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_std_allocator_std_shared_ptr_protocols_toolbox_Node_t¶: C++: protocols::toolbox::AdjacentRemainingNodes(class std::shared_ptr<class protocols::toolbox::Node>) –> class std::list<class std::shared_ptr<class protocols::toolbox::Node>, class std::allocator<class std::shared_ptr<class protocols::toolbox::Node> > >

class pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap¶

Bases: pybind11_builtins.pybind11_object

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap, arg0: pyrosetta.rosetta.core.pose.Pose) -> None

doc

__init__(self: pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap, arg0: pyrosetta.rosetta.core.pose.Pose, arg1: bool) -> None

doc

__init__(self: pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap, pose: pyrosetta.rosetta.core.pose.Pose, map_to_vanilla_pose: bool, allow_insert_res: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None
__init__(self: pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap, arg0: pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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

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

calculate_atom_id_domain_map(self: pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.map_core_id_AtomID_unsigned_long¶: C++: protocols::toolbox::AtomLevelDomainMap::calculate_atom_id_domain_map(const class core::pose::Pose &) const –> class std::map<class core::id::AtomID, unsigned long, struct std::less<class core::id::AtomID>, class std::allocator<struct std::pair<const class core::id::AtomID, unsigned long> > >

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

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

get(*args, **kwargs)¶

Overloaded function.

get(self: pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap, i: int) -> bool

C++: protocols::toolbox::AtomLevelDomainMap::get(const unsigned long &) const –> bool

get(self: pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap, atom_id: pyrosetta.rosetta.core.id.AtomID) -> bool

C++: protocols::toolbox::AtomLevelDomainMap::get(const class core::id::AtomID &) const –> bool

get(self: pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap, torsion_id: pyrosetta.rosetta.core.id.TorsionID, conformation: pyrosetta.rosetta.core.conformation.Conformation) -> bool

C++: protocols::toolbox::AtomLevelDomainMap::get(const class core::id::TorsionID &, const class core::conformation::Conformation &) const –> bool

get_domain(*args, **kwargs)¶

Overloaded function.

get_domain(self: pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap, i: int) -> int

C++: protocols::toolbox::AtomLevelDomainMap::get_domain(const unsigned long &) const –> unsigned long

get_domain(self: pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap, atom_id: pyrosetta.rosetta.core.id.AtomID) -> int

C++: protocols::toolbox::AtomLevelDomainMap::get_domain(const class core::id::AtomID &) const –> unsigned long

get_domain(self: pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap, named_atom_id: pyrosetta.rosetta.core.id.NamedAtomID, pose: pyrosetta.rosetta.core.pose.Pose) -> int

C++: protocols::toolbox::AtomLevelDomainMap::get_domain(const class core::id::NamedAtomID &, const class core::pose::Pose &) const –> unsigned long

get_jump(self: pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap, jump_number: int, conformation: pyrosetta.rosetta.core.conformation.Conformation) → bool¶: C++: protocols::toolbox::AtomLevelDomainMap::get_jump(const unsigned long &, const class core::conformation::Conformation &) const –> bool

has_domain(self: pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap, atom_id: pyrosetta.rosetta.core.id.AtomID) → bool¶: C++: protocols::toolbox::AtomLevelDomainMap::has_domain(const class core::id::AtomID &) const –> bool

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

set(*args, **kwargs)¶

Overloaded function.

set(self: pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap, i: int, setting: bool) -> None

C++: protocols::toolbox::AtomLevelDomainMap::set(const unsigned long &, const bool &) –> void

set(self: pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap, named_atom_id: pyrosetta.rosetta.core.id.NamedAtomID, pose: pyrosetta.rosetta.core.pose.Pose, setting: bool) -> None

C++: protocols::toolbox::AtomLevelDomainMap::set(const class core::id::NamedAtomID &, const class core::pose::Pose &, const bool &) –> void

set(self: pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap, atom_id: pyrosetta.rosetta.core.id.AtomID, setting: bool) -> None

C++: protocols::toolbox::AtomLevelDomainMap::set(const class core::id::AtomID &, const bool &) –> void

set(self: pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap, setting: bool) -> None

C++: protocols::toolbox::AtomLevelDomainMap::set(const bool &) –> void

set_domain(*args, **kwargs)¶

Overloaded function.

set_domain(self: pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap, i: int, setting: int) -> None

C++: protocols::toolbox::AtomLevelDomainMap::set_domain(const unsigned long &, const unsigned long &) –> void

set_domain(self: pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap, atom_id: pyrosetta.rosetta.core.id.AtomID, setting: int) -> None
set_domain(self: pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap, atom_id: pyrosetta.rosetta.core.id.AtomID, setting: int, ok_if_missing: bool) -> None

C++: protocols::toolbox::AtomLevelDomainMap::set_domain(const class core::id::AtomID &, const unsigned long &, bool) –> void

set_domain(self: pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap, atom_id: pyrosetta.rosetta.core.id.NamedAtomID, pose: pyrosetta.rosetta.core.pose.Pose, setting: int) -> None

C++: protocols::toolbox::AtomLevelDomainMap::set_domain(const class core::id::NamedAtomID &, const class core::pose::Pose &, const unsigned long &) –> void

set_domain(self: pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap, setting: int) -> None

C++: protocols::toolbox::AtomLevelDomainMap::set_domain(const unsigned long &) –> void

set_fixed_if_moving(*args, **kwargs)¶

Overloaded function.

set_fixed_if_moving(self: pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap, i: int) -> None

C++: protocols::toolbox::AtomLevelDomainMap::set_fixed_if_moving(const unsigned long &) –> void

set_fixed_if_moving(self: pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap, atom_id: pyrosetta.rosetta.core.id.AtomID) -> None

C++: protocols::toolbox::AtomLevelDomainMap::set_fixed_if_moving(const class core::id::AtomID &) –> void

set_phosphate(self: pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap, i: int, pose: pyrosetta.rosetta.core.pose.Pose, setting: bool) → None¶: C++: protocols::toolbox::AtomLevelDomainMap::set_phosphate(const unsigned long &, const class core::pose::Pose &, const bool &) –> void

set_phosphate_domain(self: pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap, i: int, pose: pyrosetta.rosetta.core.pose.Pose, setting: int) → None¶: C++: protocols::toolbox::AtomLevelDomainMap::set_phosphate_domain(const unsigned long &, const class core::pose::Pose &, const unsigned long &) –> void

set_sugar(self: pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap, i: int, pose: pyrosetta.rosetta.core.pose.Pose, setting: bool) → None¶: C++: protocols::toolbox::AtomLevelDomainMap::set_sugar(const unsigned long &, const class core::pose::Pose &, const bool &) –> void

set_sugar_domain(self: pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap, i: int, pose: pyrosetta.rosetta.core.pose.Pose, setting: int) → None¶: C++: protocols::toolbox::AtomLevelDomainMap::set_sugar_domain(const unsigned long &, const class core::pose::Pose &, const unsigned long &) –> void

setup_movemap(self: pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap, mm: pyrosetta.rosetta.core.kinematics.MoveMap, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::toolbox::AtomLevelDomainMap::setup_movemap(class core::kinematics::MoveMap &, const class core::pose::Pose &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap) -> None
show(self: pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap, out: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::toolbox::AtomLevelDomainMap::show(class std::basic_ostream<char> &) const –> void

update_to_move_chunks_with_domain(self: pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap, domain: int) → None¶: C++: protocols::toolbox::AtomLevelDomainMap::update_to_move_chunks_with_domain(const unsigned long &) –> void

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

Overloaded function.

CA_superimpose(weights: ObjexxFCL::FArray1<double>, 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_builtins.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.

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.toolbox.CalcInterNeighborGroup) -> None
__init__(self: pyrosetta.rosetta.protocols.toolbox.CalcInterNeighborGroup, arg0: pyrosetta.rosetta.utility.vector1_std_pair_std_set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_std_set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t) -> None

doc

__init__(self: pyrosetta.rosetta.protocols.toolbox.CalcInterNeighborGroup, groups: pyrosetta.rosetta.utility.vector1_std_pair_std_set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_std_set_unsigned_long_std_less_unsigned_long_std_allocator_unsigned_long_t, dist_cutoff: float) -> None
__init__(self: pyrosetta.rosetta.protocols.toolbox.CalcInterNeighborGroup, arg0: pyrosetta.rosetta.protocols.toolbox.CalcInterNeighborGroup) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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_less_unsigned_long_std_allocator_unsigned_long_std_set_unsigned_long_std_less_unsigned_long_std_allocator_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_less_unsigned_long_std_allocator_unsigned_long_std_set_unsigned_long_std_less_unsigned_long_std_allocator_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

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

class pyrosetta.rosetta.protocols.toolbox.CovalentResidueNetwork¶

Bases: pyrosetta.rosetta.protocols.toolbox.ResidueNetwork

Creates networks based on covalent connections between residues

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(self: pyrosetta.rosetta.protocols.toolbox.CovalentResidueNetwork) → None¶

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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_std_allocator_std_shared_ptr_protocols_toolbox_Node_t¶: C++: protocols::toolbox::ResidueNetwork::nodes() const –> const class std::list<class std::shared_ptr<class protocols::toolbox::Node>, class std::allocator<class std::shared_ptr<class protocols::toolbox::Node> > > &

class pyrosetta.rosetta.protocols.toolbox.DistanceResidueNetwork¶

Bases: pyrosetta.rosetta.protocols.toolbox.ResidueNetwork

Creates networks based on residue proximity in space

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(self: pyrosetta.rosetta.protocols.toolbox.DistanceResidueNetwork) → None¶

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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_std_allocator_std_shared_ptr_protocols_toolbox_Node_t¶: C++: protocols::toolbox::ResidueNetwork::nodes() const –> const class std::list<class std::shared_ptr<class protocols::toolbox::Node>, class std::allocator<class std::shared_ptr<class protocols::toolbox::Node> > > &

class pyrosetta.rosetta.protocols.toolbox.EnergyLandscapeEvaluator¶

Bases: pybind11_builtins.pybind11_object

Evaluates a set of score/rms points

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(self: pyrosetta.rosetta.protocols.toolbox.EnergyLandscapeEvaluator) → None¶

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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_std_allocator_std_shared_ptr_protocols_toolbox_Node_t) → protocols::toolbox::Node¶: C++: protocols::toolbox::ExtractSmallest(class std::list<class std::shared_ptr<class protocols::toolbox::Node>, class std::allocator<class std::shared_ptr<class protocols::toolbox::Node> > > &) –> class std::shared_ptr<class protocols::toolbox::Node>

class pyrosetta.rosetta.protocols.toolbox.GreedyKCenter¶

Bases: pyrosetta.rosetta.protocols.toolbox.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

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(self: pyrosetta.rosetta.protocols.toolbox.GreedyKCenter) → None¶

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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.KCluster¶

Bases: pybind11_builtins.pybind11_object

basic class for performing a K-style Clustering algorithm

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.toolbox.KCluster) -> None
__init__(self: pyrosetta.rosetta.protocols.toolbox.KCluster, arg0: pyrosetta.rosetta.protocols.toolbox.KCluster) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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_builtins.pybind11_object

database of a K-style Clustering algorithm

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.toolbox.KClusterData) -> None
__init__(self: pyrosetta.rosetta.protocols.toolbox.KClusterData, arg0: pyrosetta.rosetta.protocols.toolbox.KClusterData) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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) → ObjexxFCL::FArray3P<double>¶: 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(class std::basic_string<char>, 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>, class std::basic_string<char>) –> 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_builtins.pybind11_object

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.toolbox.KClusterElement) -> None
__init__(self: pyrosetta.rosetta.protocols.toolbox.KClusterElement, nd: int) -> None
__init__(self: pyrosetta.rosetta.protocols.toolbox.KClusterElement, arg0: pyrosetta.rosetta.protocols.toolbox.KClusterElement) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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: pyrosetta.rosetta.protocols.toolbox.KCluster

Typical K-Medoids Clustering Algorithm

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(self: pyrosetta.rosetta.protocols.toolbox.KMedoid) → None¶

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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: pyrosetta.rosetta.protocols.toolbox.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 ) )

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(self: pyrosetta.rosetta.protocols.toolbox.MulliganPNearEvaluator, temperature: float, lambda: float) → None¶

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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

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.ResidueNetwork¶

Bases: pybind11_builtins.pybind11_object

residuenetwork base class

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.toolbox.ResidueNetwork) -> None
__init__(self: pyrosetta.rosetta.protocols.toolbox.ResidueNetwork, arg0: pyrosetta.rosetta.protocols.toolbox.ResidueNetwork) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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_std_allocator_std_shared_ptr_protocols_toolbox_Node_t¶: C++: protocols::toolbox::ResidueNetwork::nodes() const –> const class std::list<class std::shared_ptr<class protocols::toolbox::Node>, class std::allocator<class std::shared_ptr<class protocols::toolbox::Node> > > &

class pyrosetta.rosetta.protocols.toolbox.RotamerBoltzmannWeightEvaluator¶

Bases: pyrosetta.rosetta.protocols.toolbox.EnergyLandscapeEvaluator

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

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(self: pyrosetta.rosetta.protocols.toolbox.RotamerBoltzmannWeightEvaluator, temperature: float, include_bg_point_in_sum: bool) → None¶

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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

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: ObjexxFCL::FArray1D<double>) -> None

write a CA ALA pdb

C++: protocols::toolbox::dump_as_pdb(class std::basic_string<char>, 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(class std::basic_string<char>) –> 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: ObjexxFCL::FArray1<double>, 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(class std::basic_string<char>) –> std::string

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

pyrosetta.rosetta.protocols.toolbox.reset_x(n: int, x: pyrosetta.rosetta.ObjexxFCL.FArray2_double_t, wts: ObjexxFCL::FArray1<double>, transvec: ObjexxFCL::FArray1<double>) → 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: ObjexxFCL::FArray1<double>, 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