LKB_ResidueInfo holds the coordinates of the waters attached to a Residue More...

#include <LK_BallInfo.hh>

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

Public Member Functions
	~LKB_ResidueInfo () override

	LKB_ResidueInfo (conformation::Residue const &rsd, bool compute_derivs=false)

	LKB_ResidueInfo (LKB_ResidueInfo const &src)

LKB_ResidueInfo &	operator= (LKB_ResidueInfo const &src)

	LKB_ResidueInfo ()

void	initialize (chemical::ResidueType const &rsd)

basic::datacache::CacheableDataOP	clone () const override

void	build_waters (conformation::Residue const &rsd, bool compute_derivs=false)

WaterBuilders const &	get_water_builder (conformation::Residue const &rsd, Size heavyatom) const

utility::vector1< Size > const &	n_attached_waters () const

Size	n_attached_waters (Size atom_index) const

utility::vector1< Size > const &	water_offset_for_atom () const

Size	water_offset_for_atom (Size atom_index) const

WaterCoords const &	waters () const

utility::vector1< WaterDerivMatrix > const &	atom1_derivs () const

utility::vector1< WaterDerivMatrix > const &	atom2_derivs () const

utility::vector1< WaterDerivMatrix > const &	atom3_derivs () const

bool	has_waters () const

utility::vector1< AtomWeights > const &	atom_weights () const

bool	matches_residue_type (chemical::ResidueType const &rsd_type) const

chemical::ResidueType const &	residue_type () const

Private Attributes
chemical::ResidueTypeCOP	rsd_type_

WaterBuilderForRestypeCOP	water_builders_

WaterCoords	waters_

bool	dwater_datom_ready_ = false

utility::vector1< WaterDerivMatrix >	dwater_datom1_

utility::vector1< WaterDerivMatrix >	dwater_datom2_

utility::vector1< WaterDerivMatrix >	dwater_datom3_

bool	has_waters_ = false

Detailed Description

LKB_ResidueInfo holds the coordinates of the waters attached to a Residue

Constructor & Destructor Documentation

◆ ~LKB_ResidueInfo()

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

overridedefault

Auto-generated virtual destructor

◆ LKB_ResidueInfo() [1/3]

core::scoring::lkball::LKB_ResidueInfo::LKB_ResidueInfo	(	conformation::Residue const &	rsd,
		bool	compute_derivs = `false`
	)

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

◆ LKB_ResidueInfo() [2/3]

core::scoring::lkball::LKB_ResidueInfo::LKB_ResidueInfo ( LKB_ResidueInfo const & src )

default

◆ LKB_ResidueInfo() [3/3]

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

default

Member Function Documentation

◆ atom1_derivs()

utility::vector1< WaterDerivMatrix > const& core::scoring::lkball::LKB_ResidueInfo::atom1_derivs ( ) const

inline

References dwater_datom1_, and dwater_datom_ready_.

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

◆ atom2_derivs()

utility::vector1< WaterDerivMatrix > const& core::scoring::lkball::LKB_ResidueInfo::atom2_derivs ( ) const

inline

References dwater_datom2_, and dwater_datom_ready_.

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

◆ atom3_derivs()

utility::vector1< WaterDerivMatrix > const& core::scoring::lkball::LKB_ResidueInfo::atom3_derivs ( ) const

inline

References dwater_datom3_, and dwater_datom_ready_.

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

◆ atom_weights()

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

inline

References water_builders_.

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

◆ build_waters()

void core::scoring::lkball::LKB_ResidueInfo::build_waters	(	conformation::Residue const &	rsd,
		bool	compute_derivs = `false`
	)

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

◆ clone()

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

override

◆ get_water_builder()

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

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

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

◆ has_waters()

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

inline

References has_waters_.

Referenced by core::scoring::lkball::LK_DomeEnergy::fill_occlusions_1way(), core::scoring::lkball::LKD_ResidueInfo::LKD_ResidueInfo(), and core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::prepare_lkd_infos_and_assign_waters().

◆ initialize()

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(), core::scoring::lkball::LKBallDatabase::has(), and core::scoring::lkball::LKBallDatabase::initialize_residue_type().

◆ matches_residue_type()

bool core::scoring::lkball::LKB_ResidueInfo::matches_residue_type ( chemical::ResidueType const & rsd_type ) const

References rsd_type_.

◆ n_attached_waters() [1/2]

utility::vector1< Size > const& core::scoring::lkball::LKB_ResidueInfo::n_attached_waters ( ) const

inline

References water_builders_.

Referenced by protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid(), core::scoring::lkball::LKD_ResidueInfo::clear_occlusions(), core::scoring::lkball::create_rotamer_descriptor(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::define_active_virtual_sites(), core::scoring::lkball::evaluate_lk_ball_energy_for_atom_ranges(), core::scoring::lkball::evaluate_lk_dome_energy_for_atom_ranges(), core::scoring::lkball::LK_DomeEnergy::fill_occlusions_1way(), core::scoring::lkball::LKD_ResidueInfo::LKD_ResidueInfo(), core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::prepare_lkd_infos_and_assign_waters(), core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::prepare_score_data(), core::scoring::lkball::LK_BallEnergy::sum_deriv_contributions_for_heavyatom_pair_one_way(), and core::scoring::lkball::LK_DomeEnergy::sum_deriv_contributions_for_heavyatom_pair_one_way().

◆ n_attached_waters() [2/2]

Size core::scoring::lkball::LKB_ResidueInfo::n_attached_waters ( Size atom_index ) const

inline

References water_builders_.

◆ operator=()

LKB_ResidueInfo & core::scoring::lkball::LKB_ResidueInfo::operator= ( LKB_ResidueInfo const & src )

default

Referenced by core::scoring::lkball::LKD_ResidueInfo::operator=().

◆ residue_type()

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

References rsd_type_.

◆ water_offset_for_atom() [1/2]

utility::vector1< Size > const& core::scoring::lkball::LKB_ResidueInfo::water_offset_for_atom ( ) const

inline

References water_builders_.

Referenced by protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid(), core::scoring::lkball::create_rotamer_descriptor(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::define_active_virtual_sites(), core::scoring::lkball::evaluate_lk_ball_energy_for_atom_ranges(), core::scoring::lkball::evaluate_lk_dome_energy_for_atom_ranges(), core::scoring::lkball::LK_DomeEnergy::fill_occlusions_1way(), core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::prepare_lkd_infos_and_assign_waters(), core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::prepare_score_data(), core::scoring::lkball::LK_BallEnergy::sum_deriv_contributions_for_heavyatom_pair_one_way(), and core::scoring::lkball::LK_DomeEnergy::sum_deriv_contributions_for_heavyatom_pair_one_way().

◆ water_offset_for_atom() [2/2]

Size core::scoring::lkball::LKB_ResidueInfo::water_offset_for_atom ( Size atom_index ) const

inline

References water_builders_.

◆ waters()

WaterCoords const& core::scoring::lkball::LKB_ResidueInfo::waters ( ) const

inline

References waters_.

Referenced by protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid(), core::scoring::lkball::create_rotamer_descriptor(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::define_active_virtual_sites(), core::scoring::lkball::evaluate_lk_ball_energy_for_atom_ranges(), core::scoring::lkball::evaluate_lk_dome_energy_for_atom_ranges(), core::scoring::lkball::LK_DomeEnergy::fill_occlusions_1way(), core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::prepare_lkd_infos_and_assign_waters(), core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::prepare_score_data(), core::scoring::lkball::LK_BallEnergy::sum_deriv_contributions_for_heavyatom_pair_one_way(), and core::scoring::lkball::LK_DomeEnergy::sum_deriv_contributions_for_heavyatom_pair_one_way().

Member Data Documentation

◆ dwater_datom1_

utility::vector1< WaterDerivMatrix > core::scoring::lkball::LKB_ResidueInfo::dwater_datom1_

private

Referenced by atom1_derivs().

◆ dwater_datom2_

utility::vector1< WaterDerivMatrix > core::scoring::lkball::LKB_ResidueInfo::dwater_datom2_

private

Referenced by atom2_derivs().

◆ dwater_datom3_

utility::vector1< WaterDerivMatrix > core::scoring::lkball::LKB_ResidueInfo::dwater_datom3_

private

Referenced by atom3_derivs().

◆ dwater_datom_ready_

bool core::scoring::lkball::LKB_ResidueInfo::dwater_datom_ready_ = false

private

Referenced by atom1_derivs(), atom2_derivs(), and atom3_derivs().

◆ has_waters_

bool core::scoring::lkball::LKB_ResidueInfo::has_waters_ = false

private

Referenced by has_waters().

◆ rsd_type_

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

private

Referenced by matches_residue_type(), and residue_type().

◆ water_builders_

WaterBuilderForRestypeCOP core::scoring::lkball::LKB_ResidueInfo::water_builders_

private

Referenced by atom_weights(), n_attached_waters(), and water_offset_for_atom().

◆ waters_

WaterCoords core::scoring::lkball::LKB_ResidueInfo::waters_

private

Referenced by waters().

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

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ ~LKB_ResidueInfo()

◆ LKB_ResidueInfo() [1/3]

◆ LKB_ResidueInfo() [2/3]

◆ LKB_ResidueInfo() [3/3]

Member Function Documentation

◆ atom1_derivs()

◆ atom2_derivs()

◆ atom3_derivs()

◆ atom_weights()

◆ build_waters()

◆ clone()

◆ get_water_builder()

◆ has_waters()

◆ initialize()

◆ matches_residue_type()

◆ n_attached_waters() [1/2]

◆ n_attached_waters() [2/2]

◆ operator=()

◆ residue_type()

◆ water_offset_for_atom() [1/2]

◆ water_offset_for_atom() [2/2]

◆ waters()

Member Data Documentation

◆ dwater_datom1_

◆ dwater_datom2_

◆ dwater_datom3_

◆ dwater_datom_ready_

◆ has_waters_

◆ rsd_type_

◆ water_builders_

◆ waters_