dna

Bindings for core::scoring::dna namespace

class pyrosetta.rosetta.core.scoring.dna.BasePartner

Bases: pyrosetta.rosetta.basic.datacache.CacheableData

silly vector1 wrapper class so we can derive from PoseCachedData

assign(self: pyrosetta.rosetta.core.scoring.dna.BasePartner, : pyrosetta.rosetta.core.scoring.dna.BasePartner) pyrosetta.rosetta.core.scoring.dna.BasePartner

C++: core::scoring::dna::BasePartner::operator=(const class core::scoring::dna::BasePartner &) –> class core::scoring::dna::BasePartner &

clone(self: pyrosetta.rosetta.core.scoring.dna.BasePartner) pyrosetta.rosetta.basic.datacache.CacheableData

C++: core::scoring::dna::BasePartner::clone() const –> class std::shared_ptr<class basic::datacache::CacheableData>

get_self_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) pyrosetta.rosetta.basic.datacache.CacheableData

C++: basic::datacache::CacheableData::get_self_ptr() –> class std::shared_ptr<class basic::datacache::CacheableData>

get_self_weak_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) pyrosetta.rosetta.std.weak_ptr_basic_datacache_CacheableData_t

C++: basic::datacache::CacheableData::get_self_weak_ptr() –> class std::weak_ptr<class basic::datacache::CacheableData>

resize(self: pyrosetta.rosetta.core.scoring.dna.BasePartner, size_: int) None

C++: core::scoring::dna::BasePartner::resize(const unsigned long) –> void

size(self: pyrosetta.rosetta.core.scoring.dna.BasePartner) int

C++: core::scoring::dna::BasePartner::size() const –> unsigned long

class pyrosetta.rosetta.core.scoring.dna.DNABFormPotential

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.core.scoring.dna.DNABFormPotential, : pyrosetta.rosetta.core.scoring.dna.DNABFormPotential) pyrosetta.rosetta.core.scoring.dna.DNABFormPotential

C++: core::scoring::dna::DNABFormPotential::operator=(const class core::scoring::dna::DNABFormPotential &) –> class core::scoring::dna::DNABFormPotential &

eval_dna_bform_bb_torsion_score_residue(self: pyrosetta.rosetta.core.scoring.dna.DNABFormPotential, res: pyrosetta.rosetta.core.conformation.Residue, score: float, dscore_dchi: float, torsion_id: int) None

C++: core::scoring::dna::DNABFormPotential::eval_dna_bform_bb_torsion_score_residue(const class core::conformation::Residue &, double &, double &, const unsigned long) const –> void

eval_dna_bform_chi_torsion_score_residue(self: pyrosetta.rosetta.core.scoring.dna.DNABFormPotential, res: pyrosetta.rosetta.core.conformation.Residue, score: float, dscore_dchi: float) None

C++: core::scoring::dna::DNABFormPotential::eval_dna_bform_chi_torsion_score_residue(const class core::conformation::Residue &, double &, double &) const –> void

class pyrosetta.rosetta.core.scoring.dna.DNATorsionPotential

Bases: pybind11_builtins.pybind11_object

add_sugar_ring_closure_constraints(self: pyrosetta.rosetta.core.scoring.dna.DNATorsionPotential, rsd: pyrosetta.rosetta.core.conformation.Residue, cst_set: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) None

C++: core::scoring::dna::DNATorsionPotential::add_sugar_ring_closure_constraints(const class core::conformation::Residue &, class core::scoring::constraints::ConstraintSet &) const –> void

alpha_components(self: pyrosetta.rosetta.core.scoring.dna.DNATorsionPotential) pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_scoring_func_AmberPeriodicFunc_t

C++: core::scoring::dna::DNATorsionPotential::alpha_components() –> class utility::vector1<class std::shared_ptr<class core::scoring::func::AmberPeriodicFunc>, class std::allocator<class std::shared_ptr<class core::scoring::func::AmberPeriodicFunc> > > &

beta_components(self: pyrosetta.rosetta.core.scoring.dna.DNATorsionPotential) pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_scoring_func_AmberPeriodicFunc_t

C++: core::scoring::dna::DNATorsionPotential::beta_components() –> class utility::vector1<class std::shared_ptr<class core::scoring::func::AmberPeriodicFunc>, class std::allocator<class std::shared_ptr<class core::scoring::func::AmberPeriodicFunc> > > &

delta_components(self: pyrosetta.rosetta.core.scoring.dna.DNATorsionPotential) pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_scoring_func_AmberPeriodicFunc_t

C++: core::scoring::dna::DNATorsionPotential::delta_components() –> class utility::vector1<class std::shared_ptr<class core::scoring::func::AmberPeriodicFunc>, class std::allocator<class std::shared_ptr<class core::scoring::func::AmberPeriodicFunc> > > &

delta_cutoff(self: pyrosetta.rosetta.core.scoring.dna.DNATorsionPotential) float

C++: core::scoring::dna::DNATorsionPotential::delta_cutoff() const –> double

epsilon_components(self: pyrosetta.rosetta.core.scoring.dna.DNATorsionPotential) pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_scoring_func_AmberPeriodicFunc_t

C++: core::scoring::dna::DNATorsionPotential::epsilon_components() –> class utility::vector1<class std::shared_ptr<class core::scoring::func::AmberPeriodicFunc>, class std::allocator<class std::shared_ptr<class core::scoring::func::AmberPeriodicFunc> > > &

gamma_components(self: pyrosetta.rosetta.core.scoring.dna.DNATorsionPotential) pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_scoring_func_AmberPeriodicFunc_t

C++: core::scoring::dna::DNATorsionPotential::gamma_components() –> class utility::vector1<class std::shared_ptr<class core::scoring::func::AmberPeriodicFunc>, class std::allocator<class std::shared_ptr<class core::scoring::func::AmberPeriodicFunc> > > &

nu0_components(self: pyrosetta.rosetta.core.scoring.dna.DNATorsionPotential) pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_scoring_func_AmberPeriodicFunc_t

C++: core::scoring::dna::DNATorsionPotential::nu0_components() –> class utility::vector1<class std::shared_ptr<class core::scoring::func::AmberPeriodicFunc>, class std::allocator<class std::shared_ptr<class core::scoring::func::AmberPeriodicFunc> > > &

nu1_components(self: pyrosetta.rosetta.core.scoring.dna.DNATorsionPotential) pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_scoring_func_AmberPeriodicFunc_t

C++: core::scoring::dna::DNATorsionPotential::nu1_components() –> class utility::vector1<class std::shared_ptr<class core::scoring::func::AmberPeriodicFunc>, class std::allocator<class std::shared_ptr<class core::scoring::func::AmberPeriodicFunc> > > &

nu2_components(self: pyrosetta.rosetta.core.scoring.dna.DNATorsionPotential) pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_scoring_func_AmberPeriodicFunc_t

C++: core::scoring::dna::DNATorsionPotential::nu2_components() –> class utility::vector1<class std::shared_ptr<class core::scoring::func::AmberPeriodicFunc>, class std::allocator<class std::shared_ptr<class core::scoring::func::AmberPeriodicFunc> > > &

nu3_components(self: pyrosetta.rosetta.core.scoring.dna.DNATorsionPotential) pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_scoring_func_AmberPeriodicFunc_t

C++: core::scoring::dna::DNATorsionPotential::nu3_components() –> class utility::vector1<class std::shared_ptr<class core::scoring::func::AmberPeriodicFunc>, class std::allocator<class std::shared_ptr<class core::scoring::func::AmberPeriodicFunc> > > &

nu4_components(self: pyrosetta.rosetta.core.scoring.dna.DNATorsionPotential) pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_scoring_func_AmberPeriodicFunc_t

C++: core::scoring::dna::DNATorsionPotential::nu4_components() –> class utility::vector1<class std::shared_ptr<class core::scoring::func::AmberPeriodicFunc>, class std::allocator<class std::shared_ptr<class core::scoring::func::AmberPeriodicFunc> > > &

setup_constraints(self: pyrosetta.rosetta.core.scoring.dna.DNATorsionPotential, pose: pyrosetta.rosetta.core.pose.Pose, dna_torsion_constraints: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, dna_sugar_close_constraints: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, dna_base_distance_constraints: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) None

C++: core::scoring::dna::DNATorsionPotential::setup_constraints(class core::pose::Pose &, class std::shared_ptr<class core::scoring::constraints::ConstraintSet> &, class std::shared_ptr<class core::scoring::constraints::ConstraintSet> &, class std::shared_ptr<class core::scoring::constraints::ConstraintSet> &) const –> void

zeta_components(self: pyrosetta.rosetta.core.scoring.dna.DNATorsionPotential) pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_scoring_func_AmberPeriodicFunc_t

C++: core::scoring::dna::DNATorsionPotential::zeta_components() –> class utility::vector1<class std::shared_ptr<class core::scoring::func::AmberPeriodicFunc>, class std::allocator<class std::shared_ptr<class core::scoring::func::AmberPeriodicFunc> > > &

class pyrosetta.rosetta.core.scoring.dna.DNA_BasePotential

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.core.scoring.dna.DNA_BasePotential, : pyrosetta.rosetta.core.scoring.dna.DNA_BasePotential) pyrosetta.rosetta.core.scoring.dna.DNA_BasePotential

C++: core::scoring::dna::DNA_BasePotential::operator=(const class core::scoring::dna::DNA_BasePotential &) –> class core::scoring::dna::DNA_BasePotential &

base_pair_score(self: pyrosetta.rosetta.core.scoring.dna.DNA_BasePotential, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue) float

C++: core::scoring::dna::DNA_BasePotential::base_pair_score(const class core::conformation::Residue &, const class core::conformation::Residue &) const –> double

base_step_score(self: pyrosetta.rosetta.core.scoring.dna.DNA_BasePotential, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue) float

C++: core::scoring::dna::DNA_BasePotential::base_step_score(const class core::conformation::Residue &, const class core::conformation::Residue &) const –> double

eval_base_pair_Z_scores(self: pyrosetta.rosetta.core.scoring.dna.DNA_BasePotential, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, z_scores: pyrosetta.rosetta.utility.vector1_double) None

C++: core::scoring::dna::DNA_BasePotential::eval_base_pair_Z_scores(const class core::conformation::Residue &, const class core::conformation::Residue &, class utility::vector1<double, class std::allocator<double> > &) const –> void

eval_base_pair_derivative(self: pyrosetta.rosetta.core.scoring.dna.DNA_BasePotential, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t, sign_factor: float) None

C++: core::scoring::dna::DNA_BasePotential::eval_base_pair_derivative(const class core::conformation::Residue &, const class core::conformation::Residue &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &, const double) const –> void

eval_base_step_Z_scores(self: pyrosetta.rosetta.core.scoring.dna.DNA_BasePotential, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, z_scores: pyrosetta.rosetta.utility.vector1_double) None

C++: core::scoring::dna::DNA_BasePotential::eval_base_step_Z_scores(const class core::conformation::Residue &, const class core::conformation::Residue &, class utility::vector1<double, class std::allocator<double> > &) const –> void

eval_base_step_derivative(self: pyrosetta.rosetta.core.scoring.dna.DNA_BasePotential, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t, external_sign_factor: float) None

C++: core::scoring::dna::DNA_BasePotential::eval_base_step_derivative(const class core::conformation::Residue &, const class core::conformation::Residue &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &, const double) const –> void

class pyrosetta.rosetta.core.scoring.dna.DNA_DihedralPotential

Bases: pybind11_builtins.pybind11_object

eval_harmonic_backbone_torsion_score_and_deriv(*args, **kwargs)

Overloaded function.

  1. eval_harmonic_backbone_torsion_score_and_deriv(self: pyrosetta.rosetta.core.scoring.dna.DNA_DihedralPotential, tor: int, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, score: float, dscore_dtor: float) -> None

C++: core::scoring::dna::DNA_DihedralPotential::eval_harmonic_backbone_torsion_score_and_deriv(const unsigned long, const class core::conformation::Residue &, const class core::pose::Pose &, double &, double &) const –> void

  1. eval_harmonic_backbone_torsion_score_and_deriv(self: pyrosetta.rosetta.core.scoring.dna.DNA_DihedralPotential, tor: int, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, score: float, dscore_dchi: float, dscore_deps: float, dscore_dzeta: float) -> None

C++: core::scoring::dna::DNA_DihedralPotential::eval_harmonic_backbone_torsion_score_and_deriv(const unsigned long, const class core::conformation::Residue &, const class core::pose::Pose &, double &, double &, double &, double &) const –> void

eval_harmonic_sugar_pucker_dependent_chi_torsion_score_and_deriv(self: pyrosetta.rosetta.core.scoring.dna.DNA_DihedralPotential, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, pucker: int, score: float, dscore_dchi: float) None

C++: core::scoring::dna::DNA_DihedralPotential::eval_harmonic_sugar_pucker_dependent_chi_torsion_score_and_deriv(const class core::conformation::Residue &, const class core::pose::Pose &, const unsigned long, double &, double &) const –> void

eval_sugar_torsion_score_and_deriv(self: pyrosetta.rosetta.core.scoring.dna.DNA_DihedralPotential, torsion: float, tor: int, rsd: pyrosetta.rosetta.core.conformation.Residue, pucker: int, score: float, dscore_dtor: float) None

C++: core::scoring::dna::DNA_DihedralPotential::eval_sugar_torsion_score_and_deriv(const double, const unsigned long, const class core::conformation::Residue &, const unsigned long, double &, double &) const –> void

get_mean_sugar_pucker_dependent_chi(self: pyrosetta.rosetta.core.scoring.dna.DNA_DihedralPotential, rsd: pyrosetta.rosetta.core.conformation.Residue) float

C++: core::scoring::dna::DNA_DihedralPotential::get_mean_sugar_pucker_dependent_chi(const class core::conformation::Residue &) const –> double

get_sugar_torsion_mean_and_sdev(self: pyrosetta.rosetta.core.scoring.dna.DNA_DihedralPotential, tor: int, rsd: pyrosetta.rosetta.core.conformation.Residue, pucker: int, mean: float, sdev: float) None

C++: core::scoring::dna::DNA_DihedralPotential::get_sugar_torsion_mean_and_sdev(const unsigned long, const class core::conformation::Residue &, const unsigned long, double &, double &) const –> void

class pyrosetta.rosetta.core.scoring.dna.DNA_EnvPairPotential

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.core.scoring.dna.DNA_EnvPairPotential, : pyrosetta.rosetta.core.scoring.dna.DNA_EnvPairPotential) pyrosetta.rosetta.core.scoring.dna.DNA_EnvPairPotential

C++: core::scoring::dna::DNA_EnvPairPotential::operator=(const class core::scoring::dna::DNA_EnvPairPotential &) –> class core::scoring::dna::DNA_EnvPairPotential &

centroid_xyz(self: pyrosetta.rosetta.core.scoring.dna.DNA_EnvPairPotential, rsd: pyrosetta.rosetta.core.conformation.Residue) pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::scoring::dna::DNA_EnvPairPotential::centroid_xyz(const class core::conformation::Residue &) const –> class numeric::xyzVector<double>

nbr_dis2_threshold(self: pyrosetta.rosetta.core.scoring.dna.DNA_EnvPairPotential) float

C++: core::scoring::dna::DNA_EnvPairPotential::nbr_dis2_threshold() const –> double

residue_env_score(self: pyrosetta.rosetta.core.scoring.dna.DNA_EnvPairPotential, aa: pyrosetta.rosetta.core.chemical.AA, nbr_count: int) float

C++: core::scoring::dna::DNA_EnvPairPotential::residue_env_score(const enum core::chemical::AA &, const unsigned long) const –> double

residue_pair_score(self: pyrosetta.rosetta.core.scoring.dna.DNA_EnvPairPotential, na: pyrosetta.rosetta.core.chemical.AA, aa: pyrosetta.rosetta.core.chemical.AA, dis2: float) float

C++: core::scoring::dna::DNA_EnvPairPotential::residue_pair_score(const enum core::chemical::AA &, const enum core::chemical::AA &, const double) const –> double

class pyrosetta.rosetta.core.scoring.dna.DirectReadoutPotential

Bases: pybind11_builtins.pybind11_object

1st pass implementation of Kono + Sarai’s protein-DNA interaction potential

Needs polishing, converting to mini standards in some respects, but still in trial stage.

rsd_rsd_energy(self: pyrosetta.rosetta.core.scoring.dna.DirectReadoutPotential, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue) float

C++: core::scoring::dna::DirectReadoutPotential::rsd_rsd_energy(const class core::conformation::Residue &, const class core::conformation::Residue &) const –> double

class pyrosetta.rosetta.core.scoring.dna.TorsionFourierComponent

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.core.scoring.dna.TorsionFourierComponent, : pyrosetta.rosetta.core.scoring.dna.TorsionFourierComponent) pyrosetta.rosetta.core.scoring.dna.TorsionFourierComponent

C++: core::scoring::dna::TorsionFourierComponent::operator=(const class core::scoring::dna::TorsionFourierComponent &) –> class core::scoring::dna::TorsionFourierComponent &

compute(self: pyrosetta.rosetta.core.scoring.dna.TorsionFourierComponent, torsion_angle: float, deriv: float) float

C++: core::scoring::dna::TorsionFourierComponent::compute(const double, double &) const –> double

factor(self: pyrosetta.rosetta.core.scoring.dna.TorsionFourierComponent) float

C++: core::scoring::dna::TorsionFourierComponent::factor() const –> double

periodicity(self: pyrosetta.rosetta.core.scoring.dna.TorsionFourierComponent) float

C++: core::scoring::dna::TorsionFourierComponent::periodicity() const –> double

phase(self: pyrosetta.rosetta.core.scoring.dna.TorsionFourierComponent) float

C++: core::scoring::dna::TorsionFourierComponent::phase() const –> double

pyrosetta.rosetta.core.scoring.dna.find_basepairs(pose: pyrosetta.rosetta.core.pose.Pose, partner: pyrosetta.rosetta.utility.vector1_unsigned_long) None

C++: core::scoring::dna::find_basepairs(const class core::pose::Pose &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

pyrosetta.rosetta.core.scoring.dna.get_DNA_backbone_bin(rsd: pyrosetta.rosetta.core.conformation.Residue) str

C++: core::scoring::dna::get_DNA_backbone_bin(const class core::conformation::Residue &) –> std::string

pyrosetta.rosetta.core.scoring.dna.get_base_pair_params(rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, params: pyrosetta.rosetta.utility.vector1_double) None

C++: core::scoring::dna::get_base_pair_params(const class core::conformation::Residue &, const class core::conformation::Residue &, class utility::vector1<double, class std::allocator<double> > &) –> void

pyrosetta.rosetta.core.scoring.dna.get_base_pair_stub_slow(rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue) pyrosetta.rosetta.core.kinematics.Stub

C++: core::scoring::dna::get_base_pair_stub_slow(const class core::conformation::Residue &, const class core::conformation::Residue &) –> class core::kinematics::Stub

pyrosetta.rosetta.core.scoring.dna.get_base_step_params(*args, **kwargs)

Overloaded function.

  1. get_base_step_params(rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, params: pyrosetta.rosetta.utility.vector1_double) -> None

C++: core::scoring::dna::get_base_step_params(const class core::conformation::Residue &, const class core::conformation::Residue &, class utility::vector1<double, class std::allocator<double> > &) –> void

  1. get_base_step_params(rsd11: pyrosetta.rosetta.core.conformation.Residue, rsd12: pyrosetta.rosetta.core.conformation.Residue, rsd21: pyrosetta.rosetta.core.conformation.Residue, rsd22: pyrosetta.rosetta.core.conformation.Residue, params: pyrosetta.rosetta.utility.vector1_double) -> None

C++: core::scoring::dna::get_base_step_params(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::conformation::Residue &, class utility::vector1<double, class std::allocator<double> > &) –> void

pyrosetta.rosetta.core.scoring.dna.get_base_stub(rsd: pyrosetta.rosetta.core.conformation.Residue, strand: int) pyrosetta.rosetta.core.kinematics.Stub

C++: core::scoring::dna::get_base_stub(const class core::conformation::Residue &, const int) –> class core::kinematics::Stub

pyrosetta.rosetta.core.scoring.dna.get_groove_widths(i: int, pose: pyrosetta.rosetta.core.pose.Pose, major_width: float, minor_width: float, major_length: float) None

C++: core::scoring::dna::get_groove_widths(const unsigned long, const class core::pose::Pose &, double &, double &, double &) –> void

pyrosetta.rosetta.core.scoring.dna.get_sugar_pucker_distr(rsd: pyrosetta.rosetta.core.conformation.Residue, puckerProb: pyrosetta.rosetta.utility.vector1_double) None

C++: core::scoring::dna::get_sugar_pucker_distr(const class core::conformation::Residue &, class utility::vector1<double, class std::allocator<double> > &) –> void

pyrosetta.rosetta.core.scoring.dna.get_sugar_torsions(rsd: pyrosetta.rosetta.core.conformation.Residue, torsions: pyrosetta.rosetta.utility.vector1_double) None

C++: core::scoring::dna::get_sugar_torsions(const class core::conformation::Residue &, class utility::vector1<double, class std::allocator<double> > &) –> void

pyrosetta.rosetta.core.scoring.dna.get_y_axis(rsd: pyrosetta.rosetta.core.conformation.Residue, strand: int) pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::scoring::dna::get_y_axis(const class core::conformation::Residue &, const int) –> class numeric::xyzVector<double>

pyrosetta.rosetta.core.scoring.dna.get_y_axis_atoms(rsd_type: pyrosetta.rosetta.core.chemical.ResidueType, strand: int, a1: str, a2: str) None

C++: core::scoring::dna::get_y_axis_atoms(const class core::chemical::ResidueType &, const int, std::string &, std::string &) –> void

pyrosetta.rosetta.core.scoring.dna.get_z_axis(rsd: pyrosetta.rosetta.core.conformation.Residue, y_axis: pyrosetta.rosetta.numeric.xyzVector_double_t) pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::scoring::dna::get_z_axis(const class core::conformation::Residue &, const class numeric::xyzVector<double> &) –> class numeric::xyzVector<double>

pyrosetta.rosetta.core.scoring.dna.is_orthonormal(M: pyrosetta.rosetta.numeric.xyzMatrix_double_t, tol: float) bool

C++: core::scoring::dna::is_orthonormal(const class numeric::xyzMatrix<double> &, const double) –> bool

pyrosetta.rosetta.core.scoring.dna.retrieve_base_partner_from_pose(pose: core::pose::Pose) pyrosetta.rosetta.core.scoring.dna.BasePartner

helper fcn

C++: core::scoring::dna::retrieve_base_partner_from_pose(const class core::pose::Pose &) –> const class core::scoring::dna::BasePartner &

pyrosetta.rosetta.core.scoring.dna.set_base_partner(pose: pyrosetta.rosetta.core.pose.Pose) None

C++: core::scoring::dna::set_base_partner(class core::pose::Pose &) –> void

pyrosetta.rosetta.core.scoring.dna.show_base_pair_params(*args, **kwargs)

Overloaded function.

  1. show_base_pair_params(rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue) -> None

C++: core::scoring::dna::show_base_pair_params(const class core::conformation::Residue &, const class core::conformation::Residue &) –> void

  1. show_base_pair_params(pose: pyrosetta.rosetta.core.pose.Pose, out: pyrosetta.rosetta.std.ostream) -> None

C++: core::scoring::dna::show_base_pair_params(const class core::pose::Pose &, std::ostream &) –> void

pyrosetta.rosetta.core.scoring.dna.show_base_step_params(pose: pyrosetta.rosetta.core.pose.Pose, out: pyrosetta.rosetta.std.ostream) None

C++: core::scoring::dna::show_base_step_params(const class core::pose::Pose &, std::ostream &) –> void

pyrosetta.rosetta.core.scoring.dna.show_new_base_step_params(rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue) None

C++: core::scoring::dna::show_new_base_step_params(const class core::conformation::Residue &, const class core::conformation::Residue &) –> void

pyrosetta.rosetta.core.scoring.dna.sugar_torsion_atom_names() pyrosetta.rosetta.utility.vector1_utility_vector1_std_string_std_allocator_std_string_t

C++: core::scoring::dna::sugar_torsion_atom_names() –> class utility::vector1<class utility::vector1<std::string, class std::allocator<std::string > >, class std::allocator<class utility::vector1<std::string, class std::allocator<std::string > > > >