Rosetta Core  2014.35
Public Member Functions | Protected Member Functions | Private Member Functions | Private Attributes | Friends | List of all members
core::pack::interaction_graph::InteractionGraphBase Class Referenceabstract

#include <InteractionGraphBase.hh>

Public Member Functions

virtual ~InteractionGraphBase ()
 destructor More...
 
 InteractionGraphBase (int num_nodes)
 main constructor More...
 
virtual int get_num_nodes_v () const
 
int get_num_nodes () const
 
virtual void initialize (rotamer_set::RotamerSetsBase const &rot_sets)=0
 
void set_num_states_for_node (int node, int num_states)
 sets the number of states for a node of a particular index NEW REQUIREMENT: Nodes must have their num-states set in ascending order by node index; that is, node 1 must go first, node 2 next, and so on. More...
 
int get_num_states_for_node (int node) const
 returns the number of states for a particular node More...
 
int get_num_total_states () const
 
virtual core::PackerEnergy get_one_body_energy_for_node_state (int node, int state)=0
 
void add_edge (int node1, int node2)
 creates a new edge between nodes index1 and index2. Nodes do not have to be listed in order More...
 
bool get_edge_exists (int node1, int node2)
 returns true if an edge between node1 and node2 exists More...
 
void drop_all_edges_for_node (int node)
 deletes all edges adjacent to the node specified More...
 
void print_vertices () const
 calls print() on each of the nodes in the graph More...
 
virtual void print () const
 
void output_connectivity (std::ostream &os) const
 writes out a list of all the edges in the graph More...
 
void output_dimacs (std::ostream &os) const
 writes out a connectivity description of the graph in the famous dimacs format. (where the first column "DIMACS:" should be sed'ed out) More...
 
virtual void prepare_for_simulated_annealing ()
 iterate across edges and nodes and allow them to prepare for simulated annealing More...
 
virtual void blanket_assign_state_0 ()=0
 
virtual core::PackerEnergy set_state_for_node (int node_ind, int new_state)=0
 
virtual core::PackerEnergy set_network_state (ObjexxFCL::FArray1_int &node_states)=0
 
virtual void consider_substitution (int node_ind, int new_state, core::PackerEnergy &delta_energy, core::PackerEnergy &prev_energy_for_node)=0
 
virtual core::PackerEnergy commit_considered_substitution ()=0
 
virtual core::PackerEnergy get_energy_current_state_assignment ()=0
 
void set_edge_weight (int node1, int node2, Real edge_weight)
 
Real get_edge_weight (int node1, int node2) const
 
virtual int get_edge_memory_usage () const =0
 
virtual void print_current_state_assignment () const =0
 
virtual void set_errorfull_deltaE_threshold (core::PackerEnergy deltaE)=0
 
bool any_vertex_state_unassigned () const
 Returns true if any node in the graph is in state 0, the unassigned state. More...
 
void add_to_one_body_energies (ObjexxFCL::FArray1< core::PackerEnergy > &one_body_energies)
 takes one FArray of energies – one energy for each state for each node More...
 
void update_one_body_energies (ObjexxFCL::FArray1< core::PackerEnergy > &old_energy1b, ObjexxFCL::FArray1< core::PackerEnergy > &new_energy1b)
 decrements the one body energies by the values held in old_energy1b, increments the one body energies by the values held in new_energy1b, and copies new_energy1b into old_energy1b. More...
 
void zero_one_body_energies_for_node (int node)
 
void add_to_nodes_one_body_energy (int node_ind, utility::vector1< core::PackerEnergy > const &one_body_energies)
 
void add_to_nodes_one_body_energy (int node_ind, ObjexxFCL::FArray1< core::PackerEnergy > const &one_body_energies)
 
void add_to_nodes_one_body_energy (int node_ind, int state_id, core::PackerEnergy const one_body_energy)
 interface to PrecomputedPairEnergiesNode::add_to_nodes_one_body_energy More...
 
void set_number_of_energy_sum_vertex_groups (int num_groups)
 a user may define subsets of the vertex set for which they would like to know the internal energy sum. For instance in a graph with 6 vertices, {a,b,c,d,e,f} a user may be interested in the sum of the one- and two-body energies for vertices {a,b,c}. The graph will return sum of the one body energies for vertices a b and c and also any two-body energies for the edges in the subgraph induced by a,b, and c. (In this case, edges {a,b}, {a,c} and {b,c} if these edges are part of the graph. The edge {a,d} will not be counted if it is part of the graph.) More...
 
void set_vertex_member_of_group (int vertex, int group)
 a user may define subsets of the vertex set for which they would like to know the internal energy sum. For instance in a graph with 6 vertices, {a,b,c,d,e,f} a user may be interested in the sum of the one- and two-body energies for vertices {a,b,c}. The graph will return sum of the one body energies for vertices a b and c and also any two-body energies for the edges in the subgraph induced by a,b, and c. (In this case, edges {a,b}, {a,c} and {b,c} if these edges are part of the graph. The edge {a,d} will not be counted if it is part of the graph.) More...
 
void print_vertex_groups ()
 
virtual core::PackerEnergy get_energy_sum_for_vertex_group (int group_id)=0
 
int count_connected_components_and_initialize_vertex_groups ()
 makes a depth first traversal of the graph, counting the number of connected components, and initializes the vertex group memberships to reflect the connected components. Returns the number of connected components in the graph. More...
 
void note_vertex_reached (int node_index)
 marks a vertex as belonging to the connected component currently being traversed in the depth first traversal. More...
 
bool vertex_already_reached (int node_index)
 used by class NodeBase during the depth-first traversal to determine the number of connected components in the graph. returns true if the dft has already reached the node. More...
 
bool get_vertex_member_of_energy_sum_group (int node_index, int group_id)
 
virtual unsigned int getTotalMemoryUsage () const
 
void reset_edge_list_iterator_for_node (int node_index) const
 set the Graph's (single) edge list iterator to the beginning of the edge list for a particular node More...
 
void increment_edge_list_iterator () const
 increment the (single) edge list iterator to the next element More...
 
bool edge_list_iterator_at_end () const
 test: have we arrived at the edge list end? More...
 
EdgeBase const & get_edge () const
 return a const reference to an edge pointed at by the list iterator More...
 
EdgeBase const * find_edge (int node1, int node2) const
 returns the edge connecting node1 and node2 More...
 
EdgeBasefind_edge (int node1, int node2)
 
virtual NodeBasecreate_new_node (int node_index, int num_states)=0
 
virtual EdgeBasecreate_new_edge (int index1, int index2)=0
 
NodeBaseget_node (int index) const
 
int get_num_edges () const
 
std::list< EdgeBase * >::iterator get_edge_list_begin ()
 
std::list< EdgeBase * >
::const_iterator 
get_edge_list_begin () const
 
std::list< EdgeBase * >
::const_iterator 
get_edge_list_end () const
 

Protected Member Functions

virtual unsigned int count_static_memory () const =0
 
virtual unsigned int count_dynamic_memory () const
 
void drop_edge (std::list< EdgeBase * >::iterator edge)
 removes edge from edge list at iterator iter More...
 
int get_node_state_offset (int index) const
 
bool mine (EdgeBase const *edge) const
 

Private Member Functions

 InteractionGraphBase ()
 
 InteractionGraphBase (InteractionGraphBase const &)
 
InteractionGraphBaseoperator= (InteractionGraphBase const &)
 

Private Attributes

int num_ig_nodes_
 
std::vector< NodeBase * > ig_nodes_
 
std::list< EdgeBase * > ig_edge_list_
 
std::vector< intnode_state_offsets_
 
int num_total_states_
 
EdgeBasefocused_edge_
 
std::list< EdgeBase * >
::const_iterator 
focused_edge_iterator_
 
std::list< EdgeBase * >
::const_iterator 
focused_edge_iterator_end_
 
int num_energy_sum_groups_
 
ObjexxFCL::FArray2D_bool energy_sum_group_membership_
 
ObjexxFCL::FArray1D_int component_membership_
 

Friends

class NodeBase
 
class EdgeBase
 

Constructor & Destructor Documentation

core::pack::interaction_graph::InteractionGraphBase::~InteractionGraphBase ( )
virtual

destructor

InteractionGraphBase::~InteractionGraphBase

Detailed: deletes each edge in the graph and deletes each node
Parameters
par Global Read:
Global Write:
Remarks
References:
Authors
apl
Last Modified:

References ig_edge_list_, ig_nodes_, and num_ig_nodes_.

core::pack::interaction_graph::InteractionGraphBase::InteractionGraphBase ( int  num_ig_nodes)

main constructor

InteractionGraphBase::InteractionGraphBase

Detailed: no default or copy constructors provided.
Parameters
num_ig_nodes- [in] - number of nodes that this graph will contain
Global Read:
Global Write:
Remarks
References:
Authors
apl
Last Modified:
core::pack::interaction_graph::InteractionGraphBase::InteractionGraphBase ( )
private
core::pack::interaction_graph::InteractionGraphBase::InteractionGraphBase ( InteractionGraphBase const &  )
private

Member Function Documentation

void core::pack::interaction_graph::InteractionGraphBase::add_edge ( int  index1,
int  index2 
)

creates a new edge between nodes index1 and index2. Nodes do not have to be listed in order

InteractionGraphBase::add_edge

Detailed: uses factory method create_new_edge and adds
the created edge to the graph's edge list.
Parameters
index1- [in] - index of one of the two nodes the edge is to connect
index2- [in] - index of the second of the two nodes the edge is to connect
Global Read:
Global Write:
Remarks
References:
Authors
apl
Last Modified:

References create_new_edge(), focused_edge_, ig_edge_list_, and core::pack::interaction_graph::EdgeBase::set_pos_in_owners_list().

Referenced by core::pack::interaction_graph::PDInteractionGraph::add_edge().

void core::pack::interaction_graph::InteractionGraphBase::add_to_nodes_one_body_energy ( int  node_ind,
utility::vector1< core::PackerEnergy > const &  one_body_energies 
)
Parameters
node_ind- [in] - the node in question
one_body_energies- [in] - the energies to be added to the one-body energies on that node. One entry per state.
void core::pack::interaction_graph::InteractionGraphBase::add_to_nodes_one_body_energy ( int  node_ind,
ObjexxFCL::FArray1< core::PackerEnergy > const &  one_body_energies 
)
void core::pack::interaction_graph::InteractionGraphBase::add_to_nodes_one_body_energy ( int  node_ind,
int  state_id,
core::PackerEnergy const  one_body_energy 
)

interface to PrecomputedPairEnergiesNode::add_to_nodes_one_body_energy

Parameters
node_ind- [in] - the index of the node in question
state_id- [in] - the state in question
one_body_energy- [in] - the energy to be added
void core::pack::interaction_graph::InteractionGraphBase::add_to_one_body_energies ( ObjexxFCL::FArray1< core::PackerEnergy > &  one_body_energies)

takes one FArray of energies – one energy for each state for each node

InteractionGraphBase::add_to_one_body_energies

Detailed:
The input array should have {v} |S_v| entries, where S_v is the state-space for vertex v. If the graph has two vertices, with 15 and 20 states respectively, then entries 1 to 15 correspond to vertex 1, and entries 16 to 36 correspond to vertex 2. This compact enumeration scheme is the same as the enumeration scheme used by rotindex, rotcoord, etc
Parameters
one_body_energies- [in] - the array of one body energies
Global Read:
Global Write:
Remarks
References:
Authors
apl
Last Modified:
bool core::pack::interaction_graph::InteractionGraphBase::any_vertex_state_unassigned ( ) const

Returns true if any node in the graph is in state 0, the unassigned state.

InteractionGraphBase::output_dimacs

Detailed:
Useful for debugging. If simulated annealing completes, and any vertex remains in state 0, then the state assignment is not meaningful nor is the energy for that assignment. The cases in which state-0 problems turn up are from passing an annealer a list of states to restrict itself to wherein some vertex has no states listed. Such cases are bugs; this subroutine helps identify them.
Parameters
par Global Read:
Global Write:
Remarks
References:
Authors
apl
Last Modified:

References get_node(), get_num_nodes(), and core::pack::interaction_graph::NodeBase::state_unassigned().

virtual void core::pack::interaction_graph::InteractionGraphBase::blanket_assign_state_0 ( )
pure virtual
virtual core::PackerEnergy core::pack::interaction_graph::InteractionGraphBase::commit_considered_substitution ( )
pure virtual
virtual void core::pack::interaction_graph::InteractionGraphBase::consider_substitution ( int  node_ind,
int  new_state,
core::PackerEnergy delta_energy,
core::PackerEnergy prev_energy_for_node 
)
pure virtual
int core::pack::interaction_graph::InteractionGraphBase::count_connected_components_and_initialize_vertex_groups ( )

makes a depth first traversal of the graph, counting the number of connected components, and initializes the vertex group memberships to reflect the connected components. Returns the number of connected components in the graph.

InteractionGraphBase:: count_connected_components_and_initialize_vertex_groups

Detailed:
Parameters
par Global Read:
Global Write:
Remarks
References:
Authors
apl
Last Modified:

References component_membership_, energy_sum_group_membership_, ig_nodes_, num_energy_sum_groups_, num_ig_nodes_, and vertex_already_reached().

unsigned int core::pack::interaction_graph::InteractionGraphBase::count_dynamic_memory ( ) const
protectedvirtual
virtual unsigned int core::pack::interaction_graph::InteractionGraphBase::count_static_memory ( ) const
protectedpure virtual
virtual EdgeBase* core::pack::interaction_graph::InteractionGraphBase::create_new_edge ( int  index1,
int  index2 
)
pure virtual
virtual NodeBase* core::pack::interaction_graph::InteractionGraphBase::create_new_node ( int  node_index,
int  num_states 
)
pure virtual
void core::pack::interaction_graph::InteractionGraphBase::drop_all_edges_for_node ( int  node)

deletes all edges adjacent to the node specified

InteractionGraphBase::drop_all_edges_for_node

Detailed:
Parameters
node- [in] - index of the node
Global Read:
Global Write:
Remarks
References:
Authors
apl
Last Modified:

References core::pack::interaction_graph::NodeBase::drop_all_edges(), and get_node().

void core::pack::interaction_graph::InteractionGraphBase::drop_edge ( std::list< EdgeBase * >::iterator  iter)
protected

removes edge from edge list at iterator iter

InteractionGraphBase::drop_edge

Detailed:
each edge keeps track of its position in its owner's graph's edge list so it can efficiently delete itself should it need to.
Parameters
iter- [in] - the iterator pointing at the edge that's deleting itself
Global Read:
Global Write:
Remarks
References:
Authors
apl
Last Modified:

References focused_edge_, and ig_edge_list_.

Referenced by core::pack::interaction_graph::EdgeBase::~EdgeBase().

bool core::pack::interaction_graph::InteractionGraphBase::edge_list_iterator_at_end ( ) const

test: have we arrived at the edge list end?

References focused_edge_iterator_, and focused_edge_iterator_end_.

EdgeBase const * core::pack::interaction_graph::InteractionGraphBase::find_edge ( int  node1,
int  node2 
) const

returns the edge connecting node1 and node2

The following functions provide access to the nodes and edges in the graph though, their use is strongly discouraged except for in writing unit tests to ensure that the graphs are properly implemented.

InteractionGraphBase::find_edge

Detailed:
graph keeps a pointer to the last edge that was accessed to that search is fairly efficient.
Parameters
node1- [in] - index of the first node
node2- [in] - index of the second node
Global Read:
Global Write:
Remarks
References:
Authors
apl
Last Modified:

References focused_edge_, ig_nodes_, and core::pack::interaction_graph::EdgeBase::same_edge().

Referenced by core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::add_ProCorrection_values_for_edge(), core::pack::interaction_graph::DoubleLazyInteractionGraph::get_dlazy_edge(), core::pack::interaction_graph::DensePDInteractionGraph::get_dpd_edge(), get_edge_exists(), get_edge_weight(), core::pack::interaction_graph::FASTERInteractionGraph::get_faster_edge(), core::pack::interaction_graph::FixedBBInteractionGraph::get_fixedbb_edge(), core::pack::interaction_graph::LazyInteractionGraph::get_lazy_edge(), core::pack::interaction_graph::PDInteractionGraph::get_pd_edge(), core::pack::interaction_graph::OnTheFlyInteractionGraph::note_long_range_interactions_exist_for_edge(), core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::note_long_range_interactions_exist_for_edge(), core::pack::interaction_graph::OnTheFlyInteractionGraph::note_short_range_interactions_exist_for_edge(), core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::note_short_range_interactions_exist_for_edge(), set_edge_weight(), core::pack::interaction_graph::OnTheFlyInteractionGraph::set_ProCorrection_values_for_edge(), core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::set_residues_adjacent_for_subunit_pair_for_edge(), and core::pack::interaction_graph::OnTheFlyInteractionGraph::set_sparse_aa_info_for_edge().

EdgeBase * core::pack::interaction_graph::InteractionGraphBase::find_edge ( int  node1,
int  node2 
)
EdgeBase const & core::pack::interaction_graph::InteractionGraphBase::get_edge ( ) const

return a const reference to an edge pointed at by the list iterator

References focused_edge_iterator_.

bool core::pack::interaction_graph::InteractionGraphBase::get_edge_exists ( int  node1,
int  node2 
)

returns true if an edge between node1 and node2 exists

InteractionGraphBase::get_edge_exists

Detailed:
Parameters
node1- [in] - index of the one of the nodes node2 - [in] - index of the other node
Global Read:
Global Write:
Remarks
References:
Authors
apl
Last Modified:

References find_edge().

std::list< EdgeBase* >::iterator core::pack::interaction_graph::InteractionGraphBase::get_edge_list_begin ( )
inline

References ig_edge_list_.

Referenced by core::pack::interaction_graph::SymmMinimalistInteractionGraph::get_edge_memory_usage(), core::pack::interaction_graph::DoubleDensePDInteractionGraph::get_edge_memory_usage(), core::pack::interaction_graph::DensePDInteractionGraph::get_edge_memory_usage(), core::pack::interaction_graph::SymmLinearMemoryInteractionGraph::get_edge_memory_usage(), core::pack::interaction_graph::FASTERInteractionGraph::get_edge_memory_usage(), core::pack::interaction_graph::LazyInteractionGraph::get_edge_memory_usage(), core::pack::interaction_graph::LinearMemoryInteractionGraph::get_edge_memory_usage(), core::pack::interaction_graph::PDInteractionGraph::get_edge_memory_usage(), core::pack::interaction_graph::DoubleLazyInteractionGraph::get_edge_memory_usage(), core::pack::interaction_graph::FASTERInteractionGraph::get_energy_following_relaxation(), core::pack::interaction_graph::SymmMinimalistInteractionGraph::get_energy_sum_for_vertex_group(), core::pack::interaction_graph::DoubleDensePDInteractionGraph::get_energy_sum_for_vertex_group(), core::pack::interaction_graph::DensePDInteractionGraph::get_energy_sum_for_vertex_group(), core::pack::interaction_graph::SymmLinearMemoryInteractionGraph::get_energy_sum_for_vertex_group(), core::pack::interaction_graph::LazyInteractionGraph::get_energy_sum_for_vertex_group(), core::pack::interaction_graph::FASTERInteractionGraph::get_energy_sum_for_vertex_group(), core::pack::interaction_graph::LinearMemoryInteractionGraph::get_energy_sum_for_vertex_group(), core::pack::interaction_graph::DoubleLazyInteractionGraph::get_energy_sum_for_vertex_group(), core::pack::interaction_graph::PDInteractionGraph::get_energy_sum_for_vertex_group(), core::pack::interaction_graph::FASTERInteractionGraph::prepare_for_FASTER(), prepare_for_simulated_annealing(), core::pack::interaction_graph::DoubleLazyInteractionGraph::prepare_for_simulated_annealing(), core::pack::interaction_graph::SymmMinimalistInteractionGraph::print_current_state_assignment(), core::pack::interaction_graph::SymmLinearMemoryInteractionGraph::print_current_state_assignment(), core::pack::interaction_graph::LazyInteractionGraph::print_current_state_assignment(), core::pack::interaction_graph::LinearMemoryInteractionGraph::print_current_state_assignment(), core::pack::interaction_graph::DoubleLazyInteractionGraph::print_current_state_assignment(), core::pack::interaction_graph::SymmMinimalistInteractionGraph::update_internal_energy_totals(), core::pack::interaction_graph::DoubleDensePDInteractionGraph::update_internal_energy_totals(), core::pack::interaction_graph::DensePDInteractionGraph::update_internal_energy_totals(), core::pack::interaction_graph::SymmLinearMemoryInteractionGraph::update_internal_energy_totals(), core::pack::interaction_graph::FASTERInteractionGraph::update_internal_energy_totals(), core::pack::interaction_graph::LazyInteractionGraph::update_internal_energy_totals(), core::pack::interaction_graph::LinearMemoryInteractionGraph::update_internal_energy_totals(), core::pack::interaction_graph::PDInteractionGraph::update_internal_energy_totals(), core::pack::interaction_graph::DoubleLazyInteractionGraph::update_internal_energy_totals(), and core::pack::interaction_graph::DoubleLazyInteractionGraph::~DoubleLazyInteractionGraph().

std::list< EdgeBase* >::const_iterator core::pack::interaction_graph::InteractionGraphBase::get_edge_list_begin ( ) const
inline

References ig_edge_list_.

std::list< EdgeBase* >::const_iterator core::pack::interaction_graph::InteractionGraphBase::get_edge_list_end ( ) const
inline

References ig_edge_list_.

Referenced by core::pack::interaction_graph::SymmMinimalistInteractionGraph::get_edge_memory_usage(), core::pack::interaction_graph::DoubleDensePDInteractionGraph::get_edge_memory_usage(), core::pack::interaction_graph::DensePDInteractionGraph::get_edge_memory_usage(), core::pack::interaction_graph::SymmLinearMemoryInteractionGraph::get_edge_memory_usage(), core::pack::interaction_graph::FASTERInteractionGraph::get_edge_memory_usage(), core::pack::interaction_graph::LazyInteractionGraph::get_edge_memory_usage(), core::pack::interaction_graph::LinearMemoryInteractionGraph::get_edge_memory_usage(), core::pack::interaction_graph::PDInteractionGraph::get_edge_memory_usage(), core::pack::interaction_graph::DoubleLazyInteractionGraph::get_edge_memory_usage(), core::pack::interaction_graph::FASTERInteractionGraph::get_energy_following_relaxation(), core::pack::interaction_graph::SymmMinimalistInteractionGraph::get_energy_sum_for_vertex_group(), core::pack::interaction_graph::DoubleDensePDInteractionGraph::get_energy_sum_for_vertex_group(), core::pack::interaction_graph::DensePDInteractionGraph::get_energy_sum_for_vertex_group(), core::pack::interaction_graph::SymmLinearMemoryInteractionGraph::get_energy_sum_for_vertex_group(), core::pack::interaction_graph::LazyInteractionGraph::get_energy_sum_for_vertex_group(), core::pack::interaction_graph::FASTERInteractionGraph::get_energy_sum_for_vertex_group(), core::pack::interaction_graph::LinearMemoryInteractionGraph::get_energy_sum_for_vertex_group(), core::pack::interaction_graph::DoubleLazyInteractionGraph::get_energy_sum_for_vertex_group(), core::pack::interaction_graph::PDInteractionGraph::get_energy_sum_for_vertex_group(), core::pack::interaction_graph::FASTERInteractionGraph::prepare_for_FASTER(), prepare_for_simulated_annealing(), core::pack::interaction_graph::DoubleLazyInteractionGraph::prepare_for_simulated_annealing(), core::pack::interaction_graph::SymmMinimalistInteractionGraph::print_current_state_assignment(), core::pack::interaction_graph::SymmLinearMemoryInteractionGraph::print_current_state_assignment(), core::pack::interaction_graph::LazyInteractionGraph::print_current_state_assignment(), core::pack::interaction_graph::LinearMemoryInteractionGraph::print_current_state_assignment(), core::pack::interaction_graph::DoubleLazyInteractionGraph::print_current_state_assignment(), core::pack::interaction_graph::SymmMinimalistInteractionGraph::update_internal_energy_totals(), core::pack::interaction_graph::DoubleDensePDInteractionGraph::update_internal_energy_totals(), core::pack::interaction_graph::DensePDInteractionGraph::update_internal_energy_totals(), core::pack::interaction_graph::SymmLinearMemoryInteractionGraph::update_internal_energy_totals(), core::pack::interaction_graph::FASTERInteractionGraph::update_internal_energy_totals(), core::pack::interaction_graph::LazyInteractionGraph::update_internal_energy_totals(), core::pack::interaction_graph::LinearMemoryInteractionGraph::update_internal_energy_totals(), core::pack::interaction_graph::PDInteractionGraph::update_internal_energy_totals(), core::pack::interaction_graph::DoubleLazyInteractionGraph::update_internal_energy_totals(), and core::pack::interaction_graph::DoubleLazyInteractionGraph::~DoubleLazyInteractionGraph().

virtual int core::pack::interaction_graph::InteractionGraphBase::get_edge_memory_usage ( ) const
pure virtual
Real core::pack::interaction_graph::InteractionGraphBase::get_edge_weight ( int  node1,
int  node2 
) const

returns 0 if edge is not part of the graph

References core::pack::interaction_graph::EdgeBase::edge_weight(), and find_edge().

virtual core::PackerEnergy core::pack::interaction_graph::InteractionGraphBase::get_energy_current_state_assignment ( )
pure virtual
virtual core::PackerEnergy core::pack::interaction_graph::InteractionGraphBase::get_energy_sum_for_vertex_group ( int  group_id)
pure virtual
NodeBase* core::pack::interaction_graph::InteractionGraphBase::get_node ( int  index) const
inline
int core::pack::interaction_graph::InteractionGraphBase::get_node_state_offset ( int  index) const
inlineprotected
int core::pack::interaction_graph::InteractionGraphBase::get_num_edges ( ) const
inline
int core::pack::interaction_graph::InteractionGraphBase::get_num_nodes ( ) const
inline

References num_ig_nodes_.

Referenced by any_vertex_state_unassigned(), core::pack::interaction_graph::FASTERInteractionGraph::assign_BMEC(), core::pack::interaction_graph::DoubleDensePDInteractionGraph::blanket_assign_state_0(), core::pack::interaction_graph::SymmMinimalistInteractionGraph::blanket_assign_state_0(), core::pack::interaction_graph::DensePDInteractionGraph::blanket_assign_state_0(), core::pack::interaction_graph::SymmLinearMemoryInteractionGraph::blanket_assign_state_0(), core::pack::interaction_graph::FASTERInteractionGraph::blanket_assign_state_0(), core::pack::interaction_graph::LazyInteractionGraph::blanket_assign_state_0(), core::pack::interaction_graph::LinearMemoryInteractionGraph::blanket_assign_state_0(), core::pack::interaction_graph::PDInteractionGraph::blanket_assign_state_0(), core::pack::interaction_graph::DoubleLazyInteractionGraph::blanket_assign_state_0(), core::pack::interaction_graph::FASTERInteractionGraph::commit_relaxation(), core::pack::interaction_graph::FASTERInteractionGraph::get_current_network_state(), core::pack::interaction_graph::FASTERInteractionGraph::get_energy_following_relaxation(), core::pack::interaction_graph::SymmMinimalistInteractionGraph::get_energy_sum_for_vertex_group(), core::pack::interaction_graph::DoubleDensePDInteractionGraph::get_energy_sum_for_vertex_group(), core::pack::interaction_graph::DensePDInteractionGraph::get_energy_sum_for_vertex_group(), core::pack::interaction_graph::SymmLinearMemoryInteractionGraph::get_energy_sum_for_vertex_group(), core::pack::interaction_graph::LazyInteractionGraph::get_energy_sum_for_vertex_group(), core::pack::interaction_graph::FASTERInteractionGraph::get_energy_sum_for_vertex_group(), core::pack::interaction_graph::LinearMemoryInteractionGraph::get_energy_sum_for_vertex_group(), core::pack::interaction_graph::DoubleLazyInteractionGraph::get_energy_sum_for_vertex_group(), core::pack::interaction_graph::PDInteractionGraph::get_energy_sum_for_vertex_group(), get_num_nodes_v(), core::pack::interaction_graph::PDInteractionGraph::get_weighted_energy(), core::pack::interaction_graph::FASTERInteractionGraph::prepare_for_FASTER(), prepare_for_simulated_annealing(), core::pack::interaction_graph::SymmMinimalistInteractionGraph::print_current_state_assignment(), core::pack::interaction_graph::DoubleDensePDInteractionGraph::print_current_state_assignment(), core::pack::interaction_graph::DensePDInteractionGraph::print_current_state_assignment(), core::pack::interaction_graph::SymmLinearMemoryInteractionGraph::print_current_state_assignment(), core::pack::interaction_graph::LazyInteractionGraph::print_current_state_assignment(), core::pack::interaction_graph::FASTERInteractionGraph::print_current_state_assignment(), core::pack::interaction_graph::LinearMemoryInteractionGraph::print_current_state_assignment(), core::pack::interaction_graph::PDInteractionGraph::print_current_state_assignment(), core::pack::interaction_graph::DoubleLazyInteractionGraph::print_current_state_assignment(), print_vertex_groups(), core::pack::interaction_graph::FASTERInteractionGraph::probabilistically_commit_relaxation(), core::pack::interaction_graph::FASTERInteractionGraph::relax_in_current_context(), core::pack::interaction_graph::DoubleDensePDInteractionGraph::set_network_state(), core::pack::interaction_graph::SymmMinimalistInteractionGraph::set_network_state(), core::pack::interaction_graph::DensePDInteractionGraph::set_network_state(), core::pack::interaction_graph::SymmLinearMemoryInteractionGraph::set_network_state(), core::pack::interaction_graph::FASTERInteractionGraph::set_network_state(), core::pack::interaction_graph::LazyInteractionGraph::set_network_state(), core::pack::interaction_graph::LinearMemoryInteractionGraph::set_network_state(), core::pack::interaction_graph::PDInteractionGraph::set_network_state(), core::pack::interaction_graph::DoubleLazyInteractionGraph::set_network_state(), core::pack::interaction_graph::SymmLinearMemoryInteractionGraph::set_recent_history_sizes(), core::pack::interaction_graph::LinearMemoryInteractionGraph::set_recent_history_sizes(), core::pack::interaction_graph::SymmMinimalistInteractionGraph::update_internal_energy_totals(), core::pack::interaction_graph::DoubleDensePDInteractionGraph::update_internal_energy_totals(), core::pack::interaction_graph::DensePDInteractionGraph::update_internal_energy_totals(), core::pack::interaction_graph::SymmLinearMemoryInteractionGraph::update_internal_energy_totals(), core::pack::interaction_graph::FASTERInteractionGraph::update_internal_energy_totals(), core::pack::interaction_graph::LazyInteractionGraph::update_internal_energy_totals(), core::pack::interaction_graph::LinearMemoryInteractionGraph::update_internal_energy_totals(), core::pack::interaction_graph::PDInteractionGraph::update_internal_energy_totals(), and core::pack::interaction_graph::DoubleLazyInteractionGraph::update_internal_energy_totals().

virtual int core::pack::interaction_graph::InteractionGraphBase::get_num_nodes_v ( ) const
inlinevirtual

References get_num_nodes().

int core::pack::interaction_graph::InteractionGraphBase::get_num_states_for_node ( int  node_index) const

returns the number of states for a particular node

InteractionGraphBase::get_num_states_for_node

Detailed:
Parameters
node_index- [in] - the index of the node in question
Global Read:
Global Write:
Remarks
References:
Authors
apl
Last Modified:

References ig_nodes_.

int core::pack::interaction_graph::InteractionGraphBase::get_num_total_states ( ) const
inline

References num_total_states_.

virtual core::PackerEnergy core::pack::interaction_graph::InteractionGraphBase::get_one_body_energy_for_node_state ( int  node,
int  state 
)
pure virtual
bool core::pack::interaction_graph::InteractionGraphBase::get_vertex_member_of_energy_sum_group ( int  node_index,
int  group_id 
)
inline
unsigned int core::pack::interaction_graph::InteractionGraphBase::getTotalMemoryUsage ( ) const
virtual
void core::pack::interaction_graph::InteractionGraphBase::increment_edge_list_iterator ( ) const

increment the (single) edge list iterator to the next element

References focused_edge_iterator_, and focused_edge_iterator_end_.

virtual void core::pack::interaction_graph::InteractionGraphBase::initialize ( rotamer_set::RotamerSetsBase const &  rot_sets)
pure virtual
bool core::pack::interaction_graph::InteractionGraphBase::mine ( EdgeBase const *  edge) const
inlineprotected
void core::pack::interaction_graph::InteractionGraphBase::note_vertex_reached ( int  node_index)

marks a vertex as belonging to the connected component currently being traversed in the depth first traversal.

InteractionGraphBase::note_vertex_reached

Detailed:
Parameters
node_index- [in] - the index of the node invoking this method.
Global Read:
Global Write:
Remarks
This method should be used by the NodeBase class only.
References:
Authors
apl
Last Modified:

References component_membership_, and num_energy_sum_groups_.

Referenced by core::pack::interaction_graph::NodeBase::depth_first_connected_component_counting().

InteractionGraphBase& core::pack::interaction_graph::InteractionGraphBase::operator= ( InteractionGraphBase const &  )
private
void core::pack::interaction_graph::InteractionGraphBase::output_connectivity ( std::ostream &  os) const

writes out a list of all the edges in the graph

InteractionGraphBase::output_connectivity

Detailed:
Parameters
os- [in] - the output stream to write to
Global Read:
Global Write:
Remarks
References:
Authors
apl
Last Modified:

References ig_edge_list_.

void core::pack::interaction_graph::InteractionGraphBase::output_dimacs ( std::ostream &  os) const

writes out a connectivity description of the graph in the famous dimacs format. (where the first column "DIMACS:" should be sed'ed out)

InteractionGraphBase::output_dimacs

Detailed:
Parameters
os- [in] - the output stream to write to
Global Read:
Global Write:
Remarks
References:
Authors
apl
Last Modified:

References ig_edge_list_, and num_ig_nodes_.

void core::pack::interaction_graph::InteractionGraphBase::prepare_for_simulated_annealing ( )
virtual
virtual void core::pack::interaction_graph::InteractionGraphBase::print ( ) const
inlinevirtual

Referenced by print_vertices().

virtual void core::pack::interaction_graph::InteractionGraphBase::print_current_state_assignment ( ) const
pure virtual
void core::pack::interaction_graph::InteractionGraphBase::print_vertex_groups ( )
void core::pack::interaction_graph::InteractionGraphBase::print_vertices ( ) const

calls print() on each of the nodes in the graph

InteractionGraphBase::print_vertices

Detailed:
Parameters
par Global Read:
Global Write:
Remarks
References:
Authors
apl
Last Modified:

References ig_nodes_, num_ig_nodes_, and print().

void core::pack::interaction_graph::InteractionGraphBase::reset_edge_list_iterator_for_node ( int  node_index) const

set the Graph's (single) edge list iterator to the beginning of the edge list for a particular node

Methods for iterating across edges of the interaction graph. Protected access since the raw edge lists contain non-const pointers.

References focused_edge_iterator_, focused_edge_iterator_end_, and ig_nodes_.

void core::pack::interaction_graph::InteractionGraphBase::set_edge_weight ( int  node1,
int  node2,
Real  edge_weight 
)

invokes polymorphic method of EdgeBase class; no-op if edge is not part of the graph.

References find_edge(), core::pack::interaction_graph::EdgeBase::set_edge_weight(), and utility_exit_with_message.

virtual void core::pack::interaction_graph::InteractionGraphBase::set_errorfull_deltaE_threshold ( core::PackerEnergy  deltaE)
pure virtual
virtual core::PackerEnergy core::pack::interaction_graph::InteractionGraphBase::set_network_state ( ObjexxFCL::FArray1_int &  node_states)
pure virtual
void core::pack::interaction_graph::InteractionGraphBase::set_num_states_for_node ( int  node_index,
int  num_states 
)

sets the number of states for a node of a particular index NEW REQUIREMENT: Nodes must have their num-states set in ascending order by node index; that is, node 1 must go first, node 2 next, and so on.

InteractionGraphBase::set_num_states_for_node

Detailed: once the graph knows how many states a node has, it instantiates
a new node using the NodeBase(int) constructor through the graph's factory method create_new_node()
Parameters
node_index- [in] - the index of the node
num_states- [in] - the number of states for that node
Global Read:
Global Write:
Remarks
References:
Authors
apl
Last Modified:

Referenced by core::pack::interaction_graph::DoubleDensePDInteractionGraph::initialize(), core::pack::interaction_graph::DensePDInteractionGraph::initialize(), core::pack::interaction_graph::OnTheFlyInteractionGraph::initialize(), core::pack::interaction_graph::FASTERInteractionGraph::initialize(), core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::initialize(), and core::pack::interaction_graph::PDInteractionGraph::initialize().

void core::pack::interaction_graph::InteractionGraphBase::set_number_of_energy_sum_vertex_groups ( int  num_groups)

a user may define subsets of the vertex set for which they would like to know the internal energy sum. For instance in a graph with 6 vertices, {a,b,c,d,e,f} a user may be interested in the sum of the one- and two-body energies for vertices {a,b,c}. The graph will return sum of the one body energies for vertices a b and c and also any two-body energies for the edges in the subgraph induced by a,b, and c. (In this case, edges {a,b}, {a,c} and {b,c} if these edges are part of the graph. The edge {a,d} will not be counted if it is part of the graph.)

InteractionGraphBase::set_number_of_energy_sum_vertex_groups

First you must declare how many groups you are interested in. Do that with this method. Second you must declare which node is a member of each group. Only tell the graph which node is a member, do not tell the graph if a node is not a member. Third, when you want to know the energy sum for the group in the graph's current state assignment, call get_energy_sum_for_vertex_group( group_id)

Detailed:
Parameters
num_groups- [in] - the number of groups; set this at most once.
Global Read:
Global Write:
Remarks
References:
Authors
apl
Last Modified:

References energy_sum_group_membership_, num_energy_sum_groups_, and num_ig_nodes_.

virtual core::PackerEnergy core::pack::interaction_graph::InteractionGraphBase::set_state_for_node ( int  node_ind,
int  new_state 
)
pure virtual
void core::pack::interaction_graph::InteractionGraphBase::set_vertex_member_of_group ( int  vertex,
int  group 
)

a user may define subsets of the vertex set for which they would like to know the internal energy sum. For instance in a graph with 6 vertices, {a,b,c,d,e,f} a user may be interested in the sum of the one- and two-body energies for vertices {a,b,c}. The graph will return sum of the one body energies for vertices a b and c and also any two-body energies for the edges in the subgraph induced by a,b, and c. (In this case, edges {a,b}, {a,c} and {b,c} if these edges are part of the graph. The edge {a,d} will not be counted if it is part of the graph.)

InteractionGraphBase::set_vertex_member_of_group

Detailed:
tell the graph which vertices you want to be part of which groups
Parameters
vertex- [in] - the index of the vertex you wish to include in the group group - [in] - the group index you wish to add the vertex to.
Global Read:
Global Write:
Remarks
References:
Authors
apl
Last Modified:

References energy_sum_group_membership_.

void core::pack::interaction_graph::InteractionGraphBase::update_one_body_energies ( ObjexxFCL::FArray1< core::PackerEnergy > &  old_energy1b,
ObjexxFCL::FArray1< core::PackerEnergy > &  new_energy1b 
)

decrements the one body energies by the values held in old_energy1b, increments the one body energies by the values held in new_energy1b, and copies new_energy1b into old_energy1b.

InteractionGraphBase::add_to_one_body_energies

Detailed:
Parameters
old_energy1b- [in/out] - the one body energies representing interactions with portions of the background that are no longer valid new_energy1b - [in] - the one body energies representing interactions with the background after the background has changed
Global Read:
Global Write:
Remarks
useful if you want to move something in the background like a ligand. moving the background does not invalidate the two-body energies.
References:
Authors
apl
Last Modified:
bool core::pack::interaction_graph::InteractionGraphBase::vertex_already_reached ( int  node_index)

used by class NodeBase during the depth-first traversal to determine the number of connected components in the graph. returns true if the dft has already reached the node.

InteractionGraphBase:: vertex_already_reached

Detailed:
Parameters
node_index- [in] - the index of the node calling the method.
Global Read:
Global Write:
Remarks
This method should be used by the NodeBase class only.
References:
Authors
apl
Last Modified:

References component_membership_.

Referenced by count_connected_components_and_initialize_vertex_groups(), and core::pack::interaction_graph::NodeBase::depth_first_connected_component_counting().

void core::pack::interaction_graph::InteractionGraphBase::zero_one_body_energies_for_node ( int  node)

References ig_nodes_.

Friends And Related Function Documentation

friend class EdgeBase
friend
friend class NodeBase
friend

Member Data Documentation

ObjexxFCL::FArray1D_int core::pack::interaction_graph::InteractionGraphBase::component_membership_
private
ObjexxFCL::FArray2D_bool core::pack::interaction_graph::InteractionGraphBase::energy_sum_group_membership_
private
EdgeBase* core::pack::interaction_graph::InteractionGraphBase::focused_edge_
mutableprivate

Referenced by add_edge(), drop_edge(), and find_edge().

std::list< EdgeBase * >::const_iterator core::pack::interaction_graph::InteractionGraphBase::focused_edge_iterator_
mutableprivate
std::list< EdgeBase * >::const_iterator core::pack::interaction_graph::InteractionGraphBase::focused_edge_iterator_end_
mutableprivate
std::list< EdgeBase* > core::pack::interaction_graph::InteractionGraphBase::ig_edge_list_
private
std::vector< NodeBase* > core::pack::interaction_graph::InteractionGraphBase::ig_nodes_
private
std::vector< int > core::pack::interaction_graph::InteractionGraphBase::node_state_offsets_
private

Referenced by get_node_state_offset().

int core::pack::interaction_graph::InteractionGraphBase::num_energy_sum_groups_
private
int core::pack::interaction_graph::InteractionGraphBase::num_ig_nodes_
private
int core::pack::interaction_graph::InteractionGraphBase::num_total_states_
private

Referenced by get_num_total_states().


The documentation for this class was generated from the following files: