graph

Bindings for core::scoring::hbonds::graph namespace

class pyrosetta.rosetta.core.scoring.hbonds.graph.AtomInfo

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.scoring.hbonds.graph.AtomInfo, : pyrosetta.rosetta.core.scoring.hbonds.graph.AtomInfo) → pyrosetta.rosetta.core.scoring.hbonds.graph.AtomInfo

C++: core::scoring::hbonds::graph::AtomInfo::operator=(const class core::scoring::hbonds::graph::AtomInfo &) –> class core::scoring::hbonds::graph::AtomInfo &

is_acceptor(*args, **kwargs)

Overloaded function.

  1. is_acceptor(self: pyrosetta.rosetta.core.scoring.hbonds.graph.AtomInfo, setting: bool) -> None

C++: core::scoring::hbonds::graph::AtomInfo::is_acceptor(bool) –> void

  1. is_acceptor(self: pyrosetta.rosetta.core.scoring.hbonds.graph.AtomInfo) -> bool

C++: core::scoring::hbonds::graph::AtomInfo::is_acceptor() const –> bool

is_backbone(*args, **kwargs)

Overloaded function.

  1. is_backbone(self: pyrosetta.rosetta.core.scoring.hbonds.graph.AtomInfo, setting: bool) -> None

C++: core::scoring::hbonds::graph::AtomInfo::is_backbone(bool) –> void

  1. is_backbone(self: pyrosetta.rosetta.core.scoring.hbonds.graph.AtomInfo) -> bool

C++: core::scoring::hbonds::graph::AtomInfo::is_backbone() const –> bool

is_donor(*args, **kwargs)

Overloaded function.

  1. is_donor(self: pyrosetta.rosetta.core.scoring.hbonds.graph.AtomInfo, setting: bool) -> None

C++: core::scoring::hbonds::graph::AtomInfo::is_donor(bool) –> void

  1. is_donor(self: pyrosetta.rosetta.core.scoring.hbonds.graph.AtomInfo) -> bool

C++: core::scoring::hbonds::graph::AtomInfo::is_donor() const –> bool

is_hydrogen(*args, **kwargs)

Overloaded function.

  1. is_hydrogen(self: pyrosetta.rosetta.core.scoring.hbonds.graph.AtomInfo, setting: bool) -> None

C++: core::scoring::hbonds::graph::AtomInfo::is_hydrogen(bool) –> void

  1. is_hydrogen(self: pyrosetta.rosetta.core.scoring.hbonds.graph.AtomInfo) -> bool

C++: core::scoring::hbonds::graph::AtomInfo::is_hydrogen() const –> bool

is_hydroxyl(*args, **kwargs)

Overloaded function.

  1. is_hydroxyl(self: pyrosetta.rosetta.core.scoring.hbonds.graph.AtomInfo, setting: bool) -> None

C++: core::scoring::hbonds::graph::AtomInfo::is_hydroxyl(bool) –> void

  1. is_hydroxyl(self: pyrosetta.rosetta.core.scoring.hbonds.graph.AtomInfo) -> bool

C++: core::scoring::hbonds::graph::AtomInfo::is_hydroxyl() const –> bool

local_atom_id(*args, **kwargs)

Overloaded function.

  1. local_atom_id(self: pyrosetta.rosetta.core.scoring.hbonds.graph.AtomInfo, local_atom_id: int) -> None

C++: core::scoring::hbonds::graph::AtomInfo::local_atom_id(unsigned short) –> void

  1. local_atom_id(self: pyrosetta.rosetta.core.scoring.hbonds.graph.AtomInfo) -> int

C++: core::scoring::hbonds::graph::AtomInfo::local_atom_id() const –> unsigned short

xyz(*args, **kwargs)

Overloaded function.

  1. xyz(self: pyrosetta.rosetta.core.scoring.hbonds.graph.AtomInfo, setting: pyrosetta.rosetta.numeric.xyzVector_float_t) -> None

C++: core::scoring::hbonds::graph::AtomInfo::xyz(const class numeric::xyzVector<float> &) –> void

  1. xyz(self: pyrosetta.rosetta.core.scoring.hbonds.graph.AtomInfo) -> pyrosetta.rosetta.numeric.xyzVector_float_t

C++: core::scoring::hbonds::graph::AtomInfo::xyz() const –> const class numeric::xyzVector<float> &

class pyrosetta.rosetta.core.scoring.hbonds.graph.AtomInfoSet

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.scoring.hbonds.graph.AtomInfoSet, : pyrosetta.rosetta.core.scoring.hbonds.graph.AtomInfoSet) → pyrosetta.rosetta.core.scoring.hbonds.graph.AtomInfoSet

C++: core::scoring::hbonds::graph::AtomInfoSet::operator=(const class core::scoring::hbonds::graph::AtomInfoSet &) –> class core::scoring::hbonds::graph::AtomInfoSet &

contains(self: pyrosetta.rosetta.core.scoring.hbonds.graph.AtomInfoSet, local_atom_id: int) → bool

C++: core::scoring::hbonds::graph::AtomInfoSet::contains(unsigned short) const –> bool

class pyrosetta.rosetta.core.scoring.hbonds.graph.HBondEdge

Bases: LowMemEdge

Each HBondEdge represents a hydrogen bond

assign(self: pyrosetta.rosetta.core.scoring.hbonds.graph.HBondEdge, src: pyrosetta.rosetta.core.scoring.hbonds.graph.HBondEdge) → pyrosetta.rosetta.core.scoring.hbonds.graph.HBondEdge

C++: core::scoring::hbonds::graph::HBondEdge::operator=(const class core::scoring::hbonds::graph::HBondEdge &) –> class core::scoring::hbonds::graph::HBondEdge &

count_dynamic_memory(self: pyrosetta.rosetta.core.scoring.hbonds.graph.HBondEdge) → int

C++: core::scoring::hbonds::graph::HBondEdge::count_dynamic_memory() const –> unsigned long

count_static_memory(self: pyrosetta.rosetta.core.scoring.hbonds.graph.HBondEdge) → int

C++: core::scoring::hbonds::graph::HBondEdge::count_static_memory() const –> unsigned long

energy(self: pyrosetta.rosetta.core.scoring.hbonds.graph.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++: core::scoring::hbonds::graph::HBondEdge::energy() const –> float

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

returns the index of the lower node

C++: utility::graph::LowMemEdge::get_first_node_ind() const –> unsigned int

get_other_ind(self: pyrosetta.rosetta.utility.graph.LowMemEdge, node_ind: 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::LowMemEdge::get_other_ind(unsigned int) const –> unsigned int

get_other_node(*args, **kwargs)

Overloaded function.

  1. get_other_node(self: pyrosetta.rosetta.utility.graph.LowMemEdge, node_index: int, graph: pyrosetta.rosetta.utility.graph.LowMemGraphBase) -> pyrosetta.rosetta.utility.graph.LowMemNode

returns a 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::LowMemEdge::get_other_node(unsigned int, const class utility::graph::LowMemGraphBase &) const –> const class utility::graph::LowMemNode *

  1. get_other_node(self: pyrosetta.rosetta.utility.graph.LowMemEdge, node_index: int, graph: pyrosetta.rosetta.utility.graph.LowMemGraphBase) -> pyrosetta.rosetta.utility.graph.LowMemNode

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::LowMemEdge::get_other_node(unsigned int, class utility::graph::LowMemGraphBase &) –> class utility::graph::LowMemNode *

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

returns the index of the upper node

C++: utility::graph::LowMemEdge::get_second_node_ind() const –> unsigned int

hbonds(self: pyrosetta.rosetta.core.scoring.hbonds.graph.HBondEdge) → pyrosetta.rosetta.std.vector_core_scoring_hbonds_graph_HBondInfo

C++: core::scoring::hbonds::graph::HBondEdge::hbonds() –> class std::vector<class core::scoring::hbonds::graph::HBondInfo, class std::allocator<class core::scoring::hbonds::graph::HBondInfo> > &

internal_delete_self(self: pyrosetta.rosetta.utility.graph.LowMemEdge) → None

Don’t call this!!! Only to be called by LowMemGraph

C++: utility::graph::LowMemEdge::internal_delete_self() –> void

merge_data(self: pyrosetta.rosetta.core.scoring.hbonds.graph.HBondEdge, other: pyrosetta.rosetta.core.scoring.hbonds.graph.HBondEdge, other_node_to_my_node: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Only merges new data added by this class. Flips first_node_is_donor if necessary

other_node_to_my_node is a map of node indices from the other graph

to node indices in this graph.

other_node_to_my_node.size() == other_graph.num_nodes()

C++: core::scoring::hbonds::graph::HBondEdge::merge_data(const class core::scoring::hbonds::graph::HBondEdge &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

register_hbond(self: pyrosetta.rosetta.core.scoring.hbonds.graph.HBondEdge, first_node_is_donor: bool, local_atom_id_A: int, local_atom_id_D: int, local_atom_id_H: int, energy: float) → None

C++: core::scoring::hbonds::graph::HBondEdge::register_hbond(bool, unsigned short, unsigned short, unsigned short, float) –> void

same_edge(self: pyrosetta.rosetta.utility.graph.LowMemEdge, 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::LowMemEdge::same_edge(unsigned int, unsigned int) const –> bool

score(self: pyrosetta.rosetta.core.scoring.hbonds.graph.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++: core::scoring::hbonds::graph::HBondEdge::score() const –> float

set_energy(self: pyrosetta.rosetta.core.scoring.hbonds.graph.HBondEdge, energy: float) → None

C++: core::scoring::hbonds::graph::HBondEdge::set_energy(double) –> void

set_score(self: pyrosetta.rosetta.core.scoring.hbonds.graph.HBondEdge, energy: float) → None

C++: core::scoring::hbonds::graph::HBondEdge::set_score(double) –> void

class pyrosetta.rosetta.core.scoring.hbonds.graph.HBondGraph

Bases: LowMemGraph_core_scoring_hbonds_graph_HBondNode_core_scoring_hbonds_graph_HBondEdge_t

add_edge(self: pyrosetta.rosetta.utility.graph.LowMemGraph_core_scoring_hbonds_graph_HBondNode_core_scoring_hbonds_graph_HBondEdge_t, example_edge: pyrosetta.rosetta.utility.graph.LowMemEdge) → pyrosetta.rosetta.core.scoring.hbonds.graph.HBondEdge

C++: utility::graph::LowMemGraph<core::scoring::hbonds::graph::HBondNode, core::scoring::hbonds::graph::HBondEdge>::add_edge(const class utility::graph::LowMemEdge *) –> class core::scoring::hbonds::graph::HBondEdge *

assign(self: pyrosetta.rosetta.core.scoring.hbonds.graph.HBondGraph, : pyrosetta.rosetta.core.scoring.hbonds.graph.HBondGraph) → pyrosetta.rosetta.core.scoring.hbonds.graph.HBondGraph

C++: core::scoring::hbonds::graph::HBondGraph::operator=(const class core::scoring::hbonds::graph::HBondGraph &) –> class core::scoring::hbonds::graph::HBondGraph &

const_edge_list_begin(self: pyrosetta.rosetta.utility.graph.LowMemGraph_core_scoring_hbonds_graph_HBondNode_core_scoring_hbonds_graph_HBondEdge_t) → utility::graph::LowMemEdgeListConstIter

C++: utility::graph::LowMemGraph<core::scoring::hbonds::graph::HBondNode, core::scoring::hbonds::graph::HBondEdge>::const_edge_list_begin() const –> class utility::graph::LowMemEdgeListConstIter

const_edge_list_end(self: pyrosetta.rosetta.utility.graph.LowMemGraph_core_scoring_hbonds_graph_HBondNode_core_scoring_hbonds_graph_HBondEdge_t) → utility::graph::LowMemEdgeListConstIter

C++: utility::graph::LowMemGraph<core::scoring::hbonds::graph::HBondNode, core::scoring::hbonds::graph::HBondEdge>::const_edge_list_end() const –> class utility::graph::LowMemEdgeListConstIter

count_dynamic_memory(self: pyrosetta.rosetta.core.scoring.hbonds.graph.HBondGraph) → int

C++: core::scoring::hbonds::graph::HBondGraph::count_dynamic_memory() const –> unsigned long

count_static_memory(self: pyrosetta.rosetta.core.scoring.hbonds.graph.HBondGraph) → int

C++: core::scoring::hbonds::graph::HBondGraph::count_static_memory() const –> unsigned long

delete_edge(self: pyrosetta.rosetta.utility.graph.LowMemGraph_core_scoring_hbonds_graph_HBondNode_core_scoring_hbonds_graph_HBondEdge_t, edge: pyrosetta.rosetta.utility.graph.LowMemEdge) → None

C++: utility::graph::LowMemGraph<core::scoring::hbonds::graph::HBondNode, core::scoring::hbonds::graph::HBondEdge>::delete_edge(class utility::graph::LowMemEdge *) –> void

delete_everything(self: pyrosetta.rosetta.utility.graph.LowMemGraph_core_scoring_hbonds_graph_HBondNode_core_scoring_hbonds_graph_HBondEdge_t) → None

C++: utility::graph::LowMemGraph<core::scoring::hbonds::graph::HBondNode, core::scoring::hbonds::graph::HBondEdge>::delete_everything() –> void

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

C++: utility::graph::LowMemGraph<core::scoring::hbonds::graph::HBondNode, core::scoring::hbonds::graph::HBondEdge>::drop_all_edges() –> void

drop_all_edges_for_node(*args, **kwargs)

Overloaded function.

  1. drop_all_edges_for_node(self: pyrosetta.rosetta.utility.graph.LowMemGraph_core_scoring_hbonds_graph_HBondNode_core_scoring_hbonds_graph_HBondEdge_t, index: int) -> None

C++: utility::graph::LowMemGraph<core::scoring::hbonds::graph::HBondNode, core::scoring::hbonds::graph::HBondEdge>::drop_all_edges_for_node(unsigned int) –> void

  1. drop_all_edges_for_node(self: pyrosetta.rosetta.utility.graph.LowMemGraph_core_scoring_hbonds_graph_HBondNode_core_scoring_hbonds_graph_HBondEdge_t, index: int) -> None

C++: utility::graph::LowMemGraphBase::drop_all_edges_for_node(unsigned int) –> void

edge_list_begin(self: pyrosetta.rosetta.utility.graph.LowMemGraph_core_scoring_hbonds_graph_HBondNode_core_scoring_hbonds_graph_HBondEdge_t) → utility::graph::LowMemEdgeListIter

C++: utility::graph::LowMemGraph<core::scoring::hbonds::graph::HBondNode, core::scoring::hbonds::graph::HBondEdge>::edge_list_begin() –> class utility::graph::LowMemEdgeListIter

edge_list_end(self: pyrosetta.rosetta.utility.graph.LowMemGraph_core_scoring_hbonds_graph_HBondNode_core_scoring_hbonds_graph_HBondEdge_t) → utility::graph::LowMemEdgeListIter

C++: utility::graph::LowMemGraph<core::scoring::hbonds::graph::HBondNode, core::scoring::hbonds::graph::HBondEdge>::edge_list_end() –> class utility::graph::LowMemEdgeListIter

find_edge(self: pyrosetta.rosetta.utility.graph.LowMemGraph_core_scoring_hbonds_graph_HBondNode_core_scoring_hbonds_graph_HBondEdge_t, node1: int, node2: int) → pyrosetta.rosetta.core.scoring.hbonds.graph.HBondEdge

C++: utility::graph::LowMemGraph<core::scoring::hbonds::graph::HBondNode, core::scoring::hbonds::graph::HBondEdge>::find_edge(unsigned long, unsigned long) –> class core::scoring::hbonds::graph::HBondEdge *

getTotalMemoryUsage(self: pyrosetta.rosetta.utility.graph.LowMemGraph_core_scoring_hbonds_graph_HBondNode_core_scoring_hbonds_graph_HBondEdge_t) → int

C++: utility::graph::LowMemGraph<core::scoring::hbonds::graph::HBondNode, core::scoring::hbonds::graph::HBondEdge>::getTotalMemoryUsage() –> unsigned long

get_edge_exists(self: pyrosetta.rosetta.utility.graph.LowMemGraph_core_scoring_hbonds_graph_HBondNode_core_scoring_hbonds_graph_HBondEdge_t, node1: int, node2: int) → bool

C++: utility::graph::LowMemGraph<core::scoring::hbonds::graph::HBondNode, core::scoring::hbonds::graph::HBondEdge>::get_edge_exists(unsigned int, unsigned int) const –> bool

get_node(*args, **kwargs)

Overloaded function.

  1. get_node(self: pyrosetta.rosetta.utility.graph.LowMemGraph_core_scoring_hbonds_graph_HBondNode_core_scoring_hbonds_graph_HBondEdge_t, index: int) -> pyrosetta.rosetta.core.scoring.hbonds.graph.HBondNode

C++: utility::graph::LowMemGraph<core::scoring::hbonds::graph::HBondNode, core::scoring::hbonds::graph::HBondEdge>::get_node(unsigned int) –> class core::scoring::hbonds::graph::HBondNode *

  1. get_node(self: pyrosetta.rosetta.utility.graph.LowMemGraph_core_scoring_hbonds_graph_HBondNode_core_scoring_hbonds_graph_HBondEdge_t, index: int) -> pyrosetta.rosetta.utility.graph.LowMemNode

C++: utility::graph::LowMemGraphBase::get_node(unsigned int) –> class utility::graph::LowMemNode *

internal_edge_list_size(*args, **kwargs)

Overloaded function.

  1. internal_edge_list_size(self: pyrosetta.rosetta.utility.graph.LowMemGraph_core_scoring_hbonds_graph_HBondNode_core_scoring_hbonds_graph_HBondEdge_t) -> int

C++: utility::graph::LowMemGraph<core::scoring::hbonds::graph::HBondNode, core::scoring::hbonds::graph::HBondEdge>::internal_edge_list_size() const –> unsigned long

  1. internal_edge_list_size(self: pyrosetta.rosetta.utility.graph.LowMemGraph_core_scoring_hbonds_graph_HBondNode_core_scoring_hbonds_graph_HBondEdge_t) -> int

C++: utility::graph::LowMemGraphBase::internal_edge_list_size() const –> unsigned long

merge(self: pyrosetta.rosetta.core.scoring.hbonds.graph.HBondGraph, other: pyrosetta.rosetta.core.scoring.hbonds.graph.HBondGraph, merge_nodes_with_OR_logic: bool) → None
Merges all info from other into this graph. All nodes from other must

be present in this graph (by rotamer_id and mres_id).

There are two ways to merge the atoms of a node.

OR_logic - Take the union of the atoms at each node AND_logic - Take the intersection of the atoms at each node

C++: core::scoring::hbonds::graph::HBondGraph::merge(const class core::scoring::hbonds::graph::HBondGraph &, bool) –> void

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

C++: utility::graph::LowMemGraph<core::scoring::hbonds::graph::HBondNode, core::scoring::hbonds::graph::HBondEdge>::num_edges() const –> unsigned long

num_nodes(self: pyrosetta.rosetta.utility.graph.LowMemGraph_core_scoring_hbonds_graph_HBondNode_core_scoring_hbonds_graph_HBondEdge_t) → int

C++: utility::graph::LowMemGraph<core::scoring::hbonds::graph::HBondNode, core::scoring::hbonds::graph::HBondEdge>::num_nodes() const –> unsigned long

print_vertices(self: pyrosetta.rosetta.utility.graph.LowMemGraph_core_scoring_hbonds_graph_HBondNode_core_scoring_hbonds_graph_HBondEdge_t) → None

C++: utility::graph::LowMemGraph<core::scoring::hbonds::graph::HBondNode, core::scoring::hbonds::graph::HBondEdge>::print_vertices() const –> void

register_hbond(self: pyrosetta.rosetta.core.scoring.hbonds.graph.HBondGraph, rotamerA: int, rotamerB: int, score: float) → pyrosetta.rosetta.core.scoring.hbonds.graph.HBondEdge

C++: core::scoring::hbonds::graph::HBondGraph::register_hbond(unsigned long, unsigned long, double) –> class core::scoring::hbonds::graph::HBondEdge *

set_num_nodes(self: pyrosetta.rosetta.utility.graph.LowMemGraph_core_scoring_hbonds_graph_HBondNode_core_scoring_hbonds_graph_HBondEdge_t, num_nodes: int) → None

C++: utility::graph::LowMemGraph<core::scoring::hbonds::graph::HBondNode, core::scoring::hbonds::graph::HBondEdge>::set_num_nodes(unsigned int) –> void

class pyrosetta.rosetta.core.scoring.hbonds.graph.HBondInfo

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.scoring.hbonds.graph.HBondInfo, : pyrosetta.rosetta.core.scoring.hbonds.graph.HBondInfo) → pyrosetta.rosetta.core.scoring.hbonds.graph.HBondInfo

C++: core::scoring::hbonds::graph::HBondInfo::operator=(const class core::scoring::hbonds::graph::HBondInfo &) –> class core::scoring::hbonds::graph::HBondInfo &

first_node_is_donor(*args, **kwargs)

Overloaded function.

  1. first_node_is_donor(self: pyrosetta.rosetta.core.scoring.hbonds.graph.HBondInfo) -> bool

C++: core::scoring::hbonds::graph::HBondInfo::first_node_is_donor() const –> bool

  1. first_node_is_donor(self: pyrosetta.rosetta.core.scoring.hbonds.graph.HBondInfo, setting: bool) -> None

C++: core::scoring::hbonds::graph::HBondInfo::first_node_is_donor(bool) –> void

local_atom_id_A(*args, **kwargs)

Overloaded function.

  1. local_atom_id_A(self: pyrosetta.rosetta.core.scoring.hbonds.graph.HBondInfo) -> int

C++: core::scoring::hbonds::graph::HBondInfo::local_atom_id_A() const –> unsigned short

  1. local_atom_id_A(self: pyrosetta.rosetta.core.scoring.hbonds.graph.HBondInfo, setting: int) -> None

C++: core::scoring::hbonds::graph::HBondInfo::local_atom_id_A(unsigned short) –> void

local_atom_id_D(*args, **kwargs)

Overloaded function.

  1. local_atom_id_D(self: pyrosetta.rosetta.core.scoring.hbonds.graph.HBondInfo) -> int

C++: core::scoring::hbonds::graph::HBondInfo::local_atom_id_D() const –> unsigned short

  1. local_atom_id_D(self: pyrosetta.rosetta.core.scoring.hbonds.graph.HBondInfo, setting: int) -> None

C++: core::scoring::hbonds::graph::HBondInfo::local_atom_id_D(unsigned short) –> void

local_atom_id_H(*args, **kwargs)

Overloaded function.

  1. local_atom_id_H(self: pyrosetta.rosetta.core.scoring.hbonds.graph.HBondInfo) -> int

C++: core::scoring::hbonds::graph::HBondInfo::local_atom_id_H() const –> unsigned short

  1. local_atom_id_H(self: pyrosetta.rosetta.core.scoring.hbonds.graph.HBondInfo, setting: int) -> None

C++: core::scoring::hbonds::graph::HBondInfo::local_atom_id_H(unsigned short) –> void

score(*args, **kwargs)

Overloaded function.

  1. score(self: pyrosetta.rosetta.core.scoring.hbonds.graph.HBondInfo) -> float

C++: core::scoring::hbonds::graph::HBondInfo::score() const –> float

  1. score(self: pyrosetta.rosetta.core.scoring.hbonds.graph.HBondInfo, score: float) -> None

C++: core::scoring::hbonds::graph::HBondInfo::score(float) –> void

class pyrosetta.rosetta.core.scoring.hbonds.graph.HBondNode

Bases: LowMemNode

Each HBondNode represents a rotamer from the RotamerSets object

add_polar_atom(self: pyrosetta.rosetta.core.scoring.hbonds.graph.HBondNode, local_atom_id: int, atom_position: pyrosetta.rosetta.numeric.xyzVector_float_t, is_hydrogen: bool, is_donor: bool, is_acceptor: bool, is_hydroxyl: bool, is_backbone: bool) → None

C++: core::scoring::hbonds::graph::HBondNode::add_polar_atom(unsigned short, const class numeric::xyzVector<float> &, bool, bool, bool, bool, bool) –> void

add_polar_atom_if_doesnt_exist(self: pyrosetta.rosetta.core.scoring.hbonds.graph.HBondNode, info: pyrosetta.rosetta.core.scoring.hbonds.graph.AtomInfo) → None

The polar atoms are sorted, so we have to cleverly insert and maintain the order

Used by merge

C++: core::scoring::hbonds::graph::HBondNode::add_polar_atom_if_doesnt_exist(const class core::scoring::hbonds::graph::AtomInfo &) –> void

assign(self: pyrosetta.rosetta.core.scoring.hbonds.graph.HBondNode, src: pyrosetta.rosetta.core.scoring.hbonds.graph.HBondNode) → pyrosetta.rosetta.core.scoring.hbonds.graph.HBondNode

C++: core::scoring::hbonds::graph::HBondNode::operator=(const class core::scoring::hbonds::graph::HBondNode &) –> class core::scoring::hbonds::graph::HBondNode &

clashes(self: pyrosetta.rosetta.core.scoring.hbonds.graph.HBondNode, node_id: pyrosetta.rosetta.utility.StrongT_unsigned_long_core_scoring_hbonds_graph_NodeIDSize_t) → bool

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

C++: core::scoring::hbonds::graph::HBondNode::clashes(struct utility::StrongT<unsigned long, struct core::scoring::hbonds::graph::NodeIDSize_>) const –> bool

const_edge_list_begin(self: pyrosetta.rosetta.utility.graph.LowMemNode, graph: pyrosetta.rosetta.utility.graph.LowMemGraphBase) → utility::graph::LowMemEdgeListConstIter

returns a const iterator to the beginning of its edge list

C++: utility::graph::LowMemNode::const_edge_list_begin(const class utility::graph::LowMemGraphBase &) const –> class utility::graph::LowMemEdgeListConstIter

const_edge_list_end(self: pyrosetta.rosetta.utility.graph.LowMemNode, graph: pyrosetta.rosetta.utility.graph.LowMemGraphBase) → utility::graph::LowMemEdgeListConstIter

returns a const iterator to the end of its edge list

C++: utility::graph::LowMemNode::const_edge_list_end(const class utility::graph::LowMemGraphBase &) const –> class utility::graph::LowMemEdgeListConstIter

count_dynamic_memory(self: pyrosetta.rosetta.core.scoring.hbonds.graph.HBondNode) → int

C++: core::scoring::hbonds::graph::HBondNode::count_dynamic_memory() const –> unsigned long

count_static_memory(self: pyrosetta.rosetta.core.scoring.hbonds.graph.HBondNode) → int

C++: core::scoring::hbonds::graph::HBondNode::count_static_memory() const –> unsigned long

drop_all_edges(self: pyrosetta.rosetta.utility.graph.LowMemNode, graph: pyrosetta.rosetta.utility.graph.LowMemGraphBase) → None

deletes all edges incident upon this node

Although edges are deleted, the memory for the edges is not freed.

C++: utility::graph::LowMemNode::drop_all_edges(class utility::graph::LowMemGraphBase &) –> void

edge_list_begin(self: pyrosetta.rosetta.utility.graph.LowMemNode, graph: pyrosetta.rosetta.utility.graph.LowMemGraphBase) → utility::graph::LowMemEdgeListIter

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

C++: utility::graph::LowMemNode::edge_list_begin(class utility::graph::LowMemGraphBase &) –> class utility::graph::LowMemEdgeListIter

edge_list_end(self: pyrosetta.rosetta.utility.graph.LowMemNode, graph: pyrosetta.rosetta.utility.graph.LowMemGraphBase) → utility::graph::LowMemEdgeListIter

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

C++: utility::graph::LowMemNode::edge_list_end(class utility::graph::LowMemGraphBase &) –> class utility::graph::LowMemEdgeListIter

find_edge(*args, **kwargs)

Overloaded function.

  1. find_edge(self: pyrosetta.rosetta.utility.graph.LowMemNode, other_node_ind: int, graph: pyrosetta.rosetta.utility.graph.LowMemGraphBase) -> utility::graph::LowMemEdge

a “slow” (linear) search for an edge.

C++: utility::graph::LowMemNode::find_edge(unsigned int, const class utility::graph::LowMemGraphBase &) const –> const class utility::graph::LowMemEdge *

  1. find_edge(self: pyrosetta.rosetta.utility.graph.LowMemNode, other_node_ind: int, graph: pyrosetta.rosetta.utility.graph.LowMemGraphBase) -> utility::graph::LowMemEdge

a “slow” (linear) search for an edge.

C++: utility::graph::LowMemNode::find_edge(unsigned int, class utility::graph::LowMemGraphBase &) –> class utility::graph::LowMemEdge *

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

the index for this node

C++: utility::graph::LowMemNode::get_node_index() const –> unsigned int

global_rotamer_id(self: pyrosetta.rosetta.core.scoring.hbonds.graph.HBondNode) → int

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

C++: core::scoring::hbonds::graph::HBondNode::global_rotamer_id() const –> unsigned long

internal_add_edge(self: pyrosetta.rosetta.utility.graph.LowMemNode, edge_offset: int) → None

Don’t call this!!!. Adds an edge from the edge list to this node

Only made public so we don’t have to friend the templated LowMemGraph

C++: utility::graph::LowMemNode::internal_add_edge(unsigned long) –> void

internal_drop_edge(self: pyrosetta.rosetta.utility.graph.LowMemNode, edge: utility::graph::LowMemEdge, graph: pyrosetta.rosetta.utility.graph.LowMemGraphBase) → int

Don’t call this!!!. It only locally deletes the edge from this node.

Only made public so we don’t have to friend the templated LowMemGraph.

Returns offset in the global edge list

C++: utility::graph::LowMemNode::internal_drop_edge(const class utility::graph::LowMemEdge *, const class utility::graph::LowMemGraphBase &) –> unsigned long

internal_get_edge_list(self: pyrosetta.rosetta.utility.graph.LowMemNode) → pyrosetta.rosetta.std.vector_unsigned_long

Don’t call this!!!. Only to be used by LowMemGraph

Only made public so we don’t have to friend the templated LowMemGraph

C++: utility::graph::LowMemNode::internal_get_edge_list() const –> const class std::vector<unsigned long, class std::allocator<unsigned long> > &

local_rotamer_id(self: pyrosetta.rosetta.core.scoring.hbonds.graph.HBondNode) → int

get local rotamer id (local to the residue position)

this is equivalent to pack_basic::RotamerSetsBase::rotid_on_moltenresidue( this->get_node_index() )

C++: core::scoring::hbonds::graph::HBondNode::local_rotamer_id() const –> unsigned int

merge_data(self: pyrosetta.rosetta.core.scoring.hbonds.graph.HBondNode, other: pyrosetta.rosetta.core.scoring.hbonds.graph.HBondNode, other_node_to_my_node: pyrosetta.rosetta.utility.vector1_unsigned_long, merge_with_OR_logic: bool) → None

Only merges new data added by this class. Does not merge edges!!!

There are two ways to merge the atoms.

OR_logic - Take the union of the atoms at each node AND_logic - Take the intersection of the atoms at each node

other_node_to_my_node is a map of node indices from the other graph

to node indices in this graph.

other_node_to_my_node.size() == other_graph.num_nodes()

C++: core::scoring::hbonds::graph::HBondNode::merge_data(const class core::scoring::hbonds::graph::HBondNode &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, bool) –> void

moltenres(self: pyrosetta.rosetta.core.scoring.hbonds.graph.HBondNode) → int

get molten residue id for this rotamer

C++: core::scoring::hbonds::graph::HBondNode::moltenres() const –> unsigned int

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

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

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

polar_sc_atoms_not_satisfied_by_background(self: pyrosetta.rosetta.core.scoring.hbonds.graph.HBondNode) → pyrosetta.rosetta.core.scoring.hbonds.graph.AtomInfoSet

C++: core::scoring::hbonds::graph::HBondNode::polar_sc_atoms_not_satisfied_by_background() –> class core::scoring::hbonds::graph::AtomInfoSet &

print(self: pyrosetta.rosetta.core.scoring.hbonds.graph.HBondNode) → None

C++: core::scoring::hbonds::graph::HBondNode::print() const –> void

register_clash(self: pyrosetta.rosetta.core.scoring.hbonds.graph.HBondNode, node_id: pyrosetta.rosetta.utility.StrongT_unsigned_long_core_scoring_hbonds_graph_NodeIDSize_t) → 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++: core::scoring::hbonds::graph::HBondNode::register_clash(struct utility::StrongT<unsigned long, struct core::scoring::hbonds::graph::NodeIDSize_>) –> void

remove_atom_info(self: pyrosetta.rosetta.core.scoring.hbonds.graph.HBondNode, local_atom_id: int) → None

O( N )

C++: core::scoring::hbonds::graph::HBondNode::remove_atom_info(unsigned short) –> void

set_local_rotamer_id(self: pyrosetta.rosetta.core.scoring.hbonds.graph.HBondNode, rot_id: pyrosetta.rosetta.utility.StrongT_unsigned_long_core_scoring_hbonds_graph_RotamerIDSize_t) → None

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

C++: core::scoring::hbonds::graph::HBondNode::set_local_rotamer_id(struct utility::StrongT<unsigned long, struct core::scoring::hbonds::graph::RotamerIDSize_>) –> void

set_moltenres(self: pyrosetta.rosetta.core.scoring.hbonds.graph.HBondNode, mres: pyrosetta.rosetta.utility.StrongT_unsigned_long_core_scoring_hbonds_graph_MResIDSize_t) → None

set molten residue id for this rotamer.

C++: core::scoring::hbonds::graph::HBondNode::set_moltenres(struct utility::StrongT<unsigned long, struct core::scoring::hbonds::graph::MResIDSize_>) –> void

class pyrosetta.rosetta.core.scoring.hbonds.graph.LKHBondInfo

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.scoring.hbonds.graph.LKHBondInfo, : pyrosetta.rosetta.core.scoring.hbonds.graph.LKHBondInfo) → pyrosetta.rosetta.core.scoring.hbonds.graph.LKHBondInfo

C++: core::scoring::hbonds::graph::LKHBondInfo::operator=(const class core::scoring::hbonds::graph::LKHBondInfo &) –> class core::scoring::hbonds::graph::LKHBondInfo &