pcs

Bindings for protocols::nmr::pcs namespace

class pyrosetta.rosetta.protocols.nmr.pcs.AtomGrid

Bases: pyrosetta.rosetta.numeric.VoxelGrid_protocols_nmr_pcs_AtomGridPoint_t

Clear(self: pyrosetta.rosetta.numeric.VoxelGrid_protocols_nmr_pcs_AtomGridPoint_t) None

C++: numeric::VoxelGrid<protocols::nmr::pcs::AtomGridPoint>::Clear() –> void

ExtractPosition(self: pyrosetta.rosetta.protocols.nmr.pcs.AtomGrid, point: pyrosetta.rosetta.protocols.nmr.pcs.AtomGridPoint) pyrosetta.rosetta.numeric.xyzVector_double_t

Extract the 3D coordinate of a given object of type VoxelGridPoint.

C++: protocols::nmr::pcs::AtomGrid::ExtractPosition(const class protocols::nmr::pcs::AtomGridPoint &) const –> const class numeric::xyzVector<double> *

GetBoundingBox(self: pyrosetta.rosetta.numeric.VoxelGrid_protocols_nmr_pcs_AtomGridPoint_t) pyrosetta.rosetta.numeric.geometry.BoundingBox_numeric_xyzVector_double_t

C++: numeric::VoxelGrid<protocols::nmr::pcs::AtomGridPoint>::GetBoundingBox() const –> const class numeric::geometry::BoundingBox<class numeric::xyzVector<double> > &

GetDimension(self: pyrosetta.rosetta.numeric.VoxelGrid_protocols_nmr_pcs_AtomGridPoint_t) int

C++: numeric::VoxelGrid<protocols::nmr::pcs::AtomGridPoint>::GetDimension() const –> unsigned long

GetGridItems(self: pyrosetta.rosetta.numeric.VoxelGrid_protocols_nmr_pcs_AtomGridPoint_t) pyrosetta.rosetta.utility.vector1_utility_vector1_std_pair_const_protocols_nmr_pcs_AtomGridPoint_*_const_numeric_xyzVector_double_*_std_allocator_std_pair_const_protocols_nmr_pcs_AtomGridPoint_*_const_numeric_xyzVector_double_*_t

C++: numeric::VoxelGrid<protocols::nmr::pcs::AtomGridPoint>::GetGridItems() const –> const class utility::vector1<class utility::vector1<struct std::pair<const class protocols::nmr::pcs::AtomGridPoint *, const class numeric::xyzVector<double> *>, class std::allocator<struct std::pair<const class protocols::nmr::pcs::AtomGridPoint *, const class numeric::xyzVector<double> *> > >, class std::allocator<class utility::vector1<struct std::pair<const class protocols::nmr::pcs::AtomGridPoint *, const class numeric::xyzVector<double> *>, class std::allocator<struct std::pair<const class protocols::nmr::pcs::AtomGridPoint *, const class numeric::xyzVector<double> *> > > > > &

GetNumberItems(self: pyrosetta.rosetta.numeric.VoxelGrid_protocols_nmr_pcs_AtomGridPoint_t) int

C++: numeric::VoxelGrid<protocols::nmr::pcs::AtomGridPoint>::GetNumberItems() const –> unsigned long

GetResolution(self: pyrosetta.rosetta.numeric.VoxelGrid_protocols_nmr_pcs_AtomGridPoint_t) float

C++: numeric::VoxelGrid<protocols::nmr::pcs::AtomGridPoint>::GetResolution() const –> double

HasNeighbors(*args, **kwargs)

Overloaded function.

  1. HasNeighbors(self: pyrosetta.rosetta.numeric.VoxelGrid_protocols_nmr_pcs_AtomGridPoint_t, input: protocols::nmr::pcs::AtomGridPoint, neighborhood: float) -> bool

  2. HasNeighbors(self: pyrosetta.rosetta.numeric.VoxelGrid_protocols_nmr_pcs_AtomGridPoint_t, input: protocols::nmr::pcs::AtomGridPoint, neighborhood: float, check_relevance: bool) -> bool

C++: numeric::VoxelGrid<protocols::nmr::pcs::AtomGridPoint>::HasNeighbors(const class protocols::nmr::pcs::AtomGridPoint &, const double &, bool) const –> bool

InsertObject(*args, **kwargs)

Overloaded function.

  1. InsertObject(self: pyrosetta.rosetta.numeric.VoxelGrid_protocols_nmr_pcs_AtomGridPoint_t, new_item: protocols::nmr::pcs::AtomGridPoint) -> None

  2. InsertObject(self: pyrosetta.rosetta.numeric.VoxelGrid_protocols_nmr_pcs_AtomGridPoint_t, new_item: protocols::nmr::pcs::AtomGridPoint, check_relevance: bool) -> None

C++: numeric::VoxelGrid<protocols::nmr::pcs::AtomGridPoint>::InsertObject(const class protocols::nmr::pcs::AtomGridPoint &, bool) –> void

IsRelevantItem(self: pyrosetta.rosetta.protocols.nmr.pcs.AtomGrid, point: pyrosetta.rosetta.protocols.nmr.pcs.AtomGridPoint) bool

Check if this item is relevant for neighbor search

C++: protocols::nmr::pcs::AtomGrid::IsRelevantItem(const class protocols::nmr::pcs::AtomGridPoint &) const –> bool

IsSameItem(self: pyrosetta.rosetta.protocols.nmr.pcs.AtomGrid, point1: pyrosetta.rosetta.protocols.nmr.pcs.AtomGridPoint, point2: pyrosetta.rosetta.protocols.nmr.pcs.AtomGridPoint) bool

Check if two grid points are the same.

C++: protocols::nmr::pcs::AtomGrid::IsSameItem(const class protocols::nmr::pcs::AtomGridPoint &, const class protocols::nmr::pcs::AtomGridPoint &) const –> bool

RemoveObject(self: pyrosetta.rosetta.numeric.VoxelGrid_protocols_nmr_pcs_AtomGridPoint_t, item_to_remove: protocols::nmr::pcs::AtomGridPoint) None

C++: numeric::VoxelGrid<protocols::nmr::pcs::AtomGridPoint>::RemoveObject(const class protocols::nmr::pcs::AtomGridPoint &) –> void

Translate(self: pyrosetta.rosetta.numeric.VoxelGrid_protocols_nmr_pcs_AtomGridPoint_t, translation: pyrosetta.rosetta.numeric.xyzVector_double_t) None

C++: numeric::VoxelGrid<protocols::nmr::pcs::AtomGridPoint>::Translate(const class numeric::xyzVector<double> &) –> void

assign(self: pyrosetta.rosetta.protocols.nmr.pcs.AtomGrid, : pyrosetta.rosetta.protocols.nmr.pcs.AtomGrid) pyrosetta.rosetta.protocols.nmr.pcs.AtomGrid

C++: protocols::nmr::pcs::AtomGrid::operator=(const class protocols::nmr::pcs::AtomGrid &) –> class protocols::nmr::pcs::AtomGrid &

class pyrosetta.rosetta.protocols.nmr.pcs.AtomGridPoint

Bases: pybind11_builtins.pybind11_object

Two utility classes used by the PCSLigandTranformMover

assign(self: pyrosetta.rosetta.protocols.nmr.pcs.AtomGridPoint, : pyrosetta.rosetta.protocols.nmr.pcs.AtomGridPoint) pyrosetta.rosetta.protocols.nmr.pcs.AtomGridPoint

C++: protocols::nmr::pcs::AtomGridPoint::operator=(const class protocols::nmr::pcs::AtomGridPoint &) –> class protocols::nmr::pcs::AtomGridPoint &

atom_name(self: pyrosetta.rosetta.protocols.nmr.pcs.AtomGridPoint) str

C++: protocols::nmr::pcs::AtomGridPoint::atom_name() const –> std::string

get_coordinates(self: pyrosetta.rosetta.protocols.nmr.pcs.AtomGridPoint) pyrosetta.rosetta.numeric.xyzVector_double_t

C++: protocols::nmr::pcs::AtomGridPoint::get_coordinates() const –> const class numeric::xyzVector<double> &

id(self: pyrosetta.rosetta.protocols.nmr.pcs.AtomGridPoint) int

C++: protocols::nmr::pcs::AtomGridPoint::id() const –> unsigned long

is_relevant_neighbor(self: pyrosetta.rosetta.protocols.nmr.pcs.AtomGridPoint) bool

Is relevant for neighbor search

C++: protocols::nmr::pcs::AtomGridPoint::is_relevant_neighbor() const –> bool

residue(self: pyrosetta.rosetta.protocols.nmr.pcs.AtomGridPoint) pyrosetta.rosetta.core.conformation.Residue

C++: protocols::nmr::pcs::AtomGridPoint::residue() const –> const class core::conformation::Residue *

set_coordinates(self: pyrosetta.rosetta.protocols.nmr.pcs.AtomGridPoint, v: pyrosetta.rosetta.numeric.xyzVector_double_t) None

C++: protocols::nmr::pcs::AtomGridPoint::set_coordinates(const class numeric::xyzVector<double> &) –> void

class pyrosetta.rosetta.protocols.nmr.pcs.PCSEnergy

Bases: pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy

assign(self: pyrosetta.rosetta.protocols.nmr.pcs.PCSEnergy, : pyrosetta.rosetta.protocols.nmr.pcs.PCSEnergy) pyrosetta.rosetta.protocols.nmr.pcs.PCSEnergy

C++: protocols::nmr::pcs::PCSEnergy::operator=(const class protocols::nmr::pcs::PCSEnergy &) –> class protocols::nmr::pcs::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

calcualate_total_score_and_tensors(self: pyrosetta.rosetta.protocols.nmr.pcs.PCSEnergy, pose: pyrosetta.rosetta.core.pose.Pose) float

Calculate the total PCS score from PCSData retrieved from the pose

C++: protocols::nmr::pcs::PCSEnergy::calcualate_total_score_and_tensors(class core::pose::Pose &) const –> double

clone(self: pyrosetta.rosetta.protocols.nmr.pcs.PCSEnergy) pyrosetta.rosetta.core.scoring.methods.EnergyMethod

C++: protocols::nmr::pcs::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.protocols.nmr.pcs.PCSEnergy, id: pyrosetta.rosetta.core.id.AtomID, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t, : pyrosetta.rosetta.core.scoring.ScoreFunction, weights: pyrosetta.rosetta.core.scoring.EMapVector, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t) None
Evaluate the xyz derivative of the PCS 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, setup_for_minimizing() accumulates its contribution from the xyz derivatives of atom id

C++: protocols::nmr::pcs::PCSEnergy::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.nmr.pcs.PCSEnergy, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, totals: pyrosetta.rosetta.core.scoring.EMapVector) None

Calculate the PCS score and write it into the pose’s total energy EnergyMap

C++: protocols::nmr::pcs::PCSEnergy::finalize_total_energy(class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

get_pcs_data_from_pose(self: pyrosetta.rosetta.protocols.nmr.pcs.PCSEnergy, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.scoring.nmr.pcs.PCSData

Return PCSData from pose. Create PCSData if not present and attach them to the pose.

C++: protocols::nmr::pcs::PCSEnergy::get_pcs_data_from_pose(class core::pose::Pose &) const –> class core::scoring::nmr::pcs::PCSData &

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.nmr.pcs.PCSEnergy, : pyrosetta.rosetta.utility.vector1_bool) None
Indicate in the context-graphs-required list which

context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed.

C++: protocols::nmr::pcs::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.protocols.nmr.pcs.PCSEnergy, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, : pyrosetta.rosetta.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. Here, the function creates and updates the atom_id_to_pcs_xyz_deriv_map_ which is needed by the eval_atom_derivative() function.

C++: protocols::nmr::pcs::PCSEnergy::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(*args, **kwargs)

Overloaded function.

  1. show_additional_info(self: pyrosetta.rosetta.protocols.nmr.pcs.PCSEnergy, TR: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) -> None

  2. show_additional_info(self: pyrosetta.rosetta.protocols.nmr.pcs.PCSEnergy, TR: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose, verbose: bool) -> None

show additional information of the energy method

C++: protocols::nmr::pcs::PCSEnergy::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.nmr.pcs.PCSEnergy) int

Return the version of the energy method

C++: protocols::nmr::pcs::PCSEnergy::version() const –> unsigned long

class pyrosetta.rosetta.protocols.nmr.pcs.PCSEnergyCreator

Bases: pyrosetta.rosetta.core.scoring.methods.EnergyMethodCreator

assign(self: pyrosetta.rosetta.protocols.nmr.pcs.PCSEnergyCreator, : pyrosetta.rosetta.protocols.nmr.pcs.PCSEnergyCreator) pyrosetta.rosetta.protocols.nmr.pcs.PCSEnergyCreator

C++: protocols::nmr::pcs::PCSEnergyCreator::operator=(const class protocols::nmr::pcs::PCSEnergyCreator &) –> class protocols::nmr::pcs::PCSEnergyCreator &

create_energy_method(self: pyrosetta.rosetta.protocols.nmr.pcs.PCSEnergyCreator, : pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) pyrosetta.rosetta.core.scoring.methods.EnergyMethod

C++: protocols::nmr::pcs::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.nmr.pcs.PCSEnergyCreator) pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType

C++: protocols::nmr::pcs::PCSEnergyCreator::score_types_for_method() const –> class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> >

class pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

apply(self: pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover, pose: pyrosetta.rosetta.core.pose.Pose) None

Perform grid search of ligand position by minimizing the PCS score

C++: protocols::nmr::pcs::PCSLigandTransformMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover, rhs: pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover) pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover

Assignment operator

C++: protocols::nmr::pcs::PCSLigandTransformMover::operator=(const class protocols::nmr::pcs::PCSLigandTransformMover &) –> class protocols::nmr::pcs::PCSLigandTransformMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover) pyrosetta.rosetta.protocols.moves.Mover

Return a clone of the Mover object.

C++: protocols::nmr::pcs::PCSLigandTransformMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

do_optimized_transform(self: pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover) None

C++: protocols::nmr::pcs::PCSLigandTransformMover::do_optimized_transform() –> void

fresh_instance(self: pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover) pyrosetta.rosetta.protocols.moves.Mover

Generates a new Mover object freshly created with the default ctor.

C++: protocols::nmr::pcs::PCSLigandTransformMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_chain(self: pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover) str

C++: protocols::nmr::pcs::PCSLigandTransformMover::get_chain() const –> char

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_gridsearch_range(self: pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover) pyrosetta.rosetta.numeric.geometry.BoundingBox_numeric_xyzVector_double_t

C++: protocols::nmr::pcs::PCSLigandTransformMover::get_gridsearch_range() const –> const class numeric::geometry::BoundingBox<class numeric::xyzVector<double> > &

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover) str

Get the name of this mover

C++: protocols::nmr::pcs::PCSLigandTransformMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_pcs_data(self: pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover) pyrosetta.rosetta.core.scoring.nmr.pcs.PCSData

C++: protocols::nmr::pcs::PCSLigandTransformMover::get_pcs_data() const –> const class core::scoring::nmr::pcs::PCSData &

get_resolution_damping(self: pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover) float

C++: protocols::nmr::pcs::PCSLigandTransformMover::get_resolution_damping() const –> double

get_rot_step(self: pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover) float

C++: protocols::nmr::pcs::PCSLigandTransformMover::get_rot_step() const –> double

get_scorefunction(self: pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover) pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::nmr::pcs::PCSLigandTransformMover::get_scorefunction() –> class std::shared_ptr<const class core::scoring::ScoreFunction>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_trans_step(self: pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover) float

C++: protocols::nmr::pcs::PCSLigandTransformMover::get_trans_step() const –> double

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str

C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_t

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() str

C++: protocols::nmr::pcs::PCSLigandTransformMover::mover_name() –> std::string

static name() str

C++: protocols::moves::Mover::name() –> std::string

optimized_transform(self: pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover) bool

C++: protocols::nmr::pcs::PCSLigandTransformMover::optimized_transform() const –> bool

parse_my_tag(self: pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) None

Parse tags of XML script

C++: protocols::nmr::pcs::PCSLigandTransformMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : 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 movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

Create XML schema definition for PREMover

C++: protocols::nmr::pcs::PCSLigandTransformMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() None

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on

each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_chain(self: pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover, c: str) None

C++: protocols::nmr::pcs::PCSLigandTransformMover::set_chain(const char) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None

C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_gridsearch_range(*args, **kwargs)

Overloaded function.

  1. set_gridsearch_range(self: pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover, box: pyrosetta.rosetta.numeric.geometry.BoundingBox_numeric_xyzVector_double_t) -> None

C++: protocols::nmr::pcs::PCSLigandTransformMover::set_gridsearch_range(const class numeric::geometry::BoundingBox<class numeric::xyzVector<double> > &) –> void

  1. set_gridsearch_range(self: pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover, lower: pyrosetta.rosetta.numeric.xyzVector_double_t, upper: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

C++: protocols::nmr::pcs::PCSLigandTransformMover::set_gridsearch_range(const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_resolution_damping(self: pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover, damping: float) None

C++: protocols::nmr::pcs::PCSLigandTransformMover::set_resolution_damping(double) –> void

set_rot_step(self: pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover, step: float) None

C++: protocols::nmr::pcs::PCSLigandTransformMover::set_rot_step(double) –> void

set_scorefunction(self: pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: protocols::nmr::pcs::PCSLigandTransformMover::set_scorefunction(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_trans_step(self: pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover, step: float) None

C++: protocols::nmr::pcs::PCSLigandTransformMover::set_trans_step(double) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

  2. show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None
: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)

Overloaded function.

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

undo_optimized_transform(self: pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMover) None

C++: protocols::nmr::pcs::PCSLigandTransformMover::undo_optimized_transform() –> void

class pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMoverCreator, : pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMoverCreator) pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMoverCreator

C++: protocols::nmr::pcs::PCSLigandTransformMoverCreator::operator=(const class protocols::nmr::pcs::PCSLigandTransformMoverCreator &) –> class protocols::nmr::pcs::PCSLigandTransformMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::nmr::pcs::PCSLigandTransformMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMoverCreator) str

C++: protocols::nmr::pcs::PCSLigandTransformMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.nmr.pcs.PCSLigandTransformMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::nmr::pcs::PCSLigandTransformMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.nmr.pcs.PCSTensorOptimizer

Bases: pyrosetta.rosetta.core.optimization.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

assign(self: pyrosetta.rosetta.protocols.nmr.pcs.PCSTensorOptimizer, : pyrosetta.rosetta.protocols.nmr.pcs.PCSTensorOptimizer) pyrosetta.rosetta.protocols.nmr.pcs.PCSTensorOptimizer

C++: protocols::nmr::pcs::PCSTensorOptimizer::operator=(const class protocols::nmr::pcs::PCSTensorOptimizer &) –> class protocols::nmr::pcs::PCSTensorOptimizer &

dfunc(self: pyrosetta.rosetta.protocols.nmr.pcs.PCSTensorOptimizer, tensor_params: pyrosetta.rosetta.utility.vector1_double, dPCS_dparams: pyrosetta.rosetta.utility.vector1_double) None

gradient function used in optimization of the PCS tensor parameter

C++: protocols::nmr::pcs::PCSTensorOptimizer::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.nmr.pcs.pcs_lmmin(par: float, : int, data: capsule, fvec: float, : int) None

C++: protocols::nmr::pcs::pcs_lmmin(const double *, int, const void *, double *, int *) –> void