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protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph Member List

This is the complete list of members for protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph, including all inherited members.

add_edge(int node1, int node2)core::pack::interaction_graph::InteractionGraphBase
add_to_nodes_one_body_energy(int node_ind, utility::vector1< core::PackerEnergy > const &one_body_energies)core::pack::interaction_graph::InteractionGraphBase
add_to_nodes_one_body_energy(int node_ind, ObjexxFCL::FArray1< core::PackerEnergy > const &one_body_energies)core::pack::interaction_graph::InteractionGraphBase
add_to_nodes_one_body_energy(int node_ind, int state_id, core::PackerEnergy const one_body_energy)core::pack::interaction_graph::InteractionGraphBase
add_to_one_body_energies(ObjexxFCL::FArray1< core::PackerEnergy > &one_body_energies)core::pack::interaction_graph::InteractionGraphBase
any_vertex_state_unassigned() const core::pack::interaction_graph::InteractionGraphBase
blanket_assign_state_0()protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraphvirtual
BOTH_SC_AND_BB enum valueprotocols::flexpack::interaction_graph::FlexbbInteractionGraph
cast_flexbb_edge(EdgeBase const *edge) const protocols::flexpack::interaction_graph::FlexbbInteractionGraphinlineprotected
cast_flexbb_edge(EdgeBase *edge)protocols::flexpack::interaction_graph::FlexbbInteractionGraphinlineprotected
cast_minimalist_flexbb_edge(EdgeBase const *edge) const protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraphinlineprotected
cast_minimalist_flexbb_edge(EdgeBase *edge)protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraphinlineprotected
cast_otfflexbb_edge(EdgeBase const *edge) const protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraphinlineprotected
cast_otfflexbb_edge(EdgeBase *edge)protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraphinlineprotected
commit_considered_backbone_move(ObjexxFCL::FArray1_int &rotamer_on_node)protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraphprivatevirtual
commit_considered_substitution()protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraphvirtual
complete_deltaE_prediction_for_bbmove(core::PackerEnergy &delta_energy, core::PackerEnergy &prev_energy_for_flexseg, bool &valid_motion, int &num_nodes_changing_state)protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraphprotected
consider_backbone_move(int bb_id, core::PackerEnergy &delta_energy, core::PackerEnergy &prev_flexseg_energy, bool &valid_motion, int &num_nodes_changing_state)protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraphvirtual
consider_bbmove_w_state_substitution(int node_ind, int new_state, core::PackerEnergy &delta_energy, core::PackerEnergy &prev_energy_for_flexseg, bool &valid_motion, int &num_nodes_changing_state)protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraphvirtual
consider_substitution(int node_ind, int new_state, PackerEnergy &delta_energy, PackerEnergy &prev_energy_for_node)protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraphvirtual
count_connected_components_and_initialize_vertex_groups()core::pack::interaction_graph::InteractionGraphBase
count_dynamic_memory() const protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraphprotectedvirtual
count_static_memory() const protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraphprotectedvirtual
create_new_edge(int index1, int index2)protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraphprotectedvirtual
create_new_node(int node_index, int num_states)protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraphprotectedvirtual
debug_note_accepted_substitution()protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
debug_note_considered_substitution(core::conformation::Residue const &alt_rotamer, int index)protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
debug_note_projected_deltaE_of_considered_substitution(PackerEnergy deltaE, PackerEnergy node_alt_total, bool require_match=true)protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
debug_note_rejected_substitution()protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
drop_all_edges_for_node(int node)core::pack::interaction_graph::InteractionGraphBase
drop_edge(std::list< EdgeBase * >::iterator edge)core::pack::interaction_graph::InteractionGraphBaseprotected
edge_list_iterator_at_end() const core::pack::interaction_graph::InteractionGraphBase
EdgeBase typedefprotocols::flexpack::interaction_graph::FlexbbInteractionGraph
find_edge(int node1, int node2) const core::pack::interaction_graph::InteractionGraphBase
find_edge(int node1, int node2)core::pack::interaction_graph::InteractionGraphBase
find_flexbb_edge(int node1, int node2) const protocols::flexpack::interaction_graph::FlexbbInteractionGraphinlineprotected
find_flexbb_edge(int node1, int node2)protocols::flexpack::interaction_graph::FlexbbInteractionGraphinlineprotected
find_minimalist_flexbb_edge(int node1, int node2) const protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraphinlineprotected
find_minimalist_flexbb_edge(int node1, int node2)protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraphinlineprotected
find_otfflexbb_edge(int node1, int node2) const protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraphinlineprotected
find_otfflexbb_edge(int node1, int node2)protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraphinlineprotected
FlexbbInteractionGraph(int num_nodes)protocols::flexpack::interaction_graph::FlexbbInteractionGraph
flexseg_considering_alt_bb() const protocols::flexpack::interaction_graph::FlexbbInteractionGraphinlineprotected
flexseg_for_moltenres(int moltenres) const protocols::flexpack::interaction_graph::FlexbbInteractionGraphinlineprotected
flexseg_members(int flexseg) const protocols::flexpack::interaction_graph::FlexbbInteractionGraphinline
get_accessible_states(Subsitution move_mode, utility::vector1< Size > &rotlist) const protocols::flexpack::interaction_graph::FlexbbInteractionGraph
get_backbone_currently_assigned(int bbid) const protocols::flexpack::interaction_graph::FlexbbInteractionGraph
get_backbone_list(utility::vector1< Size > &bblist) const protocols::flexpack::interaction_graph::FlexbbInteractionGraph
get_bb_for_state(int node, int state) const protocols::flexpack::interaction_graph::FlexbbInteractionGraph
get_edge() const core::pack::interaction_graph::InteractionGraphBase
get_edge_exists(int node1, int node2)core::pack::interaction_graph::InteractionGraphBase
get_edge_list_begin()core::pack::interaction_graph::InteractionGraphBaseinline
get_edge_list_begin() const core::pack::interaction_graph::InteractionGraphBaseinline
get_edge_list_end() const core::pack::interaction_graph::InteractionGraphBaseinline
get_edge_memory_usage() const protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraphvirtual
get_edge_weight(int node1, int node2) const core::pack::interaction_graph::InteractionGraphBase
get_energy_current_state_assignment()protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraphvirtual
get_energy_sum_for_vertex_group(int group_id)protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraphvirtual
get_enforce_bb_contiguity() const protocols::flexpack::interaction_graph::FlexbbInteractionGraph
get_flexbb_node(int index) const protocols::flexpack::interaction_graph::FlexbbInteractionGraphinlineprotected
get_flexbb_node(int index)protocols::flexpack::interaction_graph::FlexbbInteractionGraphinlineprotected
get_flexseg_bb_offset(int flexseg_id) const protocols::flexpack::interaction_graph::FlexbbInteractionGraphinline
get_flexseg_for_bb(int bb) const protocols::flexpack::interaction_graph::FlexbbInteractionGraphinline
get_minimalistflexbb_node(int index) const protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraphinlineprotected
get_minimalistflexbb_node(int index)protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraphinlineprotected
get_node(int index) const core::pack::interaction_graph::InteractionGraphBaseinline
get_node_state_offset(int index) const core::pack::interaction_graph::InteractionGraphBaseinlineprotected
get_num_aa_types() const protocols::flexpack::interaction_graph::FlexbbInteractionGraphinline
get_num_edges() const core::pack::interaction_graph::InteractionGraphBaseinline
get_num_nodes() const core::pack::interaction_graph::InteractionGraphBaseinline
get_num_nodes_changing_state() const protocols::flexpack::interaction_graph::FlexbbInteractionGraphprotected
get_num_nodes_v() const core::pack::interaction_graph::InteractionGraphBaseinlinevirtual
get_num_states_for_node(int node) const core::pack::interaction_graph::InteractionGraphBase
get_num_states_per_backbone_for_node(int node, int bb) const protocols::flexpack::interaction_graph::FlexbbInteractionGraph
get_num_total_states() const core::pack::interaction_graph::InteractionGraphBaseinline
get_one_body_energy_for_node_state(int node, int state)protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraphvirtual
get_otfflexbb_node(int index) const protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraphinlineprotected
get_otfflexbb_node(int index)protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraphinlineprotected
get_pose() const protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
get_scorefxn() const protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
get_vertex_member_of_energy_sum_group(int node_index, int group_id)core::pack::interaction_graph::InteractionGraphBaseinline
getTotalMemoryUsage() const core::pack::interaction_graph::InteractionGraphBasevirtual
increment_count_nodes_in_flexseg()protocols::flexpack::interaction_graph::FlexbbInteractionGraph
increment_edge_list_iterator() const core::pack::interaction_graph::InteractionGraphBase
initialize(core::pack::rotamer_set::RotamerSetsBase const &rot_sets)protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraphvirtual
InteractionGraphBase(int num_nodes)core::pack::interaction_graph::InteractionGraphBase
last_considered_backbone_sub_unresolved() const protocols::flexpack::interaction_graph::FlexbbInteractionGraphinlineprotected
last_considered_backbone_sub_valid() const protocols::flexpack::interaction_graph::FlexbbInteractionGraphinlineprotected
last_considered_substitution_kept_backbone_fixed() const protocols::flexpack::interaction_graph::FlexbbInteractionGraphinlineprotected
last_considered_substitution_moved_the_backbone() const protocols::flexpack::interaction_graph::FlexbbInteractionGraphinlineprotected
last_considered_substitution_unresolved() const protocols::flexpack::interaction_graph::FlexbbInteractionGraphinlineprotected
mine(EdgeBase const *edge) const core::pack::interaction_graph::InteractionGraphBaseinlineprotected
MinimalistFlexbbInteractionGraph(int num_nodes)protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph
node_considering_alt_state() const protocols::flexpack::interaction_graph::FlexbbInteractionGraphinlineprotected
nodes_from_same_flexseg(int node1, int node2) const protocols::flexpack::interaction_graph::FlexbbInteractionGraph
note_bbjump_substitution()protocols::flexpack::interaction_graph::FlexbbInteractionGraphinlineprotected
note_fixedbb_substitution()protocols::flexpack::interaction_graph::FlexbbInteractionGraphinlineprotected
note_last_considered_substitution_resolved()protocols::flexpack::interaction_graph::FlexbbInteractionGraphprotected
note_long_range_interactions_exist_for_edge(int node1, int node2)protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
note_vertex_reached(int node_index)core::pack::interaction_graph::InteractionGraphBase
OTFFlexbbInteractionGraph(int num_nodes)protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
output_connectivity(std::ostream &os) const core::pack::interaction_graph::InteractionGraphBase
output_dimacs(std::ostream &os) const core::pack::interaction_graph::InteractionGraphBase
PackerEnergy typedefprotocols::flexpack::interaction_graph::FlexbbInteractionGraph
parent typedefprotocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph
Pose typedefprotocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
PoseCOP typedefprotocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
PoseOP typedefprotocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
prepare_for_simulated_annealing()core::pack::interaction_graph::InteractionGraphBasevirtual
print() const core::pack::interaction_graph::InteractionGraphBaseinlinevirtual
print_current_state_assignment() const protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraphvirtual
print_vertex_groups()core::pack::interaction_graph::InteractionGraphBase
print_vertices() const core::pack::interaction_graph::InteractionGraphBase
project_deltaE_for_substitution(int alternate_state, PackerEnergy &prev_energy_for_node)protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraphprivate
Real typedefprotocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
reset_edge_list_iterator_for_node(int node_index) const core::pack::interaction_graph::InteractionGraphBase
reset_node_in_moving_flexseg_count()protocols::flexpack::interaction_graph::FlexbbInteractionGraphprotected
resolve_uncommitted_substitution()protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraphprotected
SC_ONLY enum valueprotocols::flexpack::interaction_graph::FlexbbInteractionGraph
ScoreFunction typedefprotocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
ScoreFunctionCOP typedefprotocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
ScoreFunctionOP typedefprotocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
set_edge_weight(int node1, int node2, Real edge_weight)core::pack::interaction_graph::InteractionGraphBase
set_enforce_bb_contiguity(bool)protocols::flexpack::interaction_graph::FlexbbInteractionGraphprotected
set_errorfull_deltaE_threshold(PackerEnergy deltaE)protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraphvirtual
set_flexseg_considering_alt_bb(int setting)protocols::flexpack::interaction_graph::FlexbbInteractionGraphinlineprotected
set_GlyCorrection_values_for_edge(int node1, int node2, int node_not_necessarily_glycine, int state, int other_bb, PackerEnergy bb_nonglybb_E, PackerEnergy bb_glybb_E, PackerEnergy sc_nonglybb_E, PackerEnergy sc_glybb_E)protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
set_last_considered_backbone_sub_valid(bool setting)protocols::flexpack::interaction_graph::FlexbbInteractionGraphinlineprotected
set_network_state(ObjexxFCL::FArray1_int &node_states)protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraphvirtual
set_node_considering_alt_state(int setting)protocols::flexpack::interaction_graph::FlexbbInteractionGraphinlineprotected
set_num_states_for_node(int node, int num_states)core::pack::interaction_graph::InteractionGraphBase
set_number_of_energy_sum_vertex_groups(int num_groups)core::pack::interaction_graph::InteractionGraphBase
set_pose(Pose const &pose)protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraphvirtual
set_ProCorrection_values_for_edge(int node1, int node2, int node_not_necessarily_proline, int state, int other_bb, PackerEnergy bb_nonprobb_E, PackerEnergy bb_probb_E, PackerEnergy sc_nonprobb_E, PackerEnergy sc_probb_E)protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
set_scorefxn(ScoreFunction const &sfxn)protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraphvirtual
set_state_for_node(int node_ind, int new_state)protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraphvirtual
set_total_energy_alternate_state_assignment(PackerEnergy setting)protocols::flexpack::interaction_graph::FlexbbInteractionGraphinlineprotected
set_total_energy_current_state_assignment(PackerEnergy setting)protocols::flexpack::interaction_graph::FlexbbInteractionGraphprotected
set_vertex_member_of_group(int vertex, int group)core::pack::interaction_graph::InteractionGraphBase
Subsitution enum nameprotocols::flexpack::interaction_graph::FlexbbInteractionGraph
total_energy_alternate_state_assignment() const protocols::flexpack::interaction_graph::FlexbbInteractionGraphinlineprotected
total_energy_current_state_assignment() const protocols::flexpack::interaction_graph::FlexbbInteractionGraphinlineprotected
update_internal_energy_totals()protocols::flexpack::interaction_graph::FlexbbInteractionGraphprotectedvirtual
update_one_body_energies(ObjexxFCL::FArray1< core::PackerEnergy > &old_energy1b, ObjexxFCL::FArray1< core::PackerEnergy > &new_energy1b)core::pack::interaction_graph::InteractionGraphBase
vertex_already_reached(int node_index)core::pack::interaction_graph::InteractionGraphBase
zero_one_body_energies_for_node(int node)core::pack::interaction_graph::InteractionGraphBase
~FlexbbInteractionGraph()protocols::flexpack::interaction_graph::FlexbbInteractionGraphvirtual
~InteractionGraphBase()core::pack::interaction_graph::InteractionGraphBasevirtual
~MinimalistFlexbbInteractionGraph()protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraphvirtual
~OTFFlexbbInteractionGraph()protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraphvirtual