core::graph Namespace Reference

Classes
class	Array0
	Class Array0 is a c-style array wrapper that does bounds checking in debug mode. It indexes from 0 just like regular c-arrays. Class Array0 does not manage it's own memory. It does not allocate memory if you want to make it larger, nor does it deallocate memory when you destroy it. Bounds checking only ensures that the user does not go outside of the memory Array0 thinks it's in charge of. If the user should happen to point the array0 at memory that has not been allocated, Array0 is not responsible for segmentation fault that will likely occur. Garbage in, garbage out. More...
class	ArrayPool
class	ArrayPoolElement
class	DisjointSets
struct	DS_Node
class	Edge
class	EdgeList
	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. More...
class	EdgeListConstIterator
	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 * >. More...
class	EdgeListElement
	An extensible graph class. More...
class	EdgeListIterator
	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 * >. More...
class	Graph
	A Graph with constant time edge insertion and deletion. Extensible. More...
class	NegSpaceElement
	NegSpaceElement represents a single element in the singly-linked list of negative space in an array pool. More...
class	Node
class	UEEdge
class	UEVertex
class	UpperEdgeGraph

Typedefs
typedef utility::pointer::owning_ptr < ArrayPool< platform::Real > >	RealArrayPoolOP
typedef utility::pointer::owning_ptr < ArrayPool< platform::Real > const >	RealArrayPoolCOP
typedef utility::pointer::shared_ptr < Graph >	GraphOP
typedef utility::pointer::shared_ptr < Graph const >	GraphCOP

Functions
std::string	neg_space_element_allocation_error_message (Size block_size, Size neg_space_element_size)
std::string	block_allocation_error_message (Size block_size, Size array_size, Size t_size)
bool	all_visited (utility::vector1< bool > const &visited)
utility::vector1< std::pair < platform::Size, platform::Size > >	find_connected_components (Graph const &g)
	returns a vector1 of connected component descriptions: each entry holds the connected-component size and a representative vertex from that connected component. O( V+E ). More...
void	delete_all_intragroup_edges (Graph &g, utility::vector1< platform::Size > const &node_groups)

Variables
bool	output_interaction_graph_memory_usage = false

Typedef Documentation

typedef utility::pointer::shared_ptr< Graph const > core::graph::GraphCOP

typedef utility::pointer::shared_ptr< Graph > core::graph::GraphOP

typedef utility::pointer::owning_ptr< ArrayPool< platform::Real > const > core::graph::RealArrayPoolCOP

typedef utility::pointer::owning_ptr< ArrayPool< platform::Real > > core::graph::RealArrayPoolOP

Function Documentation

bool core::graph::all_visited

(

utility::vector1< bool > const &

visited

)

Referenced by find_connected_components().

std::string core::graph::block_allocation_error_message	(	Size	block_size,
		Size	array_size,
		Size	t_size
	)

References core::id::to_string().

Referenced by core::graph::ArrayPool< Real >::create_new_block().

void core::graph::delete_all_intragroup_edges	(	Graph &	g,
		utility::vector1< platform::Size > const &	node_groups
	)

References core::graph::Graph::delete_edge(), core::graph::Graph::edge_list_begin(), core::graph::Graph::edge_list_end(), and core::graph::Graph::num_nodes().

Referenced by protocols::enzdes::EnzdesFlexibleRegion::calculate_rotamer_set_design_targets_partition_sum().

utility::vector1< std::pair< platform::Size, platform::Size > > core::graph::find_connected_components

(

Graph const &

g

)

returns a vector1 of connected component descriptions: each entry holds the connected-component size and a representative vertex from that connected component. O( V+E ).

DFS search to identify connected components O(V) memory, O(V+E) time.

References all_visited(), core::graph::Node::const_edge_list_begin(), core::graph::Node::const_edge_list_end(), core::graph::Graph::get_node(), and core::graph::Graph::num_nodes().

std::string core::graph::neg_space_element_allocation_error_message	(	Size	block_size,
		Size	neg_space_element_size
	)

References core::id::to_string().

Referenced by core::graph::ArrayPool< Real >::create_new_block().

Variable Documentation

bool core::graph::output_interaction_graph_memory_usage = false