_ResidueInfo::has_waters_

private

Referenced by has_waters().

chemical::ResidueTypeCOP core::scoring::lkball::LKB_ResidueInfo::rsd_type_

private

Referenced by matches_residue_type(), and residue_type().

LKB_ResidueInfo::WaterBuilderMap core::scoring::lkball::LKB_ResidueInfo::water_builder_map_

staticprivate

note that this number is re-defined in hbonds.cc !!

Not doing backbone waters on protein or DNA

Referenced by remove_irrelevant_waters(), and reset_arrays_danger_expert_only().

utility::vector1< Vectors > core::scoring::lkball::LKB_ResidueInfo::waters_

private

Referenced by waters().

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

• src/core/scoring/lkball/LK_BallInfo.hh
• src/core/scoring/lkball/LK_BallInfo.cc