graph

Bindings for utility::graph namespace

class pyrosetta.rosetta.utility.graph.ArrayPoolElement_double_t

Bases: pybind11_builtins.pybind11_object

copy_array_contents(self: pyrosetta.rosetta.utility.graph.ArrayPoolElement_double_t, other: pyrosetta.rosetta.utility.graph.ArrayPoolElement_double_t) None

C++: utility::graph::ArrayPoolElement<double>::copy_array_contents(const class utility::graph::ArrayPoolElement<double> &) –> void

size(self: pyrosetta.rosetta.utility.graph.ArrayPoolElement_double_t) int

C++: utility::graph::ArrayPoolElement<double>::size() const –> unsigned long

valid(self: pyrosetta.rosetta.utility.graph.ArrayPoolElement_double_t) bool

C++: utility::graph::ArrayPoolElement<double>::valid() const –> bool

class pyrosetta.rosetta.utility.graph.ArrayPool_double_t

Bases: pybind11_builtins.pybind11_object

array_size(self: pyrosetta.rosetta.utility.graph.ArrayPool_double_t) int

C++: utility::graph::ArrayPool<double>::array_size() const –> unsigned long

assign(self: pyrosetta.rosetta.utility.graph.ArrayPool_double_t, : pyrosetta.rosetta.utility.graph.ArrayPool_double_t) pyrosetta.rosetta.utility.graph.ArrayPool_double_t

C++: utility::graph::ArrayPool<double>::operator=(const class utility::graph::ArrayPool<double> &) –> class utility::graph::ArrayPool<double> &

block_size(self: pyrosetta.rosetta.utility.graph.ArrayPool_double_t) int

C++: utility::graph::ArrayPool<double>::block_size() const –> unsigned long

deallocate_array(self: pyrosetta.rosetta.utility.graph.ArrayPool_double_t, element: pyrosetta.rosetta.utility.graph.ArrayPoolElement_double_t) None

C++: utility::graph::ArrayPool<double>::deallocate_array(const class utility::graph::ArrayPoolElement<double> &) –> void

empty(self: pyrosetta.rosetta.utility.graph.ArrayPool_double_t) bool

C++: utility::graph::ArrayPool<double>::empty() const –> bool

footprint(self: pyrosetta.rosetta.utility.graph.ArrayPool_double_t) int

C++: utility::graph::ArrayPool<double>::footprint() const –> unsigned long

nallocated(self: pyrosetta.rosetta.utility.graph.ArrayPool_double_t) int

C++: utility::graph::ArrayPool<double>::nallocated() const –> unsigned long

nblocks(self: pyrosetta.rosetta.utility.graph.ArrayPool_double_t) int

C++: utility::graph::ArrayPool<double>::nblocks() const –> unsigned long

new_array(self: pyrosetta.rosetta.utility.graph.ArrayPool_double_t) pyrosetta.rosetta.utility.graph.ArrayPoolElement_double_t

C++: utility::graph::ArrayPool<double>::new_array() –> class utility::graph::ArrayPoolElement<double>

noutstanding(self: pyrosetta.rosetta.utility.graph.ArrayPool_double_t) int

C++: utility::graph::ArrayPool<double>::noutstanding() const –> unsigned long

set_array_size(self: pyrosetta.rosetta.utility.graph.ArrayPool_double_t, size: int) None

C++: utility::graph::ArrayPool<double>::set_array_size(unsigned long) –> void

set_block_size(self: pyrosetta.rosetta.utility.graph.ArrayPool_double_t, size: int) None

C++: utility::graph::ArrayPool<double>::set_block_size(unsigned long) –> void

class pyrosetta.rosetta.utility.graph.DS_Node

Bases: pybind11_builtins.pybind11_object

property index
property parent
property rank
class pyrosetta.rosetta.utility.graph.Digraph

Bases: pybind11_builtins.pybind11_object

A Digraph with constant time edge insertion and deletion. Extensible.

add_edge(*args, **kwargs)

Overloaded function.

  1. add_edge(self: pyrosetta.rosetta.utility.graph.Digraph, tail_node: int, head_node: int) -> pyrosetta.rosetta.utility.graph.DirectedEdge

add a directed edge between two vertices. Invokes “create_edge” from the derived class.

Returns a pointer to the edge after its been added, allowing the calling function to immediately set data for this edge.

C++: utility::graph::Digraph::add_edge(unsigned long, unsigned long) –> class utility::graph::DirectedEdge *

  1. add_edge(self: pyrosetta.rosetta.utility.graph.Digraph, example_edge: pyrosetta.rosetta.utility.graph.DirectedEdge) -> pyrosetta.rosetta.utility.graph.DirectedEdge

add an edge to this graph copying the data from an edge in another graph.

Returns a pointer to the edge after its been added, allowing the calling function to immediately set data for this edge.

C++: utility::graph::Digraph::add_edge(const class utility::graph::DirectedEdge *) –> class utility::graph::DirectedEdge *

add_node(self: pyrosetta.rosetta.utility.graph.Digraph) None

Add a new node to the graph; preserve all of the existing edges in the graph

C++: utility::graph::Digraph::add_node() –> void

assign(self: pyrosetta.rosetta.utility.graph.Digraph, source: pyrosetta.rosetta.utility.graph.Digraph) pyrosetta.rosetta.utility.graph.Digraph

assignment operator. source and this must have the same type.

C++: utility::graph::Digraph::operator=(const class utility::graph::Digraph &) –> class utility::graph::Digraph &

const_edge_list_begin(self: pyrosetta.rosetta.utility.graph.Digraph) pyrosetta.rosetta.utility.graph.DirectedEdgeListConstIterator
returns a const iterator to the beginning of the (unordered) edge list for the graph.

this edge list contains all the edges in the graph, not simply those for a particular vertex

C++: utility::graph::Digraph::const_edge_list_begin() const –> class utility::graph::DirectedEdgeListConstIterator

const_edge_list_end(self: pyrosetta.rosetta.utility.graph.Digraph) pyrosetta.rosetta.utility.graph.DirectedEdgeListConstIterator
returns a const iterator to the end of the (unordered) edge list for the graph.

this edge list contains all the edges in the graph, not simply those for a particular vertex

C++: utility::graph::Digraph::const_edge_list_end() const –> class utility::graph::DirectedEdgeListConstIterator

copy_connectivity(self: pyrosetta.rosetta.utility.graph.Digraph, source: pyrosetta.rosetta.utility.graph.Digraph) None
copy the edge connectivity from a source graph with a potentially

unknown type.

C++: utility::graph::Digraph::copy_connectivity(const class utility::graph::Digraph &) –> void

delete_edge(self: pyrosetta.rosetta.utility.graph.Digraph, edge: pyrosetta.rosetta.utility.graph.DirectedEdge) None
remove an edge from the graph. (NEW AS OF 12/9/07) Never call C++’s

“delete” function on an edge pointer directly. Derived classes must implement this function. If they wish to use unordered_object_pools to manage their memory

C++: utility::graph::Digraph::delete_edge(class utility::graph::DirectedEdge *) –> void

drop_all_edges(self: pyrosetta.rosetta.utility.graph.Digraph) None

delete all the edges present in the graph

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

drop_all_edges_for_node(self: pyrosetta.rosetta.utility.graph.Digraph, node: int) None

delete all the edges for a single vertex in the graph

C++: utility::graph::Digraph::drop_all_edges_for_node(unsigned long) –> void

edge_list_begin(self: pyrosetta.rosetta.utility.graph.Digraph) pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator
returns a non-const iterator to the beginning of the (unordered) edge list for the graph.

this edge list contains all the edges in the graph, not simply those for a particular vertex

C++: utility::graph::Digraph::edge_list_begin() –> class utility::graph::DirectedEdgeListIterator

edge_list_end(self: pyrosetta.rosetta.utility.graph.Digraph) pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator
returns a non-const iterator to the end of the (unordered) edge list for the graph.

this edge list contains all the edges in the graph, not simply those for a particular vertex

C++: utility::graph::Digraph::edge_list_end() –> class utility::graph::DirectedEdgeListIterator

find_edge(self: pyrosetta.rosetta.utility.graph.Digraph, tail_node: int, head_node: int) pyrosetta.rosetta.utility.graph.DirectedEdge
returns a pointer to the directed edge connecting nodes tail_node and head_node, if that edge exists

in the graph, o.w. returns 0. Focuses the graph on this edge for fast subsequent retrieval.

C++: utility::graph::Digraph::find_edge(unsigned long, unsigned long) –> class utility::graph::DirectedEdge *

focused_edge(self: pyrosetta.rosetta.utility.graph.Digraph) pyrosetta.rosetta.utility.graph.DirectedEdge

returns a pointer to the focused edge

C++: utility::graph::Digraph::focused_edge() –> class utility::graph::DirectedEdge *

getTotalMemoryUsage(self: pyrosetta.rosetta.utility.graph.Digraph) int
returns a count of all the memory used by every vertex and edge in a graph

by invoking the polymorphic count_static_memory and count_dynamic_memory of each (possibly derived) node and edge object as well as for the (possibly derived) graph class.

C++: utility::graph::Digraph::getTotalMemoryUsage() const –> unsigned long

get_edge_exists(self: pyrosetta.rosetta.utility.graph.Digraph, tail_node: int, head_node: int) bool

is an edge already present in the graph? O(V) worst case. O(1) iff all vertices have O(1) edges

C++: utility::graph::Digraph::get_edge_exists(unsigned long, unsigned long) const –> bool

get_node(self: pyrosetta.rosetta.utility.graph.Digraph, index: int) pyrosetta.rosetta.utility.graph.DirectedNode

C++: utility::graph::Digraph::get_node(unsigned long) –> class utility::graph::DirectedNode *

get_self_ptr(self: pyrosetta.rosetta.utility.graph.Digraph) pyrosetta.rosetta.utility.graph.Digraph

C++: utility::graph::Digraph::get_self_ptr() –> class std::shared_ptr<class utility::graph::Digraph>

num_edges(self: pyrosetta.rosetta.utility.graph.Digraph) int

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

num_nodes(self: pyrosetta.rosetta.utility.graph.Digraph) int

the number of nodes in the graph

C++: utility::graph::Digraph::num_nodes() const –> unsigned long

output_connectivity(self: pyrosetta.rosetta.utility.graph.Digraph, os: pyrosetta.rosetta.std.ostream) None

send an edge list to the stream os.

C++: utility::graph::Digraph::output_connectivity(std::ostream &) const –> void

output_dimacs(self: pyrosetta.rosetta.utility.graph.Digraph, os: pyrosetta.rosetta.std.ostream) None

describe this graph in dimacs form to the stream os.

C++: utility::graph::Digraph::output_dimacs(std::ostream &) const –> void

print_vertices(self: pyrosetta.rosetta.utility.graph.Digraph) None

send summary information to the screen for all vertices in the graph

C++: utility::graph::Digraph::print_vertices() const –> void

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

set the number of nodes in the graph – deletes any existing edges in the graph

C++: utility::graph::Digraph::set_num_nodes(unsigned long) –> void

class pyrosetta.rosetta.utility.graph.DirectedEdge

Bases: pybind11_builtins.pybind11_object

copy_from(self: pyrosetta.rosetta.utility.graph.DirectedEdge, source: pyrosetta.rosetta.utility.graph.DirectedEdge) None

copy-from for use in Digraph::operator= and copy ctors

C++: utility::graph::DirectedEdge::copy_from(const class utility::graph::DirectedEdge *) –> void

count_dynamic_memory(self: pyrosetta.rosetta.utility.graph.DirectedEdge) int
how much memory is dynamically allocated by this edge – must be recursively invoked

by a derived class.

C++: utility::graph::DirectedEdge::count_dynamic_memory() const –> unsigned long

count_static_memory(self: pyrosetta.rosetta.utility.graph.DirectedEdge) int

how much memory is statically allocated by this edge

C++: utility::graph::DirectedEdge::count_static_memory() const –> unsigned long

get_head_node(self: pyrosetta.rosetta.utility.graph.DirectedEdge) pyrosetta.rosetta.utility.graph.DirectedNode

returns a pointer to the head node

C++: utility::graph::DirectedEdge::get_head_node() –> class utility::graph::DirectedNode *

get_head_node_ind(self: pyrosetta.rosetta.utility.graph.DirectedEdge) int

returns the index of the upper node

C++: utility::graph::DirectedEdge::get_head_node_ind() const –> unsigned long

get_other_ind(self: pyrosetta.rosetta.utility.graph.DirectedEdge, 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::DirectedEdge::get_other_ind(unsigned long) const –> unsigned long

get_other_node(self: pyrosetta.rosetta.utility.graph.DirectedEdge, node_index: int) pyrosetta.rosetta.utility.graph.DirectedNode
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::DirectedEdge::get_other_node(unsigned long) –> class utility::graph::DirectedNode *

get_tail_node(self: pyrosetta.rosetta.utility.graph.DirectedEdge) pyrosetta.rosetta.utility.graph.DirectedNode

returns a pointer to the tail node

C++: utility::graph::DirectedEdge::get_tail_node() –> class utility::graph::DirectedNode *

get_tail_node_ind(self: pyrosetta.rosetta.utility.graph.DirectedEdge) int

returns the index of the tail node

C++: utility::graph::DirectedEdge::get_tail_node_ind() const –> unsigned long

is_head_node(self: pyrosetta.rosetta.utility.graph.DirectedEdge, node_index: int) bool

C++: utility::graph::DirectedEdge::is_head_node(unsigned long) –> bool

is_tail_node(self: pyrosetta.rosetta.utility.graph.DirectedEdge, node_index: int) bool

C++: utility::graph::DirectedEdge::is_tail_node(unsigned long) –> bool

same_edge(self: pyrosetta.rosetta.utility.graph.DirectedEdge, tail_node: int, head_node: int) bool
Is this the same edge as another edge (tail_node,head_node)? Note:

this graph does not work for multi-graphs. DirectedEdges must be unique.

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

set_pos_in_owners_list(self: pyrosetta.rosetta.utility.graph.DirectedEdge, edge_iterator: pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator) None
called only by class Digraph, this function gives the DirectedEdge the data it needs

to later delete itself from its owner’s edge list in constant time.

C++: utility::graph::DirectedEdge::set_pos_in_owners_list(class utility::graph::DirectedEdgeListIterator) –> void

class pyrosetta.rosetta.utility.graph.DirectedEdgeList

Bases: pybind11_builtins.pybind11_object

Custom edge list class. Returns const-iterators which only return DirectedEdge const ‘s and non-const-iterators which can return either const or non-const DirectedEdge’s. Manages its own memory using an unordered-object-pool for fast insertion and deletion of DirectedEdgeListElements. Implemented as a doubly linked list, though there’s no practical way to start at the end of a list and work backward since decrementing the end iterator is not a valid operation.

begin(self: pyrosetta.rosetta.utility.graph.DirectedEdgeList) pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator

returns a non-const iterator to the front of the list

C++: utility::graph::DirectedEdgeList::begin() –> class utility::graph::DirectedEdgeListIterator

const_begin(self: pyrosetta.rosetta.utility.graph.DirectedEdgeList) pyrosetta.rosetta.utility.graph.DirectedEdgeListConstIterator

returns a const iterator to the front of the list

C++: utility::graph::DirectedEdgeList::const_begin() const –> class utility::graph::DirectedEdgeListConstIterator

const_end(self: pyrosetta.rosetta.utility.graph.DirectedEdgeList) pyrosetta.rosetta.utility.graph.DirectedEdgeListConstIterator

returns a const iterator to the end of the list

C++: utility::graph::DirectedEdgeList::const_end() const –> class utility::graph::DirectedEdgeListConstIterator

const_last(self: pyrosetta.rosetta.utility.graph.DirectedEdgeList) pyrosetta.rosetta.utility.graph.DirectedEdgeListConstIterator

returns a const iterator to the last element in the list

C++: utility::graph::DirectedEdgeList::const_last() const –> class utility::graph::DirectedEdgeListConstIterator

end(self: pyrosetta.rosetta.utility.graph.DirectedEdgeList) pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator

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

C++: utility::graph::DirectedEdgeList::end() –> class utility::graph::DirectedEdgeListIterator

erase(self: pyrosetta.rosetta.utility.graph.DirectedEdgeList, to_erase: pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator) None

removes an element from the list pointed to by the input iterator

C++: utility::graph::DirectedEdgeList::erase(class utility::graph::DirectedEdgeListIterator) –> void

insert(self: pyrosetta.rosetta.utility.graph.DirectedEdgeList, element_to_insert_before: pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator, edgeptr: utility::graph::DirectedEdge) pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator
insert a new edge-list element in the list infront of the input iterator and

return an iterator to the position of the new element

C++: utility::graph::DirectedEdgeList::insert(const class utility::graph::DirectedEdgeListIterator &, class utility::graph::DirectedEdge *) –> class utility::graph::DirectedEdgeListIterator

is_end_element(self: pyrosetta.rosetta.utility.graph.DirectedEdgeList, element: pyrosetta.rosetta.utility.graph.DirectedEdgeListElement) bool
method invoked by the DirectedEdgeListIterator class: is an iterator the special

end iterator for a list?

C++: utility::graph::DirectedEdgeList::is_end_element(const class utility::graph::DirectedEdgeListElement *) const –> bool

last(self: pyrosetta.rosetta.utility.graph.DirectedEdgeList) pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator

returns a non-const iterator to the last element in the list

C++: utility::graph::DirectedEdgeList::last() –> class utility::graph::DirectedEdgeListIterator

push_back(self: pyrosetta.rosetta.utility.graph.DirectedEdgeList, edgeptr: utility::graph::DirectedEdge) None

create a new edge-list element and insert it at the front of the list

C++: utility::graph::DirectedEdgeList::push_back(class utility::graph::DirectedEdge *) –> void

push_front(self: pyrosetta.rosetta.utility.graph.DirectedEdgeList, edgeptr: utility::graph::DirectedEdge) None

create a new edge-list element and insert it at the end of the list

C++: utility::graph::DirectedEdgeList::push_front(class utility::graph::DirectedEdge *) –> void

size(self: pyrosetta.rosetta.utility.graph.DirectedEdgeList) int

O(N)

C++: utility::graph::DirectedEdgeList::size() const –> unsigned long

class pyrosetta.rosetta.utility.graph.DirectedEdgeListConstIterator

Bases: pybind11_builtins.pybind11_object

Custom DirectedEdge list const iterator class, which returns only const DirectedEdge pointers. This iterator cannot be used to change the structure of its list without access to that list directly. Customized since STL’s const-iterator cannot be prevented from giving non-const access to its data.

assign(self: pyrosetta.rosetta.utility.graph.DirectedEdgeListConstIterator, rhs: pyrosetta.rosetta.utility.graph.DirectedEdgeListConstIterator) pyrosetta.rosetta.utility.graph.DirectedEdgeListConstIterator

assignmnet operator

C++: utility::graph::DirectedEdgeListConstIterator::operator=(const class utility::graph::DirectedEdgeListConstIterator &) –> class utility::graph::DirectedEdgeListConstIterator &

minus_minus(self: pyrosetta.rosetta.utility.graph.DirectedEdgeListConstIterator) pyrosetta.rosetta.utility.graph.DirectedEdgeListConstIterator

decrement operator. Point this iterator at the previous element in the list.

C++: utility::graph::DirectedEdgeListConstIterator::operator–() –> const class utility::graph::DirectedEdgeListConstIterator &

plus_plus(self: pyrosetta.rosetta.utility.graph.DirectedEdgeListConstIterator) pyrosetta.rosetta.utility.graph.DirectedEdgeListConstIterator

increment operator. Point this iterator at the next element in the list.

C++: utility::graph::DirectedEdgeListConstIterator::operator++() –> const class utility::graph::DirectedEdgeListConstIterator &

valid(self: pyrosetta.rosetta.utility.graph.DirectedEdgeListConstIterator) bool

Is this a valid iterator?

C++: utility::graph::DirectedEdgeListConstIterator::valid() const –> bool

class pyrosetta.rosetta.utility.graph.DirectedEdgeListElement

Bases: pybind11_builtins.pybind11_object

Custom written edge list element class. Little more than a struct. Defined so that edge list memory management could rely on boost::pool like object

const_edge(self: pyrosetta.rosetta.utility.graph.DirectedEdgeListElement) utility::graph::DirectedEdge

C++: utility::graph::DirectedEdgeListElement::const_edge() const –> const class utility::graph::DirectedEdge *

const_next(self: pyrosetta.rosetta.utility.graph.DirectedEdgeListElement) pyrosetta.rosetta.utility.graph.DirectedEdgeListElement

C++: utility::graph::DirectedEdgeListElement::const_next() const –> const class utility::graph::DirectedEdgeListElement *

const_previous(self: pyrosetta.rosetta.utility.graph.DirectedEdgeListElement) pyrosetta.rosetta.utility.graph.DirectedEdgeListElement

C++: utility::graph::DirectedEdgeListElement::const_previous() const –> const class utility::graph::DirectedEdgeListElement *

edge(*args, **kwargs)

Overloaded function.

  1. edge(self: pyrosetta.rosetta.utility.graph.DirectedEdgeListElement) -> utility::graph::DirectedEdge

C++: utility::graph::DirectedEdgeListElement::edge() –> class utility::graph::DirectedEdge *

  1. edge(self: pyrosetta.rosetta.utility.graph.DirectedEdgeListElement, setting: utility::graph::DirectedEdge) -> None

C++: utility::graph::DirectedEdgeListElement::edge(class utility::graph::DirectedEdge *) –> void

next(*args, **kwargs)

Overloaded function.

  1. next(self: pyrosetta.rosetta.utility.graph.DirectedEdgeListElement) -> pyrosetta.rosetta.utility.graph.DirectedEdgeListElement

C++: utility::graph::DirectedEdgeListElement::next() –> class utility::graph::DirectedEdgeListElement *

  1. next(self: pyrosetta.rosetta.utility.graph.DirectedEdgeListElement, setting: pyrosetta.rosetta.utility.graph.DirectedEdgeListElement) -> None

C++: utility::graph::DirectedEdgeListElement::next(class utility::graph::DirectedEdgeListElement *) –> void

previous(*args, **kwargs)

Overloaded function.

  1. previous(self: pyrosetta.rosetta.utility.graph.DirectedEdgeListElement) -> pyrosetta.rosetta.utility.graph.DirectedEdgeListElement

C++: utility::graph::DirectedEdgeListElement::previous() –> class utility::graph::DirectedEdgeListElement *

  1. previous(self: pyrosetta.rosetta.utility.graph.DirectedEdgeListElement, setting: pyrosetta.rosetta.utility.graph.DirectedEdgeListElement) -> None

C++: utility::graph::DirectedEdgeListElement::previous(class utility::graph::DirectedEdgeListElement *) –> void

class pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator

Bases: pybind11_builtins.pybind11_object

Custom DirectedEdge list (non-const) iterator class, which can return non-const DirectedEdge pointers. This iterator cannot be used to change the structure of its list without access to that list directly. Customized since STL’s const-iterator cannot be prevented from giving non-const access to its data. The former workaround to this problem was to define two sets of edge lists on each vertex: a list< DirectedEdge * > and a list< DirectedEdge const * >.

assign(self: pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator, rhs: pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator) pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator

assignmnet operator

C++: utility::graph::DirectedEdgeListIterator::operator=(const class utility::graph::DirectedEdgeListIterator &) –> class utility::graph::DirectedEdgeListIterator &

minus_minus(self: pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator) pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator

decrement operator. Point this iterator at the previous element in the list.

C++: utility::graph::DirectedEdgeListIterator::operator–() –> const class utility::graph::DirectedEdgeListIterator &

plus_plus(self: pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator) pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator

increment operator. Point this iterator at the next element in the list.

C++: utility::graph::DirectedEdgeListIterator::operator++() –> const class utility::graph::DirectedEdgeListIterator &

valid(self: pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator) bool
check that this iterator is valid. Will not guarantee that the iterator points at an element

that has not been destroyed.

C++: utility::graph::DirectedEdgeListIterator::valid() const –> bool

class pyrosetta.rosetta.utility.graph.DirectedNode

Bases: pybind11_builtins.pybind11_object

add_incoming_edge(self: pyrosetta.rosetta.utility.graph.DirectedNode, edge_ptr: utility::graph::DirectedEdge, : pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator) None
adds an edge pointer to node’s edge list as an incoming edge

i.e. this node is the head of the arrow; returns an iterator to the new list element. Virtual so derived classes can observe when incoming edges are added.

C++: utility::graph::DirectedNode::add_incoming_edge(class utility::graph::DirectedEdge *, class utility::graph::DirectedEdgeListIterator &) –> void

add_outgoing_edge(self: pyrosetta.rosetta.utility.graph.DirectedNode, edge_ptr: utility::graph::DirectedEdge, : pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator) None
adds an edge pointer to node’s edge list as an outgoing edge

i.e. this node is the tail of the arrow; returns an iterator to the new list element. Virtual so derived classes can observe when incoming edges are added.

C++: utility::graph::DirectedNode::add_outgoing_edge(class utility::graph::DirectedEdge *, class utility::graph::DirectedEdgeListIterator &) –> void

const_edge_list_begin(self: pyrosetta.rosetta.utility.graph.DirectedNode) pyrosetta.rosetta.utility.graph.DirectedEdgeListConstIterator

returns a const iterator to the beginning of its edge list

C++: utility::graph::DirectedNode::const_edge_list_begin() const –> class utility::graph::DirectedEdgeListConstIterator

const_edge_list_end(self: pyrosetta.rosetta.utility.graph.DirectedNode) pyrosetta.rosetta.utility.graph.DirectedEdgeListConstIterator

returns a const iterator to the end of its edge list

C++: utility::graph::DirectedNode::const_edge_list_end() const –> class utility::graph::DirectedEdgeListConstIterator

const_incoming_edge_list_begin(self: pyrosetta.rosetta.utility.graph.DirectedNode) pyrosetta.rosetta.utility.graph.DirectedEdgeListConstIterator

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

C++: utility::graph::DirectedNode::const_incoming_edge_list_begin() const –> class utility::graph::DirectedEdgeListConstIterator

const_incoming_edge_list_end(self: pyrosetta.rosetta.utility.graph.DirectedNode) pyrosetta.rosetta.utility.graph.DirectedEdgeListConstIterator

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

C++: utility::graph::DirectedNode::const_incoming_edge_list_end() const –> class utility::graph::DirectedEdgeListConstIterator

const_outgoing_edge_list_begin(self: pyrosetta.rosetta.utility.graph.DirectedNode) pyrosetta.rosetta.utility.graph.DirectedEdgeListConstIterator

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

C++: utility::graph::DirectedNode::const_outgoing_edge_list_begin() const –> class utility::graph::DirectedEdgeListConstIterator

const_outgoing_edge_list_end(self: pyrosetta.rosetta.utility.graph.DirectedNode) pyrosetta.rosetta.utility.graph.DirectedEdgeListConstIterator

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

C++: utility::graph::DirectedNode::const_outgoing_edge_list_end() const –> class utility::graph::DirectedEdgeListConstIterator

copy_from(self: pyrosetta.rosetta.utility.graph.DirectedNode, source: pyrosetta.rosetta.utility.graph.DirectedNode) None
invoked during graph assignment operators to copy any

node data from one graph to another graph. The source node must be the same type as this node.

C++: utility::graph::DirectedNode::copy_from(const class utility::graph::DirectedNode *) –> void

count_dynamic_memory(self: pyrosetta.rosetta.utility.graph.DirectedNode) int

memory accounting scheme

C++: utility::graph::DirectedNode::count_dynamic_memory() const –> unsigned long

count_static_memory(self: pyrosetta.rosetta.utility.graph.DirectedNode) int

memory accounting scheme

C++: utility::graph::DirectedNode::count_static_memory() const –> unsigned long

drop_all_edges(self: pyrosetta.rosetta.utility.graph.DirectedNode) None

deletes all edges incident upon this node

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

drop_edge(self: pyrosetta.rosetta.utility.graph.DirectedNode, edge_iterator: pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator) None

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

C++: utility::graph::DirectedNode::drop_edge(class utility::graph::DirectedEdgeListIterator) –> void

edge_list_begin(self: pyrosetta.rosetta.utility.graph.DirectedNode) pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator

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

C++: utility::graph::DirectedNode::edge_list_begin() –> class utility::graph::DirectedEdgeListIterator

edge_list_end(self: pyrosetta.rosetta.utility.graph.DirectedNode) pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator

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

C++: utility::graph::DirectedNode::edge_list_end() –> class utility::graph::DirectedEdgeListIterator

find_edge_from(self: pyrosetta.rosetta.utility.graph.DirectedNode, head_node: int) utility::graph::DirectedEdge

a “slow” (linear) search for an edge.

C++: utility::graph::DirectedNode::find_edge_from(unsigned long) –> class utility::graph::DirectedEdge *

find_edge_to(self: pyrosetta.rosetta.utility.graph.DirectedNode, tail_node: int) utility::graph::DirectedEdge

a “slow” (linear) search for an edge.

C++: utility::graph::DirectedNode::find_edge_to(unsigned long) –> class utility::graph::DirectedEdge *

get_node_index(self: pyrosetta.rosetta.utility.graph.DirectedNode) int

the index for this node

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

incoming_edge_list_begin(self: pyrosetta.rosetta.utility.graph.DirectedNode) pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator

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

C++: utility::graph::DirectedNode::incoming_edge_list_begin() –> class utility::graph::DirectedEdgeListIterator

incoming_edge_list_end(self: pyrosetta.rosetta.utility.graph.DirectedNode) pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator

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

C++: utility::graph::DirectedNode::incoming_edge_list_end() –> class utility::graph::DirectedEdgeListIterator

indegree(self: pyrosetta.rosetta.utility.graph.DirectedNode) int

the number of incoming edges

C++: utility::graph::DirectedNode::indegree() const –> unsigned long

num_edges(self: pyrosetta.rosetta.utility.graph.DirectedNode) int

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

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

num_neighbors_counting_self(self: pyrosetta.rosetta.utility.graph.DirectedNode) int

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

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

outdegree(self: pyrosetta.rosetta.utility.graph.DirectedNode) int

the number of outgoing edges

C++: utility::graph::DirectedNode::outdegree() const –> unsigned long

outgoing_edge_list_begin(self: pyrosetta.rosetta.utility.graph.DirectedNode) pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator

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

C++: utility::graph::DirectedNode::outgoing_edge_list_begin() –> class utility::graph::DirectedEdgeListIterator

outgoing_edge_list_end(self: pyrosetta.rosetta.utility.graph.DirectedNode) pyrosetta.rosetta.utility.graph.DirectedEdgeListIterator

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

C++: utility::graph::DirectedNode::outgoing_edge_list_end() –> class utility::graph::DirectedEdgeListIterator

print(self: pyrosetta.rosetta.utility.graph.DirectedNode) None

send summaray data about this node to the screen

C++: utility::graph::DirectedNode::print() const –> void

class pyrosetta.rosetta.utility.graph.DisjointSets

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.utility.graph.DisjointSets, : pyrosetta.rosetta.utility.graph.DisjointSets) pyrosetta.rosetta.utility.graph.DisjointSets

C++: utility::graph::DisjointSets::operator=(const class utility::graph::DisjointSets &) –> class utility::graph::DisjointSets &

disjoint_set_sizes(self: pyrosetta.rosetta.utility.graph.DisjointSets) pyrosetta.rosetta.utility.vector1_unsigned_long

count the size of each disjoint set. O(N)

C++: utility::graph::DisjointSets::disjoint_set_sizes() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

ds_find(self: pyrosetta.rosetta.utility.graph.DisjointSets, node_id: int) int

return the representative for a node

C++: utility::graph::DisjointSets::ds_find(unsigned long) const –> unsigned long

ds_make_set(self: pyrosetta.rosetta.utility.graph.DisjointSets) None
add a new node – as implemented, O(N) operation

use the DS(platform::Size) constructor for better speed.

C++: utility::graph::DisjointSets::ds_make_set() –> void

ds_union(self: pyrosetta.rosetta.utility.graph.DisjointSets, node1: int, node2: int) None

make it so that two nodes end up in the same set

C++: utility::graph::DisjointSets::ds_union(unsigned long, unsigned long) –> void

n_disjoint_sets(self: pyrosetta.rosetta.utility.graph.DisjointSets) int

count the number of disjoint sets. O(N)

C++: utility::graph::DisjointSets::n_disjoint_sets() const –> unsigned long

n_nodes(self: pyrosetta.rosetta.utility.graph.DisjointSets) int

C++: utility::graph::DisjointSets::n_nodes() const –> unsigned long

node(self: pyrosetta.rosetta.utility.graph.DisjointSets, node_id: int) pyrosetta.rosetta.utility.graph.DS_Node

DS_Node read access

C++: utility::graph::DisjointSets::node(unsigned long) const –> const struct utility::graph::DS_Node &

nodes_in_set(self: pyrosetta.rosetta.utility.graph.DisjointSets, node_id: int) pyrosetta.rosetta.utility.vector1_unsigned_long

return the nodes in the set containing the specified node.

C++: utility::graph::DisjointSets::nodes_in_set(unsigned long) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

sets(self: pyrosetta.rosetta.utility.graph.DisjointSets) pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_unsigned_long_std_allocator_unsigned_long_t
return a map from the representative node of each set to

the list of nodes in their sets

C++: utility::graph::DisjointSets::sets() const –> class std::map<unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> >, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > > > >

class pyrosetta.rosetta.utility.graph.EXCN_Stop_BFS

Bases: pyrosetta.rosetta.utility.excn.Exception

Class to raise to do an immediate stop of a breadth first search. ONLY THROW FROM WITHIN A VISITOR PASSED TO breadth_first_visit_prune/breadth_first_search_prune

add_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None

C++: utility::excn::Exception::add_msg(const std::string &) –> void

assign(self: pyrosetta.rosetta.utility.graph.EXCN_Stop_BFS, : pyrosetta.rosetta.utility.graph.EXCN_Stop_BFS) pyrosetta.rosetta.utility.graph.EXCN_Stop_BFS

C++: utility::graph::EXCN_Stop_BFS::operator=(const class utility::graph::EXCN_Stop_BFS &) –> class utility::graph::EXCN_Stop_BFS &

crash_log(self: pyrosetta.rosetta.utility.excn.Exception) None
Invoke a crash log for throwing this exception.

If your exception is one which is a “non-error” exception, override this function to do nothing.

C++: utility::excn::Exception::crash_log() const –> void

display(self: pyrosetta.rosetta.utility.excn.Exception) None
Present this exception to the user.

Will invoke crash log reporting, if applicable

C++: utility::excn::Exception::display() const –> void

file(self: pyrosetta.rosetta.utility.excn.Exception) str

C++: utility::excn::Exception::file() –> const std::string &

line(self: pyrosetta.rosetta.utility.excn.Exception) int

C++: utility::excn::Exception::line() –> int

msg(*args, **kwargs)

Overloaded function.

  1. msg(self: pyrosetta.rosetta.utility.excn.Exception) -> str

Will return a formatted message (with file/line information)

C++: utility::excn::Exception::msg() const –> std::string

  1. msg(self: pyrosetta.rosetta.utility.excn.Exception, m: str) -> None

Will set the raw message.

C++: utility::excn::Exception::msg(const std::string &) –> void

prepend_to_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None

C++: utility::excn::Exception::prepend_to_msg(const std::string &) –> void

raw_msg(self: pyrosetta.rosetta.utility.excn.Exception) str

Will return the raw message (without file/line information)

C++: utility::excn::Exception::raw_msg() const –> std::string

show(self: pyrosetta.rosetta.utility.excn.Exception, : pyrosetta.rosetta.std.ostream) None

C++: utility::excn::Exception::show(std::ostream &) const –> void

traceback(self: pyrosetta.rosetta.utility.excn.Exception) str

C++: utility::excn::Exception::traceback() –> const std::string &

what(self: pyrosetta.rosetta.std.exception) str

C++: std::exception::what() const –> const char *

class pyrosetta.rosetta.utility.graph.Edge

Bases: pybind11_builtins.pybind11_object

copy_from(self: pyrosetta.rosetta.utility.graph.Edge, source: pyrosetta.rosetta.utility.graph.Edge) None

copy-from for use in Graph::operator= and copy ctors

C++: utility::graph::Edge::copy_from(const class utility::graph::Edge *) –> void

count_dynamic_memory(self: pyrosetta.rosetta.utility.graph.Edge) int
how much memory is dynamically allocated by this edge – must be recursively invoked

by a derived class.

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

count_static_memory(self: pyrosetta.rosetta.utility.graph.Edge) int

how much memory is statically allocated by this edge

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

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

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

class pyrosetta.rosetta.utility.graph.EdgeList

Bases: pybind11_builtins.pybind11_object

Custom edge list class. Returns const-iterators which only return Edge const ‘s and non-const-iterators which can return either const or non-const Edge’s. Manages its own memory using an unordered-object-pool for fast insertion and deletion of EdgeListElements. Implemented as a doubly linked list, though there’s no practical way to start at the end of a list and work backward since decrementing the end iterator is not a valid operation.

begin(self: pyrosetta.rosetta.utility.graph.EdgeList) pyrosetta.rosetta.utility.graph.EdgeListIterator

returns a non-const iterator to the front of the list

C++: utility::graph::EdgeList::begin() –> class utility::graph::EdgeListIterator

const_begin(self: pyrosetta.rosetta.utility.graph.EdgeList) pyrosetta.rosetta.utility.graph.EdgeListConstIterator

returns a const iterator to the front of the list

C++: utility::graph::EdgeList::const_begin() const –> class utility::graph::EdgeListConstIterator

const_end(self: pyrosetta.rosetta.utility.graph.EdgeList) pyrosetta.rosetta.utility.graph.EdgeListConstIterator

returns a const iterator to the end of the list

C++: utility::graph::EdgeList::const_end() const –> class utility::graph::EdgeListConstIterator

const_last(self: pyrosetta.rosetta.utility.graph.EdgeList) pyrosetta.rosetta.utility.graph.EdgeListConstIterator

returns a const iterator to the last element in the list

C++: utility::graph::EdgeList::const_last() const –> class utility::graph::EdgeListConstIterator

end(self: pyrosetta.rosetta.utility.graph.EdgeList) pyrosetta.rosetta.utility.graph.EdgeListIterator

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

C++: utility::graph::EdgeList::end() –> class utility::graph::EdgeListIterator

erase(self: pyrosetta.rosetta.utility.graph.EdgeList, to_erase: pyrosetta.rosetta.utility.graph.EdgeListIterator) None

removes an element from the list pointed to by the input iterator

C++: utility::graph::EdgeList::erase(class utility::graph::EdgeListIterator) –> void

insert(self: pyrosetta.rosetta.utility.graph.EdgeList, element_to_insert_before: pyrosetta.rosetta.utility.graph.EdgeListIterator, edgeptr: utility::graph::Edge) pyrosetta.rosetta.utility.graph.EdgeListIterator
insert a new edge-list element in the list infront of the input iterator and

return an iterator to the position of the new element

C++: utility::graph::EdgeList::insert(const class utility::graph::EdgeListIterator &, class utility::graph::Edge *) –> class utility::graph::EdgeListIterator

is_end_element(self: pyrosetta.rosetta.utility.graph.EdgeList, element: pyrosetta.rosetta.utility.graph.EdgeListElement) bool
method invoked by the EdgeListIterator class: is an iterator the special

end iterator for a list?

C++: utility::graph::EdgeList::is_end_element(const class utility::graph::EdgeListElement *) const –> bool

last(self: pyrosetta.rosetta.utility.graph.EdgeList) pyrosetta.rosetta.utility.graph.EdgeListIterator

returns a non-const iterator to the last element in the list

C++: utility::graph::EdgeList::last() –> class utility::graph::EdgeListIterator

push_back(self: pyrosetta.rosetta.utility.graph.EdgeList, edgeptr: utility::graph::Edge) None

create a new edge-list element and insert it at the front of the list

C++: utility::graph::EdgeList::push_back(class utility::graph::Edge *) –> void

push_front(self: pyrosetta.rosetta.utility.graph.EdgeList, edgeptr: utility::graph::Edge) None

create a new edge-list element and insert it at the end of the list

C++: utility::graph::EdgeList::push_front(class utility::graph::Edge *) –> void

size(self: pyrosetta.rosetta.utility.graph.EdgeList) int

O(N)

C++: utility::graph::EdgeList::size() const –> unsigned long

class pyrosetta.rosetta.utility.graph.EdgeListConstIterator

Bases: pybind11_builtins.pybind11_object

Custom Edge list const iterator class, which returns only const Edge pointers. This iterator cannot be used to change the structure of its list without access to that list directly. Customized since STL’s const-iterator cannot be prevented from giving non-const access to its data. The former workaround to this problem was to define two sets of edge lists on each vertex: a list< Edge * > and a list< Edge const * >.

assign(self: pyrosetta.rosetta.utility.graph.EdgeListConstIterator, rhs: pyrosetta.rosetta.utility.graph.EdgeListConstIterator) pyrosetta.rosetta.utility.graph.EdgeListConstIterator

assignmnet operator

C++: utility::graph::EdgeListConstIterator::operator=(const class utility::graph::EdgeListConstIterator &) –> class utility::graph::EdgeListConstIterator &

minus_minus(self: pyrosetta.rosetta.utility.graph.EdgeListConstIterator) pyrosetta.rosetta.utility.graph.EdgeListConstIterator

decrement operator. Point this iterator at the previous element in the list.

C++: utility::graph::EdgeListConstIterator::operator–() –> const class utility::graph::EdgeListConstIterator &

plus_plus(self: pyrosetta.rosetta.utility.graph.EdgeListConstIterator) pyrosetta.rosetta.utility.graph.EdgeListConstIterator

increment operator. Point this iterator at the next element in the list.

C++: utility::graph::EdgeListConstIterator::operator++() –> const class utility::graph::EdgeListConstIterator &

valid(self: pyrosetta.rosetta.utility.graph.EdgeListConstIterator) bool

Is this a valid iterator?

C++: utility::graph::EdgeListConstIterator::valid() const –> bool

class pyrosetta.rosetta.utility.graph.EdgeListElement

Bases: pybind11_builtins.pybind11_object

Custom written edge list element class. Little more than a struct. Defined so that edge list memory management could rely on boost::pool like object

const_edge(self: pyrosetta.rosetta.utility.graph.EdgeListElement) utility::graph::Edge

C++: utility::graph::EdgeListElement::const_edge() const –> const class utility::graph::Edge *

const_next(self: pyrosetta.rosetta.utility.graph.EdgeListElement) pyrosetta.rosetta.utility.graph.EdgeListElement

C++: utility::graph::EdgeListElement::const_next() const –> const class utility::graph::EdgeListElement *

const_previous(self: pyrosetta.rosetta.utility.graph.EdgeListElement) pyrosetta.rosetta.utility.graph.EdgeListElement

C++: utility::graph::EdgeListElement::const_previous() const –> const class utility::graph::EdgeListElement *

edge(*args, **kwargs)

Overloaded function.

  1. edge(self: pyrosetta.rosetta.utility.graph.EdgeListElement) -> utility::graph::Edge

C++: utility::graph::EdgeListElement::edge() –> class utility::graph::Edge *

  1. edge(self: pyrosetta.rosetta.utility.graph.EdgeListElement, setting: utility::graph::Edge) -> None

C++: utility::graph::EdgeListElement::edge(class utility::graph::Edge *) –> void

next(*args, **kwargs)

Overloaded function.

  1. next(self: pyrosetta.rosetta.utility.graph.EdgeListElement) -> pyrosetta.rosetta.utility.graph.EdgeListElement

C++: utility::graph::EdgeListElement::next() –> class utility::graph::EdgeListElement *

  1. next(self: pyrosetta.rosetta.utility.graph.EdgeListElement, setting: pyrosetta.rosetta.utility.graph.EdgeListElement) -> None

C++: utility::graph::EdgeListElement::next(class utility::graph::EdgeListElement *) –> void

previous(*args, **kwargs)

Overloaded function.

  1. previous(self: pyrosetta.rosetta.utility.graph.EdgeListElement) -> pyrosetta.rosetta.utility.graph.EdgeListElement

C++: utility::graph::EdgeListElement::previous() –> class utility::graph::EdgeListElement *

  1. previous(self: pyrosetta.rosetta.utility.graph.EdgeListElement, setting: pyrosetta.rosetta.utility.graph.EdgeListElement) -> None

C++: utility::graph::EdgeListElement::previous(class utility::graph::EdgeListElement *) –> void

class pyrosetta.rosetta.utility.graph.EdgeListIterator

Bases: pybind11_builtins.pybind11_object

Custom Edge list (non-const) iterator class, which can return non-const Edge pointers. This iterator cannot be used to change the structure of its list without access to that list directly. Customized since STL’s const-iterator cannot be prevented from giving non-const access to its data. The former workaround to this problem was to define two sets of edge lists on each vertex: a list< Edge * > and a list< Edge const * >.

assign(self: pyrosetta.rosetta.utility.graph.EdgeListIterator, rhs: pyrosetta.rosetta.utility.graph.EdgeListIterator) pyrosetta.rosetta.utility.graph.EdgeListIterator

assignmnet operator

C++: utility::graph::EdgeListIterator::operator=(const class utility::graph::EdgeListIterator &) –> class utility::graph::EdgeListIterator &

minus_minus(self: pyrosetta.rosetta.utility.graph.EdgeListIterator) pyrosetta.rosetta.utility.graph.EdgeListIterator

decrement operator. Point this iterator at the previous element in the list.

C++: utility::graph::EdgeListIterator::operator–() –> const class utility::graph::EdgeListIterator &

plus_plus(self: pyrosetta.rosetta.utility.graph.EdgeListIterator) pyrosetta.rosetta.utility.graph.EdgeListIterator

increment operator. Point this iterator at the next element in the list.

C++: utility::graph::EdgeListIterator::operator++() –> const class utility::graph::EdgeListIterator &

valid(self: pyrosetta.rosetta.utility.graph.EdgeListIterator) bool
check that this iterator is valid. Will not guarantee that the iterator points at an element

that has not been destroyed.

C++: utility::graph::EdgeListIterator::valid() const –> bool

class pyrosetta.rosetta.utility.graph.Graph

Bases: pybind11_builtins.pybind11_object

A Graph with constant time edge insertion and deletion. Extensible.

add_edge(*args, **kwargs)

Overloaded function.

  1. add_edge(self: pyrosetta.rosetta.utility.graph.Graph, node1: int, node2: int) -> pyrosetta.rosetta.utility.graph.Edge

add an edge between two vertices. Invokes “create_edge” from the derived class.

Returns a pointer to the edge after its been added, allowing the calling function to immediately set data for this edge.

C++: utility::graph::Graph::add_edge(unsigned long, unsigned long) –> class utility::graph::Edge *

  1. add_edge(self: pyrosetta.rosetta.utility.graph.Graph, example_edge: pyrosetta.rosetta.utility.graph.Edge) -> pyrosetta.rosetta.utility.graph.Edge

add an edge to this graph copying the data from an edge in another graph.

Returns a pointer to the edge after its been added, allowing the calling function to immediately set data for this edge.

C++: utility::graph::Graph::add_edge(const class utility::graph::Edge *) –> class utility::graph::Edge *

all_pairs_shortest_paths(self: pyrosetta.rosetta.utility.graph.Graph) pyrosetta.rosetta.ObjexxFCL.FArray2D_int_t
O(V^3). Computes all pairs shortest paths using Warshall’s algorithm

and writes all the path distances to the two-dimensional table.

C++: utility::graph::Graph::all_pairs_shortest_paths() const –> class ObjexxFCL::FArray2D<int>

assign(self: pyrosetta.rosetta.utility.graph.Graph, source: pyrosetta.rosetta.utility.graph.Graph) pyrosetta.rosetta.utility.graph.Graph

assignment operator. source and this must have the same type.

C++: utility::graph::Graph::operator=(const class utility::graph::Graph &) –> class utility::graph::Graph &

const_edge_list_begin(self: pyrosetta.rosetta.utility.graph.Graph) pyrosetta.rosetta.utility.graph.EdgeListConstIterator
returns a const iterator to the beginning of the (unordered) edge list for the graph.

this edge list contains all the edges in the graph, not simply those for a particular vertex

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

const_edge_list_end(self: pyrosetta.rosetta.utility.graph.Graph) pyrosetta.rosetta.utility.graph.EdgeListConstIterator
returns a const iterator to the end of the (unordered) edge list for the graph.

this edge list contains all the edges in the graph, not simply those for a particular vertex

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

copy_connectivity(self: pyrosetta.rosetta.utility.graph.Graph, source: pyrosetta.rosetta.utility.graph.Graph) None
copy the edge connectivity from a source graph with a potentially

unknown type.

C++: utility::graph::Graph::copy_connectivity(const class utility::graph::Graph &) –> void

delete_edge(self: pyrosetta.rosetta.utility.graph.Graph, edge: pyrosetta.rosetta.utility.graph.Edge) None
remove an edge from the graph. (NEW AS OF 12/9/07) Never call C++’s

“delete” function on an edge pointer directly. Derived classes must implement this function. If they wish to use unordered_object_pools to manage their memory

C++: utility::graph::Graph::delete_edge(class utility::graph::Edge *) –> void

drop_all_edges(self: pyrosetta.rosetta.utility.graph.Graph) None

delete all the edges present in the graph

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

drop_all_edges_for_node(self: pyrosetta.rosetta.utility.graph.Graph, node: int) None

delete all the edges for a single vertex in the graph

C++: utility::graph::Graph::drop_all_edges_for_node(unsigned long) –> void

edge_list_begin(self: pyrosetta.rosetta.utility.graph.Graph) pyrosetta.rosetta.utility.graph.EdgeListIterator
returns a non-const iterator to the beginning of the (unordered) edge list for the graph.

this edge list contains all the edges in the graph, not simply those for a particular vertex

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

edge_list_end(self: pyrosetta.rosetta.utility.graph.Graph) pyrosetta.rosetta.utility.graph.EdgeListIterator
returns a non-const iterator to the end of the (unordered) edge list for the graph.

this edge list contains all the edges in the graph, not simply those for a particular vertex

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

find_edge(self: pyrosetta.rosetta.utility.graph.Graph, node1: int, node2: int) pyrosetta.rosetta.utility.graph.Edge
returns a pointer to the edge connecting nodes node1 and node2, if that edge exists

in the graph, o.w. returns 0. Focuses the graph on this edge for fast subsequent retrieval.

C++: utility::graph::Graph::find_edge(unsigned long, unsigned long) –> class utility::graph::Edge *

focused_edge(self: pyrosetta.rosetta.utility.graph.Graph) pyrosetta.rosetta.utility.graph.Edge

returns a pointer to the focused edge

C++: utility::graph::Graph::focused_edge() –> class utility::graph::Edge *

getTotalMemoryUsage(self: pyrosetta.rosetta.utility.graph.Graph) int
returns a count of all the memory used by every vertex and edge in a graph

by invoking the polymorphic count_static_memory and count_dynamic_memory of each (possibly derived) node and edge object as well as for the (possibly derived) graph class.

C++: utility::graph::Graph::getTotalMemoryUsage() const –> unsigned long

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

is an edge already present in the graph? O(V) worst case. O(1) iff all vertices have O(1) edges

C++: utility::graph::Graph::get_edge_exists(unsigned long, unsigned long) const –> bool

get_node(self: pyrosetta.rosetta.utility.graph.Graph, index: int) pyrosetta.rosetta.utility.graph.Node

C++: utility::graph::Graph::get_node(unsigned long) –> class utility::graph::Node *

get_self_ptr(self: pyrosetta.rosetta.utility.graph.Graph) pyrosetta.rosetta.utility.graph.Graph

C++: utility::graph::Graph::get_self_ptr() –> class std::shared_ptr<class utility::graph::Graph>

num_edges(self: pyrosetta.rosetta.utility.graph.Graph) int

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

num_nodes(self: pyrosetta.rosetta.utility.graph.Graph) int

the number of nodes in the graph

C++: utility::graph::Graph::num_nodes() const –> unsigned long

output_connectivity(self: pyrosetta.rosetta.utility.graph.Graph, os: pyrosetta.rosetta.std.ostream) None

send an edge list to the stream os.

C++: utility::graph::Graph::output_connectivity(std::ostream &) const –> void

output_dimacs(self: pyrosetta.rosetta.utility.graph.Graph, os: pyrosetta.rosetta.std.ostream) None

describe this graph in dimacs form to the stream os.

C++: utility::graph::Graph::output_dimacs(std::ostream &) const –> void

print_vertices(self: pyrosetta.rosetta.utility.graph.Graph) None

send summary information to the screen for all vertices in the graph

C++: utility::graph::Graph::print_vertices() const –> void

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

set the number of nodes in the graph – deletes any existing edges in the graph

C++: utility::graph::Graph::set_num_nodes(unsigned long) –> void

class pyrosetta.rosetta.utility.graph.LowMemEdge

Bases: pybind11_builtins.pybind11_object

An Edge class for LowMemGraph. Will often be overriden.

Be careful with this class! It doesn’t use actual virtual
functions. Never do this:

LowMemEdgeOP op = MyDerivedEdgeOP()

Instead, if you wish to use an owning pointer, you must do this:

MyDerivedEdgeOP op = MyDerivedEdgeOP()

Having any virtual functions increases a class’s footprint by 8 bytes

If writing a derived class, “override” these three functions:

~LowMemNode() count_static_memory() count_dynamic_memory()

See core/scoring/hbonds/graph/HBondGraph.hh for example

count_dynamic_memory(self: pyrosetta.rosetta.utility.graph.LowMemEdge) int
how much memory is dynamically allocated by this edge – must be recursively invoked

by a derived class.

This function isn’t technically virtual, but if you override

it, your code WILL be called by getTotalMemoryUsage()

C++: utility::graph::LowMemEdge::count_dynamic_memory() const –> unsigned long

count_static_memory(self: pyrosetta.rosetta.utility.graph.LowMemEdge) int

how much memory is statically allocated by this edge

This function isn’t technically virtual, but if you override

it, your code WILL be called by getTotalMemoryUsage()

C++: utility::graph::LowMemEdge::count_static_memory() const –> unsigned long

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

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

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

class pyrosetta.rosetta.utility.graph.LowMemEdgeListConstIter

Bases: pybind11_builtins.pybind11_object

Const iterator for edges

minus_minus(self: pyrosetta.rosetta.utility.graph.LowMemEdgeListConstIter) pyrosetta.rosetta.utility.graph.LowMemEdgeListConstIter

decrement operator. Point this iterator at the previous element in the list.

C++: utility::graph::LowMemEdgeListConstIter::operator–() –> const class utility::graph::LowMemEdgeListConstIter &

plus_plus(self: pyrosetta.rosetta.utility.graph.LowMemEdgeListConstIter) pyrosetta.rosetta.utility.graph.LowMemEdgeListConstIter

increment operator. Point this iterator at the next element in the list.

C++: utility::graph::LowMemEdgeListConstIter::operator++() –> const class utility::graph::LowMemEdgeListConstIter &

valid(self: pyrosetta.rosetta.utility.graph.LowMemEdgeListConstIter) bool
check that this iterator is valid. Will not guarantee that the iterator points at an element

that has not been destroyed.

C++: utility::graph::LowMemEdgeListConstIter::valid() const –> bool

class pyrosetta.rosetta.utility.graph.LowMemEdgeListIter

Bases: pybind11_builtins.pybind11_object

Non-const iterator for edges

minus_minus(self: pyrosetta.rosetta.utility.graph.LowMemEdgeListIter) pyrosetta.rosetta.utility.graph.LowMemEdgeListIter

decrement operator. Point this iterator at the previous element in the list.

C++: utility::graph::LowMemEdgeListIter::operator–() –> const class utility::graph::LowMemEdgeListIter &

plus_plus(self: pyrosetta.rosetta.utility.graph.LowMemEdgeListIter) pyrosetta.rosetta.utility.graph.LowMemEdgeListIter

increment operator. Point this iterator at the next element in the list.

C++: utility::graph::LowMemEdgeListIter::operator++() –> const class utility::graph::LowMemEdgeListIter &

valid(self: pyrosetta.rosetta.utility.graph.LowMemEdgeListIter) bool
check that this iterator is valid. Will not guarantee that the iterator points at an element

that has not been destroyed.

C++: utility::graph::LowMemEdgeListIter::valid() const –> bool

class pyrosetta.rosetta.utility.graph.LowMemGraphBase

Bases: pybind11_builtins.pybind11_object

Pure virtual baseclass that was required to avoid templating Edges and Nodes

assign(self: pyrosetta.rosetta.utility.graph.LowMemGraphBase, : pyrosetta.rosetta.utility.graph.LowMemGraphBase) pyrosetta.rosetta.utility.graph.LowMemGraphBase

C++: utility::graph::LowMemGraphBase::operator=(const class utility::graph::LowMemGraphBase &) –> class utility::graph::LowMemGraphBase &

drop_all_edges_for_node(self: pyrosetta.rosetta.utility.graph.LowMemGraphBase, index: int) None

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

get_node(self: pyrosetta.rosetta.utility.graph.LowMemGraphBase, index: int) utility::graph::LowMemNode

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

internal_edge_list_size(self: pyrosetta.rosetta.utility.graph.LowMemGraphBase) int

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

class pyrosetta.rosetta.utility.graph.LowMemGraph_core_scoring_hbonds_graph_HBondNode_core_scoring_hbonds_graph_HBondEdge_t

Bases: pyrosetta.rosetta.utility.graph.LowMemGraphBase

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(*args, **kwargs)

Overloaded function.

  1. assign(self: pyrosetta.rosetta.utility.graph.LowMemGraph_core_scoring_hbonds_graph_HBondNode_core_scoring_hbonds_graph_HBondEdge_t, : pyrosetta.rosetta.utility.graph.LowMemGraph_core_scoring_hbonds_graph_HBondNode_core_scoring_hbonds_graph_HBondEdge_t) -> pyrosetta.rosetta.utility.graph.LowMemGraph_core_scoring_hbonds_graph_HBondNode_core_scoring_hbonds_graph_HBondEdge_t

C++: utility::graph::LowMemGraph<core::scoring::hbonds::graph::HBondNode, core::scoring::hbonds::graph::HBondEdge>::operator=(const class utility::graph::LowMemGraph<class core::scoring::hbonds::graph::HBondNode, class core::scoring::hbonds::graph::HBondEdge> &) –> class utility::graph::LowMemGraph<class core::scoring::hbonds::graph::HBondNode, class core::scoring::hbonds::graph::HBondEdge> &

  1. assign(self: pyrosetta.rosetta.utility.graph.LowMemGraph_core_scoring_hbonds_graph_HBondNode_core_scoring_hbonds_graph_HBondEdge_t, : pyrosetta.rosetta.utility.graph.LowMemGraphBase) -> pyrosetta.rosetta.utility.graph.LowMemGraphBase

C++: utility::graph::LowMemGraphBase::operator=(const class utility::graph::LowMemGraphBase &) –> class utility::graph::LowMemGraphBase &

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.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>::count_dynamic_memory() const –> unsigned long

count_static_memory(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>::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

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

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.utility.graph.LowMemNode

Bases: pybind11_builtins.pybind11_object

An Node class for LowMemGraph. Will often be overriden

Be careful with this class! It doesn’t use actual virtual
functions. Never do this:

LowMemNodeOP op = MyDerivedNodeOP()

Instead, if you wish to use an owning pointer, you must do this:

MyDerivedNodeOP op = MyDerivedNodeOP()

Having any virtual functions increases a class’s footprint by 8 bytes

If writing a derived class, “override” these four functions:

~LowMemNode() print() count_static_memory() count_dynamic_memory()

See core/scoring/hbonds/graph/HBondGraph.hh for example

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.utility.graph.LowMemNode) int
how much memory is dynamically allocated by this node – must be recursively invoked

by a derived class.

This function isn’t technically virtual, but if you override

it, your code WILL be called by getTotalMemoryUsage()

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

count_static_memory(self: pyrosetta.rosetta.utility.graph.LowMemNode) int

how much memory is statically allocated by this node

This function isn’t technically virtual, but if you override

it, your code WILL be called by getTotalMemoryUsage()

C++: utility::graph::LowMemNode::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

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> > &

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

print(self: pyrosetta.rosetta.utility.graph.LowMemNode) None

send summaray data about this node to the screen

This function isn’t technically virtual, but if you override

it, your code WILL be called by print_vertices()

C++: utility::graph::LowMemNode::print() const –> void

class pyrosetta.rosetta.utility.graph.NegSpaceElement_double_t

Bases: pybind11_builtins.pybind11_object

allocated(self: pyrosetta.rosetta.utility.graph.NegSpaceElement_double_t) bool

C++: utility::graph::NegSpaceElement<double>::allocated() const –> bool

array(self: pyrosetta.rosetta.utility.graph.NegSpaceElement_double_t) float

C++: utility::graph::NegSpaceElement<double>::array() const –> double *

assign(self: pyrosetta.rosetta.utility.graph.NegSpaceElement_double_t, : pyrosetta.rosetta.utility.graph.NegSpaceElement_double_t) pyrosetta.rosetta.utility.graph.NegSpaceElement_double_t

C++: utility::graph::NegSpaceElement<double>::operator=(const class utility::graph::NegSpaceElement<double> &) –> class utility::graph::NegSpaceElement<double> &

insert_after(self: pyrosetta.rosetta.utility.graph.NegSpaceElement_double_t, element: pyrosetta.rosetta.utility.graph.NegSpaceElement_double_t) None

C++: utility::graph::NegSpaceElement<double>::insert_after(class utility::graph::NegSpaceElement<double> *) –> void

next(self: pyrosetta.rosetta.utility.graph.NegSpaceElement_double_t) pyrosetta.rosetta.utility.graph.NegSpaceElement_double_t

C++: utility::graph::NegSpaceElement<double>::next() const –> class utility::graph::NegSpaceElement<double> *

pop(self: pyrosetta.rosetta.utility.graph.NegSpaceElement_double_t) pyrosetta.rosetta.utility.graph.NegSpaceElement_double_t

C++: utility::graph::NegSpaceElement<double>::pop() –> class utility::graph::NegSpaceElement<double> *

set_allocated(self: pyrosetta.rosetta.utility.graph.NegSpaceElement_double_t, setting: bool) None

C++: utility::graph::NegSpaceElement<double>::set_allocated(bool) –> void

set_array(self: pyrosetta.rosetta.utility.graph.NegSpaceElement_double_t, array: float) None

C++: utility::graph::NegSpaceElement<double>::set_array(double *) –> void

set_next(self: pyrosetta.rosetta.utility.graph.NegSpaceElement_double_t, next: pyrosetta.rosetta.utility.graph.NegSpaceElement_double_t) None

C++: utility::graph::NegSpaceElement<double>::set_next(class utility::graph::NegSpaceElement<double> *) –> void

class pyrosetta.rosetta.utility.graph.Node

Bases: pybind11_builtins.pybind11_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

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.utility.graph.Node, source: pyrosetta.rosetta.utility.graph.Node) None
invoked during graph assignment operators to copy any

node data from one graph to another graph. The source node must be the same type as this node.

C++: utility::graph::Node::copy_from(const class utility::graph::Node *) –> void

count_dynamic_memory(self: pyrosetta.rosetta.utility.graph.Node) int

memory accounting scheme

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

count_static_memory(self: pyrosetta.rosetta.utility.graph.Node) int

memory accounting scheme

C++: utility::graph::Node::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

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

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.utility.graph.Node) None

send summaray data about this node to the screen

C++: utility::graph::Node::print() const –> 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

class pyrosetta.rosetta.utility.graph.UEEdge_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t

Bases: pybind11_builtins.pybind11_object

data(self: pyrosetta.rosetta.utility.graph.UEEdge_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t) core::conformation::PointGraphEdgeData

C++: utility::graph::UEEdge<core::conformation::PointGraphVertexData, core::conformation::PointGraphEdgeData>::data() –> class core::conformation::PointGraphEdgeData &

delete_edge(self: pyrosetta.rosetta.utility.graph.UEEdge_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t) None

C++: utility::graph::UEEdge<core::conformation::PointGraphVertexData, core::conformation::PointGraphEdgeData>::delete_edge() –> void

deleted(self: pyrosetta.rosetta.utility.graph.UEEdge_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t) bool

C++: utility::graph::UEEdge<core::conformation::PointGraphVertexData, core::conformation::PointGraphEdgeData>::deleted() const –> bool

upper_vertex(self: pyrosetta.rosetta.utility.graph.UEEdge_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t) int

C++: utility::graph::UEEdge<core::conformation::PointGraphVertexData, core::conformation::PointGraphEdgeData>::upper_vertex() const –> unsigned long

class pyrosetta.rosetta.utility.graph.UEEdge_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.utility.graph.UEEdge_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t, : pyrosetta.rosetta.utility.graph.UEEdge_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t) pyrosetta.rosetta.utility.graph.UEEdge_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t

C++: utility::graph::UEEdge<protocols::pose_metric_calculators::EmptyVertexData, protocols::pose_metric_calculators::EnergiesData>::operator=(const class utility::graph::UEEdge<class protocols::pose_metric_calculators::EmptyVertexData, class protocols::pose_metric_calculators::EnergiesData> &) –> class utility::graph::UEEdge<class protocols::pose_metric_calculators::EmptyVertexData, class protocols::pose_metric_calculators::EnergiesData> &

data(self: pyrosetta.rosetta.utility.graph.UEEdge_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t) protocols::pose_metric_calculators::EnergiesData

C++: utility::graph::UEEdge<protocols::pose_metric_calculators::EmptyVertexData, protocols::pose_metric_calculators::EnergiesData>::data() –> class protocols::pose_metric_calculators::EnergiesData &

delete_edge(self: pyrosetta.rosetta.utility.graph.UEEdge_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t) None

C++: utility::graph::UEEdge<protocols::pose_metric_calculators::EmptyVertexData, protocols::pose_metric_calculators::EnergiesData>::delete_edge() –> void

deleted(self: pyrosetta.rosetta.utility.graph.UEEdge_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t) bool

C++: utility::graph::UEEdge<protocols::pose_metric_calculators::EmptyVertexData, protocols::pose_metric_calculators::EnergiesData>::deleted() const –> bool

upper_vertex(self: pyrosetta.rosetta.utility.graph.UEEdge_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t) int

C++: utility::graph::UEEdge<protocols::pose_metric_calculators::EmptyVertexData, protocols::pose_metric_calculators::EnergiesData>::upper_vertex() const –> unsigned long

class pyrosetta.rosetta.utility.graph.UEVertex_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.utility.graph.UEVertex_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t, : pyrosetta.rosetta.utility.graph.UEVertex_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t) pyrosetta.rosetta.utility.graph.UEVertex_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t

C++: utility::graph::UEVertex<core::conformation::PointGraphVertexData, core::conformation::PointGraphEdgeData>::operator=(const class utility::graph::UEVertex<class core::conformation::PointGraphVertexData, class core::conformation::PointGraphEdgeData> &) –> class utility::graph::UEVertex<class core::conformation::PointGraphVertexData, class core::conformation::PointGraphEdgeData> &

const_upper_edge_list_begin(self: pyrosetta.rosetta.utility.graph.UEVertex_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t) __gnu_cxx::__normal_iterator<utility::graph::UEEdge<core::conformation::PointGraphVertexData, core::conformation::PointGraphEdgeData> const*, std::vector<utility::graph::UEEdge<core::conformation::PointGraphVertexData, core::conformation::PointGraphEdgeData>, std::allocator<utility::graph::UEEdge<core::conformation::PointGraphVertexData, core::conformation::PointGraphEdgeData> > > >

C++: utility::graph::UEVertex<core::conformation::PointGraphVertexData, core::conformation::PointGraphEdgeData>::const_upper_edge_list_begin() const –> class __gnu_cxx::__normal_iterator<const class utility::graph::UEEdge<class core::conformation::PointGraphVertexData, class core::conformation::PointGraphEdgeData> *, class std::vector<class utility::graph::UEEdge<class core::conformation::PointGraphVertexData, class core::conformation::PointGraphEdgeData>, class std::allocator<class utility::graph::UEEdge<class core::conformation::PointGraphVertexData, class core::conformation::PointGraphEdgeData> > > >

const_upper_edge_list_end(self: pyrosetta.rosetta.utility.graph.UEVertex_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t) __gnu_cxx::__normal_iterator<utility::graph::UEEdge<core::conformation::PointGraphVertexData, core::conformation::PointGraphEdgeData> const*, std::vector<utility::graph::UEEdge<core::conformation::PointGraphVertexData, core::conformation::PointGraphEdgeData>, std::allocator<utility::graph::UEEdge<core::conformation::PointGraphVertexData, core::conformation::PointGraphEdgeData> > > >

C++: utility::graph::UEVertex<core::conformation::PointGraphVertexData, core::conformation::PointGraphEdgeData>::const_upper_edge_list_end() const –> class __gnu_cxx::__normal_iterator<const class utility::graph::UEEdge<class core::conformation::PointGraphVertexData, class core::conformation::PointGraphEdgeData> *, class std::vector<class utility::graph::UEEdge<class core::conformation::PointGraphVertexData, class core::conformation::PointGraphEdgeData>, class std::allocator<class utility::graph::UEEdge<class core::conformation::PointGraphVertexData, class core::conformation::PointGraphEdgeData> > > >

data(self: pyrosetta.rosetta.utility.graph.UEVertex_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t) core::conformation::PointGraphVertexData

C++: utility::graph::UEVertex<core::conformation::PointGraphVertexData, core::conformation::PointGraphEdgeData>::data() –> class core::conformation::PointGraphVertexData &

drop_all_edges(self: pyrosetta.rosetta.utility.graph.UEVertex_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t) None

C++: utility::graph::UEVertex<core::conformation::PointGraphVertexData, core::conformation::PointGraphEdgeData>::drop_all_edges() –> void

edge_exists(self: pyrosetta.rosetta.utility.graph.UEVertex_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t, upper_vertex_id: int) bool

C++: utility::graph::UEVertex<core::conformation::PointGraphVertexData, core::conformation::PointGraphEdgeData>::edge_exists(unsigned long) –> bool

get_edge(self: pyrosetta.rosetta.utility.graph.UEVertex_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t, upper_vertex_id: int) utility::graph::UEEdge<core::conformation::PointGraphVertexData, core::conformation::PointGraphEdgeData>

C++: utility::graph::UEVertex<core::conformation::PointGraphVertexData, core::conformation::PointGraphEdgeData>::get_edge(unsigned long) –> class utility::graph::UEEdge<class core::conformation::PointGraphVertexData, class core::conformation::PointGraphEdgeData> *

num_lower_neighbors(self: pyrosetta.rosetta.utility.graph.UEVertex_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t) int

C++: utility::graph::UEVertex<core::conformation::PointGraphVertexData, core::conformation::PointGraphEdgeData>::num_lower_neighbors() const –> unsigned long

num_neighbors(self: pyrosetta.rosetta.utility.graph.UEVertex_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t) int

C++: utility::graph::UEVertex<core::conformation::PointGraphVertexData, core::conformation::PointGraphEdgeData>::num_neighbors() const –> unsigned long

num_neighbors_counting_self(self: pyrosetta.rosetta.utility.graph.UEVertex_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t) int

C++: utility::graph::UEVertex<core::conformation::PointGraphVertexData, core::conformation::PointGraphEdgeData>::num_neighbors_counting_self() const –> unsigned long

num_upper_neighbors(self: pyrosetta.rosetta.utility.graph.UEVertex_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t) int

C++: utility::graph::UEVertex<core::conformation::PointGraphVertexData, core::conformation::PointGraphEdgeData>::num_upper_neighbors() const –> unsigned long

reserve_edge_space(self: pyrosetta.rosetta.utility.graph.UEVertex_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t) None

C++: utility::graph::UEVertex<core::conformation::PointGraphVertexData, core::conformation::PointGraphEdgeData>::reserve_edge_space() –> void

upper_edge_list_begin(self: pyrosetta.rosetta.utility.graph.UEVertex_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t) __gnu_cxx::__normal_iterator<utility::graph::UEEdge<core::conformation::PointGraphVertexData, core::conformation::PointGraphEdgeData>*, std::vector<utility::graph::UEEdge<core::conformation::PointGraphVertexData, core::conformation::PointGraphEdgeData>, std::allocator<utility::graph::UEEdge<core::conformation::PointGraphVertexData, core::conformation::PointGraphEdgeData> > > >

C++: utility::graph::UEVertex<core::conformation::PointGraphVertexData, core::conformation::PointGraphEdgeData>::upper_edge_list_begin() –> class __gnu_cxx::__normal_iterator<class utility::graph::UEEdge<class core::conformation::PointGraphVertexData, class core::conformation::PointGraphEdgeData> *, class std::vector<class utility::graph::UEEdge<class core::conformation::PointGraphVertexData, class core::conformation::PointGraphEdgeData>, class std::allocator<class utility::graph::UEEdge<class core::conformation::PointGraphVertexData, class core::conformation::PointGraphEdgeData> > > >

upper_edge_list_end(self: pyrosetta.rosetta.utility.graph.UEVertex_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t) __gnu_cxx::__normal_iterator<utility::graph::UEEdge<core::conformation::PointGraphVertexData, core::conformation::PointGraphEdgeData>*, std::vector<utility::graph::UEEdge<core::conformation::PointGraphVertexData, core::conformation::PointGraphEdgeData>, std::allocator<utility::graph::UEEdge<core::conformation::PointGraphVertexData, core::conformation::PointGraphEdgeData> > > >

C++: utility::graph::UEVertex<core::conformation::PointGraphVertexData, core::conformation::PointGraphEdgeData>::upper_edge_list_end() –> class __gnu_cxx::__normal_iterator<class utility::graph::UEEdge<class core::conformation::PointGraphVertexData, class core::conformation::PointGraphEdgeData> *, class std::vector<class utility::graph::UEEdge<class core::conformation::PointGraphVertexData, class core::conformation::PointGraphEdgeData>, class std::allocator<class utility::graph::UEEdge<class core::conformation::PointGraphVertexData, class core::conformation::PointGraphEdgeData> > > >

class pyrosetta.rosetta.utility.graph.UEVertex_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.utility.graph.UEVertex_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t, : pyrosetta.rosetta.utility.graph.UEVertex_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t) pyrosetta.rosetta.utility.graph.UEVertex_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t

C++: utility::graph::UEVertex<protocols::pose_metric_calculators::EmptyVertexData, protocols::pose_metric_calculators::EnergiesData>::operator=(const class utility::graph::UEVertex<class protocols::pose_metric_calculators::EmptyVertexData, class protocols::pose_metric_calculators::EnergiesData> &) –> class utility::graph::UEVertex<class protocols::pose_metric_calculators::EmptyVertexData, class protocols::pose_metric_calculators::EnergiesData> &

const_upper_edge_list_begin(self: pyrosetta.rosetta.utility.graph.UEVertex_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t) __gnu_cxx::__normal_iterator<utility::graph::UEEdge<protocols::pose_metric_calculators::EmptyVertexData, protocols::pose_metric_calculators::EnergiesData> const*, std::vector<utility::graph::UEEdge<protocols::pose_metric_calculators::EmptyVertexData, protocols::pose_metric_calculators::EnergiesData>, std::allocator<utility::graph::UEEdge<protocols::pose_metric_calculators::EmptyVertexData, protocols::pose_metric_calculators::EnergiesData> > > >

C++: utility::graph::UEVertex<protocols::pose_metric_calculators::EmptyVertexData, protocols::pose_metric_calculators::EnergiesData>::const_upper_edge_list_begin() const –> class __gnu_cxx::__normal_iterator<const class utility::graph::UEEdge<class protocols::pose_metric_calculators::EmptyVertexData, class protocols::pose_metric_calculators::EnergiesData> *, class std::vector<class utility::graph::UEEdge<class protocols::pose_metric_calculators::EmptyVertexData, class protocols::pose_metric_calculators::EnergiesData>, class std::allocator<class utility::graph::UEEdge<class protocols::pose_metric_calculators::EmptyVertexData, class protocols::pose_metric_calculators::EnergiesData> > > >

const_upper_edge_list_end(self: pyrosetta.rosetta.utility.graph.UEVertex_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t) __gnu_cxx::__normal_iterator<utility::graph::UEEdge<protocols::pose_metric_calculators::EmptyVertexData, protocols::pose_metric_calculators::EnergiesData> const*, std::vector<utility::graph::UEEdge<protocols::pose_metric_calculators::EmptyVertexData, protocols::pose_metric_calculators::EnergiesData>, std::allocator<utility::graph::UEEdge<protocols::pose_metric_calculators::EmptyVertexData, protocols::pose_metric_calculators::EnergiesData> > > >

C++: utility::graph::UEVertex<protocols::pose_metric_calculators::EmptyVertexData, protocols::pose_metric_calculators::EnergiesData>::const_upper_edge_list_end() const –> class __gnu_cxx::__normal_iterator<const class utility::graph::UEEdge<class protocols::pose_metric_calculators::EmptyVertexData, class protocols::pose_metric_calculators::EnergiesData> *, class std::vector<class utility::graph::UEEdge<class protocols::pose_metric_calculators::EmptyVertexData, class protocols::pose_metric_calculators::EnergiesData>, class std::allocator<class utility::graph::UEEdge<class protocols::pose_metric_calculators::EmptyVertexData, class protocols::pose_metric_calculators::EnergiesData> > > >

data(self: pyrosetta.rosetta.utility.graph.UEVertex_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t) protocols::pose_metric_calculators::EmptyVertexData

C++: utility::graph::UEVertex<protocols::pose_metric_calculators::EmptyVertexData, protocols::pose_metric_calculators::EnergiesData>::data() –> class protocols::pose_metric_calculators::EmptyVertexData &

drop_all_edges(self: pyrosetta.rosetta.utility.graph.UEVertex_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t) None

C++: utility::graph::UEVertex<protocols::pose_metric_calculators::EmptyVertexData, protocols::pose_metric_calculators::EnergiesData>::drop_all_edges() –> void

edge_exists(self: pyrosetta.rosetta.utility.graph.UEVertex_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t, upper_vertex_id: int) bool

C++: utility::graph::UEVertex<protocols::pose_metric_calculators::EmptyVertexData, protocols::pose_metric_calculators::EnergiesData>::edge_exists(unsigned long) –> bool

get_edge(self: pyrosetta.rosetta.utility.graph.UEVertex_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t, upper_vertex_id: int) utility::graph::UEEdge<protocols::pose_metric_calculators::EmptyVertexData, protocols::pose_metric_calculators::EnergiesData>

C++: utility::graph::UEVertex<protocols::pose_metric_calculators::EmptyVertexData, protocols::pose_metric_calculators::EnergiesData>::get_edge(unsigned long) –> class utility::graph::UEEdge<class protocols::pose_metric_calculators::EmptyVertexData, class protocols::pose_metric_calculators::EnergiesData> *

num_lower_neighbors(self: pyrosetta.rosetta.utility.graph.UEVertex_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t) int

C++: utility::graph::UEVertex<protocols::pose_metric_calculators::EmptyVertexData, protocols::pose_metric_calculators::EnergiesData>::num_lower_neighbors() const –> unsigned long

num_neighbors(self: pyrosetta.rosetta.utility.graph.UEVertex_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t) int

C++: utility::graph::UEVertex<protocols::pose_metric_calculators::EmptyVertexData, protocols::pose_metric_calculators::EnergiesData>::num_neighbors() const –> unsigned long

num_neighbors_counting_self(self: pyrosetta.rosetta.utility.graph.UEVertex_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t) int

C++: utility::graph::UEVertex<protocols::pose_metric_calculators::EmptyVertexData, protocols::pose_metric_calculators::EnergiesData>::num_neighbors_counting_self() const –> unsigned long

num_upper_neighbors(self: pyrosetta.rosetta.utility.graph.UEVertex_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t) int

C++: utility::graph::UEVertex<protocols::pose_metric_calculators::EmptyVertexData, protocols::pose_metric_calculators::EnergiesData>::num_upper_neighbors() const –> unsigned long

reserve_edge_space(self: pyrosetta.rosetta.utility.graph.UEVertex_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t) None

C++: utility::graph::UEVertex<protocols::pose_metric_calculators::EmptyVertexData, protocols::pose_metric_calculators::EnergiesData>::reserve_edge_space() –> void

upper_edge_list_begin(self: pyrosetta.rosetta.utility.graph.UEVertex_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t) __gnu_cxx::__normal_iterator<utility::graph::UEEdge<protocols::pose_metric_calculators::EmptyVertexData, protocols::pose_metric_calculators::EnergiesData>*, std::vector<utility::graph::UEEdge<protocols::pose_metric_calculators::EmptyVertexData, protocols::pose_metric_calculators::EnergiesData>, std::allocator<utility::graph::UEEdge<protocols::pose_metric_calculators::EmptyVertexData, protocols::pose_metric_calculators::EnergiesData> > > >

C++: utility::graph::UEVertex<protocols::pose_metric_calculators::EmptyVertexData, protocols::pose_metric_calculators::EnergiesData>::upper_edge_list_begin() –> class __gnu_cxx::__normal_iterator<class utility::graph::UEEdge<class protocols::pose_metric_calculators::EmptyVertexData, class protocols::pose_metric_calculators::EnergiesData> *, class std::vector<class utility::graph::UEEdge<class protocols::pose_metric_calculators::EmptyVertexData, class protocols::pose_metric_calculators::EnergiesData>, class std::allocator<class utility::graph::UEEdge<class protocols::pose_metric_calculators::EmptyVertexData, class protocols::pose_metric_calculators::EnergiesData> > > >

upper_edge_list_end(self: pyrosetta.rosetta.utility.graph.UEVertex_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t) __gnu_cxx::__normal_iterator<utility::graph::UEEdge<protocols::pose_metric_calculators::EmptyVertexData, protocols::pose_metric_calculators::EnergiesData>*, std::vector<utility::graph::UEEdge<protocols::pose_metric_calculators::EmptyVertexData, protocols::pose_metric_calculators::EnergiesData>, std::allocator<utility::graph::UEEdge<protocols::pose_metric_calculators::EmptyVertexData, protocols::pose_metric_calculators::EnergiesData> > > >

C++: utility::graph::UEVertex<protocols::pose_metric_calculators::EmptyVertexData, protocols::pose_metric_calculators::EnergiesData>::upper_edge_list_end() –> class __gnu_cxx::__normal_iterator<class utility::graph::UEEdge<class protocols::pose_metric_calculators::EmptyVertexData, class protocols::pose_metric_calculators::EnergiesData> *, class std::vector<class utility::graph::UEEdge<class protocols::pose_metric_calculators::EmptyVertexData, class protocols::pose_metric_calculators::EnergiesData>, class std::allocator<class utility::graph::UEEdge<class protocols::pose_metric_calculators::EmptyVertexData, class protocols::pose_metric_calculators::EnergiesData> > > >

class pyrosetta.rosetta.utility.graph.UpperEdgeGraph_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t

Bases: pybind11_builtins.pybind11_object

add_edge(*args, **kwargs)

Overloaded function.

  1. add_edge(self: pyrosetta.rosetta.utility.graph.UpperEdgeGraph_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t, lower_vertex: int, upper_vertex: int) -> None

C++: utility::graph::UpperEdgeGraph<core::conformation::PointGraphVertexData, core::conformation::PointGraphEdgeData>::add_edge(unsigned long, unsigned long) –> void

  1. add_edge(self: pyrosetta.rosetta.utility.graph.UpperEdgeGraph_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t, lower_vertex: int, upper_vertex: int, edge_data: core::conformation::PointGraphEdgeData) -> None

C++: utility::graph::UpperEdgeGraph<core::conformation::PointGraphVertexData, core::conformation::PointGraphEdgeData>::add_edge(unsigned long, unsigned long, const class core::conformation::PointGraphEdgeData &) –> void

assign(self: pyrosetta.rosetta.utility.graph.UpperEdgeGraph_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t, other: pyrosetta.rosetta.utility.graph.UpperEdgeGraph_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t) pyrosetta.rosetta.utility.graph.UpperEdgeGraph_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t

C++: utility::graph::UpperEdgeGraph<core::conformation::PointGraphVertexData, core::conformation::PointGraphEdgeData>::operator=(const class utility::graph::UpperEdgeGraph<class core::conformation::PointGraphVertexData, class core::conformation::PointGraphEdgeData> &) –> const class utility::graph::UpperEdgeGraph<class core::conformation::PointGraphVertexData, class core::conformation::PointGraphEdgeData> &

drop_all_edges(self: pyrosetta.rosetta.utility.graph.UpperEdgeGraph_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t) None

C++: utility::graph::UpperEdgeGraph<core::conformation::PointGraphVertexData, core::conformation::PointGraphEdgeData>::drop_all_edges() –> void

edge_exists(self: pyrosetta.rosetta.utility.graph.UpperEdgeGraph_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t, lower_vertex: int, upper_vertex: int) bool

C++: utility::graph::UpperEdgeGraph<core::conformation::PointGraphVertexData, core::conformation::PointGraphEdgeData>::edge_exists(unsigned long, unsigned long) –> bool

get_edge(self: pyrosetta.rosetta.utility.graph.UpperEdgeGraph_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t, lower_vertex: int, upper_vertex: int) pyrosetta.rosetta.utility.graph.UEEdge_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t

C++: utility::graph::UpperEdgeGraph<core::conformation::PointGraphVertexData, core::conformation::PointGraphEdgeData>::get_edge(unsigned long, unsigned long) –> class utility::graph::UEEdge<class core::conformation::PointGraphVertexData, class core::conformation::PointGraphEdgeData> *

get_vertex(self: pyrosetta.rosetta.utility.graph.UpperEdgeGraph_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t, index: int) pyrosetta.rosetta.utility.graph.UEVertex_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t

C++: utility::graph::UpperEdgeGraph<core::conformation::PointGraphVertexData, core::conformation::PointGraphEdgeData>::get_vertex(unsigned long) –> class utility::graph::UEVertex<class core::conformation::PointGraphVertexData, class core::conformation::PointGraphEdgeData> &

num_edges(self: pyrosetta.rosetta.utility.graph.UpperEdgeGraph_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t) int

C++: utility::graph::UpperEdgeGraph<core::conformation::PointGraphVertexData, core::conformation::PointGraphEdgeData>::num_edges() const –> unsigned long

num_vertices(self: pyrosetta.rosetta.utility.graph.UpperEdgeGraph_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t) int

C++: utility::graph::UpperEdgeGraph<core::conformation::PointGraphVertexData, core::conformation::PointGraphEdgeData>::num_vertices() const –> unsigned long

set_num_vertices(self: pyrosetta.rosetta.utility.graph.UpperEdgeGraph_core_conformation_PointGraphVertexData_core_conformation_PointGraphEdgeData_t, num_vertices: int) None

C++: utility::graph::UpperEdgeGraph<core::conformation::PointGraphVertexData, core::conformation::PointGraphEdgeData>::set_num_vertices(unsigned long) –> void

class pyrosetta.rosetta.utility.graph.UpperEdgeGraph_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t

Bases: pybind11_builtins.pybind11_object

add_edge(*args, **kwargs)

Overloaded function.

  1. add_edge(self: pyrosetta.rosetta.utility.graph.UpperEdgeGraph_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t, lower_vertex: int, upper_vertex: int) -> None

C++: utility::graph::UpperEdgeGraph<protocols::pose_metric_calculators::EmptyVertexData, protocols::pose_metric_calculators::EnergiesData>::add_edge(unsigned long, unsigned long) –> void

  1. add_edge(self: pyrosetta.rosetta.utility.graph.UpperEdgeGraph_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t, lower_vertex: int, upper_vertex: int, edge_data: protocols::pose_metric_calculators::EnergiesData) -> None

C++: utility::graph::UpperEdgeGraph<protocols::pose_metric_calculators::EmptyVertexData, protocols::pose_metric_calculators::EnergiesData>::add_edge(unsigned long, unsigned long, const class protocols::pose_metric_calculators::EnergiesData &) –> void

assign(self: pyrosetta.rosetta.utility.graph.UpperEdgeGraph_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t, other: pyrosetta.rosetta.utility.graph.UpperEdgeGraph_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t) pyrosetta.rosetta.utility.graph.UpperEdgeGraph_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t

C++: utility::graph::UpperEdgeGraph<protocols::pose_metric_calculators::EmptyVertexData, protocols::pose_metric_calculators::EnergiesData>::operator=(const class utility::graph::UpperEdgeGraph<class protocols::pose_metric_calculators::EmptyVertexData, class protocols::pose_metric_calculators::EnergiesData> &) –> const class utility::graph::UpperEdgeGraph<class protocols::pose_metric_calculators::EmptyVertexData, class protocols::pose_metric_calculators::EnergiesData> &

drop_all_edges(self: pyrosetta.rosetta.utility.graph.UpperEdgeGraph_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t) None

C++: utility::graph::UpperEdgeGraph<protocols::pose_metric_calculators::EmptyVertexData, protocols::pose_metric_calculators::EnergiesData>::drop_all_edges() –> void

edge_exists(self: pyrosetta.rosetta.utility.graph.UpperEdgeGraph_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t, lower_vertex: int, upper_vertex: int) bool

C++: utility::graph::UpperEdgeGraph<protocols::pose_metric_calculators::EmptyVertexData, protocols::pose_metric_calculators::EnergiesData>::edge_exists(unsigned long, unsigned long) –> bool

get_edge(self: pyrosetta.rosetta.utility.graph.UpperEdgeGraph_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t, lower_vertex: int, upper_vertex: int) pyrosetta.rosetta.utility.graph.UEEdge_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t

C++: utility::graph::UpperEdgeGraph<protocols::pose_metric_calculators::EmptyVertexData, protocols::pose_metric_calculators::EnergiesData>::get_edge(unsigned long, unsigned long) –> class utility::graph::UEEdge<class protocols::pose_metric_calculators::EmptyVertexData, class protocols::pose_metric_calculators::EnergiesData> *

get_vertex(self: pyrosetta.rosetta.utility.graph.UpperEdgeGraph_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t, index: int) pyrosetta.rosetta.utility.graph.UEVertex_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t

C++: utility::graph::UpperEdgeGraph<protocols::pose_metric_calculators::EmptyVertexData, protocols::pose_metric_calculators::EnergiesData>::get_vertex(unsigned long) –> class utility::graph::UEVertex<class protocols::pose_metric_calculators::EmptyVertexData, class protocols::pose_metric_calculators::EnergiesData> &

num_edges(self: pyrosetta.rosetta.utility.graph.UpperEdgeGraph_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t) int

C++: utility::graph::UpperEdgeGraph<protocols::pose_metric_calculators::EmptyVertexData, protocols::pose_metric_calculators::EnergiesData>::num_edges() const –> unsigned long

num_vertices(self: pyrosetta.rosetta.utility.graph.UpperEdgeGraph_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t) int

C++: utility::graph::UpperEdgeGraph<protocols::pose_metric_calculators::EmptyVertexData, protocols::pose_metric_calculators::EnergiesData>::num_vertices() const –> unsigned long

set_num_vertices(self: pyrosetta.rosetta.utility.graph.UpperEdgeGraph_protocols_pose_metric_calculators_EmptyVertexData_protocols_pose_metric_calculators_EnergiesData_t, num_vertices: int) None

C++: utility::graph::UpperEdgeGraph<protocols::pose_metric_calculators::EmptyVertexData, protocols::pose_metric_calculators::EnergiesData>::set_num_vertices(unsigned long) –> void

pyrosetta.rosetta.utility.graph.block_allocation_error_message(block_size: int, array_size: int, neg_space_element_size: int) str

C++: utility::graph::block_allocation_error_message(unsigned long, unsigned long, unsigned long) –> std::string

pyrosetta.rosetta.utility.graph.delete_all_intragroup_edges(g: pyrosetta.rosetta.utility.graph.Graph, node_groups: pyrosetta.rosetta.utility.vector1_unsigned_long) None

C++: utility::graph::delete_all_intragroup_edges(class utility::graph::Graph &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

pyrosetta.rosetta.utility.graph.digraph_is_a_DAG(g: pyrosetta.rosetta.utility.graph.Digraph) bool
Return whether or not the input directed graph is a DAG – this invokes

the topological_sort function and simply returns the second element in the pair that it returns.

C++: utility::graph::digraph_is_a_DAG(const class utility::graph::Digraph &) –> bool

pyrosetta.rosetta.utility.graph.find_connected_components(g: pyrosetta.rosetta.utility.graph.Graph) pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t
returns a vector1 of connected component descriptions:

each entry holds a representative vertex from that connected component (first entry in pair) and the connected-component size (second entry in pair). O( V+E ).

C++: utility::graph::find_connected_components(const class utility::graph::Graph &) –> class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > >

pyrosetta.rosetta.utility.graph.neg_space_element_allocation_error_message(block_size: int, neg_space_element_size: int) str

C++: utility::graph::neg_space_element_allocation_error_message(unsigned long, unsigned long) –> std::string

class pyrosetta.rosetta.utility.graph.null_bfs_prune_visitor

Bases: pybind11_builtins.pybind11_object

pyrosetta.rosetta.utility.graph.topological_sort(g: pyrosetta.rosetta.utility.graph.Digraph) Tuple[pyrosetta.rosetta.std.list_unsigned_long_t, bool]
Construct a topological sort for the input directed graph, if it is a DAG,

and return whether or not the input graph is actually a DAG.

C++: utility::graph::topological_sort(const class utility::graph::Digraph &) –> struct std::pair<class std::list<unsigned long, class std::allocator<unsigned long> >, bool>