sspot¶

Bindings for protocols::fldsgn::potentials::sspot namespace

class pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.HSPairPotential¶

Bases: pybind11_object

secondary structure scoring cut from classic rosetta structure.h/structure.cc

assign(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.HSPairPotential, : pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.HSPairPotential) → pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.HSPairPotential¶: C++: protocols::fldsgn::potentials::sspot::HSPairPotential::operator=(const class protocols::fldsgn::potentials::sspot::HSPairPotential &) –> class protocols::fldsgn::potentials::sspot::HSPairPotential &

score(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.HSPairPotential, pose: pyrosetta.rosetta.core.pose.Pose, ss_info: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2, hs_score: float) → None¶

score secondary structure

C++: protocols::fldsgn::potentials::sspot::HSPairPotential::score(const class core::pose::Pose &, const class protocols::fldsgn::topology::SS_Info2 &, double &) const –> void

class pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential, : pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential) → pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential¶: C++: protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::operator=(const class protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential &) –> class protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential &

hpairset(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential, hpairset: pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet) → None¶

set HelixPairingSet

C++: protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::hpairset(const class std::shared_ptr<class protocols::fldsgn::topology::HelixPairingSet>) –> void

hss_triplet_set(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential, hss3set: pyrosetta.rosetta.protocols.fldsgn.topology.HSSTripletSet) → None¶

set HSSTripletSet

C++: protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::hss_triplet_set(const class std::shared_ptr<class protocols::fldsgn::topology::HSSTripletSet>) –> void

score(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential, ss_info: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2, hh_score: float, hs_score: float) → None¶

calc score

C++: protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::score(const class std::shared_ptr<const class protocols::fldsgn::topology::SS_Info2>, double &, double &) const –> void

set_angle_params_helices_on_sheet(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential, hh_align_angle_wts: float, hh_align_angle: float, hh_align_angle_sigma2: float) → None¶

set angle parameters for helices projected onto sheet

C++: protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::set_angle_params_helices_on_sheet(const double, const double, const double) –> void

set_angle_params_helix_sheet(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential, hs_angle_wts: float, hs_angle: float, hs_angle_sigma2: float) → None¶

set angle parameters for helix-sheet interaction

C++: protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::set_angle_params_helix_sheet(const double, const double, const double) –> void

set_atrdist_params_helix_strands(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential, hs_dist_wts: float, hs_dist: float, hs_dist_sigma2: float) → None¶

set dist parameters for helix-strands interaction

C++: protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::set_atrdist_params_helix_strands(const double, const double, const double) –> void

set_hh_angle(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential, r: float) → None¶: C++: protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::set_hh_angle(const double) –> void

set_hh_angle_sigma2(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential, r: float) → None¶: C++: protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::set_hh_angle_sigma2(const double) –> void

set_hh_angle_wts(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential, r: float) → None¶: C++: protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::set_hh_angle_wts(const double) –> void

set_hs_angle(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential, r: float) → None¶: C++: protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::set_hs_angle(const double) –> void

set_hs_angle_sigma2(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential, r: float) → None¶: C++: protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::set_hs_angle_sigma2(const double) –> void

set_hs_angle_wts(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential, r: float) → None¶: C++: protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::set_hs_angle_wts(const double) –> void

set_hs_atr_dist(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential, r: float) → None¶: C++: protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::set_hs_atr_dist(const double) –> void

set_hs_atr_dist_sigma2(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential, r: float) → None¶: C++: protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::set_hs_atr_dist_sigma2(const double) –> void

set_hs_atr_dist_wts(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential, r: float) → None¶

set dist parameters for helix-sheet interaction

C++: protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::set_hs_atr_dist_wts(const double) –> void

set_hsheet_repl_dist(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential, r: float) → None¶: C++: protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::set_hsheet_repl_dist(const double) –> void

set_params(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential) → None¶

set parameters

C++: protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::set_params() –> void

set_repldist_params_helix_sheet(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential, hsheet_dist_repulsive: float) → None¶: C++: protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::set_repldist_params_helix_sheet(const double) –> void

show_params(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential) → None¶

shows parameters for score calculation

C++: protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential::show_params() const –> void

class pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential, : pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential) → pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential¶: C++: protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::operator=(const class protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential &) –> class protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential &

score(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential, ss_info: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2, hh_score: float) → None¶

score secondary structure

C++: protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::score(const class std::shared_ptr<const class protocols::fldsgn::topology::SS_Info2>, double &) const –> void

set_angle(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential, r: float) → None¶: C++: protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::set_angle(const double) –> void

set_angle_sigma2(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential, r: float) → None¶: C++: protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::set_angle_sigma2(const double) –> void

set_angle_wts(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential, r: float) → None¶: C++: protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::set_angle_wts(const double) –> void

set_bendangle(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential, r: float) → None¶

set bend angle

C++: protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::set_bendangle(double) –> void

set_dist(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential, r: float) → None¶

set distance parmeter

C++: protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::set_dist(const double) –> void

set_dist_sigma2(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential, r: float) → None¶: C++: protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::set_dist_sigma2(const double) –> void

set_dist_wts(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential, r: float) → None¶: C++: protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::set_dist_wts(const double) –> void

set_hpairset(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential, hpairset: pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet) → None¶: C++: protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::set_hpairset(const class std::shared_ptr<class protocols::fldsgn::topology::HelixPairingSet>) –> void

set_params(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential) → None¶: C++: protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::set_params() –> void

set_params_angle_pot(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential, w: float, d: float, s: float) → None¶

set parameters for angle score of helix pair

C++: protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::set_params_angle_pot(double, double, double) –> void

set_params_distance_pot(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential, w: float, d: float, s: float) → None¶

set parameters for distance score between mid points of helices

C++: protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::set_params_distance_pot(double, double, double) –> void

show(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::show(const class core::pose::Pose &) const –> void

show_params(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential) → None¶

show parameters

C++: protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential::show_params() const –> void

class pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy¶

Bases: WholeStructureEnergy

assign(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy, : pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy) → pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy¶: C++: protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::operator=(const class protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy &) –> class protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy &

atomic_interaction_cutoff(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy) → float¶

The NatbiasSecondaryStructureEnergy class requires that the EnergyGraph: span 12 Angstroms between centroids. The centroids residues build-in a 3 Angstrom radius each.

C++: protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::atomic_interaction_cutoff() const –> double

atomistic_energy(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, atmno: int, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, scorefxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None¶

Evaluate the (one body) energy associated with a particular atom

This may be a “self” energy, or it may be the single atom contribution from a whole structure term. NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here. For most terms this is likely a no-op. Terms which implement this non-trivially should return true from has_atomistic_energies()

This is return-by-reference in the EnergyMap - Implementations should accumulate, not replace.

C++: core::scoring::methods::EnergyMethod::atomistic_energy(unsigned long, const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

atomistic_pair_energy(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, atmno1: int, rsd1: pyrosetta.rosetta.core.conformation.Residue, atomno2: int, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, scorefxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector) → None¶

Evaluate the energy for a particular pair of atoms

This function may be fed the same residue with different atom numbers NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here. For most terms this is likely a no-op. Terms which implement this non-trivially should return true from has_atomistic_pairwise_energies()

This is return-by-reference in the EnergyMap - Implementations should accumulate, not replace.

C++: core::scoring::methods::EnergyMethod::atomistic_pair_energy(unsigned long, const class core::conformation::Residue &, unsigned long, const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

clone(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy) → pyrosetta.rosetta.core.scoring.methods.EnergyMethod¶

clone

C++: protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::clone() const –> class std::shared_ptr<class core::scoring::methods::EnergyMethod>

defines_high_order_terms(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose) → bool¶

Should this EnergyMethod have score and derivative evaluation: evaluated both in the context of the whole Pose and in the context of residue or residue-pairs? This covers scoring terms like env-smooth wherein the CBeta’s get derivatives for increasing the neighbor counts for surrounding residues, and terms like constraints, which are definable on arbitrary number of residues (e.g. more than 2); both of these terms could be used in RTMin, and both should use the residue and residue-pair evaluation scheme with the MinimizationGraph for the majority of the work they do. (Now, high-order constraints (3-body or above) will not be properly evaluated within RTMin.). The default implementation returns “false”.

C++: core::scoring::methods::EnergyMethod::defines_high_order_terms(const class core::pose::Pose &) const –> bool

eval_atom_derivative(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, id: pyrosetta.rosetta.core.id.AtomID, pose: core::pose::Pose, domain_map: pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t) → None¶

Evaluate the XYZ derivative for an atom in the pose.

Called during the atomtree derivative calculation, atom_tree_minimize.cc, through the ScoreFunction::eval_atom_derivative intermediary. F1 and F2 should not zeroed, rather, this class should accumulate its contribution from this atom’s XYZ derivative

The derivative scheme is based on that of Abe, Braun, Noguti and Go (1984) “Rapid Calculation of First and Second Derivatives of Conformational Energy with Respect to Dihedral Angles for Proteins. General Recurrent Equations” Computers & Chemistry 8(4) pp. 239-247. F1 and F2 correspond roughly to Fa and Ga, respectively, of equations 7a & 7b in that paper.

C++: core::scoring::methods::EnergyMethod::eval_atom_derivative(const class core::id::AtomID &, const class core::pose::Pose &, const class ObjexxFCL::FArray1D<int> &, const class core::scoring::ScoreFunction &, const class core::scoring::EMapVector &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &) const –> void

finalize_after_derivatives(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : core::scoring::ScoreFunction) → None¶

called at the end of derivatives evaluation

C++: core::scoring::methods::EnergyMethod::finalize_after_derivatives(class core::pose::Pose &, const class core::scoring::ScoreFunction &) const –> void

finalize_after_minimizing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, pose: core::pose::Pose) → None¶

Called after minimization, allowing a derived class to do some

teardown steps.

Base class function does nothing. Derived classes may override.

Vikram K. Mulligan (vmullig.edu).

C++: core::scoring::methods::EnergyMethod::finalize_after_minimizing(class core::pose::Pose &) const –> void

finalize_total_energy(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, totals: pyrosetta.rosetta.core.scoring.EMapVector) → None¶

scoring

C++: protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::finalize_total_energy(class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

has_atomistic_energies(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod) → bool¶

Does this EnergyMethod have a non-trivial implementation of the (one body) atomistic energy method?: Note that this may return false even if the score term theoretically could support atomistic energies. And even if this function returns true, it’s not necessarily the case that all atoms will get assigned an energy, or that the sum over all atoms (or atom pairs) will result in the same energy as the residue-level approach. The atomistic functions are intended for supplemental informational purposes only. The residue-level energies are the main interface for EnergyMethods.

C++: core::scoring::methods::EnergyMethod::has_atomistic_energies() const –> bool

has_atomistic_pairwise_energies(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod) → bool¶

Does this EnergyMethod have a non-trivial implementation of the pairwise atomistic energy method?: NOTE: all the cautions of EnergyMethod::has_atomistic_energies() apply here.

C++: core::scoring::methods::EnergyMethod::has_atomistic_pairwise_energies() const –> bool

indicate_required_context_graphs(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy, context_graphs_required: pyrosetta.rosetta.utility.vector1_bool) → None¶: C++: protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::indicate_required_context_graphs(class utility::vector1<bool, class std::allocator<bool> > &) const –> void

method_type(self: pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy) → pyrosetta.rosetta.core.scoring.methods.EnergyMethodType¶: C++: core::scoring::methods::WholeStructureEnergy::method_type() const –> enum core::scoring::methods::EnergyMethodType

minimize_in_whole_structure_context(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose) → bool¶

Should this EnergyMethod have score and derivative evaluation: evaluated only in the context of the whole Pose, or can it be included in a decomposed manner for a residue or a set of residue-pairs that are not part of the Pose that’s serving as their context? The default method implemented in the base class returns true in order to grandfather in EnergyMethods that have not had their derivatives changed to take advantage of the new derivative-evaluation machinery. Methods that return “true” will not have their residue-energy(-ext) / residue-pair-energy(-ext) methods invoked by the ScoreFunction during its traversal of the MinimizationGraph, and instead will be asked to perform all their work during finalize_total_energies(). Similarly, they will be expected to perform all their work during eval_atom_deriv() instead of during the ScoreFunction’s traversal of the MinimizationGraph for derivative evaluation. IMPORTANT: Methods that return “true” cannot be included in RTMin.

C++: core::scoring::methods::EnergyMethod::minimize_in_whole_structure_context(const class core::pose::Pose &) const –> bool

native_secstruct(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy, secstruct: str) → None¶

set native secondary structure

C++: protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::native_secstruct(const std::string &) –> void

prepare_rotamers_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : pyrosetta.rosetta.core.conformation.RotamerSetBase) → None¶

If an energy method needs to cache data in a packing::RotamerSet object before: rotamer energies are calculated, it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::prepare_rotamers_for_packing(const class core::pose::Pose &, class core::conformation::RotamerSetBase &) const –> void

provide_citation_info(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None¶

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by energy methods wishing to provide citation information.

C++: core::scoring::methods::EnergyMethod::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

requires_a_setup_for_scoring_for_residue_opportunity_during_regular_scoring(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, pose: core::pose::Pose) → bool¶

Does this EnergyMethod require the opportunity to examine the residue before (regular) scoring begins? Not: all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so. The default implmentation of this function returns false

C++: core::scoring::methods::EnergyMethod::requires_a_setup_for_scoring_for_residue_opportunity_during_regular_scoring(const class core::pose::Pose &) const –> bool

score_types(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod) → pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType¶

Returns the score types that this energy method computes.

C++: core::scoring::methods::EnergyMethod::score_types() const –> const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &

set_natbias_helices_sheet_pot(*args, **kwargs)¶

Overloaded function.

set_natbias_helices_sheet_pot(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy, hss3set: pyrosetta.rosetta.protocols.fldsgn.topology.HSSTripletSet) -> None

set NatbiasHelicesSheetPotential

C++: protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::set_natbias_helices_sheet_pot(const class std::shared_ptr<class protocols::fldsgn::topology::HSSTripletSet>) –> void

set_natbias_helices_sheet_pot(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy, hspot: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential) -> None

set NatbiasHelicesSheetPotential

C++: protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::set_natbias_helices_sheet_pot(const class std::shared_ptr<class protocols::fldsgn::potentials::sspot::NatbiasHelicesSheetPotential>) –> void

set_natbias_hpairpot(*args, **kwargs)¶

Overloaded function.

set_natbias_hpairpot(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy, hpairset: pyrosetta.rosetta.protocols.fldsgn.topology.HelixPairingSet) -> None

set NatbiasHelixPairPotential

C++: protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::set_natbias_hpairpot(const class std::shared_ptr<class protocols::fldsgn::topology::HelixPairingSet>) –> void

set_natbias_hpairpot(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy, hhpot: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential) -> None

set NatbiasHelixPairPotential

C++: protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::set_natbias_hpairpot(const class std::shared_ptr<class protocols::fldsgn::potentials::sspot::NatbiasHelixPairPotential>) –> void

set_natbias_spairpot(*args, **kwargs)¶

Overloaded function.

set_natbias_spairpot(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy, spairset: protocols::fldsgn::topology::StrandPairingSet) -> None

set NatbiasStrandPairPotential

C++: protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::set_natbias_spairpot(const class std::shared_ptr<class protocols::fldsgn::topology::StrandPairingSet>) –> void

set_natbias_spairpot(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy, sspot: protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential) -> None

set native NatbiasStrandPairPotential

C++: protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::set_natbias_spairpot(const class std::shared_ptr<class protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential>) –> void

setup_for_derivatives(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction) → None¶

Called immediately before atom- and DOF-derivatives are calculated: allowing the derived class a chance to prepare for future calls.

C++: core::scoring::methods::EnergyMethod::setup_for_derivatives(class core::pose::Pose &, const class core::scoring::ScoreFunction &) const –> void

setup_for_minimizing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : core::scoring::ScoreFunction, : core::kinematics::MinimizerMapBase) → None¶

Called at the beginning of atom tree minimization, this method: allows the derived class the opportunity to initialize pertinent data that will be used during minimization. During minimzation, the chemical structure of the pose is constant, so assumptions on the number of atoms per residue and their identities are safe so long as the pose’s Energies object’s “use_nblist()” method returns true.

C++: core::scoring::methods::EnergyMethod::setup_for_minimizing(class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::kinematics::MinimizerMapBase &) const –> void

setup_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : pyrosetta.rosetta.utility.vector1_bool, : pyrosetta.rosetta.utility.vector1_bool) → None¶

if an energy method needs to cache data in the Energies object,: before packing begins, then it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::setup_for_packing(class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<bool, class std::allocator<bool> > &) const –> void

setup_for_packing_with_rotsets(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, pose: core::pose::Pose, rotsets: core::pack_basic::RotamerSetsBase, sfxn: core::scoring::ScoreFunction) → None¶

if an energy method needs to cache data in the Energies object,

before packing begins and requires access to the RotamerSets object, then it does so during this function. The default behavior is to do nothing.

The exact order of events when setting up for packing are as follows:

setup_for_packing() is called for all energy methods
rotamers are built
setup_for_packing_with_rotsets() is called for all energy methods
prepare_rotamers_for_packing() is called for all energy methods
The energy methods are asked to score all rotamers and rotamer pairs
Annealing

The pose is specifically non-const here so that energy methods can store data in it

: Used in ApproximateBuriedUnsatPenalty to pre-compute compatible rotamers

C++: core::scoring::methods::EnergyMethod::setup_for_packing_with_rotsets(class core::pose::Pose &, const class std::shared_ptr<class core::pack_basic::RotamerSetsBase> &, const class core::scoring::ScoreFunction &) const –> void

setup_for_scoring(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None¶

scoring

C++: protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::setup_for_scoring(class core::pose::Pose &, const class core::scoring::ScoreFunction &) const –> void

setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) → None¶

Do any setup work before scoring, caching any slow-to-compute data that will be used during: energy evaluation inside of the input Residue object’s data cache. (The Residue on the whole is given as a constant reference, but non-constant access to its data cache is granted.)

C++: core::scoring::methods::EnergyMethod::setup_for_scoring_for_residue(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class basic::datacache::BasicDataCache &) const –> void

show_additional_info(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : pyrosetta.rosetta.std.ostream, : core::pose::Pose, : bool) → None¶

show additional information of the energy method

C++: core::scoring::methods::EnergyMethod::show_additional_info(std::ostream &, class core::pose::Pose &, bool) const –> void

update_residue_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, resid: int) → None¶

If the pose changes in the middle of a packing (as happens in rotamer trials) and if: an energy method needs to cache data in the pose that corresponds to its current state, then the method must update that data when this function is called. The packer must ensure this function gets called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::update_residue_for_packing(class core::pose::Pose &, unsigned long) const –> void

use_nobias(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy, b: bool) → None¶

use use original secondary structure potential

C++: protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::use_nobias(const bool) –> void

version(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy) → int¶: C++: protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergy::version() const –> unsigned long

class pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergyCreator¶

Bases: EnergyMethodCreator

assign(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergyCreator, : pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergyCreator) → pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergyCreator¶: C++: protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergyCreator::operator=(const class protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergyCreator &) –> class protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergyCreator &

create_energy_method(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergyCreator, : pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) → pyrosetta.rosetta.core.scoring.methods.EnergyMethod¶

Instantiate a new NatbiasSecondaryStructureEnergy2

C++: protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergyCreator::create_energy_method(const class core::scoring::methods::EnergyMethodOptions &) const –> class std::shared_ptr<class core::scoring::methods::EnergyMethod>

score_types_for_method(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergyCreator) → pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType¶

Return the set of score types claimed by the EnergyMethod: this EnergyMethodCreator creates in its create_energy_method() function

C++: protocols::fldsgn::potentials::sspot::NatbiasSecondaryStructureEnergyCreator::score_types_for_method() const –> class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> >

class pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasStrandPairPotential¶

Bases: pybind11_object

secondary structure scoring cut from classic rosetta structure.h/structure.cc

assign(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasStrandPairPotential, : pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasStrandPairPotential) → pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasStrandPairPotential¶: C++: protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::operator=(const class protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential &) –> class protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential &

score(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasStrandPairPotential, pose: pyrosetta.rosetta.core.pose.Pose, ss_info: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2, ss_score: float) → None¶

score secondary structure

C++: protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::score(const class core::pose::Pose &, const class protocols::fldsgn::topology::SS_Info2 &, double &) const –> void

set_native_spairset(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.NatbiasStrandPairPotential, spairset: protocols::fldsgn::topology::StrandPairingSet) → None¶: C++: protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::set_native_spairset(const class std::shared_ptr<class protocols::fldsgn::topology::StrandPairingSet>) –> void

class pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.SSPairPotential¶

Bases: pybind11_object

secondary structure scoring cut from classic rosetta structure.h/structure.cc

assign(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.SSPairPotential, : pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.SSPairPotential) → pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.SSPairPotential¶: C++: protocols::fldsgn::potentials::sspot::SSPairPotential::operator=(const class protocols::fldsgn::potentials::sspot::SSPairPotential &) –> class protocols::fldsgn::potentials::sspot::SSPairPotential &

score(self: pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.SSPairPotential, pose: pyrosetta.rosetta.core.pose.Pose, ss_info: pyrosetta.rosetta.protocols.fldsgn.topology.SS_Info2, dimer_pairs: protocols::fldsgn::topology::DimerPairings, ss_score: float) → None¶

score secondary structure

C++: protocols::fldsgn::potentials::sspot::SSPairPotential::score(const class core::pose::Pose &, const class protocols::fldsgn::topology::SS_Info2 &, class protocols::fldsgn::topology::DimerPairings &, double &) const –> void

pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.get_foldtree_seqsep(*args, **kwargs)¶

Overloaded function.

get_foldtree_seqsep(pose: pyrosetta.rosetta.core.pose.Pose, pos1: int, pos2: int) -> int
get_foldtree_seqsep(pose: pyrosetta.rosetta.core.pose.Pose, pos1: int, pos2: int, gap_size: int) -> int

identifies the sequence separation along the fold tree: add the gap_size (default 10 ) into seqsep when there is chain break between pos1 and pos2

C++: protocols::fldsgn::potentials::sspot::get_foldtree_seqsep(const class core::pose::Pose &, unsigned long, unsigned long, unsigned long) –> unsigned long

pyrosetta.rosetta.protocols.fldsgn.potentials.sspot.spherical(a2: pyrosetta.rosetta.numeric.xyzVector_double_t, a4: pyrosetta.rosetta.numeric.xyzVector_double_t, phi: float, theta: float, cen1: pyrosetta.rosetta.numeric.xyzVector_double_t, cen2: pyrosetta.rosetta.numeric.xyzVector_double_t, v21: pyrosetta.rosetta.numeric.xyzVector_double_t) → None¶: C++: protocols::fldsgn::potentials::sspot::spherical(const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, double &, double &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &) –> void