core::scoring::rna::RNP_LowResPotential Class Reference

#include <RNP_LowResPotential.hh>

Inheritance diagram for core::scoring::rna::RNP_LowResPotential:

Public Member Functions
	RNP_LowResPotential ()
	c-tor More...
void	initialize_rnp_base_pair ()
void	initialize_rnp_pair ()
void	initialize_rnp_aa_rna_backbone ()
void	evaluate_rnp_base_pair_score (conformation::Residue const &rsd1, conformation::Residue const &rsd2, Real const &x, Real const &y, Real &rnp_bp_score) const
Real	evaluate_rnp_aa_rna_backbone_score (conformation::Residue const &protein_rsd, Real const &dist_to_backbone) const
void	evaluate_rnp_pair_score (conformation::Residue const &rsd1, conformation::Residue const &rsd2, bool const &rsd1_is_interface, bool const &rsd1_is_buried, bool const &rsd2_is_interface, bool const &rsd2_is_buried, Real const &d, Real &rnp_pair_score) const

Private Attributes
Size const	max_aa_
Size const	max_base_
Size const	num_xbins_
Size const	num_ybins_
Size const	num_dbins_
Size const	num_backbone_dbins_
ObjexxFCL::FArray4D< Real >	rnp_basepair_xy_
ObjexxFCL::FArray3D< Real >	rnp_pair_base_interface_protein_buried_
ObjexxFCL::FArray3D< Real >	rnp_pair_base_interface_protein_notburied_
ObjexxFCL::FArray2D< Real >	rnp_aa_rna_backbone_

Constructor & Destructor Documentation

RNP_LowResPotential()

core::scoring::rna::RNP_LowResPotential::RNP_LowResPotential

(

)

c-tor

References initialize_rnp_aa_rna_backbone(), and initialize_rnp_base_pair().

Member Function Documentation

evaluate_rnp_aa_rna_backbone_score()

Real core::scoring::rna::RNP_LowResPotential::evaluate_rnp_aa_rna_backbone_score	(	conformation::Residue const &	protein_rsd,
		Real const &	dist_to_backbone
	)		const

References core::conformation::Residue::aa(), protocols::cluster::calibur::aa, num_backbone_dbins_, and rnp_aa_rna_backbone_.

Referenced by core::energy_methods::RNP_LowResEnergy::residue_pair_energy().

evaluate_rnp_base_pair_score()

void core::scoring::rna::RNP_LowResPotential::evaluate_rnp_base_pair_score	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2,
		Real const &	x,
		Real const &	y,
		Real &	rnp_bp_score
	)		const

References core::conformation::Residue::aa(), protocols::cluster::calibur::aa, core::chemical::rna::convert_acgu_to_1234(), core::conformation::Residue::has_variant_type(), core::conformation::Residue::is_protein(), core::conformation::Residue::is_RNA(), core::conformation::Residue::name1(), core::chemical::REPLONLY, and rnp_basepair_xy_.

Referenced by core::energy_methods::RNP_LowResEnergy::residue_pair_energy().

evaluate_rnp_pair_score()

void core::scoring::rna::RNP_LowResPotential::evaluate_rnp_pair_score	(	conformation::Residue const &	rsd1,
		conformation::Residue const &	rsd2,
		bool const &	rsd1_is_interface,
		bool const &	rsd1_is_buried,
		bool const &	rsd2_is_interface,
		bool const &	rsd2_is_buried,
		Real const &	d,
		Real &	rnp_pair_score
	)		const

References core::conformation::Residue::aa(), protocols::cluster::calibur::aa, core::chemical::rna::convert_acgu_to_1234(), core::conformation::Residue::is_protein(), core::conformation::Residue::name1(), num_dbins_, rnp_pair_base_interface_protein_buried_, and rnp_pair_base_interface_protein_notburied_.

initialize_rnp_aa_rna_backbone()

void core::scoring::rna::RNP_LowResPotential::initialize_rnp_aa_rna_backbone

(

)

References protocols::cluster::calibur::aa, protocols::abinitio::filename(), max_aa_, num_backbone_dbins_, rnp_aa_rna_backbone_, and core::scoring::TR().

Referenced by RNP_LowResPotential().

initialize_rnp_base_pair()

void core::scoring::rna::RNP_LowResPotential::initialize_rnp_base_pair

(

)

References protocols::cluster::calibur::aa, core::chemical::rna::convert_acgu_to_1234(), protocols::abinitio::filename(), max_aa_, max_base_, num_xbins_, num_ybins_, rnp_basepair_xy_, and core::scoring::TR().

Referenced by RNP_LowResPotential().

initialize_rnp_pair()

void core::scoring::rna::RNP_LowResPotential::initialize_rnp_pair

(

)

References protocols::cluster::calibur::aa, core::chemical::rna::convert_acgu_to_1234(), protocols::abinitio::filename(), max_aa_, max_base_, num_dbins_, rnp_pair_base_interface_protein_buried_, rnp_pair_base_interface_protein_notburied_, and core::scoring::TR().

Member Data Documentation

max_aa_

Size const core::scoring::rna::RNP_LowResPotential::max_aa_

private

Referenced by initialize_rnp_aa_rna_backbone(), initialize_rnp_base_pair(), and initialize_rnp_pair().

max_base_

Size const core::scoring::rna::RNP_LowResPotential::max_base_

private

Referenced by initialize_rnp_base_pair(), and initialize_rnp_pair().

num_backbone_dbins_

Size const core::scoring::rna::RNP_LowResPotential::num_backbone_dbins_

private

Referenced by evaluate_rnp_aa_rna_backbone_score(), and initialize_rnp_aa_rna_backbone().

num_dbins_

Size const core::scoring::rna::RNP_LowResPotential::num_dbins_

private

Referenced by evaluate_rnp_pair_score(), and initialize_rnp_pair().

num_xbins_

Size const core::scoring::rna::RNP_LowResPotential::num_xbins_

private

Referenced by initialize_rnp_base_pair().

num_ybins_

Size const core::scoring::rna::RNP_LowResPotential::num_ybins_

private

Referenced by initialize_rnp_base_pair().

rnp_aa_rna_backbone_

ObjexxFCL::FArray2D< Real > core::scoring::rna::RNP_LowResPotential::rnp_aa_rna_backbone_

private

Referenced by evaluate_rnp_aa_rna_backbone_score(), and initialize_rnp_aa_rna_backbone().

rnp_basepair_xy_

ObjexxFCL::FArray4D< Real > core::scoring::rna::RNP_LowResPotential::rnp_basepair_xy_

private

Referenced by evaluate_rnp_base_pair_score(), and initialize_rnp_base_pair().

rnp_pair_base_interface_protein_buried_

ObjexxFCL::FArray3D< Real > core::scoring::rna::RNP_LowResPotential::rnp_pair_base_interface_protein_buried_

private

Referenced by evaluate_rnp_pair_score(), and initialize_rnp_pair().

rnp_pair_base_interface_protein_notburied_

ObjexxFCL::FArray3D< Real > core::scoring::rna::RNP_LowResPotential::rnp_pair_base_interface_protein_notburied_

private

Referenced by evaluate_rnp_pair_score(), and initialize_rnp_pair().

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

• src/core/scoring/rna/RNP_LowResPotential.hh
• src/core/scoring/rna/RNP_LowResPotential.cc