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

#include <DNATorsionPotential.hh>

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

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

Member Function Documentation

void core::scoring::dna::DNATorsionPotential::add_dna_base_distance_constraints ( pose::Pose pose,
constraints::ConstraintSet cst_set 
) const
private
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
void core::scoring::dna::DNATorsionPotential::add_dna_torsion_tethers ( pose::Pose pose,
constraints::ConstraintSet cst_set 
) const
private
void core::scoring::dna::DNATorsionPotential::add_sugar_ring_closure_constraints ( conformation::Residue const &  rsd,
constraints::ConstraintSet cst_set 
) const
void core::scoring::dna::DNATorsionPotential::add_sugar_ring_closure_constraints ( pose::Pose pose,
constraints::ConstraintSet cst_set 
) const
private
utility::vector1< func::AmberPeriodicFuncOP >& core::scoring::dna::DNATorsionPotential::alpha_components ( )
inline

References alpha_components_.

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

References beta_components_.

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

References delta_components_.

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

References DELTA_CUTOFF_.

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

References epsilon_components_.

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

References gamma_components_.

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
void core::scoring::dna::DNATorsionPotential::init_dna_torsion_parameters ( )
private
utility::vector1< func::AmberPeriodicFuncOP >& core::scoring::dna::DNATorsionPotential::nu0_components ( )
inline

References nu0_components_.

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

References nu1_components_.

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

References nu2_components_.

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

References nu3_components_.

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

References nu4_components_.

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

References zeta_components_.

Member Data Documentation

utility::vector1< std::string > core::scoring::dna::DNATorsionPotential::alpha_atom_names_
private
utility::vector1< func::AmberPeriodicFuncOP > core::scoring::dna::DNATorsionPotential::alpha_components_
private
utility::vector1< std::string > core::scoring::dna::DNATorsionPotential::beta_atom_names_
private
utility::vector1< func::AmberPeriodicFuncOP > core::scoring::dna::DNATorsionPotential::beta_components_
private
Distance const core::scoring::dna::DNATorsionPotential::c2prime_c3prime_bond_length_
private
func::HarmonicFuncOP core::scoring::dna::DNATorsionPotential::c2prime_c3prime_dist_harm_func_
private
Distance const core::scoring::dna::DNATorsionPotential::c2prime_c3prime_sd_
private
func::HarmonicFuncOP core::scoring::dna::DNATorsionPotential::c3prime_c2prime_c1prime_angle_harm_func_
private
Real const core::scoring::dna::DNATorsionPotential::c3prime_c2prime_c1prime_bond_angle_
private
func::HarmonicFuncOP core::scoring::dna::DNATorsionPotential::c4prime_c3prime_c2prime_angle_harm_func_
private
Real const core::scoring::dna::DNATorsionPotential::c4prime_c3prime_c2prime_bond_angle_
private
utility::vector1< std::string > core::scoring::dna::DNATorsionPotential::delta_atom_names_
private
utility::vector1< func::AmberPeriodicFuncOP > core::scoring::dna::DNATorsionPotential::delta_components_
private
Real const core::scoring::dna::DNATorsionPotential::DELTA_CUTOFF_
private

Referenced by delta_cutoff().

utility::vector1< std::string > core::scoring::dna::DNATorsionPotential::epsilon_atom_names_
private
utility::vector1< func::AmberPeriodicFuncOP > core::scoring::dna::DNATorsionPotential::epsilon_components_
private
utility::vector1< std::string > core::scoring::dna::DNATorsionPotential::gamma_atom_names_
private
utility::vector1< func::AmberPeriodicFuncOP > core::scoring::dna::DNATorsionPotential::gamma_components_
private
utility::vector1< std::string > core::scoring::dna::DNATorsionPotential::nu0_atom_names_
private
utility::vector1< func::AmberPeriodicFuncOP > core::scoring::dna::DNATorsionPotential::nu0_components_
private
utility::vector1< std::string > core::scoring::dna::DNATorsionPotential::nu1_atom_names_
private
utility::vector1< func::AmberPeriodicFuncOP > core::scoring::dna::DNATorsionPotential::nu1_components_
private
utility::vector1< std::string > core::scoring::dna::DNATorsionPotential::nu2_atom_names_
private
utility::vector1< func::AmberPeriodicFuncOP > core::scoring::dna::DNATorsionPotential::nu2_components_
private
utility::vector1< std::string > core::scoring::dna::DNATorsionPotential::nu3_atom_names_
private
utility::vector1< func::AmberPeriodicFuncOP > core::scoring::dna::DNATorsionPotential::nu3_components_
private
utility::vector1< std::string > core::scoring::dna::DNATorsionPotential::nu4_atom_names_
private
utility::vector1< func::AmberPeriodicFuncOP > core::scoring::dna::DNATorsionPotential::nu4_components_
private
func::HarmonicFuncOP core::scoring::dna::DNATorsionPotential::o3prime_c3prime_c2prime_angle_harm_func_
private
Real const core::scoring::dna::DNATorsionPotential::o3prime_c3prime_c2prime_bond_angle_
private
Real const core::scoring::dna::DNATorsionPotential::scale_dna_torsion_sd_
private
Real const core::scoring::dna::DNATorsionPotential::scale_dna_torsion_tether_
private
utility::vector1< std::string > core::scoring::dna::DNATorsionPotential::zeta_atom_names_
private
utility::vector1< func::AmberPeriodicFuncOP > core::scoring::dna::DNATorsionPotential::zeta_components_
private

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