toolbox¶

Bindings for protocols::toolbox namespace

pyrosetta.rosetta.protocols.toolbox.AdjacentRemainingNodes(node: protocols::toolbox::Node) → pyrosetta.rosetta.std.list_std_shared_ptr_protocols_toolbox_Node_t¶: C++: protocols::toolbox::AdjacentRemainingNodes(class std::shared_ptr<struct protocols::toolbox::Node>) –> class std::list<class std::shared_ptr<struct protocols::toolbox::Node>, class std::allocator<class std::shared_ptr<struct protocols::toolbox::Node> > >

pyrosetta.rosetta.protocols.toolbox.CA_superimpose(*args, **kwargs)¶

Overloaded function.

CA_superimpose(weights: pyrosetta.rosetta.ObjexxFCL.FArray1_double_t, ref_pose: pyrosetta.rosetta.core.pose.Pose, fit_pose: pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::toolbox::CA_superimpose(const class ObjexxFCL::FArray1<double> &, const class core::pose::Pose &, class core::pose::Pose &) –> void

CA_superimpose(ref_pose: pyrosetta.rosetta.core.pose.Pose, fit_pose: pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::toolbox::CA_superimpose(const class core::pose::Pose &, class core::pose::Pose &) –> void

class pyrosetta.rosetta.protocols.toolbox.CalcInterNeighborGroup¶

Bases: pybind11_object

This is complicated, so pay attention. You define groups of residues within a protein (say, the N and C terminal domains). You then define which pairs of groups you are interested in. This calculator returns the union of the sets of residues at the interfaces between these domains/groups. Functionally it is intended for “interface design” at the non-chainbreak interface between domains of multidomain proteins. It contains a superset of the functionality of some of the other calculators (so I’ll be obsoleting them, maybe?). The pose does NOT have to have been scored.

“groups” string returns the input groups; of type utility::vector1< std::pair< std::set< core::Size >, std::set< core::Size > > > (not a calculated value)

“dist_cutoff” returns the input cutoff distance for neighbor finding (not a calculated value)

“neighbors” returns a std::set<core::Size> of the neighbors calculated between the group pairs.

“num_neighbors” returns the size of the neighbors set.

assign(self: pyrosetta.rosetta.protocols.toolbox.CalcInterNeighborGroup, : pyrosetta.rosetta.protocols.toolbox.CalcInterNeighborGroup) → pyrosetta.rosetta.protocols.toolbox.CalcInterNeighborGroup¶: C++: protocols::toolbox::CalcInterNeighborGroup::operator=(const class protocols::toolbox::CalcInterNeighborGroup &) –> class protocols::toolbox::CalcInterNeighborGroup &

compute(self: pyrosetta.rosetta.protocols.toolbox.CalcInterNeighborGroup, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::toolbox::CalcInterNeighborGroup::compute(const class core::pose::Pose &) –> void

dist_cutoff(*args, **kwargs)¶

Overloaded function.

dist_cutoff(self: pyrosetta.rosetta.protocols.toolbox.CalcInterNeighborGroup, cutoff: float) -> None

C++: protocols::toolbox::CalcInterNeighborGroup::dist_cutoff(double) –> void

dist_cutoff(self: pyrosetta.rosetta.protocols.toolbox.CalcInterNeighborGroup) -> float

return distance cutoff

C++: protocols::toolbox::CalcInterNeighborGroup::dist_cutoff() const –> double

groups(*args, **kwargs)¶

Overloaded function.

groups(self: pyrosetta.rosetta.protocols.toolbox.CalcInterNeighborGroup) -> pyrosetta.rosetta.utility.vector1_std_pair_std_set_unsigned_long_std_set_unsigned_long_t

C++: protocols::toolbox::CalcInterNeighborGroup::groups() const –> const class utility::vector1<struct std::pair<class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> >, class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > >, class std::allocator<struct std::pair<class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> >, class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > > > > &

groups(self: pyrosetta.rosetta.protocols.toolbox.CalcInterNeighborGroup, groups: pyrosetta.rosetta.utility.vector1_std_pair_std_set_unsigned_long_std_set_unsigned_long_t) -> None

C++: protocols::toolbox::CalcInterNeighborGroup::groups(class utility::vector1<struct std::pair<class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> >, class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > >, class std::allocator<struct std::pair<class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> >, class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > > > >) –> void

neighbors(self: pyrosetta.rosetta.protocols.toolbox.CalcInterNeighborGroup) → pyrosetta.rosetta.std.set_unsigned_long_t¶: C++: protocols::toolbox::CalcInterNeighborGroup::neighbors() –> class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> >

num_neighbors(self: pyrosetta.rosetta.protocols.toolbox.CalcInterNeighborGroup) → float¶: C++: protocols::toolbox::CalcInterNeighborGroup::num_neighbors() –> double

class pyrosetta.rosetta.protocols.toolbox.ClusterBase¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.toolbox.ClusterBase, : pyrosetta.rosetta.protocols.toolbox.ClusterBase) → pyrosetta.rosetta.protocols.toolbox.ClusterBase¶: C++: protocols::toolbox::ClusterBase::operator=(const class protocols::toolbox::ClusterBase &) –> class protocols::toolbox::ClusterBase &

dim(self: pyrosetta.rosetta.protocols.toolbox.ClusterBase) → int¶: C++: protocols::toolbox::ClusterBase::dim() const –> unsigned long

dist(self: pyrosetta.rosetta.protocols.toolbox.ClusterBase, i: int, j: int) → float¶: C++: protocols::toolbox::ClusterBase::dist(unsigned long, unsigned long) –> double &

distance_matrix(self: pyrosetta.rosetta.protocols.toolbox.ClusterBase) → pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t¶: C++: protocols::toolbox::ClusterBase::distance_matrix() –> class ObjexxFCL::FArray2D<double> &

limit_groupsize(self: pyrosetta.rosetta.protocols.toolbox.ClusterBase, limit: int) → None¶: C++: protocols::toolbox::ClusterBase::limit_groupsize(unsigned long) –> void

print_cluster_assignment(self: pyrosetta.rosetta.protocols.toolbox.ClusterBase, out: pyrosetta.rosetta.std.ostream) → None¶: C++: protocols::toolbox::ClusterBase::print_cluster_assignment(std::ostream &) const –> void

print_summary(self: pyrosetta.rosetta.protocols.toolbox.ClusterBase, tags: pyrosetta.rosetta.utility.vector1_std_string, all_energies: pyrosetta.rosetta.utility.vector1_double) → None¶: C++: protocols::toolbox::ClusterBase::print_summary(class utility::vector1<std::string, class std::allocator<std::string > >, class utility::vector1<double, class std::allocator<double> >) –> void

read(self: pyrosetta.rosetta.protocols.toolbox.ClusterBase, in: pyrosetta.rosetta.std.istream) → None¶: C++: protocols::toolbox::ClusterBase::read(std::istream &) –> void

show(self: pyrosetta.rosetta.protocols.toolbox.ClusterBase, out: pyrosetta.rosetta.std.ostream) → None¶: C++: protocols::toolbox::ClusterBase::show(std::ostream &) const –> void

size(self: pyrosetta.rosetta.protocols.toolbox.ClusterBase) → int¶: C++: protocols::toolbox::ClusterBase::size() const –> unsigned long

sort_each_group_by_energy(*args, **kwargs)¶

Overloaded function.

sort_each_group_by_energy(self: pyrosetta.rosetta.protocols.toolbox.ClusterBase, all_energies: pyrosetta.rosetta.utility.vector1_double) -> None
sort_each_group_by_energy(self: pyrosetta.rosetta.protocols.toolbox.ClusterBase, all_energies: pyrosetta.rosetta.utility.vector1_double, keep_center: bool) -> None

C++: protocols::toolbox::ClusterBase::sort_each_group_by_energy(class utility::vector1<double, class std::allocator<double> >, bool) –> void

class pyrosetta.rosetta.protocols.toolbox.ClusterOptions¶

Bases: pybind11_object

property assign_new_cluster_tag¶

property cluster_radius¶

property keep_center¶

property limit_cluster_size¶

class pyrosetta.rosetta.protocols.toolbox.ClusterPhilStyle¶

Bases: ClusterBase

assign(self: pyrosetta.rosetta.protocols.toolbox.ClusterPhilStyle, : pyrosetta.rosetta.protocols.toolbox.ClusterPhilStyle) → pyrosetta.rosetta.protocols.toolbox.ClusterPhilStyle¶: C++: protocols::toolbox::ClusterPhilStyle::operator=(const class protocols::toolbox::ClusterPhilStyle &) –> class protocols::toolbox::ClusterPhilStyle &

compute(self: pyrosetta.rosetta.protocols.toolbox.ClusterPhilStyle) → None¶: C++: protocols::toolbox::ClusterPhilStyle::compute() –> void

dim(self: pyrosetta.rosetta.protocols.toolbox.ClusterBase) → int¶: C++: protocols::toolbox::ClusterBase::dim() const –> unsigned long

dist(self: pyrosetta.rosetta.protocols.toolbox.ClusterBase, i: int, j: int) → float¶: C++: protocols::toolbox::ClusterBase::dist(unsigned long, unsigned long) –> double &

distance_matrix(self: pyrosetta.rosetta.protocols.toolbox.ClusterBase) → pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t¶: C++: protocols::toolbox::ClusterBase::distance_matrix() –> class ObjexxFCL::FArray2D<double> &

do_clustering(self: pyrosetta.rosetta.protocols.toolbox.ClusterPhilStyle) → None¶: C++: protocols::toolbox::ClusterPhilStyle::do_clustering() –> void

limit_groupsize(self: pyrosetta.rosetta.protocols.toolbox.ClusterBase, limit: int) → None¶: C++: protocols::toolbox::ClusterBase::limit_groupsize(unsigned long) –> void

print_cluster_assignment(self: pyrosetta.rosetta.protocols.toolbox.ClusterBase, out: pyrosetta.rosetta.std.ostream) → None¶: C++: protocols::toolbox::ClusterBase::print_cluster_assignment(std::ostream &) const –> void

print_summary(self: pyrosetta.rosetta.protocols.toolbox.ClusterBase, tags: pyrosetta.rosetta.utility.vector1_std_string, all_energies: pyrosetta.rosetta.utility.vector1_double) → None¶: C++: protocols::toolbox::ClusterBase::print_summary(class utility::vector1<std::string, class std::allocator<std::string > >, class utility::vector1<double, class std::allocator<double> >) –> void

read(self: pyrosetta.rosetta.protocols.toolbox.ClusterBase, in: pyrosetta.rosetta.std.istream) → None¶: C++: protocols::toolbox::ClusterBase::read(std::istream &) –> void

set_n_max_cluster(self: pyrosetta.rosetta.protocols.toolbox.ClusterPhilStyle, setting: int) → None¶: C++: protocols::toolbox::ClusterPhilStyle::set_n_max_cluster(unsigned long) –> void

set_radius(self: pyrosetta.rosetta.protocols.toolbox.ClusterPhilStyle, setting: float) → None¶: C++: protocols::toolbox::ClusterPhilStyle::set_radius(double) –> void

show(self: pyrosetta.rosetta.protocols.toolbox.ClusterBase, out: pyrosetta.rosetta.std.ostream) → None¶: C++: protocols::toolbox::ClusterBase::show(std::ostream &) const –> void

size(self: pyrosetta.rosetta.protocols.toolbox.ClusterBase) → int¶: C++: protocols::toolbox::ClusterBase::size() const –> unsigned long

sort_each_group_by_energy(*args, **kwargs)¶

Overloaded function.

sort_each_group_by_energy(self: pyrosetta.rosetta.protocols.toolbox.ClusterBase, all_energies: pyrosetta.rosetta.utility.vector1_double) -> None
sort_each_group_by_energy(self: pyrosetta.rosetta.protocols.toolbox.ClusterBase, all_energies: pyrosetta.rosetta.utility.vector1_double, keep_center: bool) -> None

C++: protocols::toolbox::ClusterBase::sort_each_group_by_energy(class utility::vector1<double, class std::allocator<double> >, bool) –> void

pyrosetta.rosetta.protocols.toolbox.Contains(nodes: pyrosetta.rosetta.std.list_std_shared_ptr_protocols_toolbox_Node_t, node: protocols::toolbox::Node) → bool¶: C++: protocols::toolbox::Contains(const class std::list<class std::shared_ptr<struct protocols::toolbox::Node>, class std::allocator<class std::shared_ptr<struct protocols::toolbox::Node> > > &, class std::shared_ptr<const struct protocols::toolbox::Node>) –> bool

class pyrosetta.rosetta.protocols.toolbox.CovalentResidueNetwork¶

Bases: ResidueNetwork

Creates networks based on covalent connections between residues

assign(self: pyrosetta.rosetta.protocols.toolbox.CovalentResidueNetwork, : pyrosetta.rosetta.protocols.toolbox.CovalentResidueNetwork) → pyrosetta.rosetta.protocols.toolbox.CovalentResidueNetwork¶: C++: protocols::toolbox::CovalentResidueNetwork::operator=(const class protocols::toolbox::CovalentResidueNetwork &) –> class protocols::toolbox::CovalentResidueNetwork &

average_shortest_path_length(self: pyrosetta.rosetta.protocols.toolbox.ResidueNetwork) → float¶

calculates the average shortest path length of the network

C++: protocols::toolbox::ResidueNetwork::average_shortest_path_length() const –> double

clear_edges(self: pyrosetta.rosetta.protocols.toolbox.ResidueNetwork) → None¶

empties edges

C++: protocols::toolbox::ResidueNetwork::clear_edges() –> void

connectivity_index(self: pyrosetta.rosetta.protocols.toolbox.ResidueNetwork, resi: int) → float¶

calculates the connectivity index of residue resi in the context of the network

C++: protocols::toolbox::ResidueNetwork::connectivity_index(const unsigned long) const –> double

create_from_pose(self: pyrosetta.rosetta.protocols.toolbox.ResidueNetwork, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

create a network from a pose

C++: protocols::toolbox::ResidueNetwork::create_from_pose(const class core::pose::Pose &) –> void

dijkstras(self: pyrosetta.rosetta.protocols.toolbox.ResidueNetwork, resi: int) → None¶

run Dijkstra’s shortest path algorithm on the given list of nodes: after execution, the “distanceFromStart” variable of each node will contain the distance from residue resi

C++: protocols::toolbox::ResidueNetwork::dijkstras(const unsigned long) const –> void

generate_edges(self: pyrosetta.rosetta.protocols.toolbox.CovalentResidueNetwork, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::toolbox::CovalentResidueNetwork::generate_edges(const class core::pose::Pose &) –> void

nodes(self: pyrosetta.rosetta.protocols.toolbox.ResidueNetwork) → pyrosetta.rosetta.std.list_std_shared_ptr_protocols_toolbox_Node_t¶: C++: protocols::toolbox::ResidueNetwork::nodes() const –> const class std::list<class std::shared_ptr<struct protocols::toolbox::Node>, class std::allocator<class std::shared_ptr<struct protocols::toolbox::Node> > > &

class pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation¶

Bases: pybind11_object

all_energies(self: pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation) → pyrosetta.rosetta.utility.vector1_double¶: C++: protocols::toolbox::DecoySetEvaluation::all_energies() const –> const class utility::vector1<double, class std::allocator<double> > &

assign(self: pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation, : pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation) → pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation¶: C++: protocols::toolbox::DecoySetEvaluation::operator=(const class protocols::toolbox::DecoySetEvaluation &) –> class protocols::toolbox::DecoySetEvaluation &

center_all(self: pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation, weights: pyrosetta.rosetta.ObjexxFCL.FArray1_double_t) → None¶: C++: protocols::toolbox::DecoySetEvaluation::center_all(const class ObjexxFCL::FArray1<double> &) –> void

center_structure(*args, **kwargs)¶

Overloaded function.

center_structure(self: pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation, i: int) -> None

C++: protocols::toolbox::DecoySetEvaluation::center_structure(unsigned long) –> void

center_structure(self: pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation, i: int, weights: pyrosetta.rosetta.ObjexxFCL.FArray1_double_t) -> None

C++: protocols::toolbox::DecoySetEvaluation::center_structure(unsigned long, const class ObjexxFCL::FArray1<double> &) –> void

clear(self: pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation) → None¶: C++: protocols::toolbox::DecoySetEvaluation::clear() –> void

compute_average_structure(self: pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation, average_structure: pyrosetta.rosetta.ObjexxFCL.FArray2_double_t) → None¶: C++: protocols::toolbox::DecoySetEvaluation::compute_average_structure(class ObjexxFCL::FArray2<double> &) const –> void

compute_distance_matrix(self: pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation, : pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t) → None¶: C++: protocols::toolbox::DecoySetEvaluation::compute_distance_matrix(class ObjexxFCL::FArray2D<double> &) const –> void

coords(*args, **kwargs)¶

Overloaded function.

coords(self: pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation) -> pyrosetta.rosetta.ObjexxFCL.FArray3D_double_t

C++: protocols::toolbox::DecoySetEvaluation::coords() const –> const class ObjexxFCL::FArray3D<double> &

coords(self: pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation, i: int) -> pyrosetta.rosetta.ObjexxFCL.FArray2P_double_t

C++: protocols::toolbox::DecoySetEvaluation::coords(unsigned long) const –> class ObjexxFCL::FArray2P<double>

create_dist_constraints(self: pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation, cst_set: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) → None¶: C++: protocols::toolbox::DecoySetEvaluation::create_dist_constraints(class core::scoring::constraints::ConstraintSet &) const –> void

create_dist_constraints_median(self: pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation, cst_set: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) → None¶: C++: protocols::toolbox::DecoySetEvaluation::create_dist_constraints_median(class core::scoring::constraints::ConstraintSet &) const –> void

create_xyz_constraints_median(self: pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation, cst_set: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, ref_pose: pyrosetta.rosetta.core.pose.Pose, root: int) → None¶: C++: protocols::toolbox::DecoySetEvaluation::create_xyz_constraints_median(class core::scoring::constraints::ConstraintSet &, const class core::pose::Pose &, unsigned long) const –> void

find_closest_to_average(self: pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation, average_structure: pyrosetta.rosetta.ObjexxFCL.FArray2_double_t) → int¶: C++: protocols::toolbox::DecoySetEvaluation::find_closest_to_average(class ObjexxFCL::FArray2<double> &) const –> unsigned long

n_atoms(self: pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation) → int¶: C++: protocols::toolbox::DecoySetEvaluation::n_atoms() const –> unsigned long

n_decoys(self: pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation) → int¶: C++: protocols::toolbox::DecoySetEvaluation::n_decoys() const –> unsigned long

n_decoys_max(self: pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation) → int¶: C++: protocols::toolbox::DecoySetEvaluation::n_decoys_max() const –> unsigned long

pop_back_CA_xyz(self: pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation) → None¶: C++: protocols::toolbox::DecoySetEvaluation::pop_back_CA_xyz() –> void

push_back(self: pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::toolbox::DecoySetEvaluation::push_back(class core::pose::Pose &) –> void

push_back_CA_xyz(self: pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation, : pyrosetta.rosetta.ObjexxFCL.FArray2_double_t, nres: int) → None¶: C++: protocols::toolbox::DecoySetEvaluation::push_back_CA_xyz(const class ObjexxFCL::FArray2<double> &, unsigned long) –> void

push_back_CA_xyz_from_silent_file(self: pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation, sfd: pyrosetta.rosetta.core.io.silent.SilentFileData, store_energies: bool) → None¶: C++: protocols::toolbox::DecoySetEvaluation::push_back_CA_xyz_from_silent_file(const class core::io::silent::SilentFileData &, bool) –> void

ref_pose(self: pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation) → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::toolbox::DecoySetEvaluation::ref_pose() –> const class core::pose::Pose &

static register_options() → None¶: C++: protocols::toolbox::DecoySetEvaluation::register_options() –> void

reserve(self: pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation, n_decoys_: int) → None¶: C++: protocols::toolbox::DecoySetEvaluation::reserve(unsigned long) –> void

rmsd(self: pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation, weights: pyrosetta.rosetta.ObjexxFCL.FArray1_double_t, xx_ref: pyrosetta.rosetta.ObjexxFCL.FArray2_double_t, xx: pyrosetta.rosetta.ObjexxFCL.FArray2_double_t) → float¶: C++: protocols::toolbox::DecoySetEvaluation::rmsd(const class ObjexxFCL::FArray1<double> &, class ObjexxFCL::FArray2<double> &, class ObjexxFCL::FArray2<double> &) const –> double

rmsf(*args, **kwargs)¶

Overloaded function.

rmsf(self: pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation, results: pyrosetta.rosetta.utility.vector1_double) -> None

C++: protocols::toolbox::DecoySetEvaluation::rmsf(class utility::vector1<double, class std::allocator<double> > &) –> void

rmsf(self: pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation, result: pyrosetta.rosetta.ObjexxFCL.FArray1_double_t) -> None

C++: protocols::toolbox::DecoySetEvaluation::rmsf(class ObjexxFCL::FArray1<double> &) –> void

set_all_energies(self: pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation, all_energies: pyrosetta.rosetta.utility.vector1_double) → None¶: C++: protocols::toolbox::DecoySetEvaluation::set_all_energies(const class utility::vector1<double, class std::allocator<double> > &) –> void

set_n_atom(self: pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation, natoms: int) → None¶: C++: protocols::toolbox::DecoySetEvaluation::set_n_atom(unsigned long) –> void

set_weights(self: pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation, weights: pyrosetta.rosetta.ObjexxFCL.FArray1_double_t) → None¶: C++: protocols::toolbox::DecoySetEvaluation::set_weights(const class ObjexxFCL::FArray1<double> &) –> void

superimpose(*args, **kwargs)¶

Overloaded function.

superimpose(self: pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation) -> None
superimpose(self: pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation, icenter: int) -> None

C++: protocols::toolbox::DecoySetEvaluation::superimpose(unsigned long) –> void

wRMSD(self: pyrosetta.rosetta.protocols.toolbox.DecoySetEvaluation, sigma2: float, tolerance: float, weights: pyrosetta.rosetta.ObjexxFCL.FArray1_double_t) → int¶: C++: protocols::toolbox::DecoySetEvaluation::wRMSD(double, double, class ObjexxFCL::FArray1<double> &) –> unsigned long

class pyrosetta.rosetta.protocols.toolbox.DistanceResidueNetwork¶

Bases: ResidueNetwork

Creates networks based on residue proximity in space

assign(self: pyrosetta.rosetta.protocols.toolbox.DistanceResidueNetwork, : pyrosetta.rosetta.protocols.toolbox.DistanceResidueNetwork) → pyrosetta.rosetta.protocols.toolbox.DistanceResidueNetwork¶: C++: protocols::toolbox::DistanceResidueNetwork::operator=(const class protocols::toolbox::DistanceResidueNetwork &) –> class protocols::toolbox::DistanceResidueNetwork &

average_shortest_path_length(self: pyrosetta.rosetta.protocols.toolbox.ResidueNetwork) → float¶

calculates the average shortest path length of the network

C++: protocols::toolbox::ResidueNetwork::average_shortest_path_length() const –> double

clear_edges(self: pyrosetta.rosetta.protocols.toolbox.ResidueNetwork) → None¶

empties edges

C++: protocols::toolbox::ResidueNetwork::clear_edges() –> void

connectivity_index(self: pyrosetta.rosetta.protocols.toolbox.ResidueNetwork, resi: int) → float¶

calculates the connectivity index of residue resi in the context of the network

C++: protocols::toolbox::ResidueNetwork::connectivity_index(const unsigned long) const –> double

create_from_pose(self: pyrosetta.rosetta.protocols.toolbox.ResidueNetwork, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

create a network from a pose

C++: protocols::toolbox::ResidueNetwork::create_from_pose(const class core::pose::Pose &) –> void

dijkstras(self: pyrosetta.rosetta.protocols.toolbox.ResidueNetwork, resi: int) → None¶

run Dijkstra’s shortest path algorithm on the given list of nodes: after execution, the “distanceFromStart” variable of each node will contain the distance from residue resi

C++: protocols::toolbox::ResidueNetwork::dijkstras(const unsigned long) const –> void

generate_edges(self: pyrosetta.rosetta.protocols.toolbox.DistanceResidueNetwork, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::toolbox::DistanceResidueNetwork::generate_edges(const class core::pose::Pose &) –> void

nodes(self: pyrosetta.rosetta.protocols.toolbox.ResidueNetwork) → pyrosetta.rosetta.std.list_std_shared_ptr_protocols_toolbox_Node_t¶: C++: protocols::toolbox::ResidueNetwork::nodes() const –> const class std::list<class std::shared_ptr<struct protocols::toolbox::Node>, class std::allocator<class std::shared_ptr<struct protocols::toolbox::Node> > > &

class pyrosetta.rosetta.protocols.toolbox.DummyClass¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.toolbox.DummyClass, : pyrosetta.rosetta.protocols.toolbox.DummyClass) → pyrosetta.rosetta.protocols.toolbox.DummyClass¶: C++: protocols::toolbox::DummyClass::operator=(const class protocols::toolbox::DummyClass &) –> class protocols::toolbox::DummyClass &

clone(self: pyrosetta.rosetta.protocols.toolbox.DummyClass) → pyrosetta.rosetta.protocols.toolbox.DummyClass¶: C++: protocols::toolbox::DummyClass::clone() const –> class std::shared_ptr<class protocols::toolbox::DummyClass>

static create() → pyrosetta.rosetta.protocols.toolbox.DummyClass¶: C++: protocols::toolbox::DummyClass::create() –> class protocols::toolbox::DummyClass *

test(self: pyrosetta.rosetta.protocols.toolbox.DummyClass) → None¶: C++: protocols::toolbox::DummyClass::test() –> void

class pyrosetta.rosetta.protocols.toolbox.EnergyLandscapeEvaluator¶

Bases: pybind11_object

Evaluates a set of score/rms points

assign(self: pyrosetta.rosetta.protocols.toolbox.EnergyLandscapeEvaluator, : pyrosetta.rosetta.protocols.toolbox.EnergyLandscapeEvaluator) → pyrosetta.rosetta.protocols.toolbox.EnergyLandscapeEvaluator¶: C++: protocols::toolbox::EnergyLandscapeEvaluator::operator=(const class protocols::toolbox::EnergyLandscapeEvaluator &) –> class protocols::toolbox::EnergyLandscapeEvaluator &

clone(self: pyrosetta.rosetta.protocols.toolbox.EnergyLandscapeEvaluator) → pyrosetta.rosetta.protocols.toolbox.EnergyLandscapeEvaluator¶: C++: protocols::toolbox::EnergyLandscapeEvaluator::clone() const –> class std::shared_ptr<class protocols::toolbox::EnergyLandscapeEvaluator>

compute(self: pyrosetta.rosetta.protocols.toolbox.EnergyLandscapeEvaluator, points: pyrosetta.rosetta.protocols.toolbox.ScoreRmsPoints) → float¶: C++: protocols::toolbox::EnergyLandscapeEvaluator::compute(const class protocols::toolbox::ScoreRmsPoints &) const –> double

pyrosetta.rosetta.protocols.toolbox.ExtractSmallest(nodes: pyrosetta.rosetta.std.list_std_shared_ptr_protocols_toolbox_Node_t) → protocols::toolbox::Node¶: C++: protocols::toolbox::ExtractSmallest(class std::list<class std::shared_ptr<struct protocols::toolbox::Node>, class std::allocator<class std::shared_ptr<struct protocols::toolbox::Node> > > &) –> class std::shared_ptr<struct protocols::toolbox::Node>

class pyrosetta.rosetta.protocols.toolbox.GreedyKCenter¶

Bases: KCluster

Greedy K-Center Clustering Algorithm

“A Fast Geometric Clustering Method on Conformation Space of Biomolecules” Jian Sun, Yuan Yao, Xuhui Huang, Vijay Pande, Gunnar Carlsson, Leonidas J. Guibas

assign(*args, **kwargs)¶

Overloaded function.

assign(self: pyrosetta.rosetta.protocols.toolbox.GreedyKCenter, : pyrosetta.rosetta.protocols.toolbox.KClusterElement, : pyrosetta.rosetta.protocols.toolbox.KClusterData) -> float

C++: protocols::toolbox::GreedyKCenter::assign(class std::shared_ptr<class protocols::toolbox::KClusterElement>, class protocols::toolbox::KClusterData &) –> double

assign(self: pyrosetta.rosetta.protocols.toolbox.GreedyKCenter, : pyrosetta.rosetta.protocols.toolbox.GreedyKCenter) -> pyrosetta.rosetta.protocols.toolbox.GreedyKCenter

C++: protocols::toolbox::GreedyKCenter::operator=(const class protocols::toolbox::GreedyKCenter &) –> class protocols::toolbox::GreedyKCenter &

cluster(*args, **kwargs)¶

Overloaded function.

cluster(self: pyrosetta.rosetta.protocols.toolbox.KCluster, : pyrosetta.rosetta.protocols.toolbox.KClusterElement, : pyrosetta.rosetta.protocols.toolbox.KClusterData) -> None
cluster(self: pyrosetta.rosetta.protocols.toolbox.KCluster, : pyrosetta.rosetta.protocols.toolbox.KClusterElement, : pyrosetta.rosetta.protocols.toolbox.KClusterData, first: int) -> None

C++: protocols::toolbox::KCluster::cluster(class std::shared_ptr<class protocols::toolbox::KClusterElement>, class protocols::toolbox::KClusterData &, unsigned long) –> void

get_threshold(self: pyrosetta.rosetta.protocols.toolbox.GreedyKCenter) → float¶: C++: protocols::toolbox::GreedyKCenter::get_threshold() –> double

init(*args, **kwargs)¶

Overloaded function.

init(self: pyrosetta.rosetta.protocols.toolbox.GreedyKCenter, : pyrosetta.rosetta.protocols.toolbox.KClusterElement) -> None
init(self: pyrosetta.rosetta.protocols.toolbox.GreedyKCenter, : pyrosetta.rosetta.protocols.toolbox.KClusterElement, first: int) -> None

C++: protocols::toolbox::GreedyKCenter::init(class std::shared_ptr<class protocols::toolbox::KClusterElement>, unsigned long) –> void

set_ncluster(self: pyrosetta.rosetta.protocols.toolbox.KCluster, nc: int) → None¶: C++: protocols::toolbox::KCluster::set_ncluster(unsigned long) –> void

set_threshold(self: pyrosetta.rosetta.protocols.toolbox.GreedyKCenter, : float) → None¶: C++: protocols::toolbox::GreedyKCenter::set_threshold(double) –> void

update(self: pyrosetta.rosetta.protocols.toolbox.GreedyKCenter, : pyrosetta.rosetta.protocols.toolbox.KClusterElement, : pyrosetta.rosetta.protocols.toolbox.KClusterData) → None¶: C++: protocols::toolbox::GreedyKCenter::update(class std::shared_ptr<class protocols::toolbox::KClusterElement>, class protocols::toolbox::KClusterData &) –> void

whoami(self: pyrosetta.rosetta.protocols.toolbox.GreedyKCenter) → bool¶: C++: protocols::toolbox::GreedyKCenter::whoami() –> bool

class pyrosetta.rosetta.protocols.toolbox.IGInterfaceEdgeUpweighter¶

Bases: IGEdgeReweighter

get_edge_reweight(self: pyrosetta.rosetta.protocols.toolbox.IGInterfaceEdgeUpweighter, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask, res1: int, res2: int) → float¶: C++: protocols::toolbox::IGInterfaceEdgeUpweighter::get_edge_reweight(const class core::pose::Pose &, const class core::pack::task::PackerTask &, unsigned long, unsigned long) const –> double

set_sec_str(self: pyrosetta.rosetta.protocols.toolbox.IGInterfaceEdgeUpweighter, sec_str_in: str) → None¶: C++: protocols::toolbox::IGInterfaceEdgeUpweighter::set_sec_str(const std::string &) –> void

set_skip_loop_chains(self: pyrosetta.rosetta.protocols.toolbox.IGInterfaceEdgeUpweighter, chain_string: str) → None¶: C++: protocols::toolbox::IGInterfaceEdgeUpweighter::set_skip_loop_chains(const std::string &) –> void

class pyrosetta.rosetta.protocols.toolbox.IGLigandDesignEdgeUpweighter¶

Bases: IGEdgeReweighter

get_edge_reweight(self: pyrosetta.rosetta.protocols.toolbox.IGLigandDesignEdgeUpweighter, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask, res1: int, res2: int) → float¶: C++: protocols::toolbox::IGLigandDesignEdgeUpweighter::get_edge_reweight(const class core::pose::Pose &, const class core::pack::task::PackerTask &, unsigned long, unsigned long) const –> double

class pyrosetta.rosetta.protocols.toolbox.InteratomicVarianceMatrix¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.toolbox.InteratomicVarianceMatrix, : pyrosetta.rosetta.protocols.toolbox.InteratomicVarianceMatrix) → pyrosetta.rosetta.protocols.toolbox.InteratomicVarianceMatrix¶: C++: protocols::toolbox::InteratomicVarianceMatrix::operator=(const class protocols::toolbox::InteratomicVarianceMatrix &) –> class protocols::toolbox::InteratomicVarianceMatrix &

init(self: pyrosetta.rosetta.protocols.toolbox.InteratomicVarianceMatrix, n_atoms: int, n_decoys: int, coords: pyrosetta.rosetta.ObjexxFCL.FArray3_double_t) → None¶: C++: protocols::toolbox::InteratomicVarianceMatrix::init(unsigned long, unsigned long, const class ObjexxFCL::FArray3<double> &) –> void

ivm(self: pyrosetta.rosetta.protocols.toolbox.InteratomicVarianceMatrix) → pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t¶: C++: protocols::toolbox::InteratomicVarianceMatrix::ivm() –> class ObjexxFCL::FArray2D<double> &

kurtosis(self: pyrosetta.rosetta.protocols.toolbox.InteratomicVarianceMatrix, T: pyrosetta.rosetta.ObjexxFCL.FArray1_double_t) → float¶: C++: protocols::toolbox::InteratomicVarianceMatrix::kurtosis(class ObjexxFCL::FArray1<double> &) –> double

n_atoms(self: pyrosetta.rosetta.protocols.toolbox.InteratomicVarianceMatrix) → int¶: C++: protocols::toolbox::InteratomicVarianceMatrix::n_atoms() const –> unsigned long

optimize_kurtosis(self: pyrosetta.rosetta.protocols.toolbox.InteratomicVarianceMatrix, ngrid: int, lb: float, ub: float) → None¶: C++: protocols::toolbox::InteratomicVarianceMatrix::optimize_kurtosis(unsigned long, double, double) –> void

order_parameter(self: pyrosetta.rosetta.protocols.toolbox.InteratomicVarianceMatrix, epsilon: float, T: pyrosetta.rosetta.ObjexxFCL.FArray1_double_t) → None¶: C++: protocols::toolbox::InteratomicVarianceMatrix::order_parameter(double, class ObjexxFCL::FArray1<double> &) –> void

class pyrosetta.rosetta.protocols.toolbox.KCluster¶

Bases: pybind11_object

basic class for performing a K-style Clustering algorithm

assign(*args, **kwargs)¶

Overloaded function.

assign(self: pyrosetta.rosetta.protocols.toolbox.KCluster, : pyrosetta.rosetta.protocols.toolbox.KClusterElement, : pyrosetta.rosetta.protocols.toolbox.KClusterData) -> float

C++: protocols::toolbox::KCluster::assign(class std::shared_ptr<class protocols::toolbox::KClusterElement>, class protocols::toolbox::KClusterData &) –> double

assign(self: pyrosetta.rosetta.protocols.toolbox.KCluster, : pyrosetta.rosetta.protocols.toolbox.KCluster) -> pyrosetta.rosetta.protocols.toolbox.KCluster

C++: protocols::toolbox::KCluster::operator=(const class protocols::toolbox::KCluster &) –> class protocols::toolbox::KCluster &

cluster(*args, **kwargs)¶

Overloaded function.

cluster(self: pyrosetta.rosetta.protocols.toolbox.KCluster, : pyrosetta.rosetta.protocols.toolbox.KClusterElement, : pyrosetta.rosetta.protocols.toolbox.KClusterData) -> None
cluster(self: pyrosetta.rosetta.protocols.toolbox.KCluster, : pyrosetta.rosetta.protocols.toolbox.KClusterElement, : pyrosetta.rosetta.protocols.toolbox.KClusterData, first: int) -> None

C++: protocols::toolbox::KCluster::cluster(class std::shared_ptr<class protocols::toolbox::KClusterElement>, class protocols::toolbox::KClusterData &, unsigned long) –> void

get_threshold(self: pyrosetta.rosetta.protocols.toolbox.KCluster) → float¶: C++: protocols::toolbox::KCluster::get_threshold() –> double

init(*args, **kwargs)¶

Overloaded function.

init(self: pyrosetta.rosetta.protocols.toolbox.KCluster, : pyrosetta.rosetta.protocols.toolbox.KClusterElement) -> None
init(self: pyrosetta.rosetta.protocols.toolbox.KCluster, : pyrosetta.rosetta.protocols.toolbox.KClusterElement, first: int) -> None

C++: protocols::toolbox::KCluster::init(class std::shared_ptr<class protocols::toolbox::KClusterElement>, unsigned long) –> void

set_ncluster(self: pyrosetta.rosetta.protocols.toolbox.KCluster, nc: int) → None¶: C++: protocols::toolbox::KCluster::set_ncluster(unsigned long) –> void

set_threshold(self: pyrosetta.rosetta.protocols.toolbox.KCluster, : float) → None¶: C++: protocols::toolbox::KCluster::set_threshold(double) –> void

update(self: pyrosetta.rosetta.protocols.toolbox.KCluster, : pyrosetta.rosetta.protocols.toolbox.KClusterElement, : pyrosetta.rosetta.protocols.toolbox.KClusterData) → None¶: C++: protocols::toolbox::KCluster::update(class std::shared_ptr<class protocols::toolbox::KClusterElement>, class protocols::toolbox::KClusterData &) –> void

whoami(self: pyrosetta.rosetta.protocols.toolbox.KCluster) → bool¶: C++: protocols::toolbox::KCluster::whoami() –> bool

class pyrosetta.rosetta.protocols.toolbox.KClusterData¶

Bases: pybind11_object

database of a K-style Clustering algorithm

assign(self: pyrosetta.rosetta.protocols.toolbox.KClusterData, : pyrosetta.rosetta.protocols.toolbox.KClusterData) → pyrosetta.rosetta.protocols.toolbox.KClusterData¶: C++: protocols::toolbox::KClusterData::operator=(const class protocols::toolbox::KClusterData &) –> class protocols::toolbox::KClusterData &

coords(self: pyrosetta.rosetta.protocols.toolbox.KClusterData) → pyrosetta.rosetta.ObjexxFCL.FArray3P_double_t¶: C++: protocols::toolbox::KClusterData::coords() –> class ObjexxFCL::FArray3P<double>

dist_square(*args, **kwargs)¶

Overloaded function.

dist_square(self: pyrosetta.rosetta.protocols.toolbox.KClusterData, : pyrosetta.rosetta.ObjexxFCL.FArray2_double_t, : pyrosetta.rosetta.ObjexxFCL.FArray2_double_t) -> float

C++: protocols::toolbox::KClusterData::dist_square(class ObjexxFCL::FArray2<double> &, class ObjexxFCL::FArray2<double> &) –> double

dist_square(self: pyrosetta.rosetta.protocols.toolbox.KClusterData, : int, : int) -> float

C++: protocols::toolbox::KClusterData::dist_square(unsigned long, unsigned long) –> double

get_natom(self: pyrosetta.rosetta.protocols.toolbox.KClusterData) → int¶: C++: protocols::toolbox::KClusterData::get_natom() const –> unsigned long

get_ndata(self: pyrosetta.rosetta.protocols.toolbox.KClusterData) → int¶: C++: protocols::toolbox::KClusterData::get_ndata() const –> unsigned long

get_tag(self: pyrosetta.rosetta.protocols.toolbox.KClusterData, i: int) → str¶: C++: protocols::toolbox::KClusterData::get_tag(unsigned long) –> std::string

load_silent_file(self: pyrosetta.rosetta.protocols.toolbox.KClusterData, : str, : int) → None¶: C++: protocols::toolbox::KClusterData::load_silent_file(std::string, unsigned long) –> void

load_silent_files(self: pyrosetta.rosetta.protocols.toolbox.KClusterData) → None¶: C++: protocols::toolbox::KClusterData::load_silent_files() –> void

mark_tags(self: pyrosetta.rosetta.protocols.toolbox.KClusterData, : pyrosetta.rosetta.protocols.toolbox.KClusterElement, : str) → None¶: C++: protocols::toolbox::KClusterData::mark_tags(class std::shared_ptr<class protocols::toolbox::KClusterElement>, std::string) –> void

save_all_in_one(self: pyrosetta.rosetta.protocols.toolbox.KClusterData) → None¶: C++: protocols::toolbox::KClusterData::save_all_in_one() –> void

save_cluster_tree(self: pyrosetta.rosetta.protocols.toolbox.KClusterData) → None¶: C++: protocols::toolbox::KClusterData::save_cluster_tree() –> void

show_cluster_assignments(self: pyrosetta.rosetta.protocols.toolbox.KClusterData) → None¶: C++: protocols::toolbox::KClusterData::show_cluster_assignments() –> void

source_filename(self: pyrosetta.rosetta.protocols.toolbox.KClusterData, i: int) → str¶: C++: protocols::toolbox::KClusterData::source_filename(unsigned long) –> std::string

class pyrosetta.rosetta.protocols.toolbox.KClusterElement¶

Bases: pybind11_object

add_new_cluster(self: pyrosetta.rosetta.protocols.toolbox.KClusterElement, ndx_data: int) → None¶

add a new cluster center’s data_ndx

C++: protocols::toolbox::KClusterElement::add_new_cluster(unsigned long) –> void

add_new_data(self: pyrosetta.rosetta.protocols.toolbox.KClusterElement, ndx_data: int) → None¶

add a new struture ndx to the data_ndx_

C++: protocols::toolbox::KClusterElement::add_new_data(unsigned long) –> void

assign(self: pyrosetta.rosetta.protocols.toolbox.KClusterElement, : pyrosetta.rosetta.protocols.toolbox.KClusterElement) → pyrosetta.rosetta.protocols.toolbox.KClusterElement¶: C++: protocols::toolbox::KClusterElement::operator=(const class protocols::toolbox::KClusterElement &) –> class protocols::toolbox::KClusterElement &

assign_type_data(self: pyrosetta.rosetta.protocols.toolbox.KClusterElement, : int, : int, : float) → None¶

assign a data into a cluster

C++: protocols::toolbox::KClusterElement::assign_type_data(unsigned long, unsigned long, double) –> void

check(self: pyrosetta.rosetta.protocols.toolbox.KClusterElement) → None¶

check the list, close edit mode

C++: protocols::toolbox::KClusterElement::check() –> void

clear(self: pyrosetta.rosetta.protocols.toolbox.KClusterElement) → None¶

clean the subcluster’s list, open edit mode

C++: protocols::toolbox::KClusterElement::clear() –> void

clear_data(self: pyrosetta.rosetta.protocols.toolbox.KClusterElement) → None¶

clean the data list

C++: protocols::toolbox::KClusterElement::clear_data() –> void

get_center_ndx(self: pyrosetta.rosetta.protocols.toolbox.KClusterElement, ndx_cluster: int) → int¶

return cluster center’s data_ndx

C++: protocols::toolbox::KClusterElement::get_center_ndx(unsigned long) const –> unsigned long

get_cur_ncluster(self: pyrosetta.rosetta.protocols.toolbox.KClusterElement) → int¶

return current cluster number

C++: protocols::toolbox::KClusterElement::get_cur_ncluster() const –> unsigned long

get_data_ndx(self: pyrosetta.rosetta.protocols.toolbox.KClusterElement, ndx_data: int) → int¶

return current data number

C++: protocols::toolbox::KClusterElement::get_data_ndx(unsigned long) const –> unsigned long

get_distance(self: pyrosetta.rosetta.protocols.toolbox.KClusterElement, ndx_data: int) → float¶

return distance between data and center

C++: protocols::toolbox::KClusterElement::get_distance(unsigned long) const –> double

get_max_dist_ndx(self: pyrosetta.rosetta.protocols.toolbox.KClusterElement) → int¶: C++: protocols::toolbox::KClusterElement::get_max_dist_ndx() const –> unsigned long

get_max_distance(self: pyrosetta.rosetta.protocols.toolbox.KClusterElement) → float¶: C++: protocols::toolbox::KClusterElement::get_max_distance() const –> double

get_ndata(self: pyrosetta.rosetta.protocols.toolbox.KClusterElement) → int¶

return current data number

C++: protocols::toolbox::KClusterElement::get_ndata() const –> unsigned long

get_ndx_list(*args, **kwargs)¶

Overloaded function.

get_ndx_list(self: pyrosetta.rosetta.protocols.toolbox.KClusterElement) -> pyrosetta.rosetta.utility.vector1_unsigned_long

return the data ndx list of this cluster

C++: protocols::toolbox::KClusterElement::get_ndx_list() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

get_ndx_list(self: pyrosetta.rosetta.protocols.toolbox.KClusterElement, c: int) -> pyrosetta.rosetta.utility.vector1_unsigned_long

return the ndx list of sub-cluster

C++: protocols::toolbox::KClusterElement::get_ndx_list(unsigned long) const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

get_subcluster(self: pyrosetta.rosetta.protocols.toolbox.KClusterElement, nc: int) → pyrosetta.rosetta.protocols.toolbox.KClusterElement¶

return the subcluster

C++: protocols::toolbox::KClusterElement::get_subcluster(unsigned long) const –> class std::shared_ptr<class protocols::toolbox::KClusterElement>

get_type(self: pyrosetta.rosetta.protocols.toolbox.KClusterElement, ndx_data: int) → int¶

return data’s type(local cluster index)

C++: protocols::toolbox::KClusterElement::get_type(unsigned long) const –> unsigned long

ncluster(self: pyrosetta.rosetta.protocols.toolbox.KClusterElement) → int¶: C++: protocols::toolbox::KClusterElement::ncluster() –> unsigned long

set_cluster(self: pyrosetta.rosetta.protocols.toolbox.KClusterElement, ndx_cluster: int, ndx_data: int) → None¶

set a cluster center’s data_ndx

C++: protocols::toolbox::KClusterElement::set_cluster(unsigned long, unsigned long) –> void

class pyrosetta.rosetta.protocols.toolbox.KMedoid¶

Bases: KCluster

Typical K-Medoids Clustering Algorithm

assign(*args, **kwargs)¶

Overloaded function.

assign(self: pyrosetta.rosetta.protocols.toolbox.KMedoid, : pyrosetta.rosetta.protocols.toolbox.KClusterElement, : pyrosetta.rosetta.protocols.toolbox.KClusterData) -> float

C++: protocols::toolbox::KMedoid::assign(class std::shared_ptr<class protocols::toolbox::KClusterElement>, class protocols::toolbox::KClusterData &) –> double

assign(self: pyrosetta.rosetta.protocols.toolbox.KMedoid, : pyrosetta.rosetta.protocols.toolbox.KMedoid) -> pyrosetta.rosetta.protocols.toolbox.KMedoid

C++: protocols::toolbox::KMedoid::operator=(const class protocols::toolbox::KMedoid &) –> class protocols::toolbox::KMedoid &

cluster(*args, **kwargs)¶

Overloaded function.

cluster(self: pyrosetta.rosetta.protocols.toolbox.KCluster, : pyrosetta.rosetta.protocols.toolbox.KClusterElement, : pyrosetta.rosetta.protocols.toolbox.KClusterData) -> None
cluster(self: pyrosetta.rosetta.protocols.toolbox.KCluster, : pyrosetta.rosetta.protocols.toolbox.KClusterElement, : pyrosetta.rosetta.protocols.toolbox.KClusterData, first: int) -> None

C++: protocols::toolbox::KCluster::cluster(class std::shared_ptr<class protocols::toolbox::KClusterElement>, class protocols::toolbox::KClusterData &, unsigned long) –> void

get_threshold(self: pyrosetta.rosetta.protocols.toolbox.KMedoid) → float¶: C++: protocols::toolbox::KMedoid::get_threshold() –> double

init(*args, **kwargs)¶

Overloaded function.

init(self: pyrosetta.rosetta.protocols.toolbox.KMedoid, : pyrosetta.rosetta.protocols.toolbox.KClusterElement) -> None
init(self: pyrosetta.rosetta.protocols.toolbox.KMedoid, : pyrosetta.rosetta.protocols.toolbox.KClusterElement, first: int) -> None

C++: protocols::toolbox::KMedoid::init(class std::shared_ptr<class protocols::toolbox::KClusterElement>, unsigned long) –> void

set_ncluster(self: pyrosetta.rosetta.protocols.toolbox.KCluster, nc: int) → None¶: C++: protocols::toolbox::KCluster::set_ncluster(unsigned long) –> void

set_threshold(self: pyrosetta.rosetta.protocols.toolbox.KMedoid, : float) → None¶: C++: protocols::toolbox::KMedoid::set_threshold(double) –> void

update(self: pyrosetta.rosetta.protocols.toolbox.KMedoid, : pyrosetta.rosetta.protocols.toolbox.KClusterElement, : pyrosetta.rosetta.protocols.toolbox.KClusterData) → None¶: C++: protocols::toolbox::KMedoid::update(class std::shared_ptr<class protocols::toolbox::KClusterElement>, class protocols::toolbox::KClusterData &) –> void

whoami(self: pyrosetta.rosetta.protocols.toolbox.KMedoid) → bool¶: C++: protocols::toolbox::KMedoid::whoami() –> bool

class pyrosetta.rosetta.protocols.toolbox.MulliganPNearEvaluator¶

Bases: EnergyLandscapeEvaluator

Evaluates a set of score/rms points using Vikram’s pnear method

PNear = SUM( e^(rms^2/lambda^2)*e^(-(score-bg_score)/temperature) ) / SUM( e^( -(score-bg_score)/temperature ) )

assign(self: pyrosetta.rosetta.protocols.toolbox.MulliganPNearEvaluator, : pyrosetta.rosetta.protocols.toolbox.MulliganPNearEvaluator) → pyrosetta.rosetta.protocols.toolbox.MulliganPNearEvaluator¶: C++: protocols::toolbox::MulliganPNearEvaluator::operator=(const class protocols::toolbox::MulliganPNearEvaluator &) –> class protocols::toolbox::MulliganPNearEvaluator &

clone(self: pyrosetta.rosetta.protocols.toolbox.MulliganPNearEvaluator) → pyrosetta.rosetta.protocols.toolbox.EnergyLandscapeEvaluator¶: C++: protocols::toolbox::MulliganPNearEvaluator::clone() const –> class std::shared_ptr<class protocols::toolbox::EnergyLandscapeEvaluator>

compute(self: pyrosetta.rosetta.protocols.toolbox.MulliganPNearEvaluator, points: pyrosetta.rosetta.protocols.toolbox.ScoreRmsPoints) → float¶: C++: protocols::toolbox::MulliganPNearEvaluator::compute(const class protocols::toolbox::ScoreRmsPoints &) const –> double

class pyrosetta.rosetta.protocols.toolbox.Node¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.toolbox.Node, : pyrosetta.rosetta.protocols.toolbox.Node) → pyrosetta.rosetta.protocols.toolbox.Node¶: C++: protocols::toolbox::Node::operator=(const struct protocols::toolbox::Node &) –> struct protocols::toolbox::Node &

property distanceFromStart¶

property id¶

property in_list¶

property neighbors¶

property resi¶

pyrosetta.rosetta.protocols.toolbox.PyReturnValuePolicyTest_DummyClassCOP() → pyrosetta.rosetta.protocols.toolbox.DummyClass¶: C++: protocols::toolbox::PyReturnValuePolicyTest_DummyClassCOP() –> class std::shared_ptr<const class protocols::toolbox::DummyClass>

pyrosetta.rosetta.protocols.toolbox.PyReturnValuePolicyTest_DummyClassOP() → pyrosetta.rosetta.protocols.toolbox.DummyClass¶: C++: protocols::toolbox::PyReturnValuePolicyTest_DummyClassOP() –> class std::shared_ptr<class protocols::toolbox::DummyClass>

pyrosetta.rosetta.protocols.toolbox.PyReturnValuePolicyTest_PoseCOP() → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::toolbox::PyReturnValuePolicyTest_PoseCOP() –> class std::shared_ptr<const class core::pose::Pose>

pyrosetta.rosetta.protocols.toolbox.PyReturnValuePolicyTest_PoseOP() → pyrosetta.rosetta.core.pose.Pose¶: C++: protocols::toolbox::PyReturnValuePolicyTest_PoseOP() –> class std::shared_ptr<class core::pose::Pose>

pyrosetta.rosetta.protocols.toolbox.PyReturnValuePolicyTest_SF_ReplicaCOP() → pyrosetta.rosetta.protocols.toolbox.SF_Replica¶: C++: protocols::toolbox::PyReturnValuePolicyTest_SF_ReplicaCOP() –> class std::shared_ptr<const class protocols::toolbox::SF_Replica>

pyrosetta.rosetta.protocols.toolbox.PyReturnValuePolicyTest_SF_ReplicaOP() → pyrosetta.rosetta.protocols.toolbox.SF_Replica¶: C++: protocols::toolbox::PyReturnValuePolicyTest_SF_ReplicaOP() –> class std::shared_ptr<class protocols::toolbox::SF_Replica>

pyrosetta.rosetta.protocols.toolbox.PyReturnValuePolicyTest_ScoreFunctionCOP() → pyrosetta.rosetta.core.scoring.ScoreFunction¶: C++: protocols::toolbox::PyReturnValuePolicyTest_ScoreFunctionCOP() –> class std::shared_ptr<const class core::scoring::ScoreFunction>

pyrosetta.rosetta.protocols.toolbox.PyReturnValuePolicyTest_ScoreFunctionCOP2() → pyrosetta.rosetta.core.scoring.ScoreFunction¶: C++: protocols::toolbox::PyReturnValuePolicyTest_ScoreFunctionCOP2() –> class std::shared_ptr<const class core::scoring::ScoreFunction>

pyrosetta.rosetta.protocols.toolbox.PyReturnValuePolicyTest_ScoreFunctionOP() → pyrosetta.rosetta.core.scoring.ScoreFunction¶: C++: protocols::toolbox::PyReturnValuePolicyTest_ScoreFunctionOP() –> class std::shared_ptr<class core::scoring::ScoreFunction>

class pyrosetta.rosetta.protocols.toolbox.ResidueGroupIGEdgeUpweighter¶

Bases: IGEdgeReweighter

get_edge_reweight(self: pyrosetta.rosetta.protocols.toolbox.ResidueGroupIGEdgeUpweighter, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask, res1: int, res2: int) → float¶: C++: protocols::toolbox::ResidueGroupIGEdgeUpweighter::get_edge_reweight(const class core::pose::Pose &, const class core::pack::task::PackerTask &, unsigned long, unsigned long) const –> double

class pyrosetta.rosetta.protocols.toolbox.ResidueNetwork¶

Bases: pybind11_object

residuenetwork base class

assign(self: pyrosetta.rosetta.protocols.toolbox.ResidueNetwork, : pyrosetta.rosetta.protocols.toolbox.ResidueNetwork) → pyrosetta.rosetta.protocols.toolbox.ResidueNetwork¶: C++: protocols::toolbox::ResidueNetwork::operator=(const class protocols::toolbox::ResidueNetwork &) –> class protocols::toolbox::ResidueNetwork &

average_shortest_path_length(self: pyrosetta.rosetta.protocols.toolbox.ResidueNetwork) → float¶

calculates the average shortest path length of the network

C++: protocols::toolbox::ResidueNetwork::average_shortest_path_length() const –> double

clear_edges(self: pyrosetta.rosetta.protocols.toolbox.ResidueNetwork) → None¶

empties edges

C++: protocols::toolbox::ResidueNetwork::clear_edges() –> void

connectivity_index(self: pyrosetta.rosetta.protocols.toolbox.ResidueNetwork, resi: int) → float¶

calculates the connectivity index of residue resi in the context of the network

C++: protocols::toolbox::ResidueNetwork::connectivity_index(const unsigned long) const –> double

create_from_pose(self: pyrosetta.rosetta.protocols.toolbox.ResidueNetwork, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

create a network from a pose

C++: protocols::toolbox::ResidueNetwork::create_from_pose(const class core::pose::Pose &) –> void

dijkstras(self: pyrosetta.rosetta.protocols.toolbox.ResidueNetwork, resi: int) → None¶

run Dijkstra’s shortest path algorithm on the given list of nodes: after execution, the “distanceFromStart” variable of each node will contain the distance from residue resi

C++: protocols::toolbox::ResidueNetwork::dijkstras(const unsigned long) const –> void

generate_edges(self: pyrosetta.rosetta.protocols.toolbox.ResidueNetwork, pose: pyrosetta.rosetta.core.pose.Pose) → None¶

generate a list of edges from the pose – MUST be reimplemented for each type of network

C++: protocols::toolbox::ResidueNetwork::generate_edges(const class core::pose::Pose &) –> void

nodes(self: pyrosetta.rosetta.protocols.toolbox.ResidueNetwork) → pyrosetta.rosetta.std.list_std_shared_ptr_protocols_toolbox_Node_t¶: C++: protocols::toolbox::ResidueNetwork::nodes() const –> const class std::list<class std::shared_ptr<struct protocols::toolbox::Node>, class std::allocator<class std::shared_ptr<struct protocols::toolbox::Node> > > &

class pyrosetta.rosetta.protocols.toolbox.RotamerBoltzmannWeightEvaluator¶

Bases: EnergyLandscapeEvaluator

Evaluates a set of score/rms points using the RotamerBoltzmann original method

assign(self: pyrosetta.rosetta.protocols.toolbox.RotamerBoltzmannWeightEvaluator, : pyrosetta.rosetta.protocols.toolbox.RotamerBoltzmannWeightEvaluator) → pyrosetta.rosetta.protocols.toolbox.RotamerBoltzmannWeightEvaluator¶: C++: protocols::toolbox::RotamerBoltzmannWeightEvaluator::operator=(const class protocols::toolbox::RotamerBoltzmannWeightEvaluator &) –> class protocols::toolbox::RotamerBoltzmannWeightEvaluator &

clone(self: pyrosetta.rosetta.protocols.toolbox.RotamerBoltzmannWeightEvaluator) → pyrosetta.rosetta.protocols.toolbox.EnergyLandscapeEvaluator¶: C++: protocols::toolbox::RotamerBoltzmannWeightEvaluator::clone() const –> class std::shared_ptr<class protocols::toolbox::EnergyLandscapeEvaluator>

compute(self: pyrosetta.rosetta.protocols.toolbox.RotamerBoltzmannWeightEvaluator, points: pyrosetta.rosetta.protocols.toolbox.ScoreRmsPoints) → float¶: C++: protocols::toolbox::RotamerBoltzmannWeightEvaluator::compute(const class protocols::toolbox::ScoreRmsPoints &) const –> double

class pyrosetta.rosetta.protocols.toolbox.SF_Replica¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.toolbox.SF_Replica, : pyrosetta.rosetta.protocols.toolbox.SF_Replica) → pyrosetta.rosetta.protocols.toolbox.SF_Replica¶: C++: protocols::toolbox::SF_Replica::operator=(const class protocols::toolbox::SF_Replica &) –> class protocols::toolbox::SF_Replica &

clone(self: pyrosetta.rosetta.protocols.toolbox.SF_Replica) → pyrosetta.rosetta.protocols.toolbox.SF_Replica¶: C++: protocols::toolbox::SF_Replica::clone() const –> class std::shared_ptr<class protocols::toolbox::SF_Replica>

class pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlus¶

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlus, : pyrosetta.rosetta.core.pose.Pose) → None¶

Apply the current rotamer to pose

C++: protocols::toolbox::SamplerPlusPlus::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlus, : pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlus) → pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlus¶: C++: protocols::toolbox::SamplerPlusPlus::operator=(const class protocols::toolbox::SamplerPlusPlus &) –> class protocols::toolbox::SamplerPlusPlus &

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.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

Return a clone of the Mover object.

C++: protocols::moves::Mover::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>

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover¶

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

C++: protocols::moves::Mover::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_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_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.toolbox.SamplerPlusPlus) → str¶

Name of the class

C++: protocols::toolbox::SamplerPlusPlus::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_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_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 > > &

init(self: pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlus) → None¶

Initialization

C++: protocols::toolbox::SamplerPlusPlus::init() –> void

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float¶: C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

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

pre_increment(self: pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlus) → None¶

Move to next rotamer

C++: protocols::toolbox::SamplerPlusPlus::operator++() –> 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 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(self: pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlus) → None¶

Reset to the first (or random if random()) rotamer

C++: protocols::toolbox::SamplerPlusPlus::reset() –> void

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_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_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_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.

show(self: pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlus) -> None
show(self: pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlus, output: pyrosetta.rosetta.std.ostream) -> None
show(self: pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlus, out: pyrosetta.rosetta.std.ostream, indent: int) -> None

output summary of class

C++: protocols::toolbox::SamplerPlusPlus::show(std::ostream &, const unsigned long) 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(self: pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlus) → pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType¶

Type of class (see enum in SamplerPlusPlusTypes.hh)

C++: protocols::toolbox::SamplerPlusPlus::type() const –> enum protocols::toolbox::SamplerPlusPlusType

class pyrosetta.rosetta.protocols.toolbox.SamplerPlusPlusType¶

Bases: pybind11_object

Members:

NO_ROTAMER_TYPE

ANY

COMB

COPY_DOF

INPUT_STREAM

JUMP

ONE_TORSION

ONE_DOF

ONE_VALUE

ONE_VALUE_COMB

PROTEIN_FRAGMENT

PROTEIN_MAIN_CHAIN

PROTEIN_BETA_ANTIPARALLEL

RESIDUE_LIST

RESIDUE_ALTERNATIVE

RESIDUE_ALTERNATIVE_COMB

RING_CONFORMERS

RIGID_BODY

RIGID_BODY_WITH_RESIDUE_LIST

RIGID_BODY_WITH_RESIDUE_ALTERNATIVES

RNA_CHI

RNA_KIC

RNA_KINEMATIC_CLOSER

MC_ANY

MC_COMB

MC_ONE_TORSION

MC_LOOP

MC_RNA_KIC

MC_RNA_MULTI_SUITE

MC_RNA_ONE_JUMP

MC_RNA_SUGAR

MC_RNA_SUITE

RNA_NUCLEOSIDE

RNA_SUGAR

RNA_SUITE

SIZED

SIZED_ANY

SIZED_COMB

ANY = <SamplerPlusPlusType.ANY: 1>¶

COMB = <SamplerPlusPlusType.COMB: 2>¶

COPY_DOF = <SamplerPlusPlusType.COPY_DOF: 3>¶

INPUT_STREAM = <SamplerPlusPlusType.INPUT_STREAM: 4>¶

JUMP = <SamplerPlusPlusType.JUMP: 5>¶

MC_ANY = <SamplerPlusPlusType.MC_ANY: 23>¶

MC_COMB = <SamplerPlusPlusType.MC_COMB: 24>¶

MC_LOOP = <SamplerPlusPlusType.MC_LOOP: 26>¶

MC_ONE_TORSION = <SamplerPlusPlusType.MC_ONE_TORSION: 25>¶

MC_RNA_KIC = <SamplerPlusPlusType.MC_RNA_KIC: 27>¶

MC_RNA_MULTI_SUITE = <SamplerPlusPlusType.MC_RNA_MULTI_SUITE: 28>¶

MC_RNA_ONE_JUMP = <SamplerPlusPlusType.MC_RNA_ONE_JUMP: 29>¶

MC_RNA_SUGAR = <SamplerPlusPlusType.MC_RNA_SUGAR: 30>¶

MC_RNA_SUITE = <SamplerPlusPlusType.MC_RNA_SUITE: 31>¶

NO_ROTAMER_TYPE = <SamplerPlusPlusType.NO_ROTAMER_TYPE: 0>¶

ONE_DOF = <SamplerPlusPlusType.ONE_DOF: 7>¶

ONE_TORSION = <SamplerPlusPlusType.ONE_TORSION: 6>¶

ONE_VALUE = <SamplerPlusPlusType.ONE_VALUE: 8>¶

ONE_VALUE_COMB = <SamplerPlusPlusType.ONE_VALUE_COMB: 9>¶

PROTEIN_BETA_ANTIPARALLEL = <SamplerPlusPlusType.PROTEIN_BETA_ANTIPARALLEL: 12>¶

PROTEIN_FRAGMENT = <SamplerPlusPlusType.PROTEIN_FRAGMENT: 10>¶

PROTEIN_MAIN_CHAIN = <SamplerPlusPlusType.PROTEIN_MAIN_CHAIN: 11>¶

RESIDUE_ALTERNATIVE = <SamplerPlusPlusType.RESIDUE_ALTERNATIVE: 14>¶

RESIDUE_ALTERNATIVE_COMB = <SamplerPlusPlusType.RESIDUE_ALTERNATIVE_COMB: 15>¶

RESIDUE_LIST = <SamplerPlusPlusType.RESIDUE_LIST: 13>¶

RIGID_BODY = <SamplerPlusPlusType.RIGID_BODY: 17>¶

RIGID_BODY_WITH_RESIDUE_ALTERNATIVES = <SamplerPlusPlusType.RIGID_BODY_WITH_RESIDUE_ALTERNATIVES: 19>¶

RIGID_BODY_WITH_RESIDUE_LIST = <SamplerPlusPlusType.RIGID_BODY_WITH_RESIDUE_LIST: 18>¶

RING_CONFORMERS = <SamplerPlusPlusType.RING_CONFORMERS: 16>¶

RNA_CHI = <SamplerPlusPlusType.RNA_CHI: 20>¶

RNA_KIC = <SamplerPlusPlusType.RNA_KIC: 21>¶

RNA_KINEMATIC_CLOSER = <SamplerPlusPlusType.RNA_KINEMATIC_CLOSER: 22>¶

RNA_NUCLEOSIDE = <SamplerPlusPlusType.RNA_NUCLEOSIDE: 32>¶

RNA_SUGAR = <SamplerPlusPlusType.RNA_SUGAR: 33>¶

RNA_SUITE = <SamplerPlusPlusType.RNA_SUITE: 34>¶

SIZED = <SamplerPlusPlusType.SIZED: 35>¶

SIZED_ANY = <SamplerPlusPlusType.SIZED_ANY: 36>¶

SIZED_COMB = <SamplerPlusPlusType.SIZED_COMB: 37>¶

property name¶

property value¶

class pyrosetta.rosetta.protocols.toolbox.ScoreRmsPoint¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.toolbox.ScoreRmsPoint, : pyrosetta.rosetta.protocols.toolbox.ScoreRmsPoint) → pyrosetta.rosetta.protocols.toolbox.ScoreRmsPoint¶: C++: protocols::toolbox::ScoreRmsPoint::operator=(const class protocols::toolbox::ScoreRmsPoint &) –> class protocols::toolbox::ScoreRmsPoint &

rms(self: pyrosetta.rosetta.protocols.toolbox.ScoreRmsPoint) → float¶: C++: protocols::toolbox::ScoreRmsPoint::rms() const –> double

score(self: pyrosetta.rosetta.protocols.toolbox.ScoreRmsPoint) → float¶: C++: protocols::toolbox::ScoreRmsPoint::score() const –> double

class pyrosetta.rosetta.protocols.toolbox.ScoreRmsPoints¶

Bases: vector1_protocols_toolbox_ScoreRmsPoint

append(self: pyrosetta.rosetta.utility.vector1_protocols_toolbox_ScoreRmsPoint, arg0: protocols::toolbox::ScoreRmsPoint) → None¶: adds an element to the end

assign(self: pyrosetta.rosetta.protocols.toolbox.ScoreRmsPoints, : pyrosetta.rosetta.protocols.toolbox.ScoreRmsPoints) → pyrosetta.rosetta.protocols.toolbox.ScoreRmsPoints¶: C++: protocols::toolbox::ScoreRmsPoints::operator=(const class protocols::toolbox::ScoreRmsPoints &) –> class protocols::toolbox::ScoreRmsPoints &

back(self: pyrosetta.rosetta.utility.vector1_protocols_toolbox_ScoreRmsPoint) → protocols::toolbox::ScoreRmsPoint¶: access the last element

bg(self: pyrosetta.rosetta.protocols.toolbox.ScoreRmsPoints) → pyrosetta.rosetta.protocols.toolbox.ScoreRmsPoint¶: C++: protocols::toolbox::ScoreRmsPoints::bg() const –> const class protocols::toolbox::ScoreRmsPoint &

capacity(self: pyrosetta.rosetta.utility.vector1_protocols_toolbox_ScoreRmsPoint) → int¶: returns the number of elements that can be held in currently allocated storage

clear(self: pyrosetta.rosetta.utility.vector1_protocols_toolbox_ScoreRmsPoint) → None¶: clears the contents

erase(self: pyrosetta.rosetta.utility.vector1_protocols_toolbox_ScoreRmsPoint, arg0: int) → None¶: erases element at index

extend(othervec)¶

front(self: pyrosetta.rosetta.utility.vector1_protocols_toolbox_ScoreRmsPoint) → protocols::toolbox::ScoreRmsPoint¶: access the first element

l(self: pyrosetta.rosetta.utility.vector1_protocols_toolbox_ScoreRmsPoint) → int¶: lower index

max_size(self: pyrosetta.rosetta.utility.vector1_protocols_toolbox_ScoreRmsPoint) → int¶: returns the maximum possible number of elements

pop(*args, **kwargs)¶

Overloaded function.

pop(self: pyrosetta.rosetta.utility.vector1_protocols_toolbox_ScoreRmsPoint) -> protocols::toolbox::ScoreRmsPoint

remove and return last item

pop(self: pyrosetta.rosetta.utility.vector1_protocols_toolbox_ScoreRmsPoint, arg0: int) -> protocols::toolbox::ScoreRmsPoint

remove and return item at index

reserve(self: pyrosetta.rosetta.utility.vector1_protocols_toolbox_ScoreRmsPoint, arg0: int) → None¶: reserves storage

shrink_to_fit(self: pyrosetta.rosetta.utility.vector1_protocols_toolbox_ScoreRmsPoint) → None¶: reduces memory usage by freeing unused memory

u(self: pyrosetta.rosetta.utility.vector1_protocols_toolbox_ScoreRmsPoint) → int¶: upper index

pyrosetta.rosetta.protocols.toolbox.apply_superposition_transform(pose: pyrosetta.rosetta.core.pose.Pose, rotation: pyrosetta.rosetta.numeric.xyzMatrix_double_t, to_init_center: pyrosetta.rosetta.numeric.xyzVector_double_t, to_fit_center: pyrosetta.rosetta.numeric.xyzVector_double_t) → None¶: C++: protocols::toolbox::apply_superposition_transform(class core::pose::Pose &, class numeric::xyzMatrix<double>, class numeric::xyzVector<double>, class numeric::xyzVector<double>) –> void

pyrosetta.rosetta.protocols.toolbox.apply_superposition_transform_to_jump(pose: pyrosetta.rosetta.core.pose.Pose, jump_id: int, rotation: pyrosetta.rosetta.numeric.xyzMatrix_double_t, to_init_center: pyrosetta.rosetta.numeric.xyzVector_double_t, to_fit_center: pyrosetta.rosetta.numeric.xyzVector_double_t) → None¶: C++: protocols::toolbox::apply_superposition_transform_to_jump(class core::pose::Pose &, unsigned long, class numeric::xyzMatrix<double>, class numeric::xyzVector<double>, class numeric::xyzVector<double>) –> void

pyrosetta.rosetta.protocols.toolbox.dump_as_pdb(*args, **kwargs)¶

Overloaded function.

dump_as_pdb(filename: str, n: int, coords: pyrosetta.rosetta.ObjexxFCL.FArray2_double_t) -> None
dump_as_pdb(filename: str, n: int, coords: pyrosetta.rosetta.ObjexxFCL.FArray2_double_t, transvec: pyrosetta.rosetta.ObjexxFCL.FArray1D_double_t) -> None

write a CA ALA pdb

C++: protocols::toolbox::dump_as_pdb(std::string, unsigned long, class ObjexxFCL::FArray2<double> &, class ObjexxFCL::FArray1D<double>) –> void

pyrosetta.rosetta.protocols.toolbox.file_full_path(: str) → str¶: C++: protocols::toolbox::file_full_path(std::string) –> std::string

pyrosetta.rosetta.protocols.toolbox.fill_CA_coords(*args, **kwargs)¶

Overloaded function.

fill_CA_coords(pose: pyrosetta.rosetta.core.pose.Pose, natoms: int, coords: pyrosetta.rosetta.ObjexxFCL.FArray2_double_t) -> None

C++: protocols::toolbox::fill_CA_coords(const class core::pose::Pose &, unsigned long, class ObjexxFCL::FArray2<double> &) –> void

fill_CA_coords(pose: pyrosetta.rosetta.core.pose.Pose, coords: pyrosetta.rosetta.ObjexxFCL.FArray2_double_t) -> None

C++: protocols::toolbox::fill_CA_coords(const class core::pose::Pose &, class ObjexxFCL::FArray2<double> &) –> void

pyrosetta.rosetta.protocols.toolbox.fit_centered_coords(natoms: int, weights: pyrosetta.rosetta.ObjexxFCL.FArray1_double_t, ref_coords: pyrosetta.rosetta.ObjexxFCL.FArray2_double_t, coords: pyrosetta.rosetta.ObjexxFCL.FArray2_double_t, R: pyrosetta.rosetta.numeric.xyzMatrix_double_t) → None¶: C++: protocols::toolbox::fit_centered_coords(unsigned long, const class ObjexxFCL::FArray1<double> &, const class ObjexxFCL::FArray2<double> &, class ObjexxFCL::FArray2<double> &, class numeric::xyzMatrix<double> &) –> void

pyrosetta.rosetta.protocols.toolbox.fix_tag_suffix(: str) → str¶: C++: protocols::toolbox::fix_tag_suffix(std::string) –> std::string

pyrosetta.rosetta.protocols.toolbox.get_K_cluster_engine(: str) → pyrosetta.rosetta.protocols.toolbox.KCluster¶: C++: protocols::toolbox::get_K_cluster_engine(const std::string &) –> class std::shared_ptr<class protocols::toolbox::KCluster>

pyrosetta.rosetta.protocols.toolbox.out_of_bounds_memory_access() → None¶: C++: protocols::toolbox::out_of_bounds_memory_access() –> void

pyrosetta.rosetta.protocols.toolbox.reset_x(n: int, x: pyrosetta.rosetta.ObjexxFCL.FArray2_double_t, wts: pyrosetta.rosetta.ObjexxFCL.FArray1_double_t, transvec: pyrosetta.rosetta.ObjexxFCL.FArray1_double_t) → None¶: C++: protocols::toolbox::reset_x(unsigned long, class ObjexxFCL::FArray2<double> &, const class ObjexxFCL::FArray1<double> &, class ObjexxFCL::FArray1<double> &) –> void

pyrosetta.rosetta.protocols.toolbox.superposition_transform(*args, **kwargs)¶

Overloaded function.

superposition_transform(init_coords: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t, ref_coords: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t, rotation: pyrosetta.rosetta.numeric.xyzMatrix_double_t, to_init_center: pyrosetta.rosetta.numeric.xyzVector_double_t, to_fit_center: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

C++: protocols::toolbox::superposition_transform(class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &, class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &, class numeric::xyzMatrix<double> &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &) –> void

superposition_transform(init_coords: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t, ref_coords: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t, coord_weights: pyrosetta.rosetta.utility.vector1_double, rotation: pyrosetta.rosetta.numeric.xyzMatrix_double_t, to_init_center: pyrosetta.rosetta.numeric.xyzVector_double_t, to_fit_center: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

C++: protocols::toolbox::superposition_transform(class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &, class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &, class utility::vector1<double, class std::allocator<double> > &, class numeric::xyzMatrix<double> &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &) –> void

superposition_transform(natoms: int, weights: pyrosetta.rosetta.ObjexxFCL.FArray1_double_t, ref_coords: pyrosetta.rosetta.ObjexxFCL.FArray2_double_t, coords: pyrosetta.rosetta.ObjexxFCL.FArray2_double_t, R: pyrosetta.rosetta.numeric.xyzMatrix_double_t, toCenter: pyrosetta.rosetta.numeric.xyzVector_double_t, toFitCenter: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

C++: protocols::toolbox::superposition_transform(unsigned long, const class ObjexxFCL::FArray1<double> &, class ObjexxFCL::FArray2<double> &, class ObjexxFCL::FArray2<double> &, class numeric::xyzMatrix<double> &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &) –> void

pyrosetta.rosetta.protocols.toolbox.take_pose_op(: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::toolbox::take_pose_op(const class std::shared_ptr<class core::pose::Pose> &) –> void