core::scoring::carbon_hbonds::CarbonHBondPotential Class Reference

#include <CarbonHBondPotential.hh>

Inheritance diagram for core::scoring::carbon_hbonds::CarbonHBondPotential:

Public Member Functions
	CarbonHBondPotential ()
	ctor, reads data file More...
Real	get_potential (Size const &atom_type, Vector const &H_A_vector, Vector const &D_H_vector, Vector const &B_A_vector, bool calculate_deriv, Vector &deriv_vector) const
	Calculate chbond energies for non-rna atom pairs. More...
Real	get_potential_RNA (Vector const &r_H_A, Vector const &z_i, bool const &update_deriv, Vector &deriv) const
	Calculate the rna-specific chbond energies. The derivative vector returned is the force vector on the acceptor atom. Multiply by -1 to get the force vector on the donor atom. More...
Real	get_potential (Size const &atom_type, Vector const &H_A_vector, Vector const &D_H_vector, Vector const &B_A_vector) const
	second declaration to allow skipping deriv; gcc 4.1.3 does not like setting default parameters for a pass-by-reference parameter More...
Real	max_dis () const

Private Member Functions
void	read_potential ()

Private Attributes
Real	bin_width_
Real	max_dist_
Real const	aroC_scale_factor_
Size const	num_carbon_donor_atoms_
Size const	num_bins_
utility::vector1 < ObjexxFCL::FArray1D< Real > >	carbon_hbond_parameter_
utility::vector1< std::string >	carbon_donors_
ObjexxFCL::FArray1D< Size >	standard_atomtype_to_carbon_donor_index_
Real const	rna_cos_theta_cutoff_
Real const	rna_cos_theta_fade_zone_
Real const	rna_ch_o_bond_distance_

Constructor & Destructor Documentation

core::scoring::carbon_hbonds::CarbonHBondPotential::CarbonHBondPotential

(

)

ctor, reads data file

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

References read_potential().

Member Function Documentation

Real core::scoring::carbon_hbonds::CarbonHBondPotential::get_potential	(	Size const &	atom_type,
		Vector const &	H_A_vector,
		Vector const &	D_H_vector,
		Vector const &	B_A_vector,
		bool	calculate_deriv,
		Vector &	deriv_vector
	)		const

Calculate chbond energies for non-rna atom pairs.

References bin_width_, carbon_hbond_parameter_, core::scoring::rna::get_fade_correction(), core::scoring::interpolate_value_and_deriv(), and standard_atomtype_to_carbon_donor_index_.

Referenced by core::scoring::carbon_hbonds::CarbonHBondEnergy::get_atom_atom_carbon_hbond_energy(), and get_potential().

Real core::scoring::carbon_hbonds::CarbonHBondPotential::get_potential	(	Size const &	atom_type_index,
		Vector const &	H_A_vector,
		Vector const &	D_H_vector,
		Vector const &	B_A_vector
	)		const

second declaration to allow skipping deriv; gcc 4.1.3 does not like setting default parameters for a pass-by-reference parameter

Locally allocated deriv_vector is passed by reference into the more general implementation of the get_potential function; moreover, the calculate-derivative flag is set to false in that call. This is the "evaluate only the score" interface to the chbond potential.

References get_potential().

Real core::scoring::carbon_hbonds::CarbonHBondPotential::get_potential_RNA	(	Vector const &	r_H_A,
		Vector const &	z_i,
		bool const &	update_deriv,
		Vector &	deriv
	)		const

Calculate the rna-specific chbond energies. The derivative vector returned is the force vector on the acceptor atom. Multiply by -1 to get the force vector on the donor atom.

References core::scoring::rna::get_fade_correction(), max_dist_, rna_ch_o_bond_distance_, rna_cos_theta_cutoff_, rna_cos_theta_fade_zone_, and protocols::hybridization::score.

Referenced by core::scoring::carbon_hbonds::CarbonHBondEnergy::get_atom_atom_carbon_hbond_energy().

Real core::scoring::carbon_hbonds::CarbonHBondPotential::max_dis ( ) const

inline

References max_dist_.

void core::scoring::carbon_hbonds::CarbonHBondPotential::read_potential ( )

private

References aroC_scale_factor_, bin_width_, carbon_donors_, carbon_hbond_parameter_, core::scoring::carbon_hbonds::get_position_in_vector(), max_dist_, num_bins_, num_carbon_donor_atoms_, protocols::hybridization::score, and standard_atomtype_to_carbon_donor_index_.

Referenced by CarbonHBondPotential().

Member Data Documentation

Real const core::scoring::carbon_hbonds::CarbonHBondPotential::aroC_scale_factor_

private

Referenced by read_potential().

Real core::scoring::carbon_hbonds::CarbonHBondPotential::bin_width_

private

Referenced by get_potential(), and read_potential().

utility::vector1< std::string > core::scoring::carbon_hbonds::CarbonHBondPotential::carbon_donors_

private

Referenced by read_potential().

utility::vector1< ObjexxFCL::FArray1D <Real> > core::scoring::carbon_hbonds::CarbonHBondPotential::carbon_hbond_parameter_

private

Referenced by get_potential(), and read_potential().

Real core::scoring::carbon_hbonds::CarbonHBondPotential::max_dist_

private

Referenced by get_potential_RNA(), max_dis(), and read_potential().

Size const core::scoring::carbon_hbonds::CarbonHBondPotential::num_bins_

private

Referenced by read_potential().

Size const core::scoring::carbon_hbonds::CarbonHBondPotential::num_carbon_donor_atoms_

private

Referenced by read_potential().

Real const core::scoring::carbon_hbonds::CarbonHBondPotential::rna_ch_o_bond_distance_

private

Referenced by get_potential_RNA().

Real const core::scoring::carbon_hbonds::CarbonHBondPotential::rna_cos_theta_cutoff_

private

Referenced by get_potential_RNA().

Real const core::scoring::carbon_hbonds::CarbonHBondPotential::rna_cos_theta_fade_zone_

private

Referenced by get_potential_RNA().

ObjexxFCL::FArray1D< Size > core::scoring::carbon_hbonds::CarbonHBondPotential::standard_atomtype_to_carbon_donor_index_

private

Referenced by get_potential(), and read_potential().

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

• src/core/scoring/carbon_hbonds/CarbonHBondPotential.hh
• src/core/scoring/carbon_hbonds/CarbonHBondPotential.cc