graph

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

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

Bases: pyrosetta.rosetta.utility.graph.Edge

Each AtomLevelHBondEdge represents a hydrogen bond

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

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

copy_from(self: pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondEdge, source: pyrosetta.rosetta.utility.graph.Edge) → None

C++: core::scoring::hbonds::graph::AtomLevelHBondEdge::copy_from(const class utility::graph::Edge *) –> void

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

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

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

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

energy(self: pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondEdge) → 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::AtomLevelHBondEdge::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

hbonds(self: pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondEdge) → pyrosetta.rosetta.utility.vector1_core_scoring_hbonds_graph_HBondInfo

C++: core::scoring::hbonds::graph::AtomLevelHBondEdge::hbonds() –> class utility::vector1<class core::scoring::hbonds::graph::HBondInfo, class std::allocator<class core::scoring::hbonds::graph::HBondInfo> > &

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

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

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

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.core.scoring.hbonds.graph.AtomLevelHBondEdge) → 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::AtomLevelHBondEdge::score() const –> float

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

C++: core::scoring::hbonds::graph::AtomLevelHBondEdge::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.core.scoring.hbonds.graph.AtomLevelHBondEdge, energy: float) → None

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

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

Bases: pyrosetta.rosetta.utility.graph.Node

Each AtomLevelHBondNode represents a rotamer from the RotamerSets object

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

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

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

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

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

clashes(self: pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondNode, node_id: int) → bool

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

C++: core::scoring::hbonds::graph::AtomLevelHBondNode::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.core.scoring.hbonds.graph.AtomLevelHBondNode, source: pyrosetta.rosetta.utility.graph.Node) → None

C++: core::scoring::hbonds::graph::AtomLevelHBondNode::copy_from(const class utility::graph::Node *) –> void

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

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

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

C++: core::scoring::hbonds::graph::AtomLevelHBondNode::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.core.scoring.hbonds.graph.AtomLevelHBondNode) → int

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

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

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

get local rotamer id (local to the residue position)

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

C++: core::scoring::hbonds::graph::AtomLevelHBondNode::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.core.scoring.hbonds.graph.AtomLevelHBondNode) → int

get molten residue id for this rotamer

C++: core::scoring::hbonds::graph::AtomLevelHBondNode::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

polar_sc_atoms_not_satisfied_by_background(self: pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondNode) → pyrosetta.rosetta.utility.vector1_core_scoring_hbonds_graph_AtomInfo

C++: core::scoring::hbonds::graph::AtomLevelHBondNode::polar_sc_atoms_not_satisfied_by_background() –> class utility::vector1<class core::scoring::hbonds::graph::AtomInfo, class std::allocator<class core::scoring::hbonds::graph::AtomInfo> > &

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

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

register_clash(self: pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondNode, 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++: core::scoring::hbonds::graph::AtomLevelHBondNode::register_clash(unsigned long) –> void

remove_atom_info_from_vec_stable(atom_vec: pyrosetta.rosetta.utility.vector1_core_scoring_hbonds_graph_AtomInfo, local_atom_id: int) → bool

returns true if the atom was present, false is absent. False does not indicate failure!

C++: core::scoring::hbonds::graph::AtomLevelHBondNode::remove_atom_info_from_vec_stable(class utility::vector1<class core::scoring::hbonds::graph::AtomInfo, class std::allocator<class core::scoring::hbonds::graph::AtomInfo> > &, unsigned short) –> bool

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

C++: core::scoring::hbonds::graph::AtomLevelHBondNode::remove_atom_info_stable(unsigned short) –> void

set_local_rotamer_id(self: pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondNode, rot_id: int) → None

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

C++: core::scoring::hbonds::graph::AtomLevelHBondNode::set_local_rotamer_id(unsigned long) –> void

set_moltenres(self: pyrosetta.rosetta.core.scoring.hbonds.graph.AtomLevelHBondNode, mres: int) → None

set molten residue id for this rotamer.

C++: core::scoring::hbonds::graph::AtomLevelHBondNode::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