core::scoring::geometric_solvation::DatabaseOccSolEne Class Reference

#include <DatabaseOccSolEne.hh>

Inheritance diagram for core::scoring::geometric_solvation::DatabaseOccSolEne:

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< bool >	don_type_has_data_
utility::vector1< bool >	acc_type_has_data_
utility::vector1< bool >	don_occ_type_has_data_
utility::vector1< bool >	acc_occ_type_has_data_
utility::vector1< Size >	don_type_mapping_
utility::vector1< Size >	acc_type_mapping_
utility::vector1< Size >	don_occ_type_mapping_
utility::vector1< Size >	acc_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
	)

ctor, reads data file

ctor, reads data file. Need to configure to allow alternate tables/atom_sets

References acc_occ_data_, acc_occ_type_has_data_, acc_occ_type_mapping_, acc_type_has_data_, atomic_interaction_cutoff_, core::chemical::AtomTypeSet::directory(), don_occ_type_has_data_, don_occ_type_mapping_, don_type_has_data_, donor_occ_data_, core::chemical::FA_STANDARD, core::scoring::FA_STANDARD_DEFAULT, init_acc_mapping(), init_atom_occ_mapping(), init_don_mapping(), core::chemical::AtomTypeSet::n_atomtypes(), and read_datafile().

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

References atomic_interaction_cutoff_.

Referenced by core::energy_methods::OccludedHbondSolEnergy_onebody::atomic_interaction_cutoff(), core::energy_methods::OccludedHbondSolEnergy::atomic_interaction_cutoff(), core::energy_methods::OccludedHbondSolEnergy::eval_residue_pair_derivatives_one_way(), and core::energy_methods::OccludedHbondSolEnergy::res_res_occ_sol_one_way().

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

maps acceptor types not having pwSHO parameters to acceptor types having them

Parameters

[in]

atom_set

atom type set

References acc_occ_data_, acc_type_has_data_, acc_type_mapping_, core::chemical::AtomTypeSet::atom_type_index(), init_to_self_mapping(), core::chemical::element::N, core::chemical::AtomTypeSet::n_atomtypes(), NO_PARAMETERS_, and core::scoring::geometric_solvation::OccFitParam_amp.

Referenced by DatabaseOccSolEne().

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_set	atom type set
[in,out]	atom_occ_type_mapping	maps occluding-atom types not having pwSHO parameters to occluding-atom types having them. Indexed by atom type.
[in]	atom_occ_type_has_data	tells 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

maps donor types not having pwSHO parameters to donor types having them

Parameters

[in]

atom_set

atom type set

References core::chemical::AtomTypeSet::atom_type_index(), don_type_has_data_, don_type_mapping_, donor_occ_data_, init_to_self_mapping(), core::chemical::element::N, core::chemical::AtomTypeSet::n_atomtypes(), NO_PARAMETERS_, and core::scoring::geometric_solvation::OccFitParam_amp.

Referenced by DatabaseOccSolEne().

void core::scoring::geometric_solvation::DatabaseOccSolEne::init_to_self_mapping ( utility::vector1< Size > &  v )

private

maps each atom type to itself

Parameters

[in]

v

vector 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

References acc_occ_data_, donor_occ_data_, and NO_PARAMETERS_.

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

References acc_occ_type_has_data_, acc_type_has_data_, core::chemical::AtomTypeSet::atom_type_index(), atomic_interaction_cutoff_, compute_jumpout_diff(), don_occ_type_has_data_, don_type_has_data_, core::chemical::AtomTypeSet::n_atomtypes(), NO_PARAMETERS_, core::scoring::geometric_solvation::OccFitParam_amp, core::scoring::geometric_solvation::OccFitParam_cos_angle_mu, core::scoring::geometric_solvation::OccFitParam_dist_mu, core::scoring::geometric_solvation::OccFitParam_max_sq_dist, core::scoring::geometric_solvation::OccFitParam_min_cos_angle, core::scoring::geometric_solvation::OccFitParam_num_params, core::scoring::geometric_solvation::OccFitParam_twice_cos_angle_sigma_sq, and core::scoring::geometric_solvation::OccFitParam_twice_dist_sigma_sq.

Referenced by DatabaseOccSolEne().

Member Data Documentation

utility::vector1< utility::vector1< utility::vector1< Real > > > core::scoring::geometric_solvation::DatabaseOccSolEne::acc_occ_data_

private

Referenced by DatabaseOccSolEne(), init_acc_mapping(), and operator()().

utility::vector1< bool > core::scoring::geometric_solvation::DatabaseOccSolEne::acc_occ_type_has_data_

private

Referenced by acc_occ_type_has_data(), DatabaseOccSolEne(), and read_datafile().

utility::vector1< Size > core::scoring::geometric_solvation::DatabaseOccSolEne::acc_occ_type_mapping_

private

Referenced by acc_occ_type_mapping(), and DatabaseOccSolEne().

utility::vector1< bool > core::scoring::geometric_solvation::DatabaseOccSolEne::acc_type_has_data_

private

Referenced by acc_type_has_data(), DatabaseOccSolEne(), init_acc_mapping(), and read_datafile().

utility::vector1< Size > core::scoring::geometric_solvation::DatabaseOccSolEne::acc_type_mapping_

private

Referenced by acc_type_mapping(), and init_acc_mapping().

Real core::scoring::geometric_solvation::DatabaseOccSolEne::atomic_interaction_cutoff_

private

Referenced by atomic_interaction_cutoff(), DatabaseOccSolEne(), and read_datafile().

utility::vector1< bool > core::scoring::geometric_solvation::DatabaseOccSolEne::don_occ_type_has_data_

private

Referenced by DatabaseOccSolEne(), don_occ_type_has_data(), and read_datafile().

utility::vector1< Size > core::scoring::geometric_solvation::DatabaseOccSolEne::don_occ_type_mapping_

private

Referenced by DatabaseOccSolEne(), and don_occ_type_mapping().

utility::vector1< bool > core::scoring::geometric_solvation::DatabaseOccSolEne::don_type_has_data_

private

Referenced by DatabaseOccSolEne(), don_type_has_data(), init_don_mapping(), and read_datafile().

utility::vector1< Size > core::scoring::geometric_solvation::DatabaseOccSolEne::don_type_mapping_

private

Referenced by don_type_mapping(), and init_don_mapping().

utility::vector1< utility::vector1< utility::vector1< Real > > > core::scoring::geometric_solvation::DatabaseOccSolEne::donor_occ_data_

private

Referenced by DatabaseOccSolEne(), init_don_mapping(), and operator()().

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

Referenced by init_acc_mapping(), init_don_mapping(), operator()(), and read_datafile().

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

• src/core/scoring/geometric_solvation/DatabaseOccSolEne.hh
• src/core/scoring/geometric_solvation/DatabaseOccSolEne.cc