core::scoring::geometric_solvation Namespace Reference

Classes
class	ContextDependentGeometricSolEnergy
class	ContextDependentGeometricSolEnergyCreator
class	ContextIndependentGeometricSolEnergy
class	ContextIndependentGeometricSolEnergyCreator
class	DatabaseOccSolEne
class	ExactOccludedHbondSolEnergy
class	ExactOccludedHbondSolEnergyCreator
class	GeometricSolEnergyEvaluator
class	GridInfo
class	OccludedHbondSolEnergy
class	OccludedHbondSolEnergy_onebody
class	OccludedHbondSolEnergy_onebodyCreator
class	OccludedHbondSolEnergyCreator
class	WaterWeightGridSet

Typedefs
typedef utility::pointer::owning_ptr < DatabaseOccSolEne >	DatabaseOccSolEneOP
typedef utility::pointer::owning_ptr < DatabaseOccSolEne const >	DatabaseOccSolEneCOP
typedef std::map < hbonds::HBEvalType, std::vector< std::vector < std::vector< core::Real > > > >::const_iterator	all_water_weights_iterator
typedef std::map < hbonds::HBEvalType, core::Real >::const_iterator	sum_water_weights_iterator
typedef utility::pointer::owning_ptr < GeometricSolEnergyEvaluator >	GeometricSolEnergyEvaluatorOP
typedef utility::pointer::owning_ptr < GeometricSolEnergyEvaluator const >	GeometricSolEnergyEvaluatorCOP

Enumerations
enum	OccFitParam {   OccFitParam_amp = 1, OccFitParam_dist_mu, OccFitParam_twice_dist_sigma_sq, OccFitParam_cos_angle_mu,   OccFitParam_twice_cos_angle_sigma_sq, OccFitParam_max_sq_dist, OccFitParam_min_cos_angle, OccFitParam_num_params = OccFitParam_min_cos_angle }

Functions
void	fill_atom_derivs_for_donor (hbonds::HBondDerivs const &deriv, core::conformation::Residue const &don_rsd, Size const don_hatm, Size const occatm, utility::vector1< DerivVectorPair > &don_atom_derivs, utility::vector1< DerivVectorPair > &occ_atom_derivs, hbonds::HBEvalTuple const &, hbonds::HBondOptions const &, Real const &weighted_energy)
void	fill_atom_derivs_for_acceptor (hbonds::HBondDerivs const &deriv, core::conformation::Residue const &acc_rsd, Size const aatm, Size const occatm, utility::vector1< DerivVectorPair > &acc_atom_derivs, utility::vector1< DerivVectorPair > &occ_atom_derivs, hbonds::HBEvalTuple const &hbe_type, hbonds::HBondOptions const &hbond_options, Real const &weighted_energy)
void	add_to_individual_sol_energies (pose::Pose &input_pose, core::Size const polar_resnum, core::Size const polar_atomno, core::scoring::etable::EtableOP etable_ptr, GridInfo const &grid_info, core::Real const &grid_constant, std::vector< std::vector< std::vector< core::Real > > > const &water_weights, std::vector< std::vector< std::vector< bool > > > &occluded_sites, bool const hydrogens_can_occlude, bool const pairwise_additive, bool const pairwise_additive_output, utility::vector1< core::Real > &residue_energies)
core::Real	compute_exact_geosol (pose::Pose &input_pose, bool const hydrogens_can_occlude, bool const pairwise_additive, bool const pairwise_additive_output, utility::vector1< core::Real > &residue_energies)

Variables
static basic::Tracer	tr ("core.scoring.DatabaseOccSolEne")
core::Real const	geosol_kT = { 0.593 }
core::Real const	max_possible_LK = { -5 }
core::Real const	LK_MATCHING_WEIGHT_EXACT = { 0.387829 }
core::Real const	SKIP_HBONDER_CUT = { -0.1 }
core::Real const	LK_MATCHING_WEIGHT_OLD_EXACT = { 0.23968 }
Vector	dummy_deriv_vector_
core::Real const	MIN_OCC_ENERGY = { 0.01 }

Typedef Documentation

typedef std::map< hbonds::HBEvalType, std::vector < std::vector < std::vector <core::Real> > > >::const_iterator core::scoring::geometric_solvation::all_water_weights_iterator

typedef utility::pointer::owning_ptr< DatabaseOccSolEne const > core::scoring::geometric_solvation::DatabaseOccSolEneCOP

typedef utility::pointer::owning_ptr< DatabaseOccSolEne > core::scoring::geometric_solvation::DatabaseOccSolEneOP

typedef utility::pointer::owning_ptr< GeometricSolEnergyEvaluator const > core::scoring::geometric_solvation::GeometricSolEnergyEvaluatorCOP

typedef utility::pointer::owning_ptr< GeometricSolEnergyEvaluator > core::scoring::geometric_solvation::GeometricSolEnergyEvaluatorOP

typedef std::map< hbonds::HBEvalType, core::Real>::const_iterator core::scoring::geometric_solvation::sum_water_weights_iterator

Enumeration Type Documentation

enum core::scoring::geometric_solvation::OccFitParam

Enumerator
OccFitParam_amp
OccFitParam_dist_mu
OccFitParam_twice_dist_sigma_sq
OccFitParam_cos_angle_mu
OccFitParam_twice_cos_angle_sigma_sq
OccFitParam_max_sq_dist
OccFitParam_min_cos_angle
OccFitParam_num_params

Function Documentation

void core::scoring::geometric_solvation::add_to_individual_sol_energies	(	pose::Pose &	input_pose,
		core::Size const	polar_resnum,
		core::Size const	polar_atomno,
		core::scoring::etable::EtableOP	etable_ptr,
		GridInfo const &	grid_info,
		core::Real const &	grid_constant,
		std::vector< std::vector< std::vector< core::Real > > > const &	water_weights,
		std::vector< std::vector< std::vector< bool > > > &	occluded_sites,
		bool const	hydrogens_can_occlude,
		bool const	pairwise_additive,
		bool const	pairwise_additive_output,
		utility::vector1< core::Real > &	residue_energies
	)

References core::conformation::Residue::atom(), core::conformation::Residue::atom_base(), core::conformation::Residue::atom_is_hydrogen(), core::conformation::Residue::atom_type_index(), core::graph::Node::const_edge_list_end(), cross_product(), numeric::xyzVector< class >::distance(), numeric::xyzVector< class >::dot(), core::pose::Pose::energies(), exit, geosol_kT, core::graph::Edge::get_node(), log(), numeric::xyzVector< class >::magnitude(), core::conformation::Residue::natoms(), numeric::xyzVector< class >::normalize(), numeric::xyzVector< class >::normalized(), core::pose::Pose::residue(), core::scoring::Energies::tenA_neighbor_graph(), core::scoring::TR, numeric::xyzVector< class >::x(), core::scoring::geometric_solvation::GridInfo::xnum_points(), core::scoring::geometric_solvation::GridInfo::xorigin(), core::scoring::geometric_solvation::GridInfo::xstep(), numeric::xyzMatrix< class >::xx(), numeric::xyzMatrix< class >::xy(), core::conformation::Atom::xyz(), numeric::xyzMatrix< class >::xz(), numeric::xyzVector< class >::y(), core::scoring::geometric_solvation::GridInfo::ynum_points(), core::scoring::geometric_solvation::GridInfo::yorigin(), core::scoring::geometric_solvation::GridInfo::ystep(), numeric::xyzMatrix< class >::yx(), numeric::xyzMatrix< class >::yy(), numeric::xyzMatrix< class >::yz(), numeric::xyzVector< class >::z(), core::scoring::geometric_solvation::GridInfo::znum_points(), core::scoring::geometric_solvation::GridInfo::zorigin(), core::scoring::geometric_solvation::GridInfo::zstep(), numeric::xyzMatrix< class >::zx(), numeric::xyzMatrix< class >::zy(), and numeric::xyzMatrix< class >::zz().

Referenced by compute_exact_geosol().

core::Real core::scoring::geometric_solvation::compute_exact_geosol	(	pose::Pose &	input_pose,
		bool const	hydrogens_can_occlude,
		bool const	pairwise_additive,
		bool const	pairwise_additive_output,
		utility::vector1< core::Real > &	residue_energies
	)

References core::conformation::Residue::accpt_pos(), add_to_individual_sol_energies(), core::conformation::Residue::atom_base(), core::conformation::Residue::atom_name(), core::conformation::Residue::atom_type_index(), core::chemical::FA_STANDARD, geosol_kT, core::scoring::hbonds::get_hb_acc_chem_type(), core::scoring::hbonds::get_hb_don_chem_type(), core::scoring::geometric_solvation::GridInfo::get_instance(), core::chemical::ChemicalManager::get_instance(), core::scoring::geometric_solvation::WaterWeightGridSet::get_instance(), core::scoring::geometric_solvation::WaterWeightGridSet::get_sum_water_weight_grid(), core::scoring::hbonds::hbacc_H2O, core::scoring::hbonds::hbdon_H2O, core::scoring::hbonds::HBEval_lookup, core::conformation::Residue::Hpos_polar(), core::conformation::Residue::is_lower_terminus(), LK_MATCHING_WEIGHT_OLD_EXACT, max_possible_LK, core::pose::Pose::residue(), core::scoring::hbonds::seq_sep_other, core::pose::Pose::total_residue(), core::scoring::TR, core::scoring::geometric_solvation::GridInfo::xnum_points(), and core::scoring::geometric_solvation::GridInfo::ynum_points().

void core::scoring::geometric_solvation::fill_atom_derivs_for_acceptor	(	hbonds::HBondDerivs const &	deriv,
		core::conformation::Residue const &	acc_rsd,
		Size const	aatm,
		Size const	occatm,
		utility::vector1< DerivVectorPair > &	acc_atom_derivs,
		utility::vector1< DerivVectorPair > &	occ_atom_derivs,
		hbonds::HBEvalTuple const &	hbe_type,
		hbonds::HBondOptions const &	hbond_options,
		Real const &	weighted_energy
	)

References core::conformation::Residue::abase2(), core::scoring::hbonds::HBondDerivs::abase2_deriv, core::scoring::hbonds::HBondDerivs::abase_deriv, core::scoring::hbonds::HBondDerivs::acc_deriv, core::scoring::hbonds::assign_abase_derivs(), core::scoring::hbonds::HBondDerivs::don_deriv, core::scoring::DerivVectorPair::f1(), core::scoring::DerivVectorPair::f2(), and core::scoring::hbonds::HBondDerivs::h_deriv.

Referenced by core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_intrares_derivatives(), and core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_residue_pair_derivatives().

void core::scoring::geometric_solvation::fill_atom_derivs_for_donor	(	hbonds::HBondDerivs const &	deriv,
		core::conformation::Residue const &	don_rsd,
		Size const	don_hatm,
		Size const	occatm,
		utility::vector1< DerivVectorPair > &	don_atom_derivs,
		utility::vector1< DerivVectorPair > &	occ_atom_derivs,
		hbonds::HBEvalTuple const &	,
		hbonds::HBondOptions const &	,
		Real const &	weighted_energy
	)

References core::scoring::hbonds::HBondDerivs::abase2_deriv, core::scoring::hbonds::HBondDerivs::abase_deriv, core::scoring::hbonds::HBondDerivs::acc_deriv, core::conformation::Residue::atom_base(), core::scoring::hbonds::HBondDerivs::don_deriv, core::scoring::DerivVectorPair::f1(), core::scoring::DerivVectorPair::f2(), and core::scoring::hbonds::HBondDerivs::h_deriv.

Referenced by core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_intrares_derivatives(), and core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::eval_residue_pair_derivatives().

Variable Documentation

Vector core::scoring::geometric_solvation::dummy_deriv_vector_

core::Real const core::scoring::geometric_solvation::geosol_kT = { 0.593 }

Referenced by add_to_individual_sol_energies(), compute_exact_geosol(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_grid_constant(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_polar_group_sol_energy(), core::scoring::geometric_solvation::WaterWeightGridSet::fill_water_grid(), and core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::residue_energy().

core::Real const core::scoring::geometric_solvation::LK_MATCHING_WEIGHT_EXACT = { 0.387829 }

Referenced by core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::residue_energy().

core::Real const core::scoring::geometric_solvation::LK_MATCHING_WEIGHT_OLD_EXACT = { 0.23968 }

Referenced by compute_exact_geosol().

core::Real const core::scoring::geometric_solvation::max_possible_LK = { -5 }

Referenced by compute_exact_geosol(), core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_grid_constant(), and core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::residue_energy().

core::Real const core::scoring::geometric_solvation::MIN_OCC_ENERGY = { 0.01 }

core::Real const core::scoring::geometric_solvation::SKIP_HBONDER_CUT = { -0.1 }

Referenced by core::scoring::geometric_solvation::ExactOccludedHbondSolEnergy::compute_polar_group_sol_energy().

basic::Tracer core::scoring::geometric_solvation::tr("core.scoring.DatabaseOccSolEne")

static

Referenced by core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::atomic_interaction_cutoff(), core::scoring::geometric_solvation::DatabaseOccSolEne::DatabaseOccSolEne(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::eval_intrares_energy(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::get_atom_atom_occ_solvation(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::OccludedHbondSolEnergy(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::OccludedHbondSolEnergy_onebody(), core::scoring::geometric_solvation::OccludedHbondSolEnergy::residue_pair_energy(), core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::setup_for_derivatives(), and core::scoring::geometric_solvation::OccludedHbondSolEnergy_onebody::setup_for_minimizing().