Rosetta 3.4
Public Member Functions | Protected Member Functions
core::pack::interaction_graph::EdgeBase Class Reference

#include <InteractionGraphBase.hh>

Inheritance diagram for core::pack::interaction_graph::EdgeBase:
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List of all members.

Public Member Functions

virtual ~EdgeBase ()
 copy constructor, do not use
 EdgeBase (InteractionGraphBase *owner, int first_node_ind, int second_node_ind)
 main constructor for edge, no default nor copy constructors
int get_other_ind (int callers_index) const
 returns the index of the other node that the edge is incident upon
NodeBase * get_other_node (int callers_index) const
 returns a pointer to the other node that the edge is incident upon
int get_first_node_ind () const
 returns the index of the smaller-indexed node
int get_second_node_ind () const
 returns the index of the larger-indexed node
void set_pos_in_owners_list (std::list< EdgeBase * >::iterator edge_iterator)
 edge keeps iterator to its position in it's owner's edge list
void set_pos_in_node_edgevector (int callers_index, int position)
 edge keeps index it has in node_ind's edge vector
bool same_edge (int node1, int node2) const
 returns true if this edge connects nodes of index node1 and node2 the order of node1 and node2 is not important
virtual void declare_energies_final ()=0
virtual void prepare_for_simulated_annealing ()=0
virtual unsigned int count_static_memory () const =0
virtual unsigned int count_dynamic_memory () const
Real edge_weight () const
virtual void set_edge_weight (Real weight)=0
InteractionGraphBase * get_owner () const

Protected Member Functions

int get_node_index (int index) const
int get_num_states_for_node (int index) const
NodeBase const * get_node (int index) const
NodeBase * get_node (int index)
int get_edges_position_in_nodes_edge_vector (int index) const
int which_node (int node_index) const
 is a node the first or second node this edge is incident upon?
void edge_weight (Real)
 protected setter of the edge weight. To be called by derived classes after they have completed the conversion from the previous edge weighting to the new edge weighting.

Constructor & Destructor Documentation

core::pack::interaction_graph::EdgeBase::~EdgeBase ( ) [virtual]

copy constructor, do not use

NodeBase::NodeBase( NodeBase const & rhs)

Detailed:
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Authors:
apl
Last Modified:
EdgeBase::~EdgeBase

destructor

Detailed: removes all record of this edge from edge-lists of
the 1) nodes this edge is incident upon and 2) the owning interaction graph
Parameters:
Global Read:
Global Write:
Remarks:
References:
Authors:
apl
Last Modified:

References core::pack::interaction_graph::NodeBase::drop_edge(), and core::pack::interaction_graph::InteractionGraphBase::drop_edge().

core::pack::interaction_graph::EdgeBase::EdgeBase ( InteractionGraphBase *  owner,
int  first_node_ind,
int  second_node_ind 
)

main constructor for edge, no default nor copy constructors

EdgeBase::EdgeBase(InteractionGraphBase, int, int)

Detailed: edge adds itself to the edge list of the two nodes its set to be
incident upon, and stores the list-iterators that the nodes return.
Parameters:
owner- [in] - owning InteractionGraph
first_node_ind- [in] - the index of the first node
second_node_ind- [in] - the index of the second node
Global Read:
Global Write:
Remarks:
References:
Authors:
apl
Last Modified:

Member Function Documentation

unsigned int core::pack::interaction_graph::EdgeBase::count_dynamic_memory ( ) const [virtual]

Reimplemented in core::pack::interaction_graph::DensePDEdge, core::pack::interaction_graph::DoubleDensePDEdge, core::pack::interaction_graph::DoubleLazyEdge, core::pack::interaction_graph::FASTEREdge, core::pack::interaction_graph::LazyEdge, core::pack::interaction_graph::LinearMemEdge, core::pack::interaction_graph::OnTheFlyEdge, core::pack::interaction_graph::PDEdge, protocols::flexpack::interaction_graph::FlexbbEdge, protocols::flexpack::interaction_graph::MinimalistFlexbbEdge, and protocols::flexpack::interaction_graph::OTFFlexbbEdge.

Referenced by protocols::flexpack::interaction_graph::FlexbbEdge::count_dynamic_memory(), and core::pack::interaction_graph::FASTEREdge::count_dynamic_memory().

virtual unsigned int core::pack::interaction_graph::EdgeBase::count_static_memory ( ) const [pure virtual]

Implemented in core::pack::interaction_graph::DensePDEdge, core::pack::interaction_graph::DoubleDensePDEdge, core::pack::interaction_graph::DoubleLazyEdge, core::pack::interaction_graph::FASTEREdge, core::pack::interaction_graph::LazyEdge, core::pack::interaction_graph::LinearMemEdge, core::pack::interaction_graph::OnTheFlyEdge, core::pack::interaction_graph::PDEdge, and protocols::flexpack::interaction_graph::MinimalistFlexbbEdge.

virtual void core::pack::interaction_graph::EdgeBase::declare_energies_final ( ) [pure virtual]

Implemented in core::pack::interaction_graph::DensePDEdge, core::pack::interaction_graph::DoubleDensePDEdge, core::pack::interaction_graph::DoubleLazyEdge, core::pack::interaction_graph::FASTEREdge, core::pack::interaction_graph::LazyEdge, core::pack::interaction_graph::LinearMemEdge, core::pack::interaction_graph::PDEdge, and protocols::flexpack::interaction_graph::MinimalistFlexbbEdge.

Referenced by core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph::declare_edge_energies_final().

void core::pack::interaction_graph::EdgeBase::edge_weight ( Real  new_weight) [protected]

protected setter of the edge weight. To be called by derived classes after they have completed the conversion from the previous edge weighting to the new edge weighting.

Real core::pack::interaction_graph::EdgeBase::edge_weight ( ) const [inline]

Referenced by protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_altbbconf_alternate_state_energy(), core::pack::interaction_graph::OnTheFlyNode::compute_rotamer_pair_energy(), protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_samebbconf_alternate_state_energy_first_node(), protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_samebbconf_alternate_state_energy_second_node(), core::pack::interaction_graph::InteractionGraphBase::get_edge_weight(), core::pack::interaction_graph::DoubleLazyEdge::get_two_body_energy_smi(), protocols::flexpack::interaction_graph::MinimalistFlexbbEdge::set_edge_weight(), core::pack::interaction_graph::PDEdge::set_edge_weight(), core::pack::interaction_graph::LinearMemEdge::set_edge_weight(), core::pack::interaction_graph::LazyEdge::set_edge_weight(), core::pack::interaction_graph::FASTEREdge::set_edge_weight(), core::pack::interaction_graph::DoubleLazyEdge::set_edge_weight(), core::pack::interaction_graph::DoubleDensePDEdge::set_edge_weight(), and core::pack::interaction_graph::DensePDEdge::set_edge_weight().

int core::pack::interaction_graph::EdgeBase::get_edges_position_in_nodes_edge_vector ( int  index) const [inline, protected]

Referenced by core::pack::interaction_graph::FASTEREdge::acknowledge_partial_state_assignment(), core::pack::interaction_graph::LinearMemEdge::acknowledge_partial_state_change(), core::pack::interaction_graph::LazyEdge::acknowledge_partial_state_change(), core::pack::interaction_graph::DoubleLazyEdge::acknowledge_partial_state_change(), core::pack::interaction_graph::FASTEREdge::acknowledge_perturbed_state(), core::pack::interaction_graph::LinearMemEdge::acknowledge_state_change(), core::pack::interaction_graph::LazyEdge::acknowledge_state_change(), core::pack::interaction_graph::DoubleLazyEdge::acknowledge_state_change(), core::pack::interaction_graph::PDEdge::acknowledge_state_zeroed(), core::pack::interaction_graph::LinearMemEdge::acknowledge_state_zeroed(), core::pack::interaction_graph::LazyEdge::acknowledge_state_zeroed(), core::pack::interaction_graph::FASTEREdge::acknowledge_state_zeroed(), core::pack::interaction_graph::DoubleLazyEdge::acknowledge_state_zeroed(), core::pack::interaction_graph::DoubleDensePDEdge::acknowledge_state_zeroed(), core::pack::interaction_graph::DensePDEdge::acknowledge_state_zeroed(), protocols::flexpack::interaction_graph::MinimalistFlexbbEdge::acknowledge_substitution(), core::pack::interaction_graph::PDEdge::acknowledge_substitution(), core::pack::interaction_graph::LinearMemEdge::acknowledge_substitution(), core::pack::interaction_graph::LazyEdge::acknowledge_substitution(), core::pack::interaction_graph::FASTEREdge::acknowledge_substitution(), core::pack::interaction_graph::DoubleLazyEdge::acknowledge_substitution(), core::pack::interaction_graph::DoubleDensePDEdge::acknowledge_substitution(), core::pack::interaction_graph::DensePDEdge::acknowledge_substitution(), core::pack::interaction_graph::LazyEdge::get_aa_submatrix_energies(), core::pack::interaction_graph::DoubleLazyEdge::get_aa_submatrix_energies(), core::pack::interaction_graph::LinearMemEdge::get_energy_following_partial_state_assignment(), core::pack::interaction_graph::LazyEdge::get_two_body_energy(), and core::pack::interaction_graph::DoubleLazyEdge::get_two_body_energy_smi().

int core::pack::interaction_graph::EdgeBase::get_first_node_ind ( ) const

returns the index of the smaller-indexed node

EdgeBase::get_first_node_ind

Detailed:
Parameters:
Global Read:
Global Write:
Remarks:
References:
Authors:
apl
Last Modified:
NodeBase* core::pack::interaction_graph::EdgeBase::get_node ( int  index) [inline, protected]
NodeBase const* core::pack::interaction_graph::EdgeBase::get_node ( int  index) const [inline, protected]

Referenced by protocols::flexpack::interaction_graph::FlexbbEdge::get_flexbb_node(), protocols::flexpack::interaction_graph::MinimalistFlexbbEdge::get_minimalistflexbb_node(), and protocols::flexpack::interaction_graph::OTFFlexbbEdge::get_otfflexbb_node().

int core::pack::interaction_graph::EdgeBase::get_node_index ( int  index) const [inline, protected]

Referenced by core::pack::interaction_graph::FASTEREdge::acknowledge_partial_state_assignment(), core::pack::interaction_graph::LinearMemEdge::acknowledge_partial_state_change(), core::pack::interaction_graph::LazyEdge::acknowledge_partial_state_change(), core::pack::interaction_graph::DoubleLazyEdge::acknowledge_partial_state_change(), core::pack::interaction_graph::FASTEREdge::acknowledge_perturbed_state(), core::pack::interaction_graph::LinearMemEdge::acknowledge_state_change(), core::pack::interaction_graph::LazyEdge::acknowledge_state_change(), core::pack::interaction_graph::DoubleLazyEdge::acknowledge_state_change(), core::pack::interaction_graph::PDEdge::acknowledge_state_zeroed(), core::pack::interaction_graph::LinearMemEdge::acknowledge_state_zeroed(), core::pack::interaction_graph::LazyEdge::acknowledge_state_zeroed(), core::pack::interaction_graph::FASTEREdge::acknowledge_state_zeroed(), core::pack::interaction_graph::DoubleLazyEdge::acknowledge_state_zeroed(), core::pack::interaction_graph::DoubleDensePDEdge::acknowledge_state_zeroed(), core::pack::interaction_graph::DensePDEdge::acknowledge_state_zeroed(), core::pack::interaction_graph::PDEdge::acknowledge_substitution(), core::pack::interaction_graph::LinearMemEdge::acknowledge_substitution(), core::pack::interaction_graph::LazyEdge::acknowledge_substitution(), core::pack::interaction_graph::FASTEREdge::acknowledge_substitution(), core::pack::interaction_graph::DoubleLazyEdge::acknowledge_substitution(), core::pack::interaction_graph::DoubleDensePDEdge::acknowledge_substitution(), core::pack::interaction_graph::DensePDEdge::acknowledge_substitution(), protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_altbbconf_alternate_state_energy(), protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_samebbconf_alternate_state_energy_first_node(), protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_samebbconf_alternate_state_energy_second_node(), core::pack::interaction_graph::FASTEREdge::get_deltaE_for_neighbor_following_perturbation(), core::pack::interaction_graph::FASTEREdge::get_energy_for_perturbed_state(), protocols::flexpack::interaction_graph::OTFFlexbbEdge::print_alt_energies(), core::pack::interaction_graph::LinearMemEdge::print_current_energy(), core::pack::interaction_graph::LazyEdge::print_current_energy(), core::pack::interaction_graph::DoubleLazyEdge::print_current_energy(), core::pack::interaction_graph::LinearMemEdge::reset_state_energies(), and core::pack::interaction_graph::OnTheFlyEdge::set_ProCorrection_values().

int core::pack::interaction_graph::EdgeBase::get_num_states_for_node ( int  index) const [inline, protected]

Referenced by core::pack::interaction_graph::FASTEREdge::get_edge_table_ptr(), core::pack::interaction_graph::DensePDEdge::get_edge_table_ptr(), core::pack::interaction_graph::OnTheFlyEdge::OnTheFlyEdge(), protocols::flexpack::interaction_graph::OTFFlexbbEdge::OTFFlexbbEdge(), core::pack::interaction_graph::LinearMemEdge::prepare_for_simulated_annealing(), and core::pack::interaction_graph::LinearMemEdge::reset_state_energies().

int core::pack::interaction_graph::EdgeBase::get_other_ind ( int  node_ind) const

returns the index of the other node that the edge is incident upon

EdgeBase::get_other_ind

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

Referenced by core::pack::interaction_graph::NodeBase::add_edge(), protocols::enzdes::EnzdesFlexibleRegion::calculate_rotamer_set_design_targets_partition_sum(), and core::pack::setup_IG_res_res_weights().

NodeBase * core::pack::interaction_graph::EdgeBase::get_other_node ( int  node_ind) const

returns a pointer to the other node that the edge is incident upon

EdgeBase::get_other_node

Detailed:
Parameters:
node_ind- [in] - the node index of the node whose index is already known
Global Read:
Global Write:
Remarks:
References:
Authors:
apl
Last Modified:
InteractionGraphBase* core::pack::interaction_graph::EdgeBase::get_owner ( ) const [inline]

Referenced by protocols::flexpack::interaction_graph::FlexbbEdge::get_flexbbig_owner(), protocols::flexpack::interaction_graph::MinimalistFlexbbEdge::get_minimalistflexbbig_owner(), protocols::flexpack::interaction_graph::OTFFlexbbEdge::get_otfflexbbig_owner(), and core::pack::interaction_graph::InteractionGraphBase::mine().

int core::pack::interaction_graph::EdgeBase::get_second_node_ind ( ) const

returns the index of the larger-indexed node

EdgeBase::get_second_node_ind()

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apl
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virtual void core::pack::interaction_graph::EdgeBase::prepare_for_simulated_annealing ( ) [pure virtual]

Implemented in core::pack::interaction_graph::DensePDEdge, core::pack::interaction_graph::DoubleDensePDEdge, core::pack::interaction_graph::DoubleLazyEdge, core::pack::interaction_graph::FASTEREdge, core::pack::interaction_graph::LazyEdge, core::pack::interaction_graph::LinearMemEdge, core::pack::interaction_graph::PDEdge, protocols::flexpack::interaction_graph::MinimalistFlexbbEdge, and protocols::flexpack::interaction_graph::OTFFlexbbEdge.

bool core::pack::interaction_graph::EdgeBase::same_edge ( int  node1,
int  node2 
) const

returns true if this edge connects nodes of index node1 and node2 the order of node1 and node2 is not important

EdgeBase::same_edge

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

Referenced by core::pack::interaction_graph::InteractionGraphBase::find_edge().

virtual void core::pack::interaction_graph::EdgeBase::set_edge_weight ( Real  weight) [pure virtual]

Implemented in core::pack::interaction_graph::DensePDEdge, core::pack::interaction_graph::DoubleDensePDEdge, core::pack::interaction_graph::DoubleLazyEdge, core::pack::interaction_graph::FASTEREdge, core::pack::interaction_graph::LazyEdge, core::pack::interaction_graph::LinearMemEdge, core::pack::interaction_graph::PDEdge, and protocols::flexpack::interaction_graph::MinimalistFlexbbEdge.

Referenced by core::pack::interaction_graph::InteractionGraphBase::set_edge_weight().

void core::pack::interaction_graph::EdgeBase::set_pos_in_node_edgevector ( int  node_ind,
int  vect_position 
)

edge keeps index it has in node_ind's edge vector

EdgeBase::set_pos_in_node_edgevector

Detailed:
Parameters:
node_ind- [in] - the index of the node calling this method
vect_position- [in] - the position for this edge in the node's edge vector
Global Read:
Global Write:
Remarks:
References:
Authors:
apl
Last Modified:
void core::pack::interaction_graph::EdgeBase::set_pos_in_owners_list ( std::list< EdgeBase * >::iterator  iter)

edge keeps iterator to its position in it's owner's edge list

EdgeBase::set_pos_in_owners_list

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

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

int core::pack::interaction_graph::EdgeBase::which_node ( int  node_index) const [inline, protected]

is a node the first or second node this edge is incident upon?

Referenced by protocols::flexpack::interaction_graph::FlexbbEdge::acknowledge_partial_state_assignment(), protocols::flexpack::interaction_graph::MinimalistFlexbbEdge::acknowledge_state_zeroed(), protocols::flexpack::interaction_graph::MinimalistFlexbbEdge::acknowledge_substitution(), protocols::flexpack::interaction_graph::FlexbbEdge::set_alt_state(), protocols::flexpack::interaction_graph::OTFFlexbbEdge::set_GlyCorrection_values(), protocols::flexpack::interaction_graph::FlexbbEdge::set_node_state_to_zero(), protocols::flexpack::interaction_graph::OTFFlexbbEdge::set_ProCorrection_values(), and core::pack::interaction_graph::OnTheFlyEdge::set_ProCorrection_values().

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