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core::scoring::rna::RNA_Mg_KnowledgeBasedPotential Class Reference

#include <RNA_Mg_KnowledgeBasedPotential.hh>

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Public Member Functions

 RNA_Mg_KnowledgeBasedPotential ()
 ctor, reads data file More...
 
Gaussian_parameter get_mg_potential_gaussian_parameter (core::conformation::Residue const &rsd, Size const j, bool &is_phosphate_oxygen) const
 
Gaussian_parameter get_mg_potential_gaussian_parameter (core::conformation::Residue const &rsd, Size const j) const
 
Gaussian_parameter get_mg_potential_indirect_gaussian_parameter (core::conformation::Residue const &rsd, Size const j) const
 
void setup_info_for_mg_calculation (core::pose::Pose &pose) const
 
Gaussian_parameter get_mg_potential_costheta_gaussian_parameter (core::conformation::Residue const &rsd, Size const j) const
 
Gaussian_parameter get_mg_potential_costheta_indirect_gaussian_parameter (core::conformation::Residue const &rsd, Size const j) const
 

Private Attributes

Gaussian_parameter const gaussian_parameter_phosphate_oxygen_
 
Gaussian_parameter const gaussian_parameter_imine_
 
Gaussian_parameter const gaussian_parameter_exocyclic_oxygen_
 
Gaussian_parameter const gaussian_parameter_o2star_
 
Gaussian_parameter const gaussian_parameter_phosphate_p_
 
Gaussian_parameter const gaussian_parameter_polar_H_
 
Gaussian_parameter const gaussian_parameter_nonpolar_H_
 
Gaussian_parameter const gaussian_parameter_phosphate_oxygen_indirect_
 
Gaussian_parameter const gaussian_parameter_imine_indirect_
 
Gaussian_parameter const gaussian_parameter_exocyclic_oxygen_indirect_
 
Gaussian_parameter const gaussian_parameter_o2star_indirect_
 
Gaussian_parameter const gaussian_parameter_costheta_phosphate_oxygen_
 
Gaussian_parameter const gaussian_parameter_costheta_imine_
 
Gaussian_parameter const gaussian_parameter_costheta_exocyclic_oxygen_
 
Gaussian_parameter const gaussian_parameter_costheta_o2star_
 
Gaussian_parameter const gaussian_parameter_costheta_polar_H_
 
Gaussian_parameter const gaussian_parameter_costheta_nonpolar_H_
 
Gaussian_parameter const gaussian_parameter_costheta_phosphate_oxygen_indirect_
 
Gaussian_parameter const gaussian_parameter_costheta_imine_indirect_
 
Gaussian_parameter const gaussian_parameter_costheta_exocyclic_oxygen_indirect_
 
Gaussian_parameter const gaussian_parameter_costheta_o2star_indirect_
 

Detailed Description

Definition at line 37 of file RNA_Mg_KnowledgeBasedPotential.hh.

Constructor & Destructor Documentation

core::scoring::rna::RNA_Mg_KnowledgeBasedPotential::RNA_Mg_KnowledgeBasedPotential ( )

ctor, reads data file

ctor

Definition at line 39 of file RNA_Mg_KnowledgeBasedPotential.cc.

Member Function Documentation

Gaussian_parameter core::scoring::rna::RNA_Mg_KnowledgeBasedPotential::get_mg_potential_costheta_gaussian_parameter ( core::conformation::Residue const &  rsd,
Size const  j 
) const

Definition at line 141 of file RNA_Mg_KnowledgeBasedPotential.cc.

References core::conformation::Residue::atom_name(), core::conformation::Residue::atom_type(), gaussian_parameter_costheta_exocyclic_oxygen_, gaussian_parameter_costheta_imine_, gaussian_parameter_costheta_nonpolar_H_, gaussian_parameter_costheta_o2star_, gaussian_parameter_costheta_phosphate_oxygen_, gaussian_parameter_costheta_polar_H_, core::conformation::Residue::is_RNA(), and core::chemical::AtomType::name().

Gaussian_parameter core::scoring::rna::RNA_Mg_KnowledgeBasedPotential::get_mg_potential_costheta_indirect_gaussian_parameter ( core::conformation::Residue const &  rsd,
Size const  j 
) const

Definition at line 168 of file RNA_Mg_KnowledgeBasedPotential.cc.

References core::conformation::Residue::atom_name(), core::conformation::Residue::atom_type(), gaussian_parameter_costheta_exocyclic_oxygen_indirect_, gaussian_parameter_costheta_imine_indirect_, gaussian_parameter_costheta_o2star_indirect_, gaussian_parameter_costheta_phosphate_oxygen_indirect_, core::conformation::Residue::is_RNA(), and core::chemical::AtomType::name().

Gaussian_parameter core::scoring::rna::RNA_Mg_KnowledgeBasedPotential::get_mg_potential_gaussian_parameter ( core::conformation::Residue const &  rsd,
Size const  j,
bool &  is_phosphate_oxygen 
) const

Definition at line 82 of file RNA_Mg_KnowledgeBasedPotential.cc.

References core::conformation::Residue::atom_name(), core::conformation::Residue::atom_type(), gaussian_parameter_exocyclic_oxygen_, gaussian_parameter_imine_, gaussian_parameter_nonpolar_H_, gaussian_parameter_o2star_, gaussian_parameter_phosphate_oxygen_, gaussian_parameter_phosphate_p_, gaussian_parameter_polar_H_, core::conformation::Residue::is_RNA(), and core::chemical::AtomType::name().

Referenced by get_mg_potential_gaussian_parameter(), and setup_info_for_mg_calculation().

Gaussian_parameter core::scoring::rna::RNA_Mg_KnowledgeBasedPotential::get_mg_potential_gaussian_parameter ( core::conformation::Residue const &  rsd,
Size const  j 
) const

Definition at line 71 of file RNA_Mg_KnowledgeBasedPotential.cc.

References get_mg_potential_gaussian_parameter().

Gaussian_parameter core::scoring::rna::RNA_Mg_KnowledgeBasedPotential::get_mg_potential_indirect_gaussian_parameter ( core::conformation::Residue const &  rsd,
Size const  j 
) const

Definition at line 117 of file RNA_Mg_KnowledgeBasedPotential.cc.

References core::conformation::Residue::atom_name(), core::conformation::Residue::atom_type(), gaussian_parameter_exocyclic_oxygen_indirect_, gaussian_parameter_imine_indirect_, gaussian_parameter_o2star_indirect_, gaussian_parameter_phosphate_oxygen_indirect_, core::conformation::Residue::is_RNA(), and core::chemical::AtomType::name().

void core::scoring::rna::RNA_Mg_KnowledgeBasedPotential::setup_info_for_mg_calculation ( core::pose::Pose &  pose) const

Definition at line 192 of file RNA_Mg_KnowledgeBasedPotential.cc.

References core::pose::Pose::annotated_sequence(), core::scoring::rna::Gaussian_parameter::center, get_mg_potential_gaussian_parameter(), core::scoring::rna::RNA_ScoringInfo::mg_calculation_annotated_sequence(), core::scoring::rna::RNA_ScoringInfo::nonconst_atom_numbers_for_mg_calculation(), core::scoring::rna::RNA_ScoringInfo::nonconst_is_magnesium(), core::scoring::rna::nonconst_rna_scoring_info_from_pose(), core::pose::Pose::residue(), core::scoring::rna::RNA_ScoringInfo::set_mg_calculation_annotated_sequence(), and core::pose::Pose::total_residue().

Member Data Documentation

Gaussian_parameter const core::scoring::rna::RNA_Mg_KnowledgeBasedPotential::gaussian_parameter_costheta_exocyclic_oxygen_
private

Definition at line 79 of file RNA_Mg_KnowledgeBasedPotential.hh.

Referenced by get_mg_potential_costheta_gaussian_parameter().

Gaussian_parameter const core::scoring::rna::RNA_Mg_KnowledgeBasedPotential::gaussian_parameter_costheta_exocyclic_oxygen_indirect_
private

Definition at line 86 of file RNA_Mg_KnowledgeBasedPotential.hh.

Referenced by get_mg_potential_costheta_indirect_gaussian_parameter().

Gaussian_parameter const core::scoring::rna::RNA_Mg_KnowledgeBasedPotential::gaussian_parameter_costheta_imine_
private

Definition at line 78 of file RNA_Mg_KnowledgeBasedPotential.hh.

Referenced by get_mg_potential_costheta_gaussian_parameter().

Gaussian_parameter const core::scoring::rna::RNA_Mg_KnowledgeBasedPotential::gaussian_parameter_costheta_imine_indirect_
private

Definition at line 85 of file RNA_Mg_KnowledgeBasedPotential.hh.

Referenced by get_mg_potential_costheta_indirect_gaussian_parameter().

Gaussian_parameter const core::scoring::rna::RNA_Mg_KnowledgeBasedPotential::gaussian_parameter_costheta_nonpolar_H_
private

Definition at line 82 of file RNA_Mg_KnowledgeBasedPotential.hh.

Referenced by get_mg_potential_costheta_gaussian_parameter().

Gaussian_parameter const core::scoring::rna::RNA_Mg_KnowledgeBasedPotential::gaussian_parameter_costheta_o2star_
private

Definition at line 80 of file RNA_Mg_KnowledgeBasedPotential.hh.

Referenced by get_mg_potential_costheta_gaussian_parameter().

Gaussian_parameter const core::scoring::rna::RNA_Mg_KnowledgeBasedPotential::gaussian_parameter_costheta_o2star_indirect_
private

Definition at line 87 of file RNA_Mg_KnowledgeBasedPotential.hh.

Referenced by get_mg_potential_costheta_indirect_gaussian_parameter().

Gaussian_parameter const core::scoring::rna::RNA_Mg_KnowledgeBasedPotential::gaussian_parameter_costheta_phosphate_oxygen_
private

Definition at line 77 of file RNA_Mg_KnowledgeBasedPotential.hh.

Referenced by get_mg_potential_costheta_gaussian_parameter().

Gaussian_parameter const core::scoring::rna::RNA_Mg_KnowledgeBasedPotential::gaussian_parameter_costheta_phosphate_oxygen_indirect_
private

Definition at line 84 of file RNA_Mg_KnowledgeBasedPotential.hh.

Referenced by get_mg_potential_costheta_indirect_gaussian_parameter().

Gaussian_parameter const core::scoring::rna::RNA_Mg_KnowledgeBasedPotential::gaussian_parameter_costheta_polar_H_
private

Definition at line 81 of file RNA_Mg_KnowledgeBasedPotential.hh.

Referenced by get_mg_potential_costheta_gaussian_parameter().

Gaussian_parameter const core::scoring::rna::RNA_Mg_KnowledgeBasedPotential::gaussian_parameter_exocyclic_oxygen_
private

Definition at line 65 of file RNA_Mg_KnowledgeBasedPotential.hh.

Referenced by get_mg_potential_gaussian_parameter().

Gaussian_parameter const core::scoring::rna::RNA_Mg_KnowledgeBasedPotential::gaussian_parameter_exocyclic_oxygen_indirect_
private

Definition at line 74 of file RNA_Mg_KnowledgeBasedPotential.hh.

Referenced by get_mg_potential_indirect_gaussian_parameter().

Gaussian_parameter const core::scoring::rna::RNA_Mg_KnowledgeBasedPotential::gaussian_parameter_imine_
private

Definition at line 64 of file RNA_Mg_KnowledgeBasedPotential.hh.

Referenced by get_mg_potential_gaussian_parameter().

Gaussian_parameter const core::scoring::rna::RNA_Mg_KnowledgeBasedPotential::gaussian_parameter_imine_indirect_
private

Definition at line 73 of file RNA_Mg_KnowledgeBasedPotential.hh.

Referenced by get_mg_potential_indirect_gaussian_parameter().

Gaussian_parameter const core::scoring::rna::RNA_Mg_KnowledgeBasedPotential::gaussian_parameter_nonpolar_H_
private

Definition at line 70 of file RNA_Mg_KnowledgeBasedPotential.hh.

Referenced by get_mg_potential_gaussian_parameter().

Gaussian_parameter const core::scoring::rna::RNA_Mg_KnowledgeBasedPotential::gaussian_parameter_o2star_
private

Definition at line 66 of file RNA_Mg_KnowledgeBasedPotential.hh.

Referenced by get_mg_potential_gaussian_parameter().

Gaussian_parameter const core::scoring::rna::RNA_Mg_KnowledgeBasedPotential::gaussian_parameter_o2star_indirect_
private

Definition at line 75 of file RNA_Mg_KnowledgeBasedPotential.hh.

Referenced by get_mg_potential_indirect_gaussian_parameter().

Gaussian_parameter const core::scoring::rna::RNA_Mg_KnowledgeBasedPotential::gaussian_parameter_phosphate_oxygen_
private

Definition at line 63 of file RNA_Mg_KnowledgeBasedPotential.hh.

Referenced by get_mg_potential_gaussian_parameter().

Gaussian_parameter const core::scoring::rna::RNA_Mg_KnowledgeBasedPotential::gaussian_parameter_phosphate_oxygen_indirect_
private

Definition at line 72 of file RNA_Mg_KnowledgeBasedPotential.hh.

Referenced by get_mg_potential_indirect_gaussian_parameter().

Gaussian_parameter const core::scoring::rna::RNA_Mg_KnowledgeBasedPotential::gaussian_parameter_phosphate_p_
private

Definition at line 68 of file RNA_Mg_KnowledgeBasedPotential.hh.

Referenced by get_mg_potential_gaussian_parameter().

Gaussian_parameter const core::scoring::rna::RNA_Mg_KnowledgeBasedPotential::gaussian_parameter_polar_H_
private

Definition at line 69 of file RNA_Mg_KnowledgeBasedPotential.hh.

Referenced by get_mg_potential_gaussian_parameter().

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