pcs2

Bindings for protocols::scoring::methods::pcs2 namespace

class pyrosetta.rosetta.protocols.scoring.methods.pcs2.GridSearchIteratorCA

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.GridSearchIteratorCA, other: pyrosetta.rosetta.protocols.scoring.methods.pcs2.GridSearchIteratorCA) → pyrosetta.rosetta.protocols.scoring.methods.pcs2.GridSearchIteratorCA

C++: protocols::scoring::methods::pcs2::GridSearchIteratorCA::operator=(const class protocols::scoring::methods::pcs2::GridSearchIteratorCA &) –> class protocols::scoring::methods::pcs2::GridSearchIteratorCA &

next_center(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.GridSearchIteratorCA, x: float, y: float, z: float) → bool

give me the next x-y-z coordinate to visit

bool return FALSE if everything has been visited

C++: protocols::scoring::methods::pcs2::GridSearchIteratorCA::next_center(double &, double &, double &) –> bool

reset(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.GridSearchIteratorCA) → None

C++: protocols::scoring::methods::pcs2::GridSearchIteratorCA::reset() –> void

class pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenter

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenter, src: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenter) → pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenter

C++: protocols::scoring::methods::pcs2::PcsDataCenter::operator=(const class protocols::scoring::methods::pcs2::PcsDataCenter &) –> class protocols::scoring::methods::pcs2::PcsDataCenter &

get_A_all(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenter) → pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t

Give me the matrix A_all_

C++: protocols::scoring::methods::pcs2::PcsDataCenter::get_A_all() const –> const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &

get_PCS_data_line_all_spin(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenter) → pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsInputLine

Give me the vector PCS_data_line_all_spin_

C++: protocols::scoring::methods::pcs2::PcsDataCenter::get_PCS_data_line_all_spin() const –> const class utility::vector1<class protocols::scoring::methods::pcs2::PcsInputLine, class std::allocator<class protocols::scoring::methods::pcs2::PcsInputLine> > &

get_X_all(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenter) → pyrosetta.rosetta.utility.vector1_double

Give me the vector X_all_

C++: protocols::scoring::methods::pcs2::PcsDataCenter::get_X_all() const –> const class utility::vector1<double, class std::allocator<double> > &

get_Y_all(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenter) → pyrosetta.rosetta.utility.vector1_double

Give me the vector Y_all_

C++: protocols::scoring::methods::pcs2::PcsDataCenter::get_Y_all() const –> const class utility::vector1<double, class std::allocator<double> > &

get_Z_all(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenter) → pyrosetta.rosetta.utility.vector1_double

Give me the vector Z_all_

C++: protocols::scoring::methods::pcs2::PcsDataCenter::get_Z_all() const –> const class utility::vector1<double, class std::allocator<double> > &

get_n_lanthanides(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenter) → int

Give me the number of lanthanides for this center

C++: protocols::scoring::methods::pcs2::PcsDataCenter::get_n_lanthanides() const –> unsigned long

get_pcs_data_per_lanthanides_all(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenter) → pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsDataLanthanide

Give me the vector PCS_data_per_lanthanides_all_

C++: protocols::scoring::methods::pcs2::PcsDataCenter::get_pcs_data_per_lanthanides_all() –> class utility::vector1<class protocols::scoring::methods::pcs2::PcsDataLanthanide, class std::allocator<class protocols::scoring::methods::pcs2::PcsDataLanthanide> > &

update_X_Y_Z_all(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenter, pose: pyrosetta.rosetta.core.pose.Pose) → None

This is called each time the pose is changed

C++: protocols::scoring::methods::pcs2::PcsDataCenter::update_X_Y_Z_all(const class core::pose::Pose &) –> void

update_matrix_A_all(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenter, X: float, Y: float, Z: float) → None

Call update_my_A_matrix for all lanthanide data.

X Y Z are the new coordinate of the center

C++: protocols::scoring::methods::pcs2::PcsDataCenter::update_matrix_A_all(const double, const double, const double) –> void

update_matrix_A_all_for_cstyle(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenter, X: float, Y: float, Z: float) → None

C++: protocols::scoring::methods::pcs2::PcsDataCenter::update_matrix_A_all_for_cstyle(const double, const double, const double) –> void

update_matrix_A_all_for_svd(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenter, X: float, Y: float, Z: float) → None

Call update_my_A_matrix for all lanthanide data.

X Y Z are the new coordinate of the center It also update individual smaller matrice for svd

C++: protocols::scoring::methods::pcs2::PcsDataCenter::update_matrix_A_all_for_svd(const double, const double, const double) –> void

where_is_line(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenter, pcs_i_l: protocols::scoring::methods::pcs2::PcsInputLine) → int

Give the index number of the PcsInputLine given

C++: protocols::scoring::methods::pcs2::PcsDataCenter::where_is_line(class protocols::scoring::methods::pcs2::PcsInputLine &) –> unsigned long

class pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenterManager

Bases: CacheableData

assign(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenterManager, : pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenterManager) → pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenterManager

C++: protocols::scoring::methods::pcs2::PcsDataCenterManager::operator=(const class protocols::scoring::methods::pcs2::PcsDataCenterManager &) –> class protocols::scoring::methods::pcs2::PcsDataCenterManager &

clone(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenterManager) → pyrosetta.rosetta.basic.datacache.CacheableData

C++: protocols::scoring::methods::pcs2::PcsDataCenterManager::clone() const –> class std::shared_ptr<class basic::datacache::CacheableData>

get_PCS_data_all(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenterManager) → pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsDataCenter

Give me the vector of PcsDataCenter

C++: protocols::scoring::methods::pcs2::PcsDataCenterManager::get_PCS_data_all() –> class utility::vector1<class protocols::scoring::methods::pcs2::PcsDataCenter, class std::allocator<class protocols::scoring::methods::pcs2::PcsDataCenter> > &

get_n_multi_data(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenterManager) → int

Give me the number of lanthanide

C++: protocols::scoring::methods::pcs2::PcsDataCenterManager::get_n_multi_data() const –> unsigned long

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>

class pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenterManagerSingleton

Bases: SingletonBase_protocols_scoring_methods_pcs2_PcsDataCenterManagerSingleton_t

get_PCS_data_all(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenterManagerSingleton) → pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsDataCenter

Give me the vector of PcsDataCenter

C++: protocols::scoring::methods::pcs2::PcsDataCenterManagerSingleton::get_PCS_data_all() –> class utility::vector1<class protocols::scoring::methods::pcs2::PcsDataCenter, class std::allocator<class protocols::scoring::methods::pcs2::PcsDataCenter> > &

static get_instance() → protocols::scoring::methods::pcs2::PcsDataCenterManagerSingleton

C++: utility::SingletonBase<protocols::scoring::methods::pcs2::PcsDataCenterManagerSingleton>::get_instance() –> class protocols::scoring::methods::pcs2::PcsDataCenterManagerSingleton *

get_n_multi_data(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenterManagerSingleton) → int

Give me the number of lanthanide

C++: protocols::scoring::methods::pcs2::PcsDataCenterManagerSingleton::get_n_multi_data() const –> unsigned long

class pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataLanthanide

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataLanthanide, other: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataLanthanide) → pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataLanthanide

C++: protocols::scoring::methods::pcs2::PcsDataLanthanide::operator=(const class protocols::scoring::methods::pcs2::PcsDataLanthanide &) –> class protocols::scoring::methods::pcs2::PcsDataLanthanide &

calculate_cost_only_with_svd(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataLanthanide) → float

C++: protocols::scoring::methods::pcs2::PcsDataLanthanide::calculate_cost_only_with_svd() –> double

calculate_tensor_and_cost_with_svd(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataLanthanide, pcs_t: protocols::scoring::methods::pcs2::PcsTensor) → float

return the score and populate the PcsTensor with svd.

C++: protocols::scoring::methods::pcs2::PcsDataLanthanide::calculate_tensor_and_cost_with_svd(class protocols::scoring::methods::pcs2::PcsTensor &) –> double

calculate_tensor_only_with_svd(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataLanthanide, pcs_t: protocols::scoring::methods::pcs2::PcsTensor) → None

populate the PcsTensor with svd.

C++: protocols::scoring::methods::pcs2::PcsDataLanthanide::calculate_tensor_only_with_svd(class protocols::scoring::methods::pcs2::PcsTensor &) –> void

get_A_index(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataLanthanide) → pyrosetta.rosetta.utility.vector1_unsigned_long

Give me the A_index_ vector

C++: protocols::scoring::methods::pcs2::PcsDataLanthanide::get_A_index() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

get_cstyle_A(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataLanthanide) → pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t

C++: protocols::scoring::methods::pcs2::PcsDataLanthanide::get_cstyle_A() const –> const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &

get_cstyle_b(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataLanthanide) → pyrosetta.rosetta.utility.vector1_double

C++: protocols::scoring::methods::pcs2::PcsDataLanthanide::get_cstyle_b() const –> const class utility::vector1<double, class std::allocator<double> > &

get_cstyle_b_individual_scale(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataLanthanide) → pyrosetta.rosetta.utility.vector1_double

C++: protocols::scoring::methods::pcs2::PcsDataLanthanide::get_cstyle_b_individual_scale() const –> const class utility::vector1<double, class std::allocator<double> > &

get_filename(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataLanthanide) → str

give me the filename associated with this PCS data

C++: protocols::scoring::methods::pcs2::PcsDataLanthanide::get_filename() const –> std::string

get_individual_scale(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataLanthanide) → float

C++: protocols::scoring::methods::pcs2::PcsDataLanthanide::get_individual_scale() const –> double

get_n_pcs(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataLanthanide) → int

give me the number of PCS data

C++: protocols::scoring::methods::pcs2::PcsDataLanthanide::get_n_pcs() const –> unsigned long

get_normalization_factor(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataLanthanide) → float

give me the normalization factor associated with this PCS data

C++: protocols::scoring::methods::pcs2::PcsDataLanthanide::get_normalization_factor() const –> double

get_normalization_factor_inversed(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataLanthanide) → float

give me the normalization factor associated with this PCS data

C++: protocols::scoring::methods::pcs2::PcsDataLanthanide::get_normalization_factor_inversed() const –> double

get_weight(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataLanthanide) → float

give me the weight associated with this PCS data

C++: protocols::scoring::methods::pcs2::PcsDataLanthanide::get_weight() const –> double

retrieve_tensor_from_svd(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataLanthanide, pcs_t: protocols::scoring::methods::pcs2::PcsTensor) → None

C++: protocols::scoring::methods::pcs2::PcsDataLanthanide::retrieve_tensor_from_svd(class protocols::scoring::methods::pcs2::PcsTensor &) –> void

set_A_index(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataLanthanide, j: int, n_pcs_spin_: int) → None

Set a value of the A_index_ vector

C++: protocols::scoring::methods::pcs2::PcsDataLanthanide::set_A_index(unsigned long, unsigned long) –> void

update_my_A_matrix_for_cstyle(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataLanthanide, A_all: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t) → None

C++: protocols::scoring::methods::pcs2::PcsDataLanthanide::update_my_A_matrix_for_cstyle(class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &) –> void

update_my_A_matrix_for_svd(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataLanthanide, A_all: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t) → None

update the A matrix given A_all matrix.

Dimensions of A_all >= dimension of A. A_all is common to all the lanthanide sharing the same center

C++: protocols::scoring::methods::pcs2::PcsDataLanthanide::update_my_A_matrix_for_svd(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.pcs2.PcsEnergy

Bases: WholeStructureEnergy

PCS_multi_data_from_noone(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergy) → pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenterManagerSingleton

C++: protocols::scoring::methods::pcs2::PcsEnergy::PCS_multi_data_from_noone() const –> class protocols::scoring::methods::pcs2::PcsDataCenterManagerSingleton &

PCS_multi_data_from_pose(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergy, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenterManager

C++: protocols::scoring::methods::pcs2::PcsEnergy::PCS_multi_data_from_pose(class core::pose::Pose &) const –> class protocols::scoring::methods::pcs2::PcsDataCenterManager &

assign(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergy, other: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergy) → pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergy

C++: protocols::scoring::methods::pcs2::PcsEnergy::operator=(const class protocols::scoring::methods::pcs2::PcsEnergy &) –> class protocols::scoring::methods::pcs2::PcsEnergy &

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_on_PCS_data_center_CA(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergy, pose: pyrosetta.rosetta.core.pose.Pose, print_to_tracer: bool, pcs_d: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsDataCenter, i_multi_data: int, grid_it: pyrosetta.rosetta.protocols.scoring.methods.pcs2.GridSearchIteratorCA) → float

Return the PCS score given the pose, the given PcsDataCenter, and the lanthanide number

C++: protocols::scoring::methods::pcs2::PcsEnergy::calculate_pcs_score_on_PCS_data_center_CA(class core::pose::Pose &, bool, class protocols::scoring::methods::pcs2::PcsDataCenter &, unsigned long, class protocols::scoring::methods::pcs2::GridSearchIteratorCA &) const –> double

clone(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergy) → pyrosetta.rosetta.core.scoring.methods.EnergyMethod

C++: protocols::scoring::methods::pcs2::PcsEnergy::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.pcs2.PcsEnergy, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, totals: pyrosetta.rosetta.core.scoring.EMapVector) → None

This is called to start the PCS machinerie and get the score (set in totals)

C++: protocols::scoring::methods::pcs2::PcsEnergy::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.pcs2.PcsEnergy, : pyrosetta.rosetta.utility.vector1_bool) → None

C++: protocols::scoring::methods::pcs2::PcsEnergy::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:

1. setup_for_packing() is called for all energy methods

2. rotamers are built

3. setup_for_packing_with_rotsets() is called for all energy methods

4. prepare_rotamers_for_packing() is called for all energy methods

5. The energy methods are asked to score all rotamers and rotamer pairs

6. 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(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

version(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergy) → int

C++: protocols::scoring::methods::pcs2::PcsEnergy::version() const –> unsigned long

class pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergyCreator

Bases: EnergyMethodCreator

assign(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergyCreator, : pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergyCreator) → pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergyCreator

C++: protocols::scoring::methods::pcs2::PcsEnergyCreator::operator=(const class protocols::scoring::methods::pcs2::PcsEnergyCreator &) –> class protocols::scoring::methods::pcs2::PcsEnergyCreator &

create_energy_method(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergyCreator, : pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) → pyrosetta.rosetta.core.scoring.methods.EnergyMethod

Instantiate a new PcsEnergy

C++: protocols::scoring::methods::pcs2::PcsEnergyCreator::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.pcs2.PcsEnergyCreator) → 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::pcs2::PcsEnergyCreator::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.pcs2.PcsEnergyParameter

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergyParameter, other: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergyParameter) → pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergyParameter

C++: protocols::scoring::methods::pcs2::PcsEnergyParameter::operator=(const class protocols::scoring::methods::pcs2::PcsEnergyParameter &) –> class protocols::scoring::methods::pcs2::PcsEnergyParameter &

get_include_only_end(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergyParameter) → int

C++: protocols::scoring::methods::pcs2::PcsEnergyParameter::get_include_only_end() const –> unsigned long

get_include_only_start(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergyParameter) → int

C++: protocols::scoring::methods::pcs2::PcsEnergyParameter::get_include_only_start() const –> unsigned long

get_individual_scale(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergyParameter) → float

C++: protocols::scoring::methods::pcs2::PcsEnergyParameter::get_individual_scale() const –> double

get_n_trial_min(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergyParameter) → int

C++: protocols::scoring::methods::pcs2::PcsEnergyParameter::get_n_trial_min() const –> unsigned long

get_pcs_weight(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergyParameter) → float

Give me the pcs_weight value

C++: protocols::scoring::methods::pcs2::PcsEnergyParameter::get_pcs_weight() const –> double

get_vector_filename(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergyParameter) → pyrosetta.rosetta.utility.vector1_std_string

Give me the vector of the name

C++: protocols::scoring::methods::pcs2::PcsEnergyParameter::get_vector_filename() const –> const class utility::vector1<std::string, class std::allocator<std::string > > &

get_vector_weight(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergyParameter) → pyrosetta.rosetta.utility.vector1_double

Give me the vector of the weight

C++: protocols::scoring::methods::pcs2::PcsEnergyParameter::get_vector_weight() const –> const class utility::vector1<double, class std::allocator<double> > &

set_grid_param(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergyParameter, include_only_start: int, include_only_end: int, n_trial_min: int, pcs_weight: float, individual_scale: float) → None

the grid parameter for this PcsEnergyParameter

C++: protocols::scoring::methods::pcs2::PcsEnergyParameter::set_grid_param(const unsigned long, const unsigned long, const unsigned long, const double, const double) –> void

set_vector_name_and_weight(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergyParameter, vec_filename: pyrosetta.rosetta.utility.vector1_std_string, vec_individual_weight: pyrosetta.rosetta.utility.vector1_double) → None

the vector an weight name for this PcsEnergyParameter

C++: protocols::scoring::methods::pcs2::PcsEnergyParameter::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.pcs2.PcsEnergyParameterManager

Bases: SingletonBase_protocols_scoring_methods_pcs2_PcsEnergyParameterManager_t

get_PcsEnergyParameter_for(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergyParameterManager, i_multi_data: int) → pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergyParameter

Give me the PcsEnergyParameter number i_multi_data

C++: protocols::scoring::methods::pcs2::PcsEnergyParameterManager::get_PcsEnergyParameter_for(unsigned long) –> class protocols::scoring::methods::pcs2::PcsEnergyParameter &

static get_instance() → protocols::scoring::methods::pcs2::PcsEnergyParameterManager

C++: utility::SingletonBase<protocols::scoring::methods::pcs2::PcsEnergyParameterManager>::get_instance() –> class protocols::scoring::methods::pcs2::PcsEnergyParameterManager *

get_n_multi_data(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergyParameterManager) → int

Give me the number of paramagnetic center

C++: protocols::scoring::methods::pcs2::PcsEnergyParameterManager::get_n_multi_data() const –> unsigned long

incremente_n_multi_data(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergyParameterManager) → None

Add a new paramagnetic center

C++: protocols::scoring::methods::pcs2::PcsEnergyParameterManager::incremente_n_multi_data() –> void

re_init(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsEnergyParameterManager) → None

Re init the singleton

C++: protocols::scoring::methods::pcs2::PcsEnergyParameterManager::re_init() –> void

class pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsGridSearchParameter

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsGridSearchParameter, other: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsGridSearchParameter) → pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsGridSearchParameter

C++: protocols::scoring::methods::pcs2::PcsGridSearchParameter::operator=(const class protocols::scoring::methods::pcs2::PcsGridSearchParameter &) –> class protocols::scoring::methods::pcs2::PcsGridSearchParameter &

control_grid_param(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsGridSearchParameter) → None

This is to make sure the grid is correctly set up

C++: protocols::scoring::methods::pcs2::PcsGridSearchParameter::control_grid_param() –> void

property filenames_

property include_only_end_stage1_

property include_only_end_stage2_

property include_only_end_stage3_

property include_only_end_stage4_

property include_only_start_stage1_

property include_only_start_stage2_

property include_only_start_stage3_

property include_only_start_stage4_

property individual_scale_stage1_

property individual_scale_stage2_

property individual_scale_stage3_

property individual_scale_stage4_

property individual_weights_

property n_trial_min_stage1_

property n_trial_min_stage2_

property n_trial_min_stage3_

property n_trial_min_stage4_

property pcs_weight_stage1_

property pcs_weight_stage2_

property pcs_weight_stage3_

property pcs_weight_stage4_

class pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsGridSearchParameterManager

Bases: SingletonBase_protocols_scoring_methods_pcs2_PcsGridSearchParameterManager_t

get_grid_search_parameters(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsGridSearchParameterManager, i_multi_data: int) → pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsGridSearchParameter

@ Give me the PcsGridSearchParamater of the center i_multi_data

C++: protocols::scoring::methods::pcs2::PcsGridSearchParameterManager::get_grid_search_parameters(unsigned long) –> class protocols::scoring::methods::pcs2::PcsGridSearchParameter &

static get_instance() → protocols::scoring::methods::pcs2::PcsGridSearchParameterManager

C++: utility::SingletonBase<protocols::scoring::methods::pcs2::PcsGridSearchParameterManager>::get_instance() –> class protocols::scoring::methods::pcs2::PcsGridSearchParameterManager *

get_n_multi_data(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsGridSearchParameterManager) → int

give me the number of paramagnetic center

C++: protocols::scoring::methods::pcs2::PcsGridSearchParameterManager::get_n_multi_data() const –> unsigned long

incremente_n_multi_data(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsGridSearchParameterManager) → None

Incremente the number of paramagnetic center

C++: protocols::scoring::methods::pcs2::PcsGridSearchParameterManager::incremente_n_multi_data() –> void

re_init(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsGridSearchParameterManager) → None

@ Re init the singleton to default value

C++: protocols::scoring::methods::pcs2::PcsGridSearchParameterManager::re_init() –> void

class pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputCenter

Bases: pybind11_object

PcsInputCenter contain all the input information for one paramagnetic center. It can contain multiple data set

assign(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputCenter, other: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputCenter) → pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputCenter

C++: protocols::scoring::methods::pcs2::PcsInputCenter::operator=(const class protocols::scoring::methods::pcs2::PcsInputCenter &) –> class protocols::scoring::methods::pcs2::PcsInputCenter &

get_PcsInputFile_all(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputCenter) → pyrosetta.rosetta.std.map_std_string_protocols_scoring_methods_pcs2_PcsInputFile

Give me all PcsInputFile

C++: protocols::scoring::methods::pcs2::PcsInputCenter::get_PcsInputFile_all() –> class std::map<std::string, class protocols::scoring::methods::pcs2::PcsInputFile, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class protocols::scoring::methods::pcs2::PcsInputFile> > > &

class pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputCenterManager

Bases: SingletonBase_protocols_scoring_methods_pcs2_PcsInputCenterManager_t

get_PcsInputCenter_for(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputCenterManager, filenames: pyrosetta.rosetta.utility.vector1_std_string, vec_weight: pyrosetta.rosetta.utility.vector1_double) → pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputCenter

Give me the PcsInputCenter given the vector of filename and vector of weight

C++: protocols::scoring::methods::pcs2::PcsInputCenterManager::get_PcsInputCenter_for(const class utility::vector1<std::string, class std::allocator<std::string > > &, const class utility::vector1<double, class std::allocator<double> > &) –> class protocols::scoring::methods::pcs2::PcsInputCenter

static get_instance() → protocols::scoring::methods::pcs2::PcsInputCenterManager

C++: utility::SingletonBase<protocols::scoring::methods::pcs2::PcsInputCenterManager>::get_instance() –> class protocols::scoring::methods::pcs2::PcsInputCenterManager *

re_init(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputCenterManager) → None

@ Re init the singleton to default value

C++: protocols::scoring::methods::pcs2::PcsInputCenterManager::re_init() –> void

class pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputFile

Bases: pybind11_object

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

assign(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputFile, other: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputFile) → pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputFile

C++: protocols::scoring::methods::pcs2::PcsInputFile::operator=(const class protocols::scoring::methods::pcs2::PcsInputFile &) –> class protocols::scoring::methods::pcs2::PcsInputFile &

get_PcsInputLine_all(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputFile) → pyrosetta.rosetta.utility.vector1_protocols_scoring_methods_pcs2_PcsInputLine

Give me the vector of all the line of the file

C++: protocols::scoring::methods::pcs2::PcsInputFile::get_PcsInputLine_all() –> class utility::vector1<class protocols::scoring::methods::pcs2::PcsInputLine, class std::allocator<class protocols::scoring::methods::pcs2::PcsInputLine> > &

get_filename(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputFile) → str

Give me the name of the file

C++: protocols::scoring::methods::pcs2::PcsInputFile::get_filename() const –> std::string

get_weight(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputFile) → float

Give me the weight associated

C++: protocols::scoring::methods::pcs2::PcsInputFile::get_weight() const –> double

class pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputLine

Bases: pybind11_object

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

assign(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputLine, other: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputLine) → pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputLine

C++: protocols::scoring::methods::pcs2::PcsInputLine::operator=(const class protocols::scoring::methods::pcs2::PcsInputLine &) –> class protocols::scoring::methods::pcs2::PcsInputLine &

get_PCS_experimental(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputLine) → float

Give me the experimental PCS of this PcsInputLine

C++: protocols::scoring::methods::pcs2::PcsInputLine::get_PCS_experimental() const –> double

get_PCS_tolerance(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputLine) → float

Give me the tolerance for the PCS of this PcsInputLine

C++: protocols::scoring::methods::pcs2::PcsInputLine::get_PCS_tolerance() const –> double

get_atom_name(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputLine) → str

Give me the atom name of this PcsInputLine

C++: protocols::scoring::methods::pcs2::PcsInputLine::get_atom_name() const –> std::string

get_residue_num(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsInputLine) → int

Give me the residue number of this PcsInputLine

C++: protocols::scoring::methods::pcs2::PcsInputLine::get_residue_num() const –> unsigned long

class pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsTensor

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsTensor, other: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsTensor) → pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsTensor

C++: protocols::scoring::methods::pcs2::PcsTensor::operator=(const class protocols::scoring::methods::pcs2::PcsTensor &) –> class protocols::scoring::methods::pcs2::PcsTensor &

get_chi_xx(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsTensor) → float

Give me chi_xx

C++: protocols::scoring::methods::pcs2::PcsTensor::get_chi_xx() const –> double

get_chi_xy(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsTensor) → float

Give me chi_xy

C++: protocols::scoring::methods::pcs2::PcsTensor::get_chi_xy() const –> double

get_chi_xz(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsTensor) → float

Give me chi_xz

C++: protocols::scoring::methods::pcs2::PcsTensor::get_chi_xz() const –> double

get_chi_yy(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsTensor) → float

Give me chi_yy

C++: protocols::scoring::methods::pcs2::PcsTensor::get_chi_yy() const –> double

get_chi_yz(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsTensor) → float

Give me chi_yz

C++: protocols::scoring::methods::pcs2::PcsTensor::get_chi_yz() const –> double

get_chi_zz(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsTensor) → float

Give me chi_zz

C++: protocols::scoring::methods::pcs2::PcsTensor::get_chi_zz() const –> double

get_delta_X_xx(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsTensor) → float

Give me delta chi_xx

C++: protocols::scoring::methods::pcs2::PcsTensor::get_delta_X_xx() const –> double

get_delta_X_yy(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsTensor) → float

Give me delta chi_yy

C++: protocols::scoring::methods::pcs2::PcsTensor::get_delta_X_yy() const –> double

get_delta_X_zz(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsTensor) → float

Give me delta chi_zz

C++: protocols::scoring::methods::pcs2::PcsTensor::get_delta_X_zz() const –> double

get_label(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsTensor) → str

Give me the tensor label

C++: protocols::scoring::methods::pcs2::PcsTensor::get_label() const –> const std::string &

reset_from_ref(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsTensor, other: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsTensor) → None

Reset the tensor from the other tensor value

C++: protocols::scoring::methods::pcs2::PcsTensor::reset_from_ref(class protocols::scoring::methods::pcs2::PcsTensor &) –> void

reset_tensor(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.PcsTensor, chi_xx: float, chi_yy: float, chi_xy: float, chi_xz: float, chi_yz: float) → None

Reset the tensor from the given values.

C++: protocols::scoring::methods::pcs2::PcsTensor::reset_tensor(const double, const double, const double, const double, const double) –> void

class pyrosetta.rosetta.protocols.scoring.methods.pcs2.TensorsOptimizer

Bases: Multifunc

abort_min(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.TensorsOptimizer, vars: pyrosetta.rosetta.utility.vector1_double) → bool

C++: protocols::scoring::methods::pcs2::TensorsOptimizer::abort_min(const class utility::vector1<double, class std::allocator<double> > &) const –> bool

dfunc(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.TensorsOptimizer, vars: pyrosetta.rosetta.utility.vector1_double, dE_dvars: pyrosetta.rosetta.utility.vector1_double) → None

OptE dfunc

C++: protocols::scoring::methods::pcs2::TensorsOptimizer::dfunc(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &) const –> void

dfunc_exact(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.TensorsOptimizer, vars: pyrosetta.rosetta.utility.vector1_double, dE_dvars: pyrosetta.rosetta.utility.vector1_double) → None

exact derivative (fast)

C++: protocols::scoring::methods::pcs2::TensorsOptimizer::dfunc_exact(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &) const –> void

dfunc_numeric(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.TensorsOptimizer, vars: pyrosetta.rosetta.utility.vector1_double, dE_dvars: pyrosetta.rosetta.utility.vector1_double) → None

numeric derivative (slow)

C++: protocols::scoring::methods::pcs2::TensorsOptimizer::dfunc_numeric(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

func(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.TensorsOptimizer, vars: pyrosetta.rosetta.utility.vector1_double) → float

C++: protocols::scoring::methods::pcs2::TensorsOptimizer::func(const class utility::vector1<double, class std::allocator<double> > &) const –> double

class pyrosetta.rosetta.protocols.scoring.methods.pcs2.TensorsOptimizerFix

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.pcs2.TensorsOptimizerFix, vars: pyrosetta.rosetta.utility.vector1_double, dE_dvars: pyrosetta.rosetta.utility.vector1_double) → None

OptE dfunc

C++: protocols::scoring::methods::pcs2::TensorsOptimizerFix::dfunc(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &) const –> void

dfunc_exact(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.TensorsOptimizerFix, vars: pyrosetta.rosetta.utility.vector1_double, dE_dvars: pyrosetta.rosetta.utility.vector1_double) → None

exact derivative (fast)

C++: protocols::scoring::methods::pcs2::TensorsOptimizerFix::dfunc_exact(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &) const –> void

dfunc_numeric(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.TensorsOptimizerFix, vars: pyrosetta.rosetta.utility.vector1_double, dE_dvars: pyrosetta.rosetta.utility.vector1_double) → None

numeric derivative (slow)

C++: protocols::scoring::methods::pcs2::TensorsOptimizerFix::dfunc_numeric(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

func(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.TensorsOptimizerFix, vars: pyrosetta.rosetta.utility.vector1_double) → float

C++: protocols::scoring::methods::pcs2::TensorsOptimizerFix::func(const class utility::vector1<double, class std::allocator<double> > &) const –> double

class pyrosetta.rosetta.protocols.scoring.methods.pcs2.TensorsOptimizerSvd

Bases: Multifunc

abort_min(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.TensorsOptimizerSvd, vars: pyrosetta.rosetta.utility.vector1_double) → bool

C++: protocols::scoring::methods::pcs2::TensorsOptimizerSvd::abort_min(const class utility::vector1<double, class std::allocator<double> > &) const –> bool

dfunc(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.TensorsOptimizerSvd, vars: pyrosetta.rosetta.utility.vector1_double, dE_dvars: pyrosetta.rosetta.utility.vector1_double) → None

OptE dfunc

C++: protocols::scoring::methods::pcs2::TensorsOptimizerSvd::dfunc(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &) const –> void

dfunc_exact(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.TensorsOptimizerSvd, vars: pyrosetta.rosetta.utility.vector1_double, dE_dvars: pyrosetta.rosetta.utility.vector1_double) → None

exact derivative (fast)

C++: protocols::scoring::methods::pcs2::TensorsOptimizerSvd::dfunc_exact(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &) const –> void

dfunc_numeric(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.TensorsOptimizerSvd, vars: pyrosetta.rosetta.utility.vector1_double, dE_dvars: pyrosetta.rosetta.utility.vector1_double) → None

numeric derivative (slow)

C++: protocols::scoring::methods::pcs2::TensorsOptimizerSvd::dfunc_numeric(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

func(self: pyrosetta.rosetta.protocols.scoring.methods.pcs2.TensorsOptimizerSvd, vars: pyrosetta.rosetta.utility.vector1_double) → float

C++: protocols::scoring::methods::pcs2::TensorsOptimizerSvd::func(const class utility::vector1<double, class std::allocator<double> > &) const –> double

pyrosetta.rosetta.protocols.scoring.methods.pcs2.do_I_skip(pcs_i_l: protocols::scoring::methods::pcs2::PcsInputLine, start: int, end: int) → bool

C++: protocols::scoring::methods::pcs2::do_I_skip(class protocols::scoring::methods::pcs2::PcsInputLine &, unsigned long, unsigned long) –> bool

pyrosetta.rosetta.protocols.scoring.methods.pcs2.fill_A_line_fast(A_line: pyrosetta.rosetta.utility.vector1_double, xM: float, yM: float, zM: float, x: float, y: float, z: float) → float

C++: protocols::scoring::methods::pcs2::fill_A_line_fast(class utility::vector1<double, class std::allocator<double> > &, const double, const double, const double, const double, const double, const double) –> double

pyrosetta.rosetta.protocols.scoring.methods.pcs2.fill_A_line_slow(A_line: pyrosetta.rosetta.utility.vector1_double, xM: float, yM: float, zM: float, x: float, y: float, z: float) → None

C++: protocols::scoring::methods::pcs2::fill_A_line_slow(class utility::vector1<double, class std::allocator<double> > &, const double, const double, const double, const double, const double, const double) –> void