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protocols::hbnet::HBNetStapleInterface Member List

This is the complete list of members for protocols::hbnet::HBNetStapleInterface, including all inherited members.

add_residue_to_network_state(NetworkState &current_state, core::scoring::hbonds::graph::HBondNode *node_being_added) const protocols::hbnet::HBNetprotected
add_start_res(core::Size res)protocols::hbnet::HBNetinline
all_helices_protocols::hbnet::HBNetStapleInterfaceprivate
allow_onebody_networks_protocols::hbnet::HBNetStapleInterfaceprivate
append_to_network_vector(utility::vector1< DecoratedNetworkState > const &designed_networks)protocols::hbnet::HBNetprotected
apply(core::pose::Pose &pose) overrideprotocols::hbnet::HBNetvirtual
at_least_one_net_fully_satisfied_protocols::hbnet::HBNetStapleInterfaceprivate
at_least_one_net_spans_all_helices_protocols::hbnet::HBNetStapleInterfaceprivate
at_least_one_net_w_aromatic_sc_protocols::hbnet::HBNetStapleInterfaceprivate
atom_hbonds_to_bridging_water(core::pose::Pose const &pose, core::id::AtomID const at_id)protocols::hbnet::HBNet
attributes_for_hbnet(utility::tag::AttributeList &)protocols::hbnet::HBNetstatic
boundary_his_must_to_hbond_pos_charge_protocols::hbnet::HBNetStapleInterfaceprivate
branch_overlapping_networks()protocols::hbnet::HBNetprotected
chain_for_moltenres(core::Size mres) const protocols::hbnet::HBNetinlineprotected
chain_for_resid(core::Size resid) const protocols::hbnet::HBNetinlineprotected
check_clash(utility::vector1< HBondResStructCOP > const &residues, platform::uint my_node_ind, core::Size mystate, core::Size myres, core::Real &init_score, bool &cycle)protocols::hbnet::HBNetprotected
clear_info()protocols::moves::Moverinlinevirtual
clone() const overrideprotocols::hbnet::HBNetStapleInterfacevirtual
combos_protocols::hbnet::HBNetStapleInterfaceprivate
create()protocols::moves::Movervirtual
create_ptask(core::pose::Pose const &pose, bool initialize_from_commandline=false)protocols::hbnet::HBNetprotected
edge_can_yield_monte_carlo_seed(core::Size resid1, core::Size resid2) const overrideprotocols::hbnet::HBNetStapleInterfaceinlineprotectedvirtual
protocols::hbnet::HBNet::edge_can_yield_monte_carlo_seed(core::pack::interaction_graph::EdgeBase const *) const protocols::hbnet::HBNetprotectedvirtual
estimate_saturation(NetworkState const &) const protocols::hbnet::HBNetprotected
find_native()protocols::hbnet::HBNetinline
find_unsats(core::pose::Pose const &pose, HBondNetStruct &i)protocols::hbnet::HBNet
fresh_instance() const overrideprotocols::hbnet::HBNetStapleInterfacevirtual
get_aa_for_state(core::Size const res, core::Size const rot) const protocols::hbnet::HBNet
get_additional_output() overrideprotocols::hbnet::HBNetvirtual
get_ala_pose()protocols::hbnet::HBNetinline
get_boundary_residues()protocols::hbnet::HBNetinline
get_boundary_selector()protocols::hbnet::HBNetinline
get_core_residues()protocols::hbnet::HBNetinline
get_core_selector()protocols::hbnet::HBNetinline
get_current_job() const protocols::moves::Mover
get_current_tag() const protocols::moves::Moverinline
get_extend_existing_networks()protocols::hbnet::HBNetinline
get_file_name(core::Size id, std::string prefix, std::string extension)protocols::hbnet::HBNet
get_helix_id(core::Size r1) const protocols::hbnet::HBNetStapleInterface
get_ind_res(core::pose::Pose const &pose, core::Size const res_i)protocols::hbnet::HBNet
get_input_pose() const protocols::moves::Mover
get_keep_existing_networks()protocols::hbnet::HBNetinline
get_last_move_status() const protocols::moves::Mover
get_max_networks_size()protocols::hbnet::HBNetinline
get_max_unsat()protocols::hbnet::HBNetinline
get_min_networks_size()protocols::hbnet::HBNetinline
get_name() const overrideprotocols::hbnet::HBNetStapleInterfacevirtual
get_native_networks(core::pose::Pose const &pose)protocols::hbnet::HBNetprotected
get_native_pose() const protocols::moves::Mover
get_native_vec()protocols::hbnet::HBNetinline
get_net_vec()protocols::hbnet::HBNetinline
get_network_by_id(core::Size id)protocols::hbnet::HBNetinline
get_networks()protocols::hbnet::HBNetinline
get_next_node(NetworkState &current_state)protocols::hbnet::HBNetprotected
get_num_native_rot(core::pose::Pose &pose, utility::vector1< HBondResStructCOP > const &residues, core::Real sc_rmsd_cut=0.25, bool super=true)protocols::hbnet::HBNet
get_num_native_seq(core::pose::Pose &pose, utility::vector1< HBondResStructCOP > const &residues)protocols::hbnet::HBNet
get_only_extend_existing()protocols::hbnet::HBNetinline
get_orig_pose()protocols::hbnet::HBNetinline
get_output_vector()protocols::hbnet::HBNetinline
get_packer_graph()protocols::hbnet::HBNetinline
get_self_ptr() const protocols::moves::Moverinline
get_self_ptr()protocols::moves::Moverinline
get_self_weak_ptr() const protocols::moves::Moverinline
get_self_weak_ptr()protocols::moves::Moverinline
get_start_res_vec()protocols::hbnet::HBNetinline
get_symm_info() const protocols::hbnet::HBNetinline
get_task() const protocols::hbnet::HBNetinline
get_type() const protocols::moves::Moverinline
has_pH_His(core::pose::Pose const &pose, HBondNetStruct &i)protocols::hbnet::HBNetStapleInterface
HBNet()protocols::hbnet::HBNet
HBNet(std::string const name)protocols::hbnet::HBNet
HBNet(core::scoring::ScoreFunctionCOP scorefxn, core::Size max_unsat, core::Size min_network_size=3, core::Real hb_threshold=-0.75, core::Size max_network_size=15, std::string des_residues="STRKHYWNQDE", bool find_native=false, bool only_native=false, bool keep_existing=false, bool extend_existing=false, bool only_extend=false)protocols::hbnet::HBNet
HBNetStapleInterface()protocols::hbnet::HBNetStapleInterface
HBNetStapleInterface(std::string const name)protocols::hbnet::HBNetStapleInterface
HBNetStapleInterface(core::scoring::ScoreFunctionCOP scorefxn, core::Size max_unsat_Hpol, core::Size min_network_size=3, core::Real hb_threshold=-0.5, core::Size max_network_size=15, std::string des_residues="STRKHYWNQDE", bool find_native=false, bool only_native=false, bool keep_existing=false, bool extend_existing=false, bool only_extend=false)protocols::hbnet::HBNetStapleInterface
helix_boundaries_protocols::hbnet::HBNetStapleInterfaceprivate
his_tyr_protocols::hbnet::HBNetStapleInterfaceprivate
info()protocols::moves::Moverinlinevirtual
info() const protocols::moves::Moverinlinevirtual
initialize_hbond_graph()protocols::hbnet::HBNetprotected
interf_distance_protocols::hbnet::HBNetStapleInterfaceprivate
interhelical_contact(utility::vector1< std::pair< core::Size, core::Size > > const helix_boundaries, core::Size const r1, core::Size const r2, core::pose::Pose const &pose)protocols::hbnet::HBNetStapleInterface
is_sub_residues(utility::vector1< HBondResStructCOP > &residues1, utility::vector1< HBondResStructCOP > &residues2)protocols::hbnet::HBNetprotected
is_sub_residues(utility::vector1< HBondResStructCOP > &residues1, utility::vector1< HBondResStructCOP > &residues2, bool &branch, bool true_if_identical=true)protocols::hbnet::HBNetprotected
jump_nums_protocols::hbnet::HBNetStapleInterfaceprivate
last_proposal_density_ratio()protocols::moves::Moverinlinevirtual
ligand()protocols::hbnet::HBNetinlinevirtual
max_networks_per_pose_protocols::hbnet::HBNetStapleInterfaceprivate
MC_branch_overlapping_networks()protocols::hbnet::HBNetprotected
MC_traverse_IG()protocols::hbnet::HBNetprotected
merge_2_branched_networks(HBondNetStruct const &i, HBondNetStruct const &j, HBondNetStructOP new_network)protocols::hbnet::HBNetprotected
merge_2_branched_networks(utility::vector1< HBondResStructCOP > const &residues1, utility::vector1< HBondResStructCOP > const &residues2, utility::vector1< HBondResStructCOP > &new_residues)protocols::hbnet::HBNetprotected
min_asp_glu_hbonds_protocols::hbnet::HBNetStapleInterfaceprivate
min_helices_contacted_by_network_protocols::hbnet::HBNetStapleInterfaceprivate
min_intermolecular_hbonds_protocols::hbnet::HBNetStapleInterfaceprivate
min_networks_per_pose_protocols::hbnet::HBNetStapleInterfaceprivate
minimize_network(core::pose::Pose &pose, HBondNetStruct &network, bool residues_already_placed=true)protocols::hbnet::HBNetprotected
monte_carlo_net_clash(utility::vector1< HBondResStructCOP > const &residues_i, utility::vector1< HBondResStructCOP > const &residues_j) const protocols::hbnet::HBNetprotected
monte_carlo_seed_is_dead_end(core::scoring::hbonds::graph::HBondEdge const *monte_carlo_seed)protocols::hbnet::HBNetprotected
Mover()protocols::moves::Mover
Mover(std::string const &type_name)protocols::moves::Mover
mover_name()protocols::hbnet::HBNetStapleInterfacestatic
multi_component() const protocols::hbnet::HBNetinline
multi_component(bool const multi_component)protocols::hbnet::HBNetinline
name()protocols::moves::Moverinlinestatic
net_clash(HBondNetStruct const &i, HBondNetStruct const &j)protocols::hbnet::HBNet
net_clash(utility::vector1< HBondResStructCOP > const &residues_i, utility::vector1< HBondResStructCOP > const &residues_j)protocols::hbnet::HBNetprotected
network_already_stored(utility::vector1< HBondResStructCOP > &residues, utility::vector1< HBondResStructCOP > &i_residues)protocols::hbnet::HBNetprotected
network_meets_final_criteria(core::pose::Pose const &pose, HBondNetStruct &network) overrideprotocols::hbnet::HBNetStapleInterfacevirtual
network_meets_initial_criteria(HBondNetStruct const &network) overrideprotocols::hbnet::HBNetStapleInterfacevirtual
network_spans_all_helices(HBondNetStruct const &i) const protocols::hbnet::HBNetStapleInterface
network_state_is_done_growing(NetworkState const &current_state, core::scoring::hbonds::graph::HBondGraphCOP hbond_graph)protocols::hbnet::HBNetprotected
network_state_is_satisfied(NetworkState &current_state) const protocols::hbnet::HBNetprotected
networks_identical_aa_sequence(HBondNetStruct const &i, HBondNetStruct const &j)protocols::hbnet::HBNetprotected
networks_unique(HBondNetStruct const &i, HBondNetStruct const &j, bool no_surface=true)protocols::hbnet::HBNetprotected
node_is_compatible(NetworkState const &current_state, core::scoring::hbonds::graph::HBondNode const *node_being_added)protocols::hbnet::HBNetprotected
num_boundary_res(HBondNetStruct const &network)protocols::hbnet::HBNet
num_core_res(HBondNetStruct const &network)protocols::hbnet::HBNet
num_helices_w_hbond(HBondNetStruct const &i) const protocols::hbnet::HBNetStapleInterface
num_helices_w_hbond(utility::vector1< HBondResStructCOP > const &residues) const protocols::hbnet::HBNetStapleInterface
num_intermolecular_hbonds(HBondNetStruct &i, core::pose::Pose const &pose)protocols::hbnet::HBNetStapleInterface
only_native()protocols::hbnet::HBNetinline
only_start_at_interface_pairs_protocols::hbnet::HBNetStapleInterfaceprivate
only_symm_interfaces_protocols::hbnet::HBNetStapleInterfaceprivate
output_networks(bool finalize=false)protocols::hbnet::HBNetprotected
pair_lists_vec_protocols::hbnet::HBNetStapleInterfaceprivate
pair_meets_starting_criteria(core::Size const res1, core::Size const rot1, core::Size const res2, core::Size const rot2) overrideprotocols::hbnet::HBNetStapleInterfacevirtual
parse_my_tag(utility::tag::TagCOP tag, basic::datacache::DataMap &) overrideprotocols::hbnet::HBNetStapleInterfacevirtual
pdb_numbering() const protocols::hbnet::HBNetinline
pdb_numbering(bool const pdb_numbering)protocols::hbnet::HBNetinline
pH_His_protocols::hbnet::HBNetStapleInterfaceprivate
place_rots_on_pose(core::pose::Pose &pose, HBondNetStruct &residues, bool use_pose=false)protocols::hbnet::HBNet
Pose typedefprotocols::moves::Mover
PoseCOP typedefprotocols::moves::Mover
prepare_output() overrideprotocols::hbnet::HBNetStapleInterfacevirtual
print_additional_headers() overrideprotocols::hbnet::HBNetStapleInterfacevirtual
print_additional_info_for_net(HBondNetStruct &i, core::pose::Pose const &pose) overrideprotocols::hbnet::HBNetStapleInterfacevirtual
provide_citation_info(basic::citation_manager::CitationCollectionList &) const overrideprotocols::hbnet::HBNetvirtual
provide_xml_schema(utility::tag::XMLSchemaDefinition &xsd)protocols::hbnet::HBNetStapleInterfacestatic
quick_and_dirty_heavy_atom_is_unsat(core::pose::Pose const &pose, core::id::AtomID const at_id)protocols::hbnet::HBNet
quick_and_dirty_network_has_heavy_atom_unsat(core::pose::Pose const &pose, HBondNetStruct const &network)protocols::hbnet::HBNet
rec_add_staple(std::vector< HBondNetStructOP >::const_iterator netit, std::set< core::Size > net_ids, core::Size staple_count)protocols::hbnet::HBNetStapleInterface
rec_set_intersection(std::vector< core::Size > add_index_vec, std::vector< core::Size > next_index_list, core::Size pos)protocols::hbnet::HBNetprotected
rec_trav_native(core::pose::Pose const &pose, core::Size new_res, core::Size prev_res, utility::vector1< HBondResStructCOP > residues, core::Real const hb_threshold)protocols::hbnet::HBNetprotected
recursive_traverse(int const new_node_ind, int const newstate, core::Size const newres, core::Size const prevres, utility::vector1< HBondResStructCOP > residues, core::Size network_rec_count, core::Real init_sc, core::Real const hb_threshold, bool const second_search=false)protocols::hbnet::HBNetprotected
register_clash(core::Size rotamerA, core::Size rotamerB)protocols::hbnet::HBNetinlineprotected
register_new_network(NetworkState &current_network_state, utility::vector0< std::list< utility::vector1< core::Size > > > &hash_table, std::list< NetworkState > &designed_networks) const protocols::hbnet::HBNetprotected
register_options()protocols::moves::Moverinlinestatic
reinitialize_for_each_job() const protocols::moves::Movervirtual
reinitialize_for_new_input() const protocols::moves::Movervirtual
remove_replicate_networks(core::Size same_max=1)protocols::hbnet::HBNetprotected
res_is_boundary(core::Size const res) const protocols::hbnet::HBNet
res_is_core(core::Size const res) const protocols::hbnet::HBNet
reset_status()protocols::moves::Mover
residues_are_interface_pairs(core::Size const res1, core::Size const res2)protocols::hbnet::HBNetStapleInterface
residues_identical(utility::vector1< HBondResStructCOP > &residues1, utility::vector1< HBondResStructCOP > &residues2)protocols::hbnet::HBNetprotected
residues_not_unique(utility::vector1< HBondResStructCOP > &residues1, utility::vector1< HBondResStructCOP > &residues2)protocols::hbnet::HBNetprotected
run(core::pose::Pose &pose)protocols::hbnet::HBNetprotected
same_helix(utility::vector1< std::pair< core::Size, core::Size > > const helix_boundaries, core::Size const r1, core::Size const r2)protocols::hbnet::HBNetStapleInterface
scale_twobody_energy(core::Real input_twobody_energy, char res1, char res2) overrideprotocols::hbnet::HBNetStapleInterfacevirtual
score_network_on_pose(core::pose::Pose &pose, HBondNetStruct &i)protocols::hbnet::HBNetprotected
score_network_state(NetworkState &state) const protocols::hbnet::HBNetprotected
search_IG_for_networks(core::pose::Pose &pose)protocols::hbnet::HBNetvirtual
select_best_networks()protocols::hbnet::HBNet
set_ala_pose(core::pose::Pose &pose)protocols::hbnet::HBNetinline
set_boundary_residues(core::select::residue_selector::ResidueSubset boundary_residues)protocols::hbnet::HBNetinline
set_constraints(core::pose::Pose &pose, core::scoring::constraints::ConstraintSet &constraints, HBondNetStruct &p, bool write_cst_file=false)protocols::hbnet::HBNetprotected
set_core_residues(core::select::residue_selector::ResidueSubset core_residues)protocols::hbnet::HBNetinline
set_current_job(protocols::jobdist::BasicJobCOP job)protocols::moves::Mover
set_current_tag(std::string const &new_tag)protocols::moves::Moverinlinevirtual
set_extend_existing_networks(bool extend_existing_networks)protocols::hbnet::HBNetinline
set_find_native(bool native)protocols::hbnet::HBNetinline
set_find_only_native(bool only)protocols::hbnet::HBNetinline
set_input_pose(PoseCOP pose)protocols::moves::Movervirtual
set_keep_existing_networks(bool keep_existing_networks)protocols::hbnet::HBNetinline
set_last_move_status(MoverStatus status)protocols::moves::Moverprotected
set_max_networks_size(core::Size max)protocols::hbnet::HBNetinline
set_max_unsat(core::Size max)protocols::hbnet::HBNetinline
set_min_networks_size(core::Size min)protocols::hbnet::HBNetinline
set_monte_carlo_branch(bool setting)protocols::hbnet::HBNetinline
set_monte_carlo_data_to_default()protocols::hbnet::HBNetinlineprotected
set_monte_carlo_seed_must_be_buried(bool setting)protocols::hbnet::HBNetinline
set_monte_carlo_seed_must_be_fully_buried(bool setting)protocols::hbnet::HBNetinline
set_monte_carlo_seed_threshold(core::Real setting)protocols::hbnet::HBNetinline
set_native_pose(PoseCOP pose)protocols::moves::Movervirtual
set_only_extend_existing(bool only_extend_existing)protocols::hbnet::HBNetinline
set_orig_pose(core::pose::Pose &pose)protocols::hbnet::HBNetinline
set_score_function(core::scoring::ScoreFunctionCOP const &sf)protocols::hbnet::HBNetinline
set_start_res_vec(std::set< core::Size > const start_resnums)protocols::hbnet::HBNetinline
set_start_resnums(std::set< core::Size > const start_resnums)protocols::hbnet::HBNetinline
set_symm_info(core::conformation::symmetry::SymmetryInfoCOP const &symminfo)protocols::hbnet::HBNetinline
set_symmetry(core::pose::Pose &pose)protocols::hbnet::HBNet
set_task(core::pack::task::PackerTaskOP const &task)protocols::hbnet::HBNetinline
set_total_num_mc_runs(core::Size setting)protocols::hbnet::HBNetinline
set_type(std::string const &setting)protocols::moves::Moverinline
set_upweight_starting_twobody(core::Real upweight_factor)protocols::hbnet::HBNetinline
setup(core::pose::Pose const &pose)protocols::hbnet::HBNetprotected
setup_packer_task_and_starting_residues(core::pose::Pose const &pose) overrideprotocols::hbnet::HBNetStapleInterfacevirtual
show(std::ostream &output=std::cout) const protocols::moves::Movervirtual
span_all_helices_protocols::hbnet::HBNetStapleInterfaceprivate
state_is_starting_aa_type(core::Size const res, core::Size const rot_id) overrideprotocols::hbnet::HBNetStapleInterfacevirtual
store_network(utility::vector1< HBondResStructCOP > residues, core::Real init_score=0.0, bool term_w_start=false, bool term_w_cycle=false, bool score_now=false, bool native=false)protocols::hbnet::HBNetprotected
store_network_scores_in_pose() const protocols::hbnet::HBNetinlineprotected
store_network_scores_in_pose(bool setting)protocols::hbnet::HBNetinlineprotected
Strings typedefprotocols::moves::Mover
symmetric() const protocols::hbnet::HBNetinline
symmetric(bool const is_symmetric_pose)protocols::hbnet::HBNetinline
TagCOP typedefprotocols::moves::Mover
task_factory(core::pack::task::TaskFactoryOP const &task_factory)protocols::hbnet::HBNetinline
task_factory() const protocols::hbnet::HBNetinline
task_is_valid(core::pose::Pose const &pose) const protocols::hbnet::HBNetprotected
test_move(Pose &pose)protocols::moves::Moverinlinevirtual
traverse_IG(core::Real const hb_threshold)protocols::hbnet::HBNetprotected
traverse_native(core::pose::Pose const &pose, core::Real const hb_threshold)protocols::hbnet::HBNetprotected
trim_additional_rotamers(core::pose::Pose &)protocols::hbnet::HBNetinlinevirtual
trim_rotamers(core::pose::Pose &pose)protocols::hbnet::HBNetprotected
type(const std::string &type_in)protocols::moves::Moverinline
type() const protocols::moves::Moverinline
update_core_and_boundary_residues(core::pose::Pose const &pose)protocols::hbnet::HBNet
upweight_starting_twobody_energy()protocols::hbnet::HBNetinline
use_aa_dependent_weights_protocols::hbnet::HBNetStapleInterfaceprivate
verbose() const protocols::hbnet::HBNetinline
verbose(bool const set_verbose)protocols::hbnet::HBNetinline
water_clashes(core::pose::Pose const &pose, core::Vector const water_O)protocols::hbnet::HBNet
water_oxygen_clashes_with_residue(core::Vector const water_oxygen, core::Size const resnum, int const rot_state)protocols::hbnet::HBNet
water_oxygen_clashes_with_residue(core::Vector const water_oxygen, core::conformation::Residue const &res)protocols::hbnet::HBNet
write_network_pdb(HBondNetStructOP &p)protocols::hbnet::HBNetprotected
~HBNet() overrideprotocols::hbnet::HBNet
~HBNetStapleInterface() overrideprotocols::hbnet::HBNetStapleInterface
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