etable¶

Bindings for core::scoring::etable namespace

class pyrosetta.rosetta.core.scoring.etable.Etable¶

Bases: pybind11_builtins.pybind11_object

Class definition for Etable

Wradius(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶: C++: core::scoring::etable::Etable::Wradius() const –> double

add_long_range_damping(self: pyrosetta.rosetta.core.scoring.etable.Etable) → bool¶: C++: core::scoring::etable::Etable::add_long_range_damping() const –> bool

analytic_etable_derivatives(self: pyrosetta.rosetta.core.scoring.etable.Etable, at1: pyrosetta.rosetta.core.conformation.Atom, at2: pyrosetta.rosetta.core.conformation.Atom, dljatrE_ddis: float, dljrepE_ddis: float, dfasolE_ddis: float, inv_d: float) → None¶

Analytically evaluate the energy derivatives for a pair of atoms

C++: core::scoring::etable::Etable::analytic_etable_derivatives(const class core::conformation::Atom &, const class core::conformation::Atom &, double &, double &, double &, double &) const –> void

analytic_etable_evaluation(self: pyrosetta.rosetta.core.scoring.etable.Etable, at1: pyrosetta.rosetta.core.conformation.Atom, at2: pyrosetta.rosetta.core.conformation.Atom, lj_atrE: float, lj_repE: float, fa_solE: float, d2: float) → None¶

Use an analytic functional form of the etable to evaluate an atom-pair energy: without reading from the enormous and uncachable tables.

C++: core::scoring::etable::Etable::analytic_etable_evaluation(const class core::conformation::Atom &, const class core::conformation::Atom &, double &, double &, double &, double &) const –> void

analytic_lk_derivatives(self: pyrosetta.rosetta.core.scoring.etable.Etable, at1: pyrosetta.rosetta.core.conformation.Atom, at2: pyrosetta.rosetta.core.conformation.Atom, dfasolE1_ddis: float, dfasolE2_ddis: float, inv_d: float) → None¶

Analytically evaluate the LK solvation derivatives for a pair of atoms, separately: computing the derivative for atom2’s desolvation of atom1 (dfasolE1_ddis) and atom1’s desolvation of atom2 (dfasolE2_ddis).

C++: core::scoring::etable::Etable::analytic_lk_derivatives(const class core::conformation::Atom &, const class core::conformation::Atom &, double &, double &, double &) const –> void

analytic_lk_energy(self: pyrosetta.rosetta.core.scoring.etable.Etable, at1: pyrosetta.rosetta.core.conformation.Atom, at2: pyrosetta.rosetta.core.conformation.Atom, fa_solE1: float, fa_solE2: float) → None¶

Use an analytic functional form of the etable to evaluate only the LK atom-pair energy: computing the desolvation of atom1 by atom2 separately from the desolvation of atom2 by atom1.

C++: core::scoring::etable::Etable::analytic_lk_energy(const class core::conformation::Atom &, const class core::conformation::Atom &, double &, double &) const –> void

analytic_params_for_pair(self: pyrosetta.rosetta.core.scoring.etable.Etable, atype1: int, atype2: int) → pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair¶: C++: core::scoring::etable::Etable::analytic_params_for_pair(unsigned long, unsigned long) const –> const struct core::scoring::etable::EtableParamsOnePair &

atom_set(self: pyrosetta.rosetta.core.scoring.etable.Etable) → pyrosetta.rosetta.std.weak_ptr_const_core_chemical_AtomTypeSet_t¶: C++: core::scoring::etable::Etable::atom_set() const –> class std::weak_ptr<const class core::chemical::AtomTypeSet>

atom_type(self: pyrosetta.rosetta.core.scoring.etable.Etable, type: int) → pyrosetta.rosetta.core.chemical.AtomType¶: C++: core::scoring::etable::Etable::atom_type(const int) –> const class core::chemical::AtomType &

cubic_polynomial_deriv(x: float, cp: pyrosetta.rosetta.core.scoring.etable.CubicPolynomial) → float¶: C++: core::scoring::etable::Etable::cubic_polynomial_deriv(const double, const struct core::scoring::etable::CubicPolynomial &) –> double

cubic_polynomial_from_spline(xlo: float, xhi: float, sp: pyrosetta.rosetta.core.scoring.etable.SplineParameters) → pyrosetta.rosetta.core.scoring.etable.CubicPolynomial¶: C++: core::scoring::etable::Etable::cubic_polynomial_from_spline(double, double, const struct core::scoring::etable::SplineParameters &) –> struct core::scoring::etable::CubicPolynomial

dljatr(self: pyrosetta.rosetta.core.scoring.etable.Etable) → ObjexxFCL::FArray3D<double>¶

const access to the deriv arrays

C++: core::scoring::etable::Etable::dljatr() const –> const class ObjexxFCL::FArray3D<double> &

dljrep(self: pyrosetta.rosetta.core.scoring.etable.Etable) → ObjexxFCL::FArray3D<double>¶: C++: core::scoring::etable::Etable::dljrep() const –> const class ObjexxFCL::FArray3D<double> &

dsolv(self: pyrosetta.rosetta.core.scoring.etable.Etable) → ObjexxFCL::FArray3D<double>¶

return the solvation derivative table that combines atom1 and atom2’s desolvations

C++: core::scoring::etable::Etable::dsolv() const –> const class ObjexxFCL::FArray3D<double> &

dsolv1(self: pyrosetta.rosetta.core.scoring.etable.Etable) → ObjexxFCL::FArray3D<double>¶

return the solvation derivative table for the desolvation of atom1 by atom2

C++: core::scoring::etable::Etable::dsolv1() const –> const class ObjexxFCL::FArray3D<double> &

epsilon(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶: C++: core::scoring::etable::Etable::epsilon() const –> double

etable_disbins(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶: C++: core::scoring::etable::Etable::etable_disbins() const –> double

eval_cubic_polynomial(x: float, sp: pyrosetta.rosetta.core.scoring.etable.CubicPolynomial) → float¶: C++: core::scoring::etable::Etable::eval_cubic_polynomial(const double, const struct core::scoring::etable::CubicPolynomial &) –> double

fa_hatr(self: pyrosetta.rosetta.core.scoring.etable.Etable) → bool¶

Do hydrogens provide attractive forces or do they only repell?

C++: core::scoring::etable::Etable::fa_hatr() const –> bool

fasol_cubic_poly_far_xhi(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶: C++: core::scoring::etable::Etable::fasol_cubic_poly_far_xhi() const –> double

fasol_cubic_poly_far_xlo(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶: C++: core::scoring::etable::Etable::fasol_cubic_poly_far_xlo() const –> double

get_bins_per_A2(self: pyrosetta.rosetta.core.scoring.etable.Etable) → int¶: C++: core::scoring::etable::Etable::get_bins_per_A2() const –> int

get_lj_hbond_OH_donor_dis(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶: C++: core::scoring::etable::Etable::get_lj_hbond_OH_donor_dis() const –> double

get_lj_hbond_dis(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶: C++: core::scoring::etable::Etable::get_lj_hbond_dis() const –> double

get_lj_hbond_hdis(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶: C++: core::scoring::etable::Etable::get_lj_hbond_hdis() const –> double

get_safe_max_dis2(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶: C++: core::scoring::etable::Etable::get_safe_max_dis2() const –> double

hydrogen_interaction_cutoff2(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶: C++: core::scoring::etable::Etable::hydrogen_interaction_cutoff2() const –> double

input_etable(self: pyrosetta.rosetta.core.scoring.etable.Etable, etable: ObjexxFCL::FArray3D<double>, label: str, in: pyrosetta.rosetta.std.istream) → None¶: C++: core::scoring::etable::Etable::input_etable(class ObjexxFCL::FArray3D<double> &, const class std::basic_string<char> &, class std::basic_istream<char> &) –> void

interpolated_analytic_etable_evaluation(self: pyrosetta.rosetta.core.scoring.etable.Etable, at1: pyrosetta.rosetta.core.conformation.Atom, at2: pyrosetta.rosetta.core.conformation.Atom, lj_atrE: float, lj_repE: float, fa_solE: float, d2: float) → None¶

Use the analytic_etable_evaluation function to evaluate the energy: of two atoms, but evaluate the function at the old grid points and then interpolate between them the way the existing etable does (in square distance space). Useful for comparing the original etable evaluation with the analytic evaluation.

C++: core::scoring::etable::Etable::interpolated_analytic_etable_evaluation(const class core::conformation::Atom &, const class core::conformation::Atom &, double &, double &, double &, double &) const –> void

lj_radius(self: pyrosetta.rosetta.core.scoring.etable.Etable, i: int) → float¶

Return the Lennard-Jones radius for an atom.

C++: core::scoring::etable::Etable::lj_radius(const int) const –> double

lj_slope_intercept(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶: C++: core::scoring::etable::Etable::lj_slope_intercept() const –> double

lj_switch_dis2sigma(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶: C++: core::scoring::etable::Etable::lj_switch_dis2sigma() const –> double

lj_use_hbond_radii(self: pyrosetta.rosetta.core.scoring.etable.Etable) → bool¶: C++: core::scoring::etable::Etable::lj_use_hbond_radii() const –> bool

lj_use_lj_deriv_slope(self: pyrosetta.rosetta.core.scoring.etable.Etable) → bool¶: C++: core::scoring::etable::Etable::lj_use_lj_deriv_slope() const –> bool

lj_use_water_radii(self: pyrosetta.rosetta.core.scoring.etable.Etable) → bool¶: C++: core::scoring::etable::Etable::lj_use_water_radii() const –> bool

lj_water_dis(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶: C++: core::scoring::etable::Etable::lj_water_dis() const –> double

lj_water_hdis(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶: C++: core::scoring::etable::Etable::lj_water_hdis() const –> double

lj_wdepth(self: pyrosetta.rosetta.core.scoring.etable.Etable, i: int) → float¶

Return the Lennard-Jones well depth for an atom

C++: core::scoring::etable::Etable::lj_wdepth(const int) const –> double

ljatr(self: pyrosetta.rosetta.core.scoring.etable.Etable) → ObjexxFCL::FArray3D<double>¶

const access to the arrays

C++: core::scoring::etable::Etable::ljatr() const –> const class ObjexxFCL::FArray3D<double> &

ljrep(self: pyrosetta.rosetta.core.scoring.etable.Etable) → ObjexxFCL::FArray3D<double>¶: C++: core::scoring::etable::Etable::ljrep() const –> const class ObjexxFCL::FArray3D<double> &

lk_dgfree(self: pyrosetta.rosetta.core.scoring.etable.Etable, i: int) → float¶

Return the Lazardis Karplus DGFree value for an atom

C++: core::scoring::etable::Etable::lk_dgfree(const int) const –> double

lk_inv_lambda2(self: pyrosetta.rosetta.core.scoring.etable.Etable, i: int) → float¶: C++: core::scoring::etable::Etable::lk_inv_lambda2(const int) const –> double

lk_lambda(self: pyrosetta.rosetta.core.scoring.etable.Etable, i: int) → float¶

Return the Lazaridis Karplus “lambda” value (correlation distance) for an atom

C++: core::scoring::etable::Etable::lk_lambda(const int) const –> double

lk_min_dis2sigma(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶: C++: core::scoring::etable::Etable::lk_min_dis2sigma() const –> double

lk_volume(self: pyrosetta.rosetta.core.scoring.etable.Etable, i: int) → float¶

Return the Lazaridis Karplus volume for an atom

C++: core::scoring::etable::Etable::lk_volume(const int) const –> double

long_range_damping_length(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶: C++: core::scoring::etable::Etable::long_range_damping_length() const –> double

max_dis(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶: C++: core::scoring::etable::Etable::max_dis() const –> double

max_dis2(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶: C++: core::scoring::etable::Etable::max_dis2() const –> double

max_heavy_heavy_cutoff(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶: C++: core::scoring::etable::Etable::max_heavy_heavy_cutoff() const –> double

max_heavy_hydrogen_cutoff(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶: C++: core::scoring::etable::Etable::max_heavy_hydrogen_cutoff() const –> double

max_hydrogen_hydrogen_cutoff(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶: C++: core::scoring::etable::Etable::max_hydrogen_hydrogen_cutoff() const –> double

max_hydrogen_lj_radius(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶

Returns the maximum lj radius for any hydrogen atom as: defined by the input atom-type-set used to create this Etable.

C++: core::scoring::etable::Etable::max_hydrogen_lj_radius() const –> double

max_non_hydrogen_lj_radius(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶

Returns the maximum lj radius for any non-hydrogen: atom as defined by the atom-type-set used to create this Etable.

C++: core::scoring::etable::Etable::max_non_hydrogen_lj_radius() const –> double

min_dis(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶: C++: core::scoring::etable::Etable::min_dis() const –> double

min_dis2(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶: C++: core::scoring::etable::Etable::min_dis2() const –> double

n_atomtypes(self: pyrosetta.rosetta.core.scoring.etable.Etable) → int¶: C++: core::scoring::etable::Etable::n_atomtypes() const –> int

nblist_dis2_cutoff_HH(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶

The square distance cutoff beyond which any hydrogen/hydrogen pair is guaranteed: to have an interaction energy of zero. This function is used by the NeighborList

C++: core::scoring::etable::Etable::nblist_dis2_cutoff_HH() const –> double

nblist_dis2_cutoff_XH(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶

The square distance cutoff beyond which a hydrogen/heavy-atom pair is: guaranteed to have an interaction energy of zero. This function is used by the NeighborList

C++: core::scoring::etable::Etable::nblist_dis2_cutoff_XH() const –> double

nblist_dis2_cutoff_XX(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶

The square distance cutoff beyond which any pair of heavy-atoms is: guaranteed to have an interaction energy of zero. This function is used by the NeighborList

C++: core::scoring::etable::Etable::nblist_dis2_cutoff_XX() const –> double

output_etable(self: pyrosetta.rosetta.core.scoring.etable.Etable, etable: ObjexxFCL::FArray3D<double>, label: str, out: pyrosetta.rosetta.std.ostream) → None¶: C++: core::scoring::etable::Etable::output_etable(class ObjexxFCL::FArray3D<double> &, class std::basic_string<char>, class std::basic_ostream<char> &) –> void

solv1(self: pyrosetta.rosetta.core.scoring.etable.Etable) → ObjexxFCL::FArray3D<double>¶: C++: core::scoring::etable::Etable::solv1() const –> const class ObjexxFCL::FArray3D<double> &

solv2(self: pyrosetta.rosetta.core.scoring.etable.Etable) → ObjexxFCL::FArray3D<double>¶: C++: core::scoring::etable::Etable::solv2() const –> const class ObjexxFCL::FArray3D<double> &

class pyrosetta.rosetta.core.scoring.etable.EtableEvaluator¶

Bases: pybind11_builtins.pybind11_object

///////////////// Evaluators ///////////////////////////////

assign(self: pyrosetta.rosetta.core.scoring.etable.EtableEvaluator, : pyrosetta.rosetta.core.scoring.etable.EtableEvaluator) → pyrosetta.rosetta.core.scoring.etable.EtableEvaluator¶: C++: core::scoring::etable::EtableEvaluator::operator=(const class core::scoring::etable::EtableEvaluator &) –> class core::scoring::etable::EtableEvaluator &

atom_pair_energy_v(*args, **kwargs)¶

Overloaded function.

atom_pair_energy_v(self: pyrosetta.rosetta.core.scoring.etable.EtableEvaluator, atom1: pyrosetta.rosetta.core.conformation.Atom, atom2: pyrosetta.rosetta.core.conformation.Atom, weight: float, atrE: float, repE: float, solE: float, d2: float) -> None

C++: core::scoring::etable::EtableEvaluator::atom_pair_energy_v(const class core::conformation::Atom &, const class core::conformation::Atom &, const double, double &, double &, double &, double &) const –> void

atom_pair_energy_v(self: pyrosetta.rosetta.core.scoring.etable.EtableEvaluator, atom1: pyrosetta.rosetta.core.conformation.Atom, atom2: pyrosetta.rosetta.core.conformation.Atom, weight: float, emap: pyrosetta.rosetta.core.scoring.EMapVector, d2: float) -> None

C++: core::scoring::etable::EtableEvaluator::atom_pair_energy_v(const class core::conformation::Atom &, const class core::conformation::Atom &, const double, class core::scoring::EMapVector &, double &) const –> void

atom_pair_lk_energy_and_deriv_v(*args, **kwargs)¶

Overloaded function.

atom_pair_lk_energy_and_deriv_v(self: pyrosetta.rosetta.core.scoring.etable.EtableEvaluator, atom1: pyrosetta.rosetta.core.conformation.Atom, atom2: pyrosetta.rosetta.core.conformation.Atom, solE1: float, dsolE1: float) -> None
atom_pair_lk_energy_and_deriv_v(self: pyrosetta.rosetta.core.scoring.etable.EtableEvaluator, atom1: pyrosetta.rosetta.core.conformation.Atom, atom2: pyrosetta.rosetta.core.conformation.Atom, solE1: float, dsolE1: float, eval_deriv: bool) -> None

C++: core::scoring::etable::EtableEvaluator::atom_pair_lk_energy_and_deriv_v(const class core::conformation::Atom &, const class core::conformation::Atom &, double &, double &, const bool) const –> void

atom_pair_lk_energy_and_deriv_v_efficient(self: pyrosetta.rosetta.core.scoring.etable.EtableEvaluator, atom1: pyrosetta.rosetta.core.conformation.Atom, atom2: pyrosetta.rosetta.core.conformation.Atom, solE1: float, solE2: float, dsolE1: float, eval_deriv: bool) → None¶: C++: core::scoring::etable::EtableEvaluator::atom_pair_lk_energy_and_deriv_v_efficient(const class core::conformation::Atom &, const class core::conformation::Atom &, double &, double &, double &, const bool) const –> void

atr_weight(self: pyrosetta.rosetta.core.scoring.etable.EtableEvaluator) → float¶: C++: core::scoring::etable::EtableEvaluator::atr_weight() const –> double

eval_dE_dR_over_r_v(self: pyrosetta.rosetta.core.scoring.etable.EtableEvaluator, atom1: pyrosetta.rosetta.core.conformation.Atom, atom2: pyrosetta.rosetta.core.conformation.Atom, weights: pyrosetta.rosetta.core.scoring.EMapVector, f1: pyrosetta.rosetta.numeric.xyzVector_double_t, f2: pyrosetta.rosetta.numeric.xyzVector_double_t) → float¶: C++: core::scoring::etable::EtableEvaluator::eval_dE_dR_over_r_v(const class core::conformation::Atom &, const class core::conformation::Atom &, const class core::scoring::EMapVector &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &) const –> double

hydrogen_interaction_cutoff2(self: pyrosetta.rosetta.core.scoring.etable.EtableEvaluator) → float¶: C++: core::scoring::etable::EtableEvaluator::hydrogen_interaction_cutoff2() const –> double

pair_energy_H_v(self: pyrosetta.rosetta.core.scoring.etable.EtableEvaluator, atom1: pyrosetta.rosetta.core.conformation.Atom, atom2: pyrosetta.rosetta.core.conformation.Atom, weight: float, emap: pyrosetta.rosetta.core.scoring.EMapVector) → None¶

A Virtual function for the evaluation of an interaction energy of an atom with: a hydrogen atom. Not to be confused with the importantly non-virtual function defined in each of the subclasses that templated atom-pair-energy-inline functions invoke (avoiding any virtual-function overhead).

C++: core::scoring::etable::EtableEvaluator::pair_energy_H_v(const class core::conformation::Atom &, const class core::conformation::Atom &, const double, class core::scoring::EMapVector &) const –> void

rep_weight(self: pyrosetta.rosetta.core.scoring.etable.EtableEvaluator) → float¶: C++: core::scoring::etable::EtableEvaluator::rep_weight() const –> double

set_scoretypes(self: pyrosetta.rosetta.core.scoring.etable.EtableEvaluator, st_atr_in: pyrosetta.rosetta.core.scoring.ScoreType, st_rep_in: pyrosetta.rosetta.core.scoring.ScoreType, st_sol_in: pyrosetta.rosetta.core.scoring.ScoreType) → None¶: C++: core::scoring::etable::EtableEvaluator::set_scoretypes(enum core::scoring::ScoreType, enum core::scoring::ScoreType, enum core::scoring::ScoreType) –> void

set_weights(self: pyrosetta.rosetta.core.scoring.etable.EtableEvaluator, weights: pyrosetta.rosetta.core.scoring.EMapVector) → None¶: C++: core::scoring::etable::EtableEvaluator::set_weights(const class core::scoring::EMapVector &) –> void

sol_weight(self: pyrosetta.rosetta.core.scoring.etable.EtableEvaluator) → float¶: C++: core::scoring::etable::EtableEvaluator::sol_weight() const –> double

st_atr(self: pyrosetta.rosetta.core.scoring.etable.EtableEvaluator) → pyrosetta.rosetta.core.scoring.ScoreType¶: C++: core::scoring::etable::EtableEvaluator::st_atr() const –> enum core::scoring::ScoreType

st_rep(self: pyrosetta.rosetta.core.scoring.etable.EtableEvaluator) → pyrosetta.rosetta.core.scoring.ScoreType¶: C++: core::scoring::etable::EtableEvaluator::st_rep() const –> enum core::scoring::ScoreType

st_sol(self: pyrosetta.rosetta.core.scoring.etable.EtableEvaluator) → pyrosetta.rosetta.core.scoring.ScoreType¶: C++: core::scoring::etable::EtableEvaluator::st_sol() const –> enum core::scoring::ScoreType

sum_energies(self: pyrosetta.rosetta.core.scoring.etable.EtableEvaluator, atr: float, rep: float, solv: float) → float¶: C++: core::scoring::etable::EtableEvaluator::sum_energies(double, double, double) const –> double

class pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair¶

Bases: pybind11_builtins.pybind11_object

%EtableParamsOnePair describes all of the parameters for a particular pair of atom types necessary to evaluate the Lennard-Jones and LK solvation energies.

class pyrosetta.rosetta.core.scoring.etable.ExtraQuadraticRepulsion¶

Bases: pybind11_builtins.pybind11_object

the ExtraQuadraticRepulsion class is used to add in extra repulsion for particular atom pairs, if needed, (e.g. for OCbb/OCbb) where the functional form is: fa_rep += (xhi - x)^2 * slope for values of x between xlo and xhi, and fa_rep += (x - xlo ) * extrapolated_slope + ylo where extrapolated slope can be anything, but, to defined a function with continuous derivatives, should be extrapolated_slope = (xhi-xlo)^2*slope. This is the analytical implementation of the “modify_pot” behavior.

class pyrosetta.rosetta.core.scoring.etable.MembEtable¶

Bases: pyrosetta.rosetta.core.scoring.etable.Etable

Table of pre-computed LK membrane solvation energies

Wradius(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶: C++: core::scoring::etable::Etable::Wradius() const –> double

add_long_range_damping(self: pyrosetta.rosetta.core.scoring.etable.Etable) → bool¶: C++: core::scoring::etable::Etable::add_long_range_damping() const –> bool

analytic_etable_derivatives(self: pyrosetta.rosetta.core.scoring.etable.Etable, at1: pyrosetta.rosetta.core.conformation.Atom, at2: pyrosetta.rosetta.core.conformation.Atom, dljatrE_ddis: float, dljrepE_ddis: float, dfasolE_ddis: float, inv_d: float) → None¶

Analytically evaluate the energy derivatives for a pair of atoms

C++: core::scoring::etable::Etable::analytic_etable_derivatives(const class core::conformation::Atom &, const class core::conformation::Atom &, double &, double &, double &, double &) const –> void

analytic_etable_evaluation(self: pyrosetta.rosetta.core.scoring.etable.Etable, at1: pyrosetta.rosetta.core.conformation.Atom, at2: pyrosetta.rosetta.core.conformation.Atom, lj_atrE: float, lj_repE: float, fa_solE: float, d2: float) → None¶

Use an analytic functional form of the etable to evaluate an atom-pair energy: without reading from the enormous and uncachable tables.

C++: core::scoring::etable::Etable::analytic_etable_evaluation(const class core::conformation::Atom &, const class core::conformation::Atom &, double &, double &, double &, double &) const –> void

analytic_lk_derivatives(self: pyrosetta.rosetta.core.scoring.etable.Etable, at1: pyrosetta.rosetta.core.conformation.Atom, at2: pyrosetta.rosetta.core.conformation.Atom, dfasolE1_ddis: float, dfasolE2_ddis: float, inv_d: float) → None¶

Analytically evaluate the LK solvation derivatives for a pair of atoms, separately: computing the derivative for atom2’s desolvation of atom1 (dfasolE1_ddis) and atom1’s desolvation of atom2 (dfasolE2_ddis).

C++: core::scoring::etable::Etable::analytic_lk_derivatives(const class core::conformation::Atom &, const class core::conformation::Atom &, double &, double &, double &) const –> void

analytic_lk_energy(self: pyrosetta.rosetta.core.scoring.etable.Etable, at1: pyrosetta.rosetta.core.conformation.Atom, at2: pyrosetta.rosetta.core.conformation.Atom, fa_solE1: float, fa_solE2: float) → None¶

Use an analytic functional form of the etable to evaluate only the LK atom-pair energy: computing the desolvation of atom1 by atom2 separately from the desolvation of atom2 by atom1.

C++: core::scoring::etable::Etable::analytic_lk_energy(const class core::conformation::Atom &, const class core::conformation::Atom &, double &, double &) const –> void

analytic_params_for_pair(self: pyrosetta.rosetta.core.scoring.etable.Etable, atype1: int, atype2: int) → pyrosetta.rosetta.core.scoring.etable.EtableParamsOnePair¶: C++: core::scoring::etable::Etable::analytic_params_for_pair(unsigned long, unsigned long) const –> const struct core::scoring::etable::EtableParamsOnePair &

atom_set(self: pyrosetta.rosetta.core.scoring.etable.Etable) → pyrosetta.rosetta.std.weak_ptr_const_core_chemical_AtomTypeSet_t¶: C++: core::scoring::etable::Etable::atom_set() const –> class std::weak_ptr<const class core::chemical::AtomTypeSet>

atom_type(self: pyrosetta.rosetta.core.scoring.etable.Etable, type: int) → pyrosetta.rosetta.core.chemical.AtomType¶: C++: core::scoring::etable::Etable::atom_type(const int) –> const class core::chemical::AtomType &

cubic_polynomial_deriv(x: float, cp: pyrosetta.rosetta.core.scoring.etable.CubicPolynomial) → float¶: C++: core::scoring::etable::Etable::cubic_polynomial_deriv(const double, const struct core::scoring::etable::CubicPolynomial &) –> double

cubic_polynomial_from_spline(xlo: float, xhi: float, sp: pyrosetta.rosetta.core.scoring.etable.SplineParameters) → pyrosetta.rosetta.core.scoring.etable.CubicPolynomial¶: C++: core::scoring::etable::Etable::cubic_polynomial_from_spline(double, double, const struct core::scoring::etable::SplineParameters &) –> struct core::scoring::etable::CubicPolynomial

dljatr(self: pyrosetta.rosetta.core.scoring.etable.Etable) → ObjexxFCL::FArray3D<double>¶

const access to the deriv arrays

C++: core::scoring::etable::Etable::dljatr() const –> const class ObjexxFCL::FArray3D<double> &

dljrep(self: pyrosetta.rosetta.core.scoring.etable.Etable) → ObjexxFCL::FArray3D<double>¶: C++: core::scoring::etable::Etable::dljrep() const –> const class ObjexxFCL::FArray3D<double> &

dsolv(self: pyrosetta.rosetta.core.scoring.etable.Etable) → ObjexxFCL::FArray3D<double>¶

return the solvation derivative table that combines atom1 and atom2’s desolvations

C++: core::scoring::etable::Etable::dsolv() const –> const class ObjexxFCL::FArray3D<double> &

dsolv1(self: pyrosetta.rosetta.core.scoring.etable.MembEtable) → ObjexxFCL::FArray3D<double>¶

Return the solvation derivative table for the desolvation of atom1 by atom2

C++: core::scoring::etable::MembEtable::dsolv1() const –> const class ObjexxFCL::FArray3D<double> &

dsolv2(self: pyrosetta.rosetta.core.scoring.etable.MembEtable) → ObjexxFCL::FArray3D<double>¶

Return the solvation derivative table that combines atom1 and atom2’s desolvations

C++: core::scoring::etable::MembEtable::dsolv2() const –> const class ObjexxFCL::FArray3D<double> &

epsilon(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶: C++: core::scoring::etable::Etable::epsilon() const –> double

etable_disbins(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶: C++: core::scoring::etable::Etable::etable_disbins() const –> double

eval_cubic_polynomial(x: float, sp: pyrosetta.rosetta.core.scoring.etable.CubicPolynomial) → float¶: C++: core::scoring::etable::Etable::eval_cubic_polynomial(const double, const struct core::scoring::etable::CubicPolynomial &) –> double

fa_hatr(self: pyrosetta.rosetta.core.scoring.etable.Etable) → bool¶

Do hydrogens provide attractive forces or do they only repell?

C++: core::scoring::etable::Etable::fa_hatr() const –> bool

fasol_cubic_poly_far_xhi(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶: C++: core::scoring::etable::Etable::fasol_cubic_poly_far_xhi() const –> double

fasol_cubic_poly_far_xlo(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶: C++: core::scoring::etable::Etable::fasol_cubic_poly_far_xlo() const –> double

get_bins_per_A2(self: pyrosetta.rosetta.core.scoring.etable.Etable) → int¶: C++: core::scoring::etable::Etable::get_bins_per_A2() const –> int

get_lj_hbond_OH_donor_dis(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶: C++: core::scoring::etable::Etable::get_lj_hbond_OH_donor_dis() const –> double

get_lj_hbond_dis(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶: C++: core::scoring::etable::Etable::get_lj_hbond_dis() const –> double

get_lj_hbond_hdis(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶: C++: core::scoring::etable::Etable::get_lj_hbond_hdis() const –> double

get_safe_max_dis2(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶: C++: core::scoring::etable::Etable::get_safe_max_dis2() const –> double

hydrogen_interaction_cutoff2(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶: C++: core::scoring::etable::Etable::hydrogen_interaction_cutoff2() const –> double

input_etable(self: pyrosetta.rosetta.core.scoring.etable.MembEtable, etable: ObjexxFCL::FArray3D<double>, label: str, in: pyrosetta.rosetta.std.istream) → None¶: C++: core::scoring::etable::MembEtable::input_etable(class ObjexxFCL::FArray3D<double> &, const class std::basic_string<char> &, class std::basic_istream<char> &) –> void

interpolated_analytic_etable_evaluation(self: pyrosetta.rosetta.core.scoring.etable.Etable, at1: pyrosetta.rosetta.core.conformation.Atom, at2: pyrosetta.rosetta.core.conformation.Atom, lj_atrE: float, lj_repE: float, fa_solE: float, d2: float) → None¶

Use the analytic_etable_evaluation function to evaluate the energy: of two atoms, but evaluate the function at the old grid points and then interpolate between them the way the existing etable does (in square distance space). Useful for comparing the original etable evaluation with the analytic evaluation.

C++: core::scoring::etable::Etable::interpolated_analytic_etable_evaluation(const class core::conformation::Atom &, const class core::conformation::Atom &, double &, double &, double &, double &) const –> void

lj_radius(self: pyrosetta.rosetta.core.scoring.etable.MembEtable, i: int) → float¶

set these up in the ctor

C++: core::scoring::etable::MembEtable::lj_radius(const int) const –> double

lj_slope_intercept(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶: C++: core::scoring::etable::Etable::lj_slope_intercept() const –> double

lj_switch_dis2sigma(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶: C++: core::scoring::etable::Etable::lj_switch_dis2sigma() const –> double

lj_use_hbond_radii(self: pyrosetta.rosetta.core.scoring.etable.Etable) → bool¶: C++: core::scoring::etable::Etable::lj_use_hbond_radii() const –> bool

lj_use_lj_deriv_slope(self: pyrosetta.rosetta.core.scoring.etable.Etable) → bool¶: C++: core::scoring::etable::Etable::lj_use_lj_deriv_slope() const –> bool

lj_use_water_radii(self: pyrosetta.rosetta.core.scoring.etable.Etable) → bool¶: C++: core::scoring::etable::Etable::lj_use_water_radii() const –> bool

lj_water_dis(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶: C++: core::scoring::etable::Etable::lj_water_dis() const –> double

lj_water_hdis(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶: C++: core::scoring::etable::Etable::lj_water_hdis() const –> double

lj_wdepth(self: pyrosetta.rosetta.core.scoring.etable.Etable, i: int) → float¶

Return the Lennard-Jones well depth for an atom

C++: core::scoring::etable::Etable::lj_wdepth(const int) const –> double

ljatr(self: pyrosetta.rosetta.core.scoring.etable.Etable) → ObjexxFCL::FArray3D<double>¶

const access to the arrays

C++: core::scoring::etable::Etable::ljatr() const –> const class ObjexxFCL::FArray3D<double> &

ljrep(self: pyrosetta.rosetta.core.scoring.etable.Etable) → ObjexxFCL::FArray3D<double>¶: C++: core::scoring::etable::Etable::ljrep() const –> const class ObjexxFCL::FArray3D<double> &

lk_dgfree(self: pyrosetta.rosetta.core.scoring.etable.MembEtable, i: int) → float¶: C++: core::scoring::etable::MembEtable::lk_dgfree(const int) const –> double

lk_dgrefce(self: pyrosetta.rosetta.core.scoring.etable.MembEtable) → ObjexxFCL::FArray1D<double>¶: C++: core::scoring::etable::MembEtable::lk_dgrefce() const –> const class ObjexxFCL::FArray1D<double> &

lk_inv_lambda2(self: pyrosetta.rosetta.core.scoring.etable.Etable, i: int) → float¶: C++: core::scoring::etable::Etable::lk_inv_lambda2(const int) const –> double

lk_lambda(self: pyrosetta.rosetta.core.scoring.etable.MembEtable, i: int) → float¶: C++: core::scoring::etable::MembEtable::lk_lambda(const int) const –> double

lk_min_dis2sigma(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶: C++: core::scoring::etable::Etable::lk_min_dis2sigma() const –> double

lk_volume(self: pyrosetta.rosetta.core.scoring.etable.MembEtable, i: int) → float¶: C++: core::scoring::etable::MembEtable::lk_volume(const int) const –> double

long_range_damping_length(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶: C++: core::scoring::etable::Etable::long_range_damping_length() const –> double

max_dis(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶: C++: core::scoring::etable::Etable::max_dis() const –> double

max_dis2(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶: C++: core::scoring::etable::Etable::max_dis2() const –> double

max_heavy_heavy_cutoff(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶: C++: core::scoring::etable::Etable::max_heavy_heavy_cutoff() const –> double

max_heavy_hydrogen_cutoff(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶: C++: core::scoring::etable::Etable::max_heavy_hydrogen_cutoff() const –> double

max_hydrogen_hydrogen_cutoff(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶: C++: core::scoring::etable::Etable::max_hydrogen_hydrogen_cutoff() const –> double

max_hydrogen_lj_radius(self: pyrosetta.rosetta.core.scoring.etable.MembEtable) → float¶

Returns the maximum lj radius for any hydrogen atom as: defined by the input atom-type-set used to create this Etable.

C++: core::scoring::etable::MembEtable::max_hydrogen_lj_radius() const –> double

max_non_hydrogen_lj_radius(self: pyrosetta.rosetta.core.scoring.etable.MembEtable) → float¶

Returns the maximum lj radius for any non-hydrogen: atom as defined by the atom-type-set used to create this Etable.

C++: core::scoring::etable::MembEtable::max_non_hydrogen_lj_radius() const –> double

memb_dsolv1(self: pyrosetta.rosetta.core.scoring.etable.MembEtable) → ObjexxFCL::FArray3D<double>¶

Return the solvation derivative table for the desolvation of atom1 by atom2

C++: core::scoring::etable::MembEtable::memb_dsolv1() const –> const class ObjexxFCL::FArray3D<double> &

memb_dsolv2(self: pyrosetta.rosetta.core.scoring.etable.MembEtable) → ObjexxFCL::FArray3D<double>¶

return the solvation derivative table that combines atom1 and atom2’s desolvations

C++: core::scoring::etable::MembEtable::memb_dsolv2() const –> const class ObjexxFCL::FArray3D<double> &

memb_lk_dgfree(self: pyrosetta.rosetta.core.scoring.etable.MembEtable, i: int) → float¶: C++: core::scoring::etable::MembEtable::memb_lk_dgfree(const int) const –> double

memb_lk_dgrefce(self: pyrosetta.rosetta.core.scoring.etable.MembEtable) → ObjexxFCL::FArray1D<double>¶: C++: core::scoring::etable::MembEtable::memb_lk_dgrefce() const –> const class ObjexxFCL::FArray1D<double> &

memb_solv1(self: pyrosetta.rosetta.core.scoring.etable.MembEtable) → ObjexxFCL::FArray3D<double>¶: C++: core::scoring::etable::MembEtable::memb_solv1() const –> const class ObjexxFCL::FArray3D<double> &

memb_solv2(self: pyrosetta.rosetta.core.scoring.etable.MembEtable) → ObjexxFCL::FArray3D<double>¶: C++: core::scoring::etable::MembEtable::memb_solv2() const –> const class ObjexxFCL::FArray3D<double> &

min_dis(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶: C++: core::scoring::etable::Etable::min_dis() const –> double

min_dis2(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶: C++: core::scoring::etable::Etable::min_dis2() const –> double

n_atomtypes(self: pyrosetta.rosetta.core.scoring.etable.Etable) → int¶: C++: core::scoring::etable::Etable::n_atomtypes() const –> int

nblist_dis2_cutoff_HH(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶

The square distance cutoff beyond which any hydrogen/hydrogen pair is guaranteed: to have an interaction energy of zero. This function is used by the NeighborList

C++: core::scoring::etable::Etable::nblist_dis2_cutoff_HH() const –> double

nblist_dis2_cutoff_XH(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶

The square distance cutoff beyond which a hydrogen/heavy-atom pair is: guaranteed to have an interaction energy of zero. This function is used by the NeighborList

C++: core::scoring::etable::Etable::nblist_dis2_cutoff_XH() const –> double

nblist_dis2_cutoff_XX(self: pyrosetta.rosetta.core.scoring.etable.Etable) → float¶

The square distance cutoff beyond which any pair of heavy-atoms is: guaranteed to have an interaction energy of zero. This function is used by the NeighborList

C++: core::scoring::etable::Etable::nblist_dis2_cutoff_XX() const –> double

output_etable(self: pyrosetta.rosetta.core.scoring.etable.MembEtable, etable: ObjexxFCL::FArray3D<double>, label: str, out: pyrosetta.rosetta.std.ostream) → None¶: C++: core::scoring::etable::MembEtable::output_etable(class ObjexxFCL::FArray3D<double> &, class std::basic_string<char>, class std::basic_ostream<char> &) –> void

solv1(self: pyrosetta.rosetta.core.scoring.etable.MembEtable) → ObjexxFCL::FArray3D<double>¶

Provide Constnat Access to Arrays

C++: core::scoring::etable::MembEtable::solv1() const –> const class ObjexxFCL::FArray3D<double> &

solv2(self: pyrosetta.rosetta.core.scoring.etable.MembEtable) → ObjexxFCL::FArray3D<double>¶: C++: core::scoring::etable::MembEtable::solv2() const –> const class ObjexxFCL::FArray3D<double> &

class pyrosetta.rosetta.core.scoring.etable.SplineParameters¶

Bases: pybind11_builtins.pybind11_object

%SplineParameters is a simple struct for holding the cubic spline polynomials used in the etable to interpolate the lennard-jones attractive and LK-solvation terms to zero smoothly. These splines have exactly two knots to represent them, and the same x values are used for all the knots: thus the only parameters needed are the y values at the knots, and the second-derivatives for the polynomials at knots.