core::scoring::dna::DNA_DihedralPotential Class Reference

#include <DNA_DihedralPotential.hh>

Public Member Functions
	DNA_DihedralPotential (std::string const &filename)
	DNA_DihedralPotential ()
void	eval_harmonic_backbone_torsion_score_and_deriv (Size const tor, conformation::Residue const &rsd, pose::Pose const &pose, Real &score, Real &dscore_dtor) const
void	eval_harmonic_backbone_torsion_score_and_deriv (Size const tor, conformation::Residue const &rsd, pose::Pose const &pose, Real &score, Real &dscore_dchi, Real &dscore_deps, Real &dscore_dzeta) const
void	eval_harmonic_sugar_pucker_dependent_chi_torsion_score_and_deriv (conformation::Residue const &rsd, pose::Pose const &pose, Size const pucker, Real &score, Real &dscore_dchi) const
Real	get_mean_sugar_pucker_dependent_chi (conformation::Residue const &rsd) const
void	eval_sugar_torsion_score_and_deriv (Real const torsion, Size const tor, conformation::Residue const &rsd, Size const pucker, Real &score, Real &dscore_dtor) const
void	get_sugar_torsion_mean_and_sdev (Size const tor, conformation::Residue const &rsd, Size const pucker, Real &mean, Real &sdev) const

Private Member Functions
bool	skip_torsion (conformation::Residue const &rsd, Size const tor) const
void	read_dna_geometry_log_file (std::string const &filename)
void	read_dna_geometry_log_file_from_database (std::string const &database_file)
void	parse_dna_geometry_log (std::istream &data)
	should only do this once More...

Private Attributes
utility::vector1< utility::vector1< Real > >	mean_backbone_torsion_
utility::vector1< utility::vector0< utility::vector1< Real > > >	mean_sugar_torsion_

Constructor & Destructor Documentation

DNA_DihedralPotential() [1/2]

core::scoring::dna::DNA_DihedralPotential::DNA_DihedralPotential

(

std::string const &

filename

)

References protocols::abinitio::filename(), and read_dna_geometry_log_file().

DNA_DihedralPotential() [2/2]

core::scoring::dna::DNA_DihedralPotential::DNA_DihedralPotential

(

)

References read_dna_geometry_log_file_from_database().

Member Function Documentation

eval_harmonic_backbone_torsion_score_and_deriv() [1/2]

void core::scoring::dna::DNA_DihedralPotential::eval_harmonic_backbone_torsion_score_and_deriv	(	Size const	tor,
		conformation::Residue const &	rsd,
		pose::Pose const &	pose,
		Real &	score,
		Real &	dscore_dchi,
		Real &	dscore_deps,
		Real &	dscore_dzeta
	)		const

References core::scoring::dna::get_b1b2_weight(), core::scoring::dna::get_db1b2_weight_deps(), core::scoring::dna::get_triple_bin(), core::conformation::Residue::is_DNA(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::mainchain_torsion(), core::simple_metrics::metrics::mean, mean_backbone_torsion_, core::pose::Pose::residue(), protocols::hybridization::score, core::conformation::Residue::seqpos(), and core::scoring::electron_density::square().

eval_harmonic_backbone_torsion_score_and_deriv() [2/2]

void core::scoring::dna::DNA_DihedralPotential::eval_harmonic_backbone_torsion_score_and_deriv	(	Size const	tor,
		conformation::Residue const &	rsd,
		pose::Pose const &	pose,
		Real &	score,
		Real &	dscore_dtor
	)		const

References protocols::hybridization::score.

Referenced by core::energy_methods::DNA_DihedralEnergy::eval_intrares_energy(), core::energy_methods::DNA_DihedralEnergy::eval_intraresidue_dof_derivative(), and core::energy_methods::DNA_DihedralEnergy::eval_residue_pair_derivatives().

eval_harmonic_sugar_pucker_dependent_chi_torsion_score_and_deriv()

void core::scoring::dna::DNA_DihedralPotential::eval_harmonic_sugar_pucker_dependent_chi_torsion_score_and_deriv	(	conformation::Residue const &	rsd,
		pose::Pose const &	pose,
		Size const	pucker,
		Real &	score,
		Real &	dscore_dchi
	)		const

References core::conformation::Residue::chi(), core::scoring::dna::get_iname1_from_name1(), core::simple_metrics::metrics::mean, mean_sugar_torsion_, core::conformation::Residue::name1(), core::scoring::dna::put_angle_in_0to360(), protocols::hybridization::score, and core::scoring::electron_density::square().

Referenced by core::energy_methods::DNA_DihedralEnergy::eval_intrares_derivatives(), core::energy_methods::DNA_DihedralEnergy::eval_intrares_energy(), and core::energy_methods::DNA_DihedralEnergy::eval_intraresidue_dof_derivative().

eval_sugar_torsion_score_and_deriv()

void core::scoring::dna::DNA_DihedralPotential::eval_sugar_torsion_score_and_deriv	(	Real const	torsion,
		Size const	tor,
		conformation::Residue const &	rsd,
		Size const	pucker,
		Real &	score,
		Real &	dscore_dtor
	)		const

1- delta 2- "chi2" 3- "chi3" 4- "chi4"

References core::scoring::dna::get_iname1_from_name1(), core::simple_metrics::metrics::mean, mean_sugar_torsion_, core::conformation::Residue::name1(), protocols::hybridization::score, and core::scoring::electron_density::square().

Referenced by core::energy_methods::DNA_DihedralEnergy::eval_intrares_derivatives(), core::energy_methods::DNA_DihedralEnergy::eval_intrares_energy(), and core::energy_methods::DNA_DihedralEnergy::eval_intraresidue_dof_derivative().

get_mean_sugar_pucker_dependent_chi()

Real core::scoring::dna::DNA_DihedralPotential::get_mean_sugar_pucker_dependent_chi

(

conformation::Residue const &

rsd

)

const

References core::scoring::dna::get_iname1_from_name1(), core::scoring::dna::get_sugar_pucker(), mean_sugar_torsion_, and core::conformation::Residue::name1().

get_sugar_torsion_mean_and_sdev()

void core::scoring::dna::DNA_DihedralPotential::get_sugar_torsion_mean_and_sdev	(	Size const	tor,
		conformation::Residue const &	rsd,
		Size const	pucker,
		Real &	mean,
		Real &	sdev
	)		const

References core::scoring::dna::get_iname1_from_name1(), core::simple_metrics::metrics::mean, mean_sugar_torsion_, and core::conformation::Residue::name1().

parse_dna_geometry_log()

void core::scoring::dna::DNA_DihedralPotential::parse_dna_geometry_log ( std::istream &  data )

private

should only do this once

References core::chemical::element::F, core::scoring::dna::filter_torsions_by_iname(), core::scoring::dna::get_b1b2_bin(), core::scoring::dna::get_iname1_from_name1(), core::scoring::dna::get_mean_median_and_sdev(), core::scoring::dna::get_triple_bin(), core::chemical::element::I, core::pose::is_lower_terminus(), core::pose::is_upper_terminus(), core::simple_metrics::metrics::mean, mean_backbone_torsion_, mean_sugar_torsion_, core::scoring::electron_density::square(), protocols::hybridization::t, and core::scoring::dna::TR().

Referenced by read_dna_geometry_log_file(), and read_dna_geometry_log_file_from_database().

read_dna_geometry_log_file()

void core::scoring::dna::DNA_DihedralPotential::read_dna_geometry_log_file ( std::string const &  filename )

private

References protocols::abinitio::filename(), and parse_dna_geometry_log().

Referenced by DNA_DihedralPotential().

read_dna_geometry_log_file_from_database()

void core::scoring::dna::DNA_DihedralPotential::read_dna_geometry_log_file_from_database ( std::string const &  database_file )

private

References parse_dna_geometry_log().

Referenced by DNA_DihedralPotential().

skip_torsion()

bool core::scoring::dna::DNA_DihedralPotential::skip_torsion ( conformation::Residue const &  rsd, Size const  tor  ) const

private

References core::conformation::Residue::is_DNA(), core::conformation::Residue::is_lower_terminus(), and core::conformation::Residue::is_upper_terminus().

Member Data Documentation

mean_backbone_torsion_

utility::vector1< utility::vector1< Real > > core::scoring::dna::DNA_DihedralPotential::mean_backbone_torsion_

private

Referenced by eval_harmonic_backbone_torsion_score_and_deriv(), and parse_dna_geometry_log().

mean_sugar_torsion_

utility::vector1< utility::vector0< utility::vector1< Real > > > core::scoring::dna::DNA_DihedralPotential::mean_sugar_torsion_

private

Referenced by eval_harmonic_sugar_pucker_dependent_chi_torsion_score_and_deriv(), eval_sugar_torsion_score_and_deriv(), get_mean_sugar_pucker_dependent_chi(), get_sugar_torsion_mean_and_sdev(), and parse_dna_geometry_log().

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

• src/core/scoring/dna/DNA_DihedralPotential.hh
• src/core/scoring/dna/DNA_DihedralPotential.cc