Rosetta Core  2014.35
Classes | Typedefs | Enumerations | Functions | Variables
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

Enumeration Type Documentation

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 
)
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 
)
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 
)

Variable Documentation

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