core::scoring::rna::RNA_AtomVDW Class Reference

#include <RNA_AtomVDW.hh>

Inheritance diagram for core::scoring::rna::RNA_AtomVDW:

Public Member Functions
	RNA_AtomVDW ()
	ctor, reads data file More...
utility::vector1< std::string > const	vdw_atom_list (chemical::ResidueType const &rt) const
void	initialize_rnp_vdw_parameters ()
Real	bump_parameter (Size const atom1, Size const atom2, chemical::ResidueType const &rsd1, chemical::ResidueType const &rsd2) const
Real	bump_parameter_rnp (Size const atom_RNA, Size const atom_protein, chemical::ResidueType const &rna_type) const

Private Types
typedef std::map< char, utility::vector1< std::string > >	AtomList

Private Attributes
AtomList	rna_vdw_atom_
ObjexxFCL::FArray4D< Real >	rna_vdw_parameter_
ObjexxFCL::FArray3D< Real >	rnp_vdw_parameter_

Member Typedef Documentation

AtomList

typedef std::map< char, utility::vector1< std::string > > core::scoring::rna::RNA_AtomVDW::AtomList

private

Constructor & Destructor Documentation

RNA_AtomVDW()

core::scoring::rna::RNA_AtomVDW::RNA_AtomVDW

(

)

ctor, reads data file

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

References core::scoring::rna::get_position_in_vector(), initialize_rnp_vdw_parameters(), core::scoring::rna::rna_residue_name_to_num(), rna_vdw_atom_, and rna_vdw_parameter_.

Member Function Documentation

bump_parameter()

Real core::scoring::rna::RNA_AtomVDW::bump_parameter	(	Size const	atom1,
		Size const	atom2,
		chemical::ResidueType const &	rsd1,
		chemical::ResidueType const &	rsd2
	)		const

References core::scoring::rna::rna_residue_type_to_num(), and rna_vdw_parameter_.

Referenced by core::energy_methods::RNA_VDW_Energy::eval_atom_derivative(), and core::energy_methods::RNA_VDW_Energy::residue_pair_energy().

bump_parameter_rnp()

Real core::scoring::rna::RNA_AtomVDW::bump_parameter_rnp	(	Size const	atom_RNA,
		Size const	atom_protein,
		chemical::ResidueType const &	rna_type
	)		const

References core::scoring::rna::rna_residue_type_to_num(), and rnp_vdw_parameter_.

Referenced by core::energy_methods::RNA_VDW_Energy::evaluate_rnp_vdw_score().

initialize_rnp_vdw_parameters()

void core::scoring::rna::RNA_AtomVDW::initialize_rnp_vdw_parameters

(

)

References protocols::abinitio::filename(), core::scoring::rna::get_position_in_vector(), core::scoring::rna::protein_atom_name_to_num(), core::scoring::rna::rna_residue_name_to_num(), rna_vdw_atom_, and rnp_vdw_parameter_.

Referenced by RNA_AtomVDW().

vdw_atom_list()

utility::vector1< std::string > const core::scoring::rna::RNA_AtomVDW::vdw_atom_list

(

chemical::ResidueType const &

rt

)

const

References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_unp, core::chemical::na_ade, core::chemical::ResidueTypeBase::na_analogue(), core::chemical::na_cyt, core::chemical::na_gua, core::chemical::na_rad, core::chemical::na_rcy, core::chemical::na_rgu, core::chemical::na_ura, core::chemical::ResidueTypeBase::name1(), rna_vdw_atom_, and core::scoring::tr().

Referenced by core::energy_methods::RNA_VDW_Energy::setup_atom_numbers_for_vdw_calculation().

Member Data Documentation

rna_vdw_atom_

AtomList core::scoring::rna::RNA_AtomVDW::rna_vdw_atom_

private

Referenced by initialize_rnp_vdw_parameters(), RNA_AtomVDW(), and vdw_atom_list().

rna_vdw_parameter_

ObjexxFCL::FArray4D< Real > core::scoring::rna::RNA_AtomVDW::rna_vdw_parameter_

private

Referenced by bump_parameter(), and RNA_AtomVDW().

rnp_vdw_parameter_

ObjexxFCL::FArray3D< Real > core::scoring::rna::RNA_AtomVDW::rnp_vdw_parameter_

private

Referenced by bump_parameter_rnp(), and initialize_rnp_vdw_parameters().

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

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