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Public Member Functions | Private Member Functions | Private Attributes | List of all members
core::scoring::geometric_solvation::DatabaseOccSolEne Class Reference

#include <DatabaseOccSolEne.hh>

Inheritance diagram for core::scoring::geometric_solvation::DatabaseOccSolEne:
Inheritance graph
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Public Member Functions

 DatabaseOccSolEne (std::string const &etable_name, Real const &min_occ_energy)
 ctor, reads data file More...
 
Real const & operator() (bool const polar_atom_donates, Size const polar_atom_type_index, Size const occ_atom_type_index, OccFitParam des_param) const
 
Real const & atomic_interaction_cutoff () const
 
bool don_type_has_data (Size atom_type_index) const
 tells, for a given atom type, if there are pwSHO parameters for donors having that atom type More...
 
bool acc_type_has_data (Size atom_type_index) const
 tells, for a given atom type, if there are pwSHO parameters for acceptors having that atom type More...
 
bool don_occ_type_has_data (Size atom_type_index) const
 tells, for a given atom type, if there are pwSHO parameters for donor-occluding atoms having that type More...
 
bool acc_occ_type_has_data (Size atom_type_index) const
 tells, for a given atom type, if there are pwSHO parameters for acceptor-occluding atoms having that type More...
 
Size don_type_mapping (Size atom_type_index) const
 maps each atom type to one for which there are pwSHO parameters when atoms of the new type are evaluated as donors More...
 
Size acc_type_mapping (Size atom_type_index) const
 maps each atom type to one for which there are pwSHO parameters when atoms of the new type are evaluated as acceptors More...
 
Size don_occ_type_mapping (Size atom_type_index) const
 maps each atom type to one for which there are pwSHO parameters when atoms of the new type are evaluated as occluding solvent H-bonds to donors More...
 
Size acc_occ_type_mapping (Size atom_type_index) const
 maps each atom type to one for which there are pwSHO parameters when atoms of the new type are evaluated as occluding solvent H-bonds to acceptors More...
 

Private Member Functions

void read_datafile (chemical::AtomTypeSet const &atom_set, std::string const &database_name, utility::vector1< utility::vector1< utility::vector1< Real > > > &occ_data_, bool const process_donors)
 
Real compute_jumpout_diff (Real const &amp, Real const &twice_sigma_sq)
 
void init_to_self_mapping (utility::vector1< Size > &v)
 maps each atom type to itself More...
 
void init_don_mapping (chemical::AtomTypeSet const &atom_set)
 maps donor types not having pwSHO parameters to donor types having them More...
 
void init_acc_mapping (chemical::AtomTypeSet const &atom_set)
 maps acceptor types not having pwSHO parameters to acceptor types having them More...
 
void init_atom_occ_mapping (chemical::AtomTypeSet const &atom_set, utility::vector1< Size > &atom_occ_type_mapping, utility::vector1< bool > const &atom_occ_type_has_data)
 maps occluding-atom types not having pwSHO parameters to occluding-atom types having them More...
 

Private Attributes

utility::vector1
< utility::vector1
< utility::vector1< Real > > > 
donor_occ_data_
 
utility::vector1
< utility::vector1
< utility::vector1< Real > > > 
acc_occ_data_
 
utility::vector1< booldon_type_has_data_
 
utility::vector1< boolacc_type_has_data_
 
utility::vector1< booldon_occ_type_has_data_
 
utility::vector1< boolacc_occ_type_has_data_
 
utility::vector1< Sizedon_type_mapping_
 
utility::vector1< Sizeacc_type_mapping_
 
utility::vector1< Sizedon_occ_type_mapping_
 
utility::vector1< Sizeacc_occ_type_mapping_
 
Real const min_occ_energy_
 
Real atomic_interaction_cutoff_
 
Real const NO_PARAMETERS_
 

Constructor & Destructor Documentation

core::scoring::geometric_solvation::DatabaseOccSolEne::DatabaseOccSolEne ( std::string const &  etable_name,
Real const &  min_occ_energy 
)

Member Function Documentation

bool core::scoring::geometric_solvation::DatabaseOccSolEne::acc_occ_type_has_data ( Size  atom_type_index) const
inline

tells, for a given atom type, if there are pwSHO parameters for acceptor-occluding atoms having that type

References acc_occ_type_has_data_.

Size core::scoring::geometric_solvation::DatabaseOccSolEne::acc_occ_type_mapping ( Size  atom_type_index) const
inline

maps each atom type to one for which there are pwSHO parameters when atoms of the new type are evaluated as occluding solvent H-bonds to acceptors

References acc_occ_type_mapping_.

Referenced by core::energy_methods::OccludedHbondSolEnergy::get_atom_atom_occ_solvation().

bool core::scoring::geometric_solvation::DatabaseOccSolEne::acc_type_has_data ( Size  atom_type_index) const
inline

tells, for a given atom type, if there are pwSHO parameters for acceptors having that atom type

References acc_type_has_data_.

Size core::scoring::geometric_solvation::DatabaseOccSolEne::acc_type_mapping ( Size  atom_type_index) const
inline

maps each atom type to one for which there are pwSHO parameters when atoms of the new type are evaluated as acceptors

References acc_type_mapping_.

Referenced by core::energy_methods::OccludedHbondSolEnergy::get_atom_atom_occ_solvation().

Real const& core::scoring::geometric_solvation::DatabaseOccSolEne::atomic_interaction_cutoff ( ) const
inline
Real core::scoring::geometric_solvation::DatabaseOccSolEne::compute_jumpout_diff ( Real const &  amp,
Real const &  twice_sigma_sq 
)
private

References min_occ_energy_.

Referenced by read_datafile().

bool core::scoring::geometric_solvation::DatabaseOccSolEne::don_occ_type_has_data ( Size  atom_type_index) const
inline

tells, for a given atom type, if there are pwSHO parameters for donor-occluding atoms having that type

References don_occ_type_has_data_.

Size core::scoring::geometric_solvation::DatabaseOccSolEne::don_occ_type_mapping ( Size  atom_type_index) const
inline

maps each atom type to one for which there are pwSHO parameters when atoms of the new type are evaluated as occluding solvent H-bonds to donors

References don_occ_type_mapping_.

Referenced by core::energy_methods::OccludedHbondSolEnergy::get_atom_atom_occ_solvation().

bool core::scoring::geometric_solvation::DatabaseOccSolEne::don_type_has_data ( Size  atom_type_index) const
inline

tells, for a given atom type, if there are pwSHO parameters for donors having that atom type

References don_type_has_data_.

Size core::scoring::geometric_solvation::DatabaseOccSolEne::don_type_mapping ( Size  atom_type_index) const
inline

maps each atom type to one for which there are pwSHO parameters when atoms of the new type are evaluated as donors

References don_type_mapping_.

Referenced by core::energy_methods::OccludedHbondSolEnergy::get_atom_atom_occ_solvation().

void core::scoring::geometric_solvation::DatabaseOccSolEne::init_acc_mapping ( chemical::AtomTypeSet const &  atom_set)
private
void core::scoring::geometric_solvation::DatabaseOccSolEne::init_atom_occ_mapping ( chemical::AtomTypeSet const &  atom_set,
utility::vector1< Size > &  atom_occ_type_mapping,
utility::vector1< bool > const &  atom_occ_type_has_data 
)
private

maps occluding-atom types not having pwSHO parameters to occluding-atom types having them

Parameters
[in]atom_setatom type set
[in,out]atom_occ_type_mappingmaps occluding-atom types not having pwSHO parameters to occluding-atom types having them. Indexed by atom type.
[in]atom_occ_type_has_datatells which occluding-atom types have pwSHO parameters. Indexed by atom type.

References core::chemical::AtomTypeSet::atom_type_index(), init_to_self_mapping(), core::chemical::element::N, and core::chemical::AtomTypeSet::n_atomtypes().

Referenced by DatabaseOccSolEne().

void core::scoring::geometric_solvation::DatabaseOccSolEne::init_don_mapping ( chemical::AtomTypeSet const &  atom_set)
private
void core::scoring::geometric_solvation::DatabaseOccSolEne::init_to_self_mapping ( utility::vector1< Size > &  v)
private

maps each atom type to itself

Parameters
[in]vvector mapping atom types

atom type of index i is mapped to atom type of index i (i=1,...,N, where N is the number of atom types)

References core::chemical::element::N.

Referenced by init_acc_mapping(), init_atom_occ_mapping(), and init_don_mapping().

Real const& core::scoring::geometric_solvation::DatabaseOccSolEne::operator() ( bool const  polar_atom_donates,
Size const  polar_atom_type_index,
Size const  occ_atom_type_index,
OccFitParam  des_param 
) const
inline
void core::scoring::geometric_solvation::DatabaseOccSolEne::read_datafile ( chemical::AtomTypeSet const &  atom_set,
std::string const &  database_name,
utility::vector1< utility::vector1< utility::vector1< Real > > > &  occ_data_,
bool const  process_donors 
)
private

Member Data Documentation

utility::vector1< utility::vector1< utility::vector1< Real > > > core::scoring::geometric_solvation::DatabaseOccSolEne::acc_occ_data_
private
utility::vector1< bool > core::scoring::geometric_solvation::DatabaseOccSolEne::acc_occ_type_has_data_
private
utility::vector1< Size > core::scoring::geometric_solvation::DatabaseOccSolEne::acc_occ_type_mapping_
private
utility::vector1< bool > core::scoring::geometric_solvation::DatabaseOccSolEne::acc_type_has_data_
private
utility::vector1< Size > core::scoring::geometric_solvation::DatabaseOccSolEne::acc_type_mapping_
private
Real core::scoring::geometric_solvation::DatabaseOccSolEne::atomic_interaction_cutoff_
private
utility::vector1< bool > core::scoring::geometric_solvation::DatabaseOccSolEne::don_occ_type_has_data_
private
utility::vector1< Size > core::scoring::geometric_solvation::DatabaseOccSolEne::don_occ_type_mapping_
private
utility::vector1< bool > core::scoring::geometric_solvation::DatabaseOccSolEne::don_type_has_data_
private
utility::vector1< Size > core::scoring::geometric_solvation::DatabaseOccSolEne::don_type_mapping_
private
utility::vector1< utility::vector1< utility::vector1< Real > > > core::scoring::geometric_solvation::DatabaseOccSolEne::donor_occ_data_
private
Real const core::scoring::geometric_solvation::DatabaseOccSolEne::min_occ_energy_
private

Referenced by compute_jumpout_diff().

Real const core::scoring::geometric_solvation::DatabaseOccSolEne::NO_PARAMETERS_
private

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