pcsTs2¶

Bindings for protocols::scoring::methods::pcsTs2 namespace

class pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.GridSearchIterator_Ts2¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.GridSearchIterator_Ts2, other: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.GridSearchIterator_Ts2) → pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.GridSearchIterator_Ts2¶: C++: protocols::scoring::methods::pcsTs2::GridSearchIterator_Ts2::operator=(const class protocols::scoring::methods::pcsTs2::GridSearchIterator_Ts2 &) –> class protocols::scoring::methods::pcsTs2::GridSearchIterator_Ts2 &

next(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.GridSearchIterator_Ts2, x: float, y: float, z: float) → bool¶: C++: protocols::scoring::methods::pcsTs2::GridSearchIterator_Ts2::next(double &, double &, double &) –> bool

next_center(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.GridSearchIterator_Ts2, x: float, y: float, z: float) → bool¶: C++: protocols::scoring::methods::pcsTs2::GridSearchIterator_Ts2::next_center(double &, double &, double &) –> bool

reset(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.GridSearchIterator_Ts2) → None¶: C++: protocols::scoring::methods::pcsTs2::GridSearchIterator_Ts2::reset() –> void

class pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_Ts2¶

Bases: WholeStructureEnergy

PCS_data_from_pose(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_Ts2, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_Ts2¶: C++: protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2::PCS_data_from_pose(class core::pose::Pose &) const –> class protocols::scoring::methods::pcsTs2::PCS_data_Ts2 &

assign(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_Ts2, other: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_Ts2) → pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_Ts2¶: C++: protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2::operator=(const class protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2 &) –> class protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2 &

atomic_interaction_cutoff(self: pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy) → float¶

how far apart must two heavy atoms be to have a zero interaction energy?

If hydrogen atoms interact at the same range as heavy atoms, then this distance should build-in a 2 * max-bound-h-distance-cutoff buffer. There is an improper mixing here between run-time aquired chemical knowledge (max-bound-h-distance-cutoff) and compile time aquired scoring knowledge (max atom cutoff); this could be resolved by adding a boolean uses_hydrogen_interaction_distance() to the SRTBEnergy class along with a method of the ChemicalManager max_bound_h_distance_cutoff().

This method allows the WholeStructureEnergy class to define which edges should be included in the EnergyGraph so that during the finalize() method the Energy class can iterate across the EnergyGraph. This iteration occurrs in the SecondaryStructureEnergy class, where the edges must span 12 angstroms between the centroids. Arguably, the SecondaryStructureEnergy class could use the TwelveANeighborGraph (a context graph) and not require that the EnergyGraph span such long distances.

C++: core::scoring::methods::WholeStructureEnergy::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

calculate_pcs_score(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_Ts2, pose: pyrosetta.rosetta.core.pose.Pose, print_to_tracer: bool) → float¶: C++: protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2::calculate_pcs_score(class core::pose::Pose &, bool) const –> double

clone(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_Ts2) → pyrosetta.rosetta.core.scoring.methods.EnergyMethod¶: C++: protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2::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.scoring.methods.pcsTs2.PCS_Energy_Ts2, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, totals: pyrosetta.rosetta.core.scoring.EMapVector) → None¶: C++: protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2::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.scoring.methods.pcsTs2.PCS_Energy_Ts2, : pyrosetta.rosetta.utility.vector1_bool) → None¶: C++: protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2::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

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> > &

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.core.scoring.methods.EnergyMethod, : core::pose::Pose, : core::scoring::ScoreFunction) → None¶

if an energy method needs to cache something in the pose (e.g. in pose.energies()),: before scoring begins, it must do so in this method. All long range energy functions must initialize their LREnergyContainers before scoring begins. The default is to do nothing.

C++: core::scoring::methods::EnergyMethod::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(*args, **kwargs)¶

Overloaded function.

show_additional_info(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_Ts2, out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) -> None
show_additional_info(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_Ts2, out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose, verbose: bool) -> None

C++: protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2::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

version(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_Ts2) → int¶: C++: protocols::scoring::methods::pcsTs2::PCS_Energy_Ts2::version() const –> unsigned long

class pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_parameters_manager_Ts2¶

Bases: SingletonBase_protocols_scoring_methods_pcsTs2_PCS_Energy_parameters_manager_Ts2_t

exclude_residues_vector_is_current(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_parameters_manager_Ts2) → None¶: C++: protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2::exclude_residues_vector_is_current() –> void

get_grid_atom_name_1(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_parameters_manager_Ts2) → str¶: C++: protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2::get_grid_atom_name_1() const –> std::string

get_grid_atom_name_2(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_parameters_manager_Ts2) → str¶: C++: protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2::get_grid_atom_name_2() const –> std::string

get_grid_cone_angle_cutoff(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_parameters_manager_Ts2) → float¶: C++: protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2::get_grid_cone_angle_cutoff() const –> double

get_grid_edge(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_parameters_manager_Ts2) → float¶: C++: protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2::get_grid_edge() const –> double

get_grid_k_vector(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_parameters_manager_Ts2) → float¶: C++: protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2::get_grid_k_vector() const –> double

get_grid_large_cutoff(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_parameters_manager_Ts2) → float¶: C++: protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2::get_grid_large_cutoff() const –> double

get_grid_residue_num_1(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_parameters_manager_Ts2) → int¶: C++: protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2::get_grid_residue_num_1() const –> unsigned long

get_grid_residue_num_2(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_parameters_manager_Ts2) → int¶: C++: protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2::get_grid_residue_num_2() const –> unsigned long

get_grid_small_cutoff(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_parameters_manager_Ts2) → float¶: C++: protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2::get_grid_small_cutoff() const –> double

get_grid_step(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_parameters_manager_Ts2) → float¶: C++: protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2::get_grid_step() const –> double

static get_instance() → protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2¶: C++: utility::SingletonBase<protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2>::get_instance() –> class protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2 *

get_minimize_best_tensor(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_parameters_manager_Ts2) → bool¶: C++: protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2::get_minimize_best_tensor() const –> bool

get_pcs_weight(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_parameters_manager_Ts2) → float¶: C++: protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2::get_pcs_weight() const –> double

get_vector_exclude_residues(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_parameters_manager_Ts2) → pyrosetta.rosetta.utility.vector1_bool¶: C++: protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2::get_vector_exclude_residues() –> class utility::vector1<bool, class std::allocator<bool> >

get_vector_filename(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_parameters_manager_Ts2) → pyrosetta.rosetta.utility.vector1_std_string¶: C++: protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2::get_vector_filename() const –> const class utility::vector1<std::string, class std::allocator<std::string > > &

get_vector_weight(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_parameters_manager_Ts2) → pyrosetta.rosetta.utility.vector1_double¶: C++: protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2::get_vector_weight() const –> const class utility::vector1<double, class std::allocator<double> > &

has_exclude_residues_vector(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_parameters_manager_Ts2) → bool¶: C++: protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2::has_exclude_residues_vector() –> bool

has_exclude_residues_vector_changed(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_parameters_manager_Ts2) → bool¶: C++: protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2::has_exclude_residues_vector_changed() –> bool

print_grid_param(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_parameters_manager_Ts2) → None¶: C++: protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2::print_grid_param() const –> void

remove_vector_exclude_residues(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_parameters_manager_Ts2) → None¶: C++: protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2::remove_vector_exclude_residues() –> void

set_grid_param(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_parameters_manager_Ts2, grid_edge: float, grid_step: float, grid_small_cutoff: float, grid_large_cutoff: float, grid_cone_angle_cutoff: float, grid_atom_name_1: str, grid_atom_name_2: str, grid_residue_num_1: int, grid_residue_num_2: int, grid_k_vector: float, minimize_best_tensor: bool, pcs_weight: float) → None¶: C++: protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2::set_grid_param(const double, const double, const double, const double, const double, const std::string, const std::string, const long, const long, const double, const bool, const double) –> void

set_vector_exclude_residues(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_parameters_manager_Ts2, vec_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶: C++: protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2::set_vector_exclude_residues(const class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void

set_vector_name_and_weight(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_Energy_parameters_manager_Ts2, vec_filename: pyrosetta.rosetta.utility.vector1_std_string, vec_individual_weight: pyrosetta.rosetta.utility.vector1_double) → None¶: C++: protocols::scoring::methods::pcsTs2::PCS_Energy_parameters_manager_Ts2::set_vector_name_and_weight(const class utility::vector1<std::string, class std::allocator<std::string > >, const class utility::vector1<double, class std::allocator<double> >) –> void

class pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_Ts2¶

Bases: CacheableData

assign(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_Ts2, : pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_Ts2) → pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_Ts2¶: C++: protocols::scoring::methods::pcsTs2::PCS_data_Ts2::operator=(const class protocols::scoring::methods::pcsTs2::PCS_data_Ts2 &) –> class protocols::scoring::methods::pcsTs2::PCS_data_Ts2 &

clone(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_Ts2) → pyrosetta.rosetta.basic.datacache.CacheableData¶: C++: protocols::scoring::methods::pcsTs2::PCS_data_Ts2::clone() const –> class std::shared_ptr<class basic::datacache::CacheableData>

get_PCS_data_line_all_spin(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_Ts2) → pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs2_PCS_line_data_Ts2¶: C++: protocols::scoring::methods::pcsTs2::PCS_data_Ts2::get_PCS_data_line_all_spin() const –> const class utility::vector1<class protocols::scoring::methods::pcsTs2::PCS_line_data_Ts2, class std::allocator<class protocols::scoring::methods::pcsTs2::PCS_line_data_Ts2> > &

get_X_all(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_Ts2) → pyrosetta.rosetta.utility.vector1_double¶: C++: protocols::scoring::methods::pcsTs2::PCS_data_Ts2::get_X_all() const –> const class utility::vector1<double, class std::allocator<double> > &

get_Y_all(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_Ts2) → pyrosetta.rosetta.utility.vector1_double¶: C++: protocols::scoring::methods::pcsTs2::PCS_data_Ts2::get_Y_all() const –> const class utility::vector1<double, class std::allocator<double> > &

get_Z_all(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_Ts2) → pyrosetta.rosetta.utility.vector1_double¶: C++: protocols::scoring::methods::pcsTs2::PCS_data_Ts2::get_Z_all() const –> const class utility::vector1<double, class std::allocator<double> > &

get_n_lanthanides(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_Ts2) → int¶: C++: protocols::scoring::methods::pcsTs2::PCS_data_Ts2::get_n_lanthanides() const –> unsigned long

get_pcs_data_per_lanthanides_all(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_Ts2) → pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs2_PCS_data_per_lanthanides_Ts2¶: C++: protocols::scoring::methods::pcsTs2::PCS_data_Ts2::get_pcs_data_per_lanthanides_all() –> class utility::vector1<class protocols::scoring::methods::pcsTs2::PCS_data_per_lanthanides_Ts2, class std::allocator<class protocols::scoring::methods::pcsTs2::PCS_data_per_lanthanides_Ts2> > &

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>

update_X_Y_Z_all(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_Ts2, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::scoring::methods::pcsTs2::PCS_data_Ts2::update_X_Y_Z_all(const class core::pose::Pose &) –> void

update_matrix_A_all(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_Ts2, X: float, Y: float, Z: float) → None¶: C++: protocols::scoring::methods::pcsTs2::PCS_data_Ts2::update_matrix_A_all(const double, const double, const double) –> void

where_is_line(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_Ts2, P_l_d: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_line_data_Ts2) → int¶: C++: protocols::scoring::methods::pcsTs2::PCS_data_Ts2::where_is_line(class protocols::scoring::methods::pcsTs2::PCS_line_data_Ts2 &) –> unsigned long

class pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_input_Ts2¶

Bases: pybind11_object

PCS_data_input_Ts2 contain all the input information for the PCS. This includes all the information from the .npc files

assign(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_input_Ts2, other: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_input_Ts2) → pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_input_Ts2¶: C++: protocols::scoring::methods::pcsTs2::PCS_data_input_Ts2::operator=(const class protocols::scoring::methods::pcsTs2::PCS_data_input_Ts2 &) –> class protocols::scoring::methods::pcsTs2::PCS_data_input_Ts2 &

get_PCS_data_input_reference(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_input_Ts2) → pyrosetta.rosetta.std.map_std_string_protocols_scoring_methods_pcsTs2_PCS_file_data_Ts2¶: C++: protocols::scoring::methods::pcsTs2::PCS_data_input_Ts2::get_PCS_data_input_reference() –> class std::map<std::string, class protocols::scoring::methods::pcsTs2::PCS_file_data_Ts2, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class protocols::scoring::methods::pcsTs2::PCS_file_data_Ts2> > > &

class pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_input_manager_Ts2¶

Bases: pybind11_object

get_input_data(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_input_manager_Ts2, filenames: pyrosetta.rosetta.utility.vector1_std_string, vec_weight: pyrosetta.rosetta.utility.vector1_double) → pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_input_Ts2¶: C++: protocols::scoring::methods::pcsTs2::PCS_data_input_manager_Ts2::get_input_data(const class utility::vector1<std::string, class std::allocator<std::string > > &, const class utility::vector1<double, class std::allocator<double> > &) –> class protocols::scoring::methods::pcsTs2::PCS_data_input_Ts2

static get_instance() → pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_input_manager_Ts2¶: C++: protocols::scoring::methods::pcsTs2::PCS_data_input_manager_Ts2::get_instance() –> class protocols::scoring::methods::pcsTs2::PCS_data_input_manager_Ts2 *

class pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_per_lanthanides_Ts2¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_per_lanthanides_Ts2, other: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_per_lanthanides_Ts2) → pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_per_lanthanides_Ts2¶: C++: protocols::scoring::methods::pcsTs2::PCS_data_per_lanthanides_Ts2::operator=(const class protocols::scoring::methods::pcsTs2::PCS_data_per_lanthanides_Ts2 &) –> class protocols::scoring::methods::pcsTs2::PCS_data_per_lanthanides_Ts2 &

calculate_tensor_and_cost_with_svd(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_per_lanthanides_Ts2, PCS_t: protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2) → float¶: C++: protocols::scoring::methods::pcsTs2::PCS_data_per_lanthanides_Ts2::calculate_tensor_and_cost_with_svd(class protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2 &) –> double

get_A_index(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_per_lanthanides_Ts2) → pyrosetta.rosetta.utility.vector1_unsigned_long¶: C++: protocols::scoring::methods::pcsTs2::PCS_data_per_lanthanides_Ts2::get_A_index() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

get_filename(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_per_lanthanides_Ts2) → str¶: C++: protocols::scoring::methods::pcsTs2::PCS_data_per_lanthanides_Ts2::get_filename() const –> std::string

get_fstyle_b(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_per_lanthanides_Ts2) → pyrosetta.rosetta.ObjexxFCL.FArray1D_double_t¶: C++: protocols::scoring::methods::pcsTs2::PCS_data_per_lanthanides_Ts2::get_fstyle_b() const –> const class ObjexxFCL::FArray1D<double> &

get_n_pcs(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_per_lanthanides_Ts2) → int¶: C++: protocols::scoring::methods::pcsTs2::PCS_data_per_lanthanides_Ts2::get_n_pcs() const –> unsigned long

get_normalization_factor(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_per_lanthanides_Ts2) → float¶: C++: protocols::scoring::methods::pcsTs2::PCS_data_per_lanthanides_Ts2::get_normalization_factor() const –> double

get_weight(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_per_lanthanides_Ts2) → float¶: C++: protocols::scoring::methods::pcsTs2::PCS_data_per_lanthanides_Ts2::get_weight() const –> double

set_A_index(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_per_lanthanides_Ts2, j: int, n_pcs_spin_: int) → None¶: C++: protocols::scoring::methods::pcsTs2::PCS_data_per_lanthanides_Ts2::set_A_index(unsigned long, unsigned long) –> void

update_my_A_matrix(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_data_per_lanthanides_Ts2, A_all: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t) → None¶: C++: protocols::scoring::methods::pcsTs2::PCS_data_per_lanthanides_Ts2::update_my_A_matrix(class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &) –> void

class pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_file_data_Ts2¶

Bases: pybind11_object

PCS_file_data_Ts2 contain all the information of a .npc file one per lanthanide.

assign(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_file_data_Ts2, other: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_file_data_Ts2) → pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_file_data_Ts2¶: C++: protocols::scoring::methods::pcsTs2::PCS_file_data_Ts2::operator=(const class protocols::scoring::methods::pcsTs2::PCS_file_data_Ts2 &) –> class protocols::scoring::methods::pcsTs2::PCS_file_data_Ts2 &

get_PCS_data_line_all_reference(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_file_data_Ts2) → pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcsTs2_PCS_line_data_Ts2¶: C++: protocols::scoring::methods::pcsTs2::PCS_file_data_Ts2::get_PCS_data_line_all_reference() –> class utility::vector1<class protocols::scoring::methods::pcsTs2::PCS_line_data_Ts2, class std::allocator<class protocols::scoring::methods::pcsTs2::PCS_line_data_Ts2> > &

get_filename(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_file_data_Ts2) → str¶: C++: protocols::scoring::methods::pcsTs2::PCS_file_data_Ts2::get_filename() const –> std::string

get_weight(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_file_data_Ts2) → float¶: C++: protocols::scoring::methods::pcsTs2::PCS_file_data_Ts2::get_weight() const –> double

class pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_line_data_Ts2¶

Bases: pybind11_object

PCS_line_data_Ts2 class: hold a line of the input file information (.npc format) One PCS_line_data_Ts2 per line in the input file

PCS_experimental(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_line_data_Ts2) → float¶: C++: protocols::scoring::methods::pcsTs2::PCS_line_data_Ts2::PCS_experimental() const –> double

PCS_tolerance(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_line_data_Ts2) → float¶: C++: protocols::scoring::methods::pcsTs2::PCS_line_data_Ts2::PCS_tolerance() const –> double

assign(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_line_data_Ts2, other: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_line_data_Ts2) → pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_line_data_Ts2¶: C++: protocols::scoring::methods::pcsTs2::PCS_line_data_Ts2::operator=(const class protocols::scoring::methods::pcsTs2::PCS_line_data_Ts2 &) –> class protocols::scoring::methods::pcsTs2::PCS_line_data_Ts2 &

atom_name(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_line_data_Ts2) → str¶: C++: protocols::scoring::methods::pcsTs2::PCS_line_data_Ts2::atom_name() const –> std::string

residue_num(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_line_data_Ts2) → int¶: C++: protocols::scoring::methods::pcsTs2::PCS_line_data_Ts2::residue_num() const –> unsigned long

class pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_tensor_Ts2¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_tensor_Ts2, other: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_tensor_Ts2) → pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_tensor_Ts2¶: C++: protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2::operator=(const class protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2 &) –> class protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2 &

chi_xx(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_tensor_Ts2) → float¶: C++: protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2::chi_xx() const –> double

chi_xy(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_tensor_Ts2) → float¶: C++: protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2::chi_xy() const –> double

chi_xz(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_tensor_Ts2) → float¶: C++: protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2::chi_xz() const –> double

chi_yy(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_tensor_Ts2) → float¶: C++: protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2::chi_yy() const –> double

chi_yz(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_tensor_Ts2) → float¶: C++: protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2::chi_yz() const –> double

copy_from_ref(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_tensor_Ts2, other: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_tensor_Ts2) → None¶: C++: protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2::copy_from_ref(class protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2 &) –> void

delta_X_xx(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_tensor_Ts2) → float¶: C++: protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2::delta_X_xx() const –> double

delta_X_yy(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_tensor_Ts2) → float¶: C++: protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2::delta_X_yy() const –> double

delta_X_zz(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_tensor_Ts2) → float¶: C++: protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2::delta_X_zz() const –> double

delta_chi_zz(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_tensor_Ts2) → float¶: C++: protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2::delta_chi_zz() const –> double

get_label(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_tensor_Ts2) → str¶: C++: protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2::get_label() const –> const std::string &

reset_tensor(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PCS_tensor_Ts2, chi_xx: float, chi_yy: float, chi_xy: float, chi_xz: float, chi_yz: float) → None¶: C++: protocols::scoring::methods::pcsTs2::PCS_tensor_Ts2::reset_tensor(const double, const double, const double, const double, const double) –> void

class pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PseudocontactShiftEnergyCreator_Ts2¶

Bases: EnergyMethodCreator

assign(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PseudocontactShiftEnergyCreator_Ts2, : pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PseudocontactShiftEnergyCreator_Ts2) → pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PseudocontactShiftEnergyCreator_Ts2¶: C++: protocols::scoring::methods::pcsTs2::PseudocontactShiftEnergyCreator_Ts2::operator=(const class protocols::scoring::methods::pcsTs2::PseudocontactShiftEnergyCreator_Ts2 &) –> class protocols::scoring::methods::pcsTs2::PseudocontactShiftEnergyCreator_Ts2 &

create_energy_method(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.PseudocontactShiftEnergyCreator_Ts2, : pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) → pyrosetta.rosetta.core.scoring.methods.EnergyMethod¶

Instantiate a new PseudoconstactShiftEnergy

C++: protocols::scoring::methods::pcsTs2::PseudocontactShiftEnergyCreator_Ts2::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.scoring.methods.pcsTs2.PseudocontactShiftEnergyCreator_Ts2) → 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::scoring::methods::pcsTs2::PseudocontactShiftEnergyCreator_Ts2::score_types_for_method() const –> class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> >

class pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.TensorsOptimizer_Ts2¶

Bases: Multifunc

abort_min(self: pyrosetta.rosetta.core.optimization.Multifunc, : pyrosetta.rosetta.utility.vector1_double) → bool¶

Christophe added the following to allow premature end of minimization: If you want to abort the minimizer under specific circonstances overload this function and return true if you want to stop, false if you want to continue. FOR THE MOMENT, ONLY IN DFPMIN!

C++: core::optimization::Multifunc::abort_min(const class utility::vector1<double, class std::allocator<double> > &) const –> bool

dfunc(self: pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.TensorsOptimizer_Ts2, vars: pyrosetta.rosetta.utility.vector1_double, dE_dvars: pyrosetta.rosetta.utility.vector1_double) → None¶

OptE dfunc

C++: protocols::scoring::methods::pcsTs2::TensorsOptimizer_Ts2::dfunc(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &) const –> void

dump(self: pyrosetta.rosetta.core.optimization.Multifunc, : pyrosetta.rosetta.utility.vector1_double, : pyrosetta.rosetta.utility.vector1_double) → None¶

Error state reached – derivative does not match gradient: Derived classes have the oportunity to now output and or analyze the two vars assignments vars, vars+delta where the derivatives are incorrect.

C++: core::optimization::Multifunc::dump(const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &) const –> void

pyrosetta.rosetta.protocols.scoring.methods.pcsTs2.fill_A_line(A_line: pyrosetta.rosetta.utility.vector1_double, xM: float, yM: float, zM: float, x: float, y: float, z: float) → None¶: C++: protocols::scoring::methods::pcsTs2::fill_A_line(class utility::vector1<double, class std::allocator<double> > &, const double, const double, const double, const double, const double, const double) –> void