core::scoring::dna::DNATorsionPotential Class Reference

#include <DNATorsionPotential.hh>

Inheritance diagram for core::scoring::dna::DNATorsionPotential:

Public Member Functions
	DNATorsionPotential ()
	~DNATorsionPotential () override
void	setup_constraints (pose::Pose &pose, constraints::ConstraintSetOP &dna_torsion_constraints, constraints::ConstraintSetOP &dna_sugar_close_constraints, constraints::ConstraintSetOP &dna_base_distance_constraints) const
Real	delta_cutoff () const
utility::vector1< func::AmberPeriodicFuncOP > &	alpha_components ()
utility::vector1< func::AmberPeriodicFuncOP > &	beta_components ()
utility::vector1< func::AmberPeriodicFuncOP > &	gamma_components ()
utility::vector1< func::AmberPeriodicFuncOP > &	delta_components ()
utility::vector1< func::AmberPeriodicFuncOP > &	epsilon_components ()
utility::vector1< func::AmberPeriodicFuncOP > &	zeta_components ()
utility::vector1< func::AmberPeriodicFuncOP > &	nu0_components ()
utility::vector1< func::AmberPeriodicFuncOP > &	nu1_components ()
utility::vector1< func::AmberPeriodicFuncOP > &	nu2_components ()
utility::vector1< func::AmberPeriodicFuncOP > &	nu3_components ()
utility::vector1< func::AmberPeriodicFuncOP > &	nu4_components ()
void	add_sugar_ring_closure_constraints (conformation::Residue const &rsd, constraints::ConstraintSet &cst_set) const

Private Member Functions
void	add_sugar_ring_closure_constraints (pose::Pose &pose, constraints::ConstraintSet &cst_set) const
void	add_dna_base_distance_constraints (pose::Pose &pose, constraints::ConstraintSet &cst_set) const
void	add_dna_torsion_tethers (pose::Pose &pose, constraints::ConstraintSet &cst_set) const
void	add_DNA_torsion_constraint (pose::Pose &pose, Size const i, constraints::ConstraintSet &cst_set, Size const dna_torsion_number, utility::vector1< func::AmberPeriodicFuncOP > const &gaussian_parameter_set) const
bool	get_atom_ids_by_torsion (Size const dna_torsion_number, pose::Pose &pose, Size const resid, id::AtomID &id1, id::AtomID &id2, id::AtomID &id3, id::AtomID &id4) const
void	init_dna_torsion_parameters ()

Private Attributes
utility::vector1< func::AmberPeriodicFuncOP >	alpha_components_
utility::vector1< func::AmberPeriodicFuncOP >	beta_components_
utility::vector1< func::AmberPeriodicFuncOP >	gamma_components_
utility::vector1< func::AmberPeriodicFuncOP >	delta_components_
utility::vector1< func::AmberPeriodicFuncOP >	epsilon_components_
utility::vector1< func::AmberPeriodicFuncOP >	zeta_components_
utility::vector1< func::AmberPeriodicFuncOP >	nu0_components_
utility::vector1< func::AmberPeriodicFuncOP >	nu1_components_
utility::vector1< func::AmberPeriodicFuncOP >	nu2_components_
utility::vector1< func::AmberPeriodicFuncOP >	nu3_components_
utility::vector1< func::AmberPeriodicFuncOP >	nu4_components_
utility::vector1< std::string >	alpha_atom_names_
utility::vector1< std::string >	beta_atom_names_
utility::vector1< std::string >	gamma_atom_names_
utility::vector1< std::string >	delta_atom_names_
utility::vector1< std::string >	epsilon_atom_names_
utility::vector1< std::string >	zeta_atom_names_
utility::vector1< std::string >	nu0_atom_names_
utility::vector1< std::string >	nu1_atom_names_
utility::vector1< std::string >	nu2_atom_names_
utility::vector1< std::string >	nu3_atom_names_
utility::vector1< std::string >	nu4_atom_names_
Real const	DELTA_CUTOFF_
Real const	scale_dna_torsion_tether_
Real const	scale_dna_torsion_sd_
Distance const	c2prime_c3prime_bond_length_
Distance const	c2prime_c3prime_sd_
func::HarmonicFuncOP	c2prime_c3prime_dist_harm_func_
Real const	c4prime_c3prime_c2prime_bond_angle_
func::HarmonicFuncOP	c4prime_c3prime_c2prime_angle_harm_func_
Real const	o3prime_c3prime_c2prime_bond_angle_
func::HarmonicFuncOP	o3prime_c3prime_c2prime_angle_harm_func_
Real const	c3prime_c2prime_c1prime_bond_angle_
func::HarmonicFuncOP	c3prime_c2prime_c1prime_angle_harm_func_

Constructor & Destructor Documentation

DNATorsionPotential()

core::scoring::dna::DNATorsionPotential::DNATorsionPotential

(

)

References init_dna_torsion_parameters().

~DNATorsionPotential()

core::scoring::dna::DNATorsionPotential::~DNATorsionPotential ( )

inlineoverride

Member Function Documentation

add_dna_base_distance_constraints()

void core::scoring::dna::DNATorsionPotential::add_dna_base_distance_constraints ( pose::Pose &  pose, constraints::ConstraintSet &  cst_set  ) const

private

References core::chemical::ResidueTypeBase::aa(), core::scoring::constraints::ConstraintSet::add_constraint(), protocols::abinitio::abscript::angle_diff(), core::conformation::Residue::atom_index(), core::scoring::dna_base_distance, core::conformation::Residue::is_DNA(), core::conformation::Residue::is_upper_terminus(), core::conformation::Residue::mainchain_torsion(), core::chemical::na_ade, core::chemical::na_gua, core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::type().

Referenced by setup_constraints().

add_DNA_torsion_constraint()

void core::scoring::dna::DNATorsionPotential::add_DNA_torsion_constraint ( pose::Pose &  pose, Size const  i, constraints::ConstraintSet &  cst_set, Size const  dna_torsion_number, utility::vector1< func::AmberPeriodicFuncOP > const &  gaussian_parameter_set  ) const

private

References core::scoring::constraints::ConstraintSet::add_constraint(), core::scoring::dna_bb_torsion, and get_atom_ids_by_torsion().

Referenced by add_dna_torsion_tethers().

add_dna_torsion_tethers()

void core::scoring::dna::DNATorsionPotential::add_dna_torsion_tethers ( pose::Pose &  pose, constraints::ConstraintSet &  cst_set  ) const

private

References add_DNA_torsion_constraint(), core::scoring::dna::ALPHA, alpha_components_, core::scoring::dna::BETA, beta_components_, core::scoring::dna::CHI, core::scoring::dna::DELTA, delta_components_, core::scoring::dna::EPSILON, epsilon_components_, core::scoring::dna::GAMMA, gamma_components_, core::conformation::Residue::is_DNA(), core::scoring::dna::NU0, nu0_components_, core::scoring::dna::NU1, nu1_components_, core::scoring::dna::NU2, nu2_components_, core::scoring::dna::NU3, nu3_components_, core::scoring::dna::NU4, nu4_components_, core::pose::Pose::residue(), core::pose::Pose::size(), core::scoring::dna::ZETA, and zeta_components_.

Referenced by setup_constraints().

add_sugar_ring_closure_constraints() [1/2]

void core::scoring::dna::DNATorsionPotential::add_sugar_ring_closure_constraints	(	conformation::Residue const &	rsd,
		constraints::ConstraintSet &	cst_set
	)		const

References core::scoring::constraints::ConstraintSet::add_constraint(), core::conformation::Residue::atom_index(), c2prime_c3prime_dist_harm_func_, c3prime_c2prime_c1prime_angle_harm_func_, c4prime_c3prime_c2prime_angle_harm_func_, core::scoring::dna_sugar_close, core::conformation::Residue::is_DNA(), o3prime_c3prime_c2prime_angle_harm_func_, and core::conformation::Residue::seqpos().

Referenced by add_sugar_ring_closure_constraints(), core::energy_methods::DNATorsionEnergy::eval_intrares_energy(), and setup_constraints().

add_sugar_ring_closure_constraints() [2/2]

void core::scoring::dna::DNATorsionPotential::add_sugar_ring_closure_constraints ( pose::Pose &  pose, constraints::ConstraintSet &  cst_set  ) const

private

References add_sugar_ring_closure_constraints(), core::pose::Pose::residue(), and core::pose::Pose::size().

alpha_components()

utility::vector1< func::AmberPeriodicFuncOP >& core::scoring::dna::DNATorsionPotential::alpha_components ( )

inline

References alpha_components_.

beta_components()

utility::vector1< func::AmberPeriodicFuncOP >& core::scoring::dna::DNATorsionPotential::beta_components ( )

inline

References beta_components_.

delta_components()

utility::vector1< func::AmberPeriodicFuncOP >& core::scoring::dna::DNATorsionPotential::delta_components ( )

inline

References delta_components_.

delta_cutoff()

Real core::scoring::dna::DNATorsionPotential::delta_cutoff ( ) const

inline

References DELTA_CUTOFF_.

epsilon_components()

utility::vector1< func::AmberPeriodicFuncOP >& core::scoring::dna::DNATorsionPotential::epsilon_components ( )

inline

References epsilon_components_.

gamma_components()

utility::vector1< func::AmberPeriodicFuncOP >& core::scoring::dna::DNATorsionPotential::gamma_components ( )

inline

References gamma_components_.

get_atom_ids_by_torsion()

bool core::scoring::dna::DNATorsionPotential::get_atom_ids_by_torsion ( Size const  dna_torsion_number, pose::Pose &  pose, Size const  resid, id::AtomID &  id1, id::AtomID &  id2, id::AtomID &  id3, id::AtomID &  id4  ) const

private

References core::scoring::dna::ALPHA, alpha_atom_names_, core::conformation::Residue::atom_index(), core::scoring::dna::BETA, beta_atom_names_, core::scoring::dna::DELTA, delta_atom_names_, core::scoring::dna::EPSILON, epsilon_atom_names_, core::scoring::dna::GAMMA, gamma_atom_names_, core::chemical::ResidueType::is_lower_terminus(), core::chemical::ResidueType::is_upper_terminus(), core::scoring::dna::NU0, nu0_atom_names_, core::scoring::dna::NU1, nu1_atom_names_, core::scoring::dna::NU2, nu2_atom_names_, core::scoring::dna::NU3, nu3_atom_names_, core::scoring::dna::NU4, nu4_atom_names_, core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::scoring::dna::ZETA, and zeta_atom_names_.

Referenced by add_DNA_torsion_constraint().

init_dna_torsion_parameters()

void core::scoring::dna::DNATorsionPotential::init_dna_torsion_parameters ( )

private

References alpha_atom_names_, alpha_components_, beta_atom_names_, beta_components_, delta_atom_names_, delta_components_, epsilon_atom_names_, epsilon_components_, gamma_atom_names_, gamma_components_, nu0_atom_names_, nu0_components_, nu1_atom_names_, nu1_components_, nu2_atom_names_, nu2_components_, nu3_atom_names_, nu3_components_, nu4_atom_names_, nu4_components_, zeta_atom_names_, and zeta_components_.

Referenced by DNATorsionPotential().

nu0_components()

utility::vector1< func::AmberPeriodicFuncOP >& core::scoring::dna::DNATorsionPotential::nu0_components ( )

inline

References nu0_components_.

nu1_components()

utility::vector1< func::AmberPeriodicFuncOP >& core::scoring::dna::DNATorsionPotential::nu1_components ( )

inline

References nu1_components_.

nu2_components()

utility::vector1< func::AmberPeriodicFuncOP >& core::scoring::dna::DNATorsionPotential::nu2_components ( )

inline

References nu2_components_.

nu3_components()

utility::vector1< func::AmberPeriodicFuncOP >& core::scoring::dna::DNATorsionPotential::nu3_components ( )

inline

References nu3_components_.

nu4_components()

utility::vector1< func::AmberPeriodicFuncOP >& core::scoring::dna::DNATorsionPotential::nu4_components ( )

inline

References nu4_components_.

setup_constraints()

void core::scoring::dna::DNATorsionPotential::setup_constraints	(	pose::Pose &	pose,
		constraints::ConstraintSetOP &	dna_torsion_constraints,
		constraints::ConstraintSetOP &	dna_sugar_close_constraints,
		constraints::ConstraintSetOP &	dna_base_distance_constraints
	)		const

References add_dna_base_distance_constraints(), add_dna_torsion_tethers(), and add_sugar_ring_closure_constraints().

Referenced by core::energy_methods::DNATorsionEnergy::setup_for_derivatives(), and core::energy_methods::DNATorsionEnergy::setup_for_scoring().

zeta_components()

utility::vector1< func::AmberPeriodicFuncOP >& core::scoring::dna::DNATorsionPotential::zeta_components ( )

inline

References zeta_components_.

Member Data Documentation

alpha_atom_names_

utility::vector1< std::string > core::scoring::dna::DNATorsionPotential::alpha_atom_names_

private

Referenced by get_atom_ids_by_torsion(), and init_dna_torsion_parameters().

alpha_components_

utility::vector1< func::AmberPeriodicFuncOP > core::scoring::dna::DNATorsionPotential::alpha_components_

private

Referenced by add_dna_torsion_tethers(), alpha_components(), and init_dna_torsion_parameters().

beta_atom_names_

utility::vector1< std::string > core::scoring::dna::DNATorsionPotential::beta_atom_names_

private

Referenced by get_atom_ids_by_torsion(), and init_dna_torsion_parameters().

beta_components_

utility::vector1< func::AmberPeriodicFuncOP > core::scoring::dna::DNATorsionPotential::beta_components_

private

Referenced by add_dna_torsion_tethers(), beta_components(), and init_dna_torsion_parameters().

c2prime_c3prime_bond_length_

Distance const core::scoring::dna::DNATorsionPotential::c2prime_c3prime_bond_length_

private

c2prime_c3prime_dist_harm_func_

func::HarmonicFuncOP core::scoring::dna::DNATorsionPotential::c2prime_c3prime_dist_harm_func_

private

Referenced by add_sugar_ring_closure_constraints().

c2prime_c3prime_sd_

Distance const core::scoring::dna::DNATorsionPotential::c2prime_c3prime_sd_

private

c3prime_c2prime_c1prime_angle_harm_func_

func::HarmonicFuncOP core::scoring::dna::DNATorsionPotential::c3prime_c2prime_c1prime_angle_harm_func_

private

Referenced by add_sugar_ring_closure_constraints().

c3prime_c2prime_c1prime_bond_angle_

Real const core::scoring::dna::DNATorsionPotential::c3prime_c2prime_c1prime_bond_angle_

private

c4prime_c3prime_c2prime_angle_harm_func_

func::HarmonicFuncOP core::scoring::dna::DNATorsionPotential::c4prime_c3prime_c2prime_angle_harm_func_

private

Referenced by add_sugar_ring_closure_constraints().

c4prime_c3prime_c2prime_bond_angle_

Real const core::scoring::dna::DNATorsionPotential::c4prime_c3prime_c2prime_bond_angle_

private

delta_atom_names_

utility::vector1< std::string > core::scoring::dna::DNATorsionPotential::delta_atom_names_

private

Referenced by get_atom_ids_by_torsion(), and init_dna_torsion_parameters().

delta_components_

utility::vector1< func::AmberPeriodicFuncOP > core::scoring::dna::DNATorsionPotential::delta_components_

private

Referenced by add_dna_torsion_tethers(), delta_components(), and init_dna_torsion_parameters().

DELTA_CUTOFF_

Real const core::scoring::dna::DNATorsionPotential::DELTA_CUTOFF_

private

Referenced by delta_cutoff().

epsilon_atom_names_

utility::vector1< std::string > core::scoring::dna::DNATorsionPotential::epsilon_atom_names_

private

Referenced by get_atom_ids_by_torsion(), and init_dna_torsion_parameters().

epsilon_components_

utility::vector1< func::AmberPeriodicFuncOP > core::scoring::dna::DNATorsionPotential::epsilon_components_

private

Referenced by add_dna_torsion_tethers(), epsilon_components(), and init_dna_torsion_parameters().

gamma_atom_names_

utility::vector1< std::string > core::scoring::dna::DNATorsionPotential::gamma_atom_names_

private

Referenced by get_atom_ids_by_torsion(), and init_dna_torsion_parameters().

gamma_components_

utility::vector1< func::AmberPeriodicFuncOP > core::scoring::dna::DNATorsionPotential::gamma_components_

private

Referenced by add_dna_torsion_tethers(), gamma_components(), and init_dna_torsion_parameters().

nu0_atom_names_

utility::vector1< std::string > core::scoring::dna::DNATorsionPotential::nu0_atom_names_

private

Referenced by get_atom_ids_by_torsion(), and init_dna_torsion_parameters().

nu0_components_

utility::vector1< func::AmberPeriodicFuncOP > core::scoring::dna::DNATorsionPotential::nu0_components_

private

Referenced by add_dna_torsion_tethers(), init_dna_torsion_parameters(), and nu0_components().

nu1_atom_names_

utility::vector1< std::string > core::scoring::dna::DNATorsionPotential::nu1_atom_names_

private

Referenced by get_atom_ids_by_torsion(), and init_dna_torsion_parameters().

nu1_components_

utility::vector1< func::AmberPeriodicFuncOP > core::scoring::dna::DNATorsionPotential::nu1_components_

private

Referenced by add_dna_torsion_tethers(), init_dna_torsion_parameters(), and nu1_components().

nu2_atom_names_

utility::vector1< std::string > core::scoring::dna::DNATorsionPotential::nu2_atom_names_

private

Referenced by get_atom_ids_by_torsion(), and init_dna_torsion_parameters().

nu2_components_

utility::vector1< func::AmberPeriodicFuncOP > core::scoring::dna::DNATorsionPotential::nu2_components_

private

Referenced by add_dna_torsion_tethers(), init_dna_torsion_parameters(), and nu2_components().

nu3_atom_names_

utility::vector1< std::string > core::scoring::dna::DNATorsionPotential::nu3_atom_names_

private

Referenced by get_atom_ids_by_torsion(), and init_dna_torsion_parameters().

nu3_components_

utility::vector1< func::AmberPeriodicFuncOP > core::scoring::dna::DNATorsionPotential::nu3_components_

private

Referenced by add_dna_torsion_tethers(), init_dna_torsion_parameters(), and nu3_components().

nu4_atom_names_

utility::vector1< std::string > core::scoring::dna::DNATorsionPotential::nu4_atom_names_

private

Referenced by get_atom_ids_by_torsion(), and init_dna_torsion_parameters().

nu4_components_

utility::vector1< func::AmberPeriodicFuncOP > core::scoring::dna::DNATorsionPotential::nu4_components_

private

Referenced by add_dna_torsion_tethers(), init_dna_torsion_parameters(), and nu4_components().

o3prime_c3prime_c2prime_angle_harm_func_

func::HarmonicFuncOP core::scoring::dna::DNATorsionPotential::o3prime_c3prime_c2prime_angle_harm_func_

private

Referenced by add_sugar_ring_closure_constraints().

o3prime_c3prime_c2prime_bond_angle_

Real const core::scoring::dna::DNATorsionPotential::o3prime_c3prime_c2prime_bond_angle_

private

scale_dna_torsion_sd_

Real const core::scoring::dna::DNATorsionPotential::scale_dna_torsion_sd_

private

scale_dna_torsion_tether_

Real const core::scoring::dna::DNATorsionPotential::scale_dna_torsion_tether_

private

zeta_atom_names_

utility::vector1< std::string > core::scoring::dna::DNATorsionPotential::zeta_atom_names_

private

Referenced by get_atom_ids_by_torsion(), and init_dna_torsion_parameters().

zeta_components_

utility::vector1< func::AmberPeriodicFuncOP > core::scoring::dna::DNATorsionPotential::zeta_components_

private

Referenced by add_dna_torsion_tethers(), init_dna_torsion_parameters(), and zeta_components().

---

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

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