hbnet¶

Bindings for protocols::hbnet namespace

class pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetwork¶

Bases: pyrosetta.rosetta.core.pack.task.operation.TaskOperation

sets allowed residue types to constrain HBNet residues in downstream design; add this Taskop to any design movers downstream of HBNet

__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.hbnet.ConstrainHBondNetwork) → 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).

apply(self: pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetwork, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None¶: C++: protocols::hbnet::ConstrainHBondNetwork::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

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

clone(self: pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetwork) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::hbnet::ConstrainHBondNetwork::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname() → str¶: C++: protocols::hbnet::ConstrainHBondNetwork::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.protocols.hbnet.ConstrainHBondNetwork, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::hbnet::ConstrainHBondNetwork::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::hbnet::ConstrainHBondNetwork::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.protocols.hbnet.HBondEdge¶

Bases: pyrosetta.rosetta.utility.graph.Edge

Each HBondEdge represents a hydrogen bond

__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.hbnet.HBondEdge, owner: pyrosetta.rosetta.utility.graph.Graph, first_node_ind: int, second_node_ind: int) -> None
__init__(self: pyrosetta.rosetta.protocols.hbnet.HBondEdge, owner: pyrosetta.rosetta.utility.graph.Graph, first_node_ind: int, second_node_ind: int, energy: 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).

copy_from(self: pyrosetta.rosetta.protocols.hbnet.HBondEdge, source: pyrosetta.rosetta.utility.graph.Edge) → None¶: C++: protocols::hbnet::HBondEdge::copy_from(const class utility::graph::Edge *) –> void

count_dynamic_memory(self: pyrosetta.rosetta.protocols.hbnet.HBondEdge) → int¶: C++: protocols::hbnet::HBondEdge::count_dynamic_memory() const –> unsigned long

count_static_memory(self: pyrosetta.rosetta.protocols.hbnet.HBondEdge) → int¶: C++: protocols::hbnet::HBondEdge::count_static_memory() const –> unsigned long

energy(self: pyrosetta.rosetta.protocols.hbnet.HBondEdge) → float¶

this is intended to be the raw energy from the interaction graph between the rotamers represented by this->get_first_node_ind() and this->get_second_node_ind()

C++: protocols::hbnet::HBondEdge::energy() const –> float

get_first_node_ind(self: pyrosetta.rosetta.utility.graph.Edge) → int¶

returns the index of the lower node

C++: utility::graph::Edge::get_first_node_ind() const –> unsigned long

get_other_ind(self: pyrosetta.rosetta.utility.graph.Edge, node_index: int) → int¶

returns the index of the one node given the index of the other.: node_index must be one of the two nodes that this edge is incident upon.

C++: utility::graph::Edge::get_other_ind(unsigned long) const –> unsigned long

get_other_node(self: pyrosetta.rosetta.utility.graph.Edge, node_index: int) → pyrosetta.rosetta.utility.graph.Node¶

returns a non-const pointer to one node given the index of the other.: node_index must be one of the two nodes that this edge is incident upon.

C++: utility::graph::Edge::get_other_node(unsigned long) –> class utility::graph::Node *

get_second_node_ind(self: pyrosetta.rosetta.utility.graph.Edge) → int¶

returns the index of the upper node

C++: utility::graph::Edge::get_second_node_ind() const –> unsigned long

is_loop(self: pyrosetta.rosetta.utility.graph.Edge) → bool¶

Is this edge a loop? In Pseudographs, loop edges are incident twice on a single vertex.

C++: utility::graph::Edge::is_loop() const –> bool

same_edge(self: pyrosetta.rosetta.utility.graph.Edge, node1: int, node2: int) → bool¶

Is this the same edge as another edge (node1,node2)? Note:: this graph does not work for multi-graphs. Edges must be unique.

C++: utility::graph::Edge::same_edge(unsigned long, unsigned long) const –> bool

score(self: pyrosetta.rosetta.protocols.hbnet.HBondEdge) → float¶

redundant interface for energy getter and setter. I find myself forgetting if the method is called “score” or “energy” so this way both are right

C++: protocols::hbnet::HBondEdge::score() const –> float

set_energy(self: pyrosetta.rosetta.protocols.hbnet.HBondEdge, energy: float) → None¶: C++: protocols::hbnet::HBondEdge::set_energy(double) –> void

set_pos_in_owners_list(self: pyrosetta.rosetta.utility.graph.Edge, edge_iterator: pyrosetta.rosetta.utility.graph.EdgeListIterator) → None¶

called only by class Graph, this function gives the Edge the data it needs: to later delete itself from its owner’s edge list in constant time.

C++: utility::graph::Edge::set_pos_in_owners_list(class utility::graph::EdgeListIterator) –> void

set_score(self: pyrosetta.rosetta.protocols.hbnet.HBondEdge, energy: float) → None¶: C++: protocols::hbnet::HBondEdge::set_score(double) –> void

class pyrosetta.rosetta.protocols.hbnet.HBondNode¶

Bases: pyrosetta.rosetta.utility.graph.Node

Each HBondNode represents a rotamer from the RotamerSets 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.hbnet.HBondNode, : pyrosetta.rosetta.utility.graph.Graph, node_id: int) -> None
__init__(self: pyrosetta.rosetta.protocols.hbnet.HBondNode, : pyrosetta.rosetta.utility.graph.Graph, node_id: int, mres_id: int, rotamer_id: int) -> 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_edge(self: pyrosetta.rosetta.utility.graph.Node, edge_ptr: utility::graph::Edge, : pyrosetta.rosetta.utility.graph.EdgeListIterator) → None¶

adds edge pointer to edge list; returns an iterator to the new: list element

C++: utility::graph::Node::add_edge(class utility::graph::Edge *, class utility::graph::EdgeListIterator &) –> void

clashes(self: pyrosetta.rosetta.protocols.hbnet.HBondNode, node_id: int) → bool¶

does this node clash with another node (at another residue position)?

C++: protocols::hbnet::HBondNode::clashes(unsigned long) const –> bool

const_edge_list_begin(self: pyrosetta.rosetta.utility.graph.Node) → pyrosetta.rosetta.utility.graph.EdgeListConstIterator¶

returns a const iterator to the beginning of its edge list

C++: utility::graph::Node::const_edge_list_begin() const –> class utility::graph::EdgeListConstIterator

const_edge_list_end(self: pyrosetta.rosetta.utility.graph.Node) → pyrosetta.rosetta.utility.graph.EdgeListConstIterator¶

returns a const iterator to the end of its edge list

C++: utility::graph::Node::const_edge_list_end() const –> class utility::graph::EdgeListConstIterator

const_lower_edge_list_begin(self: pyrosetta.rosetta.utility.graph.Node) → pyrosetta.rosetta.utility.graph.EdgeListConstIterator¶

returns a const iterator to the beginning of its lower-edge list

C++: utility::graph::Node::const_lower_edge_list_begin() const –> class utility::graph::EdgeListConstIterator

const_lower_edge_list_end(self: pyrosetta.rosetta.utility.graph.Node) → pyrosetta.rosetta.utility.graph.EdgeListConstIterator¶

returns a const iterator to the end of its lower-edge list

C++: utility::graph::Node::const_lower_edge_list_end() const –> class utility::graph::EdgeListConstIterator

const_upper_edge_list_begin(self: pyrosetta.rosetta.utility.graph.Node) → pyrosetta.rosetta.utility.graph.EdgeListConstIterator¶

returns a const iterator to the beginning of its upper-edge list

C++: utility::graph::Node::const_upper_edge_list_begin() const –> class utility::graph::EdgeListConstIterator

const_upper_edge_list_end(self: pyrosetta.rosetta.utility.graph.Node) → pyrosetta.rosetta.utility.graph.EdgeListConstIterator¶

returns a const iterator to the end of its upper-edge list

C++: utility::graph::Node::const_upper_edge_list_end() const –> class utility::graph::EdgeListConstIterator

copy_from(self: pyrosetta.rosetta.protocols.hbnet.HBondNode, source: pyrosetta.rosetta.utility.graph.Node) → None¶: C++: protocols::hbnet::HBondNode::copy_from(const class utility::graph::Node *) –> void

count_dynamic_memory(self: pyrosetta.rosetta.protocols.hbnet.HBondNode) → int¶: C++: protocols::hbnet::HBondNode::count_dynamic_memory() const –> unsigned long

count_static_memory(self: pyrosetta.rosetta.protocols.hbnet.HBondNode) → int¶: C++: protocols::hbnet::HBondNode::count_static_memory() const –> unsigned long

drop_all_edges(self: pyrosetta.rosetta.utility.graph.Node) → None¶

deletes all edges incident upon this node

C++: utility::graph::Node::drop_all_edges() –> void

drop_edge(self: pyrosetta.rosetta.utility.graph.Node, edge_iterator: pyrosetta.rosetta.utility.graph.EdgeListIterator) → None¶

removes an edge iterator from the node’s edge list. Only called by Edge class.

C++: utility::graph::Node::drop_edge(class utility::graph::EdgeListIterator) –> void

edge_list_begin(self: pyrosetta.rosetta.utility.graph.Node) → pyrosetta.rosetta.utility.graph.EdgeListIterator¶

returns a non-const iterator to the beginning of its edge list

C++: utility::graph::Node::edge_list_begin() –> class utility::graph::EdgeListIterator

edge_list_end(self: pyrosetta.rosetta.utility.graph.Node) → pyrosetta.rosetta.utility.graph.EdgeListIterator¶

returns a non-const iterator to the end of its edge list

C++: utility::graph::Node::edge_list_end() –> class utility::graph::EdgeListIterator

find_edge(self: pyrosetta.rosetta.utility.graph.Node, other_node_index: int) → utility::graph::Edge¶: C++: utility::graph::Node::find_edge(unsigned long) –> class utility::graph::Edge *

get_node_index(self: pyrosetta.rosetta.utility.graph.Node) → int¶

the index for this node

C++: utility::graph::Node::get_node_index() const –> unsigned long

get_num_edges_to_larger_indexed_nodes(self: pyrosetta.rosetta.utility.graph.Node) → int¶

the number of upper neighbors – which “self” neighborness is counted if a loop edge: is present

C++: utility::graph::Node::get_num_edges_to_larger_indexed_nodes() const –> unsigned long

get_num_edges_to_smaller_indexed_nodes(self: pyrosetta.rosetta.utility.graph.Node) → int¶

the number of lower neighbors

C++: utility::graph::Node::get_num_edges_to_smaller_indexed_nodes() const –> unsigned long

global_rotamer_id(self: pyrosetta.rosetta.protocols.hbnet.HBondNode) → int¶

duplicate interface for getting the global rotamer id. Identical to this->get_node_index() details this is equivalent to core::pack::rotamer_set::RotamerSetsBase::nrotamer_offset_for_moltenres( this->moltenres() ) + this->local_rotamer_id()

C++: protocols::hbnet::HBondNode::global_rotamer_id() const –> unsigned long

local_rotamer_id(self: pyrosetta.rosetta.protocols.hbnet.HBondNode) → int¶

get local rotamer id (local to the residue position)

this is equivalent to core::pack::rotamer_set::RotamerSetsBase::rotid_on_moltenresidue( this->get_node_index() )

C++: protocols::hbnet::HBondNode::local_rotamer_id() const –> unsigned int

loop_incident(self: pyrosetta.rosetta.utility.graph.Node) → bool¶

NOTE TO SELF: remove loop support

C++: utility::graph::Node::loop_incident() const –> bool

lower_edge_list_begin(self: pyrosetta.rosetta.utility.graph.Node) → pyrosetta.rosetta.utility.graph.EdgeListIterator¶

returns a non-const iterator to the beginning of its lower-edge list

C++: utility::graph::Node::lower_edge_list_begin() –> class utility::graph::EdgeListIterator

lower_edge_list_end(self: pyrosetta.rosetta.utility.graph.Node) → pyrosetta.rosetta.utility.graph.EdgeListIterator¶

returns a non-const iterator to the end of its lower-edge list

C++: utility::graph::Node::lower_edge_list_end() –> class utility::graph::EdgeListIterator

moltenres(self: pyrosetta.rosetta.protocols.hbnet.HBondNode) → int¶

get molten residue id for this rotamer

C++: protocols::hbnet::HBondNode::moltenres() const –> unsigned int

num_edges(self: pyrosetta.rosetta.utility.graph.Node) → int¶

the number of edges incident on this node, which may include a loop edge

C++: utility::graph::Node::num_edges() const –> unsigned long

num_neighbors_counting_self(self: pyrosetta.rosetta.utility.graph.Node) → int¶

the number of neighbors counting “self” as a neighbor.

C++: utility::graph::Node::num_neighbors_counting_self() const –> unsigned long

num_neighbors_counting_self_static(self: pyrosetta.rosetta.utility.graph.Node) → int¶

the number of neighbors counting “self” as neighbor. Defaults to: num_neighbors_counting_self() but can be set to other values as well. Useful in calculation of symmetrical structures.

C++: utility::graph::Node::num_neighbors_counting_self_static() const –> unsigned long

print(self: pyrosetta.rosetta.protocols.hbnet.HBondNode) → None¶: C++: protocols::hbnet::HBondNode::print() const –> void

register_clash(self: pyrosetta.rosetta.protocols.hbnet.HBondNode, node_id: int) → None¶

keep track of another node (rotamer) that this clashes with. You do not need to call this for all of the rotamers that share a residue position.

C++: protocols::hbnet::HBondNode::register_clash(unsigned long) –> void

set_local_rotamer_id(self: pyrosetta.rosetta.protocols.hbnet.HBondNode, rot_id: int) → None¶

set local rotamer id (local to the residue position).

C++: protocols::hbnet::HBondNode::set_local_rotamer_id(unsigned long) –> void

set_moltenres(self: pyrosetta.rosetta.protocols.hbnet.HBondNode, mres: int) → None¶

set molten residue id for this rotamer.

C++: protocols::hbnet::HBondNode::set_moltenres(unsigned long) –> void

set_num_neighbors_counting_self_static(self: pyrosetta.rosetta.utility.graph.Node, neighbor: int) → None¶

manually change the number of neighbors for a Node. Used: for symmetry scoring

C++: utility::graph::Node::set_num_neighbors_counting_self_static(unsigned long) –> void

upper_edge_list_begin(self: pyrosetta.rosetta.utility.graph.Node) → pyrosetta.rosetta.utility.graph.EdgeListIterator¶

returns a non-const iterator to the beginning of its upper-edge list

C++: utility::graph::Node::upper_edge_list_begin() –> class utility::graph::EdgeListIterator

upper_edge_list_end(self: pyrosetta.rosetta.utility.graph.Node) → pyrosetta.rosetta.utility.graph.EdgeListIterator¶

returns a non-const iterator to the end of its upper-edge list

C++: utility::graph::Node::upper_edge_list_end() –> class utility::graph::EdgeListIterator

pyrosetta.rosetta.protocols.hbnet.add_polar_atoms_to_network_state(: protocols::hbnet::NetworkState, : pyrosetta.rosetta.protocols.hbnet.HBondNode, : pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets) → None¶: C++: protocols::hbnet::add_polar_atoms_to_network_state(struct protocols::hbnet::NetworkState &, const class protocols::hbnet::HBondNode *, class std::shared_ptr<class core::pack::rotamer_set::RotamerSets>) –> void

pyrosetta.rosetta.protocols.hbnet.add_reslabels_to_pose(*args, **kwargs)¶

Overloaded function.

add_reslabels_to_pose(pose: pyrosetta.rosetta.core.pose.Pose, i: pyrosetta.rosetta.protocols.hbnet.hbond_net_struct) -> None
add_reslabels_to_pose(pose: pyrosetta.rosetta.core.pose.Pose, i: pyrosetta.rosetta.protocols.hbnet.hbond_net_struct, label: str) -> None

C++: protocols::hbnet::add_reslabels_to_pose(class core::pose::Pose &, struct protocols::hbnet::hbond_net_struct &, class std::basic_string<char>) –> void

pyrosetta.rosetta.protocols.hbnet.find_hbond_res_struct(residues: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_protocols_hbnet_hbond_res_struct_t, resnum: int) → __gnu_cxx::__normal_iterator<std::shared_ptr<protocols::hbnet::hbond_res_struct const> const*, std::vector<std::shared_ptr<protocols::hbnet::hbond_res_struct const>, std::allocator<std::shared_ptr<protocols::hbnet::hbond_res_struct const> > > >¶: C++: protocols::hbnet::find_hbond_res_struct(const class utility::vector1<class std::shared_ptr<const struct protocols::hbnet::hbond_res_struct>, class std::allocator<class std::shared_ptr<const struct protocols::hbnet::hbond_res_struct> > > &, unsigned long) –> class __gnu_cxx::__normal_iterator<const class std::shared_ptr<const struct protocols::hbnet::hbond_res_struct> *, class std::vector<class std::shared_ptr<const struct protocols::hbnet::hbond_res_struct>, class std::allocator<class std::shared_ptr<const struct protocols::hbnet::hbond_res_struct> > > >

pyrosetta.rosetta.protocols.hbnet.get_hbond_atom_pairs(*args, **kwargs)¶

Overloaded function.

get_hbond_atom_pairs(network: pyrosetta.rosetta.protocols.hbnet.hbond_net_struct, pose: pyrosetta.rosetta.core.pose.Pose) -> None
get_hbond_atom_pairs(network: pyrosetta.rosetta.protocols.hbnet.hbond_net_struct, pose: pyrosetta.rosetta.core.pose.Pose, bb_exlcusion: bool) -> None

C++: protocols::hbnet::get_hbond_atom_pairs(struct protocols::hbnet::hbond_net_struct &, class core::pose::Pose &, bool) –> void

pyrosetta.rosetta.protocols.hbnet.get_num_edges_for_res(res: int, path_dists: ObjexxFCL::FArray2D<int>) → int¶: C++: protocols::hbnet::get_num_edges_for_res(const unsigned long, class ObjexxFCL::FArray2D<int> &) –> unsigned long

pyrosetta.rosetta.protocols.hbnet.get_num_protein_sc_sc_hbonds(pose: pyrosetta.rosetta.core.pose.Pose, i: pyrosetta.rosetta.protocols.hbnet.hbond_net_struct) → int¶: C++: protocols::hbnet::get_num_protein_sc_sc_hbonds(class core::pose::Pose &, struct protocols::hbnet::hbond_net_struct &) –> unsigned long

pyrosetta.rosetta.protocols.hbnet.hbnet_one_body_energies(pose: pyrosetta.rosetta.core.pose.Pose, rotset_op: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, energies: pyrosetta.rosetta.utility.vector1_float) → None¶: C++: protocols::hbnet::hbnet_one_body_energies(const class core::pose::Pose &, class std::shared_ptr<class core::pack::rotamer_set::RotamerSet>, const class core::scoring::ScoreFunction &, class utility::vector1<float, class std::allocator<float> > &) –> void

pyrosetta.rosetta.protocols.hbnet.hbnet_symm_one_body_energies(pose: pyrosetta.rosetta.core.pose.Pose, rotset_op: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, energies: pyrosetta.rosetta.utility.vector1_float) → None¶: C++: protocols::hbnet::hbnet_symm_one_body_energies(const class core::pose::Pose &, class std::shared_ptr<class core::pack::rotamer_set::RotamerSet>, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class utility::vector1<float, class std::allocator<float> > &) –> void

pyrosetta.rosetta.protocols.hbnet.hbond_exists_in_vector(hbond_vec: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_hbonds_HBond_t, h2: pyrosetta.rosetta.core.scoring.hbonds.HBond) → bool¶: C++: protocols::hbnet::hbond_exists_in_vector(const class utility::vector1<class std::shared_ptr<const class core::scoring::hbonds::HBond>, class std::allocator<class std::shared_ptr<const class core::scoring::hbonds::HBond> > > &, class std::shared_ptr<const class core::scoring::hbonds::HBond>) –> bool

class pyrosetta.rosetta.protocols.hbnet.hbond_net_struct¶

Bases: pybind11_builtins.pybind11_object

struct that contains info needed for hbond networks

__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.hbnet.hbond_net_struct) -> None
__init__(self: pyrosetta.rosetta.protocols.hbnet.hbond_net_struct, arg0: pyrosetta.rosetta.protocols.hbnet.hbond_net_struct) -> 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.hbnet.hbond_net_struct, : pyrosetta.rosetta.protocols.hbnet.hbond_net_struct) → pyrosetta.rosetta.protocols.hbnet.hbond_net_struct¶: C++: protocols::hbnet::hbond_net_struct::operator=(const struct protocols::hbnet::hbond_net_struct &) –> struct protocols::hbnet::hbond_net_struct &

class pyrosetta.rosetta.protocols.hbnet.hbond_res_struct¶

Bases: pybind11_builtins.pybind11_object

struct that represents minimal info for residue in an h-bond network

__delattr__¶: Implement delattr(self, name).

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

__eq__(self: pyrosetta.rosetta.protocols.hbnet.hbond_res_struct, a: pyrosetta.rosetta.protocols.hbnet.hbond_res_struct) → bool¶: C++: protocols::hbnet::hbond_res_struct::operator==(const struct protocols::hbnet::hbond_res_struct &) const –> bool

__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.hbnet.hbond_res_struct) -> None
__init__(self: pyrosetta.rosetta.protocols.hbnet.hbond_res_struct, res: int, rot: int, a: str, c: str, prot: bool, solv: bool, lig: 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.hbnet.hbond_res_struct, : pyrosetta.rosetta.protocols.hbnet.hbond_res_struct) → pyrosetta.rosetta.protocols.hbnet.hbond_res_struct¶: C++: protocols::hbnet::hbond_res_struct::operator=(const struct protocols::hbnet::hbond_res_struct &) –> struct protocols::hbnet::hbond_res_struct &

pyrosetta.rosetta.protocols.hbnet.heavy_atoms_are_within_cutoff(atom1: pyrosetta.rosetta.numeric.xyzVector_double_t, atom2: pyrosetta.rosetta.numeric.xyzVector_float_t) → bool¶: C++: protocols::hbnet::heavy_atoms_are_within_cutoff(const class numeric::xyzVector<double> &, const class numeric::xyzVector<float> &) –> bool

pyrosetta.rosetta.protocols.hbnet.his_tyr_connectivity(pose: pyrosetta.rosetta.core.pose.Pose, i: pyrosetta.rosetta.protocols.hbnet.hbond_net_struct) → bool¶: C++: protocols::hbnet::his_tyr_connectivity(const class core::pose::Pose &, struct protocols::hbnet::hbond_net_struct &) –> bool

pyrosetta.rosetta.protocols.hbnet.network_contains_aa(*args, **kwargs)¶

Overloaded function.

network_contains_aa(aa_one_letter: str, i: pyrosetta.rosetta.protocols.hbnet.hbond_net_struct) -> bool

C++: protocols::hbnet::network_contains_aa(char, const struct protocols::hbnet::hbond_net_struct &) –> bool

network_contains_aa(aa_one_letter: str, residues: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_protocols_hbnet_hbond_res_struct_t) -> bool

C++: protocols::hbnet::network_contains_aa(char, const class utility::vector1<class std::shared_ptr<const struct protocols::hbnet::hbond_res_struct>, class std::allocator<class std::shared_ptr<const struct protocols::hbnet::hbond_res_struct> > > &) –> bool

class pyrosetta.rosetta.protocols.hbnet.polar_atom¶

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.hbnet.polar_atom, arg0: int, arg1: pyrosetta.rosetta.numeric.xyzVector_float_t, arg2: bool) -> None

doc

__init__(self: pyrosetta.rosetta.protocols.hbnet.polar_atom, sequence_position: int, atom_position: pyrosetta.rosetta.numeric.xyzVector_float_t, hydroxyl: bool, satisfied: bool) -> None
__init__(self: pyrosetta.rosetta.protocols.hbnet.polar_atom, arg0: pyrosetta.rosetta.protocols.hbnet.polar_atom) -> 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).

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

pyrosetta.rosetta.protocols.hbnet.print_list_to_string(*args, **kwargs)¶

Overloaded function.

print_list_to_string(network: pyrosetta.rosetta.protocols.hbnet.hbond_net_struct) -> str
print_list_to_string(network: pyrosetta.rosetta.protocols.hbnet.hbond_net_struct, chainid: bool) -> str
print_list_to_string(network: pyrosetta.rosetta.protocols.hbnet.hbond_net_struct, chainid: bool, term_w_start: bool) -> str
print_list_to_string(network: pyrosetta.rosetta.protocols.hbnet.hbond_net_struct, chainid: bool, term_w_start: bool, term_w_cycle: bool) -> str
print_list_to_string(network: pyrosetta.rosetta.protocols.hbnet.hbond_net_struct, chainid: bool, term_w_start: bool, term_w_cycle: bool, term_w_bb: bool) -> str

C++: protocols::hbnet::print_list_to_string(const struct protocols::hbnet::hbond_net_struct &, bool, bool, bool, bool) –> std::string

print_list_to_string(pose: pyrosetta.rosetta.core.pose.Pose, network: pyrosetta.rosetta.protocols.hbnet.hbond_net_struct) -> str
print_list_to_string(pose: pyrosetta.rosetta.core.pose.Pose, network: pyrosetta.rosetta.protocols.hbnet.hbond_net_struct, chainid: bool) -> str
print_list_to_string(pose: pyrosetta.rosetta.core.pose.Pose, network: pyrosetta.rosetta.protocols.hbnet.hbond_net_struct, chainid: bool, term_w_start: bool) -> str
print_list_to_string(pose: pyrosetta.rosetta.core.pose.Pose, network: pyrosetta.rosetta.protocols.hbnet.hbond_net_struct, chainid: bool, term_w_start: bool, term_w_cycle: bool) -> str
print_list_to_string(pose: pyrosetta.rosetta.core.pose.Pose, network: pyrosetta.rosetta.protocols.hbnet.hbond_net_struct, chainid: bool, term_w_start: bool, term_w_cycle: bool, term_w_bb: bool) -> str
print_list_to_string(pose: pyrosetta.rosetta.core.pose.Pose, network: pyrosetta.rosetta.protocols.hbnet.hbond_net_struct, chainid: bool, term_w_start: bool, term_w_cycle: bool, term_w_bb: bool, use_pdb_numbering: bool) -> str

C++: protocols::hbnet::print_list_to_string(const class core::pose::Pose &, const struct protocols::hbnet::hbond_net_struct &, bool, bool, bool, bool, bool) –> std::string

pyrosetta.rosetta.protocols.hbnet.print_network(*args, **kwargs)¶

Overloaded function.

print_network(i: pyrosetta.rosetta.protocols.hbnet.hbond_net_struct) -> str
print_network(i: pyrosetta.rosetta.protocols.hbnet.hbond_net_struct, chainid: bool) -> str

C++: protocols::hbnet::print_network(const struct protocols::hbnet::hbond_net_struct &, bool) –> std::string

pyrosetta.rosetta.protocols.hbnet.print_network_w_pdb_numbering(pose: pyrosetta.rosetta.core.pose.Pose, i: pyrosetta.rosetta.protocols.hbnet.hbond_net_struct, chainid: bool) → str¶: C++: protocols::hbnet::print_network_w_pdb_numbering(const class core::pose::Pose &, const struct protocols::hbnet::hbond_net_struct &, bool) –> std::string