#include <DNATorsionPotential.hh>
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void | add_sugar_ring_closure_constraints (pose::Pose &pose, constraints::ConstraintSet &cst_set) const |
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void | add_dna_base_distance_constraints (pose::Pose &pose, constraints::ConstraintSet &cst_set) const |
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void | add_dna_torsion_tethers (pose::Pose &pose, constraints::ConstraintSet &cst_set) const |
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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 |
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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 |
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void | init_dna_torsion_parameters () |
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core::scoring::dna::DNATorsionPotential::DNATorsionPotential |
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core::scoring::dna::DNATorsionPotential::~DNATorsionPotential |
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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::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::total_residue(), core::scoring::dna::ZETA, and zeta_components_.
Referenced by setup_constraints().
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::scoring::dna::DNATorsionEnergy::eval_intrares_energy(), and setup_constraints().
Real core::scoring::dna::DNATorsionPotential::delta_cutoff |
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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().
void core::scoring::dna::DNATorsionPotential::init_dna_torsion_parameters |
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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().
utility::vector1< std::string > core::scoring::dna::DNATorsionPotential::alpha_atom_names_ |
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utility::vector1< std::string > core::scoring::dna::DNATorsionPotential::beta_atom_names_ |
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Distance const core::scoring::dna::DNATorsionPotential::c2prime_c3prime_bond_length_ |
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Distance const core::scoring::dna::DNATorsionPotential::c2prime_c3prime_sd_ |
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func::HarmonicFuncOP core::scoring::dna::DNATorsionPotential::c3prime_c2prime_c1prime_angle_harm_func_ |
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Real const core::scoring::dna::DNATorsionPotential::c3prime_c2prime_c1prime_bond_angle_ |
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func::HarmonicFuncOP core::scoring::dna::DNATorsionPotential::c4prime_c3prime_c2prime_angle_harm_func_ |
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Real const core::scoring::dna::DNATorsionPotential::c4prime_c3prime_c2prime_bond_angle_ |
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utility::vector1< std::string > core::scoring::dna::DNATorsionPotential::delta_atom_names_ |
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Real const core::scoring::dna::DNATorsionPotential::DELTA_CUTOFF_ |
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utility::vector1< std::string > core::scoring::dna::DNATorsionPotential::epsilon_atom_names_ |
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utility::vector1< std::string > core::scoring::dna::DNATorsionPotential::gamma_atom_names_ |
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utility::vector1< std::string > core::scoring::dna::DNATorsionPotential::nu0_atom_names_ |
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utility::vector1< std::string > core::scoring::dna::DNATorsionPotential::nu1_atom_names_ |
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utility::vector1< std::string > core::scoring::dna::DNATorsionPotential::nu2_atom_names_ |
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utility::vector1< std::string > core::scoring::dna::DNATorsionPotential::nu3_atom_names_ |
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utility::vector1< std::string > core::scoring::dna::DNATorsionPotential::nu4_atom_names_ |
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func::HarmonicFuncOP core::scoring::dna::DNATorsionPotential::o3prime_c3prime_c2prime_angle_harm_func_ |
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Real const core::scoring::dna::DNATorsionPotential::o3prime_c3prime_c2prime_bond_angle_ |
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Real const core::scoring::dna::DNATorsionPotential::scale_dna_torsion_sd_ |
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Real const core::scoring::dna::DNATorsionPotential::scale_dna_torsion_tether_ |
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utility::vector1< std::string > core::scoring::dna::DNATorsionPotential::zeta_atom_names_ |
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The documentation for this class was generated from the following files: