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protocols::abinitio::IterativeBase Member List

This is the complete list of members for protocols::abinitio::IterativeBase, including all inherited members.

AbstractArchiveBase(ArchiveManagerAP ptr)protocols::jd2::archive::AbstractArchiveBaseinline
AbstractArchiveBase()protocols::jd2::archive::AbstractArchiveBaseinline
accepts_since_last_batch()protocols::jd2::archive::ArchiveBaseinline
accepts_since_last_batch() const protocols::jd2::archive::ArchiveBaseinline
add_core_evaluator(loops::Loops const &core, std::string const &core_tag)protocols::abinitio::IterativeBaseprivate
add_evaluated_structure(core::io::silent::SilentStructOP from_batch, Batch const &)protocols::jd2::archive::NormalizedEvaluatedArchivevirtual
add_evaluation(evaluation::PoseEvaluatorCOP, core::Real weight=0.0)protocols::jd2::archive::EvaluatedArchive
add_fullatom_flags(jd2::archive::Batch &batch)protocols::abinitio::IterativeBaseprotected
add_structure(core::io::silent::SilentStructOP, jd2::archive::Batch const &)protocols::abinitio::IterativeBasevirtual
add_structure_at_position(SilentStructs::iterator iss, core::io::silent::SilentStructOP new_decoy)protocols::jd2::archive::ArchiveBaseprotected
ArchiveBase(ArchiveManagerAP ptr=NULL)protocols::jd2::archive::ArchiveBase
bCombineNoesyCst_protocols::abinitio::IterativeBaseprivate
bDoBetaJumping_protocols::abinitio::IterativeBaseprivate
bEnumeratedLastTime_protocols::abinitio::IterativeBaseprivate
CEN2FULLATOM enum valueprotocols::abinitio::IterativeBase
cen_score() const protocols::abinitio::IterativeBaseinlineprotected
cen_score_protocols::abinitio::IterativeBaseprivate
cen_score_patch() const protocols::abinitio::IterativeBaseinlineprotected
cen_score_patch_protocols::abinitio::IterativeBaseprivate
chemshift_column() const protocols::abinitio::IterativeBaseinlineprotected
chemshift_column_protocols::abinitio::IterativeBaseprivate
cluster()protocols::abinitio::IterativeBaseprotected
collect_alternative_decoys(SilentStructs primary_decoys, std::string alternative_decoy_file, SilentStructVector &output_decoys)protocols::abinitio::IterativeBaseprivate
collect_hedge_structures(core::io::silent::SilentStructOP evaluated_decoy, jd2::archive::Batch const &batch)protocols::abinitio::IterativeBaseprivate
collect_hedgeing_decoys_from_batches(jd2::archive::Batch const &batch, core::io::silent::SilentStructOPs &start_decoys, core::Real score_cut_per_batch)protocols::abinitio::IterativeBaseprotected
compute_beta_topology()protocols::abinitio::IterativeBaseprotected
compute_cores()protocols::abinitio::IterativeBaseprotected
const_decoy_iterator typedefprotocols::jd2::archive::ArchiveBaseprotected
core(core::Size i)protocols::abinitio::IterativeBaseinlineprotected
core15_protocols::abinitio::IterativeBaseprivate
core2_protocols::abinitio::IterativeBaseprivate
core3_protocols::abinitio::IterativeBaseprivate
core4_protocols::abinitio::IterativeBaseprivate
count_removed_structures(core::Size n_removed)protocols::jd2::archive::ArchiveBaseprotected
count_structure(Batch const &batch, bool accepted)protocols::jd2::archive::ArchiveBaseprotectedvirtual
cst_data_protocols::abinitio::IterativeBasemutableprivate
cst_fa_data_protocols::abinitio::IterativeBasemutableprivate
current_acceptance_ratio() const protocols::jd2::archive::ArchiveBaseinline
current_noesy_sampling_file_protocols::abinitio::IterativeBaseprivate
decoy_iterator typedefprotocols::jd2::archive::ArchiveBaseprotected
decoys() const protocols::jd2::archive::ArchiveBaseinline
decoys()protocols::jd2::archive::ArchiveBaseinline
delay_noesy_reassign_protocols::abinitio::IterativeBaseprivate
determine_score_variations() const protocols::jd2::archive::NormalizedEvaluatedArchive
do_dynamic_patching(jd2::archive::Batch &batch, utility::io::ozstream &flags, std::string score, utility::options::FileVectorOptionKey const &key) const protocols::abinitio::IterativeBaseprivate
ENUMERATION enum valueprotocols::abinitio::IterativeBase
evaluate_local() const protocols::jd2::archive::EvaluatedArchiveinline
evaluate_silent_struct(core::io::silent::SilentStructOP from_batch) const protocols::jd2::archive::EvaluatedArchive
EvaluatedArchive(ArchiveManagerAP ptr)protocols::jd2::archive::EvaluatedArchive
EvaluatedArchive()protocols::jd2::archive::EvaluatedArchive
EvaluatorMap typedefprotocols::jd2::archive::EvaluatedArchive
evaluators() const protocols::jd2::archive::EvaluatedArchiveinline
fa_score() const protocols::abinitio::IterativeBaseinlineprotected
fa_score_protocols::abinitio::IterativeBaseprivate
fa_score_patch() const protocols::abinitio::IterativeBaseinlineprotected
fa_score_patch_protocols::abinitio::IterativeBaseprivate
finish_stage_protocols::abinitio::IterativeBaseprivate
FINISHED enum valueprotocols::abinitio::IterativeBase
finished() const protocols::abinitio::IterativeBaseinlinevirtual
first_batch_this_stage_protocols::abinitio::IterativeBaseprivate
first_fullatom_batch_protocols::abinitio::IterativeBaseprivate
first_noesy_cst_file_protocols::abinitio::IterativeBaseprivate
first_noesy_fa_cst_file_protocols::abinitio::IterativeBaseprivate
gen_cen2fullatom(jd2::archive::Batch &batch)protocols::abinitio::IterativeBaseprotected
gen_cen2fullatom_non_pool_decoys(jd2::archive::Batch &batch)protocols::abinitio::IterativeBaseprotected
gen_diversity_pool(jd2::archive::Batch &, bool fullatom=false)protocols::abinitio::IterativeBasevirtual
gen_dynamic_patches(jd2::archive::Batch &batch)protocols::abinitio::IterativeBasevirtual
gen_enumerate_pairings(jd2::archive::Batch &batch)protocols::abinitio::IterativeBaseprotected
gen_evaluation_output(jd2::archive::Batch &batch, bool fullatom=false)protocols::abinitio::IterativeBasevirtual
gen_noe_assignments(jd2::archive::Batch &batch)protocols::abinitio::IterativeBaseprotected
gen_resample_fragments(jd2::archive::Batch &batch)protocols::abinitio::IterativeBaseprotected
gen_resample_stage2(jd2::archive::Batch &batch)protocols::abinitio::IterativeBaseprotected
gen_resample_topologies(jd2::archive::Batch &batch)protocols::abinitio::IterativeBaseprotected
gen_start_structures(jd2::archive::Batch &batch)protocols::abinitio::IterativeBaseprotected
generate_batch()protocols::abinitio::IterativeBasevirtual
get_weight(std::string const &column) const protocols::jd2::archive::EvaluatedArchive
guess_pairings_from_secondary_structure(core::fragment::FragSet const &frags, std::string const &out_pairings_file, std::string const &out_frag_ss_file) const protocols::abinitio::IterativeBaseprotected
has_evaluator(std::string const &column)protocols::jd2::archive::EvaluatedArchive
hasherprotocols::abinitio::IterativeBaseprivate
hedge_archive_protocols::abinitio::IterativeBaseprivate
idle()protocols::abinitio::IterativeBasevirtual
increment_stage()protocols::abinitio::IterativeBaseprivate
init_from_decoy_set(core::io::silent::SilentFileData const &sfd)protocols::abinitio::IterativeBasevirtual
init_from_options()protocols::jd2::archive::NormalizedEvaluatedArchive
initialize()protocols::abinitio::IterativeBasevirtual
invalidate_score_variations()protocols::jd2::archive::NormalizedEvaluatedArchiveinlineprotectedvirtual
IterationStage enum nameprotocols::abinitio::IterativeBase
IterativeBase(std::string name)protocols::abinitio::IterativeBase
last_accepted_decoys_in_idle_protocols::abinitio::IterativeBaseprivate
LAST_CENTROID_START enum valueprotocols::abinitio::IterativeBase
manager()protocols::jd2::archive::AbstractArchiveBaseinline
manager_ptr()protocols::jd2::archive::AbstractArchiveBaseinlineprotected
max_nstruct_list_protocols::abinitio::IterativeBaseprivate
min_diversity_list_protocols::abinitio::IterativeBaseprivate
name() const protocols::jd2::archive::AbstractArchiveBaseinline
never_switched_noe_filter_protocols::abinitio::IterativeBaseprotected
noesy_assign_float_cycle_protocols::abinitio::IterativeBaseprivate
noesy_assign_hash_protocols::abinitio::IterativeBaseprivate
noesy_module_protocols::abinitio::IterativeBaseprivate
NOESY_PHASEII_S2_RESAMPLING enum valueprotocols::abinitio::IterativeBase
NOESY_PHASEII_TOPO enum valueprotocols::abinitio::IterativeBase
NormalizedEvaluatedArchive(ArchiveManagerAP ptr)protocols::jd2::archive::NormalizedEvaluatedArchive
NormalizedEvaluatedArchive()protocols::jd2::archive::NormalizedEvaluatedArchive
nstruct() const protocols::jd2::archive::ArchiveBaseinline
options_registered_protocols::abinitio::IterativeBaseprivatestatic
overall_cstfilter_weight() const protocols::abinitio::IterativeBaseinlineprotected
overall_cstfilter_weight_protocols::abinitio::IterativeBaseprivate
Parent typedefprotocols::abinitio::IterativeBaseprivate
proposed_since_last_batch() const protocols::jd2::archive::ArchiveBaseinline
PURE_TOPO_RESAMPLING enum valueprotocols::abinitio::IterativeBase
rdc_data_protocols::abinitio::IterativeBasemutableprivate
read_structures(core::io::silent::SilentFileData &returned_decoys, jd2::archive::Batch const &batch)protocols::abinitio::IterativeBasevirtual
ready_for_batch() const protocols::abinitio::IterativeBaseinlinevirtual
reassign_noesy_data(jd2::archive::Batch &batch)protocols::abinitio::IterativeBaseprotected
recover_centroid_structure_for_pool_protocols::abinitio::IterativeBaseprivate
reference_pose_protocols::abinitio::IterativeBaseprivate
register_options()protocols::abinitio::IterativeBasestatic
remove_evaluation(std::string const &column)protocols::jd2::archive::EvaluatedArchive
replace_noesy_filter_constraints()protocols::abinitio::IterativeBaseprivate
rescore()protocols::abinitio::IterativeBasevirtual
rescore_nonlocal_archive()protocols::abinitio::IterativeBaseprivate
reset_accept_counter()protocols::jd2::archive::ArchiveBaseinline
restore_from_file()protocols::jd2::archive::NormalizedEvaluatedArchivevirtual
restore_status(std::istream &)protocols::abinitio::IterativeBasevirtual
RIGID_CORE_RESAMPLING enum valueprotocols::abinitio::IterativeBase
save_status(std::ostream &) const protocols::abinitio::IterativeBasevirtual
save_to_file(std::string suffix="")protocols::jd2::archive::NormalizedEvaluatedArchivevirtual
score(core::pose::Pose &pose) const protocols::abinitio::IterativeBaseprivatevirtual
score_variation(std::string const &col) const protocols::jd2::archive::NormalizedEvaluatedArchivevirtual
score_variations() const protocols::jd2::archive::NormalizedEvaluatedArchivevirtual
scored_core_protocols::abinitio::IterativeBaseprotected
scorefxn() const protocols::jd2::archive::EvaluatedArchive
scorefxn_non_const()protocols::jd2::archive::EvaluatedArchiveprotected
select_score(core::io::silent::SilentStructOP evaluated_decoy)protocols::jd2::archive::EvaluatedArchive
set_evaluate_local(bool setting)protocols::jd2::archive::EvaluatedArchiveinline
set_evaluators(EvaluatorMap const &, WeightMap const &)protocols::jd2::archive::EvaluatedArchive
set_finish_stage(IterationStage setting)protocols::abinitio::IterativeBaseinline
set_manager(ArchiveManagerAP manager)protocols::jd2::archive::AbstractArchiveBaseinlinevirtual
set_max_nstruct(core::Size setting)protocols::jd2::archive::ArchiveBaseinlineprotected
set_name(std::string const &set)protocols::jd2::archive::AbstractArchiveBaseinline
set_noesy_assign_float_cycle(core::Real setting)protocols::abinitio::IterativeBaseinlineprotected
set_nstruct(core::Size set)protocols::jd2::archive::ArchiveBaseinline
set_overall_cstfilter_weight(core::Real setting)protocols::abinitio::IterativeBaseinlineprotected
set_scorefxn(core::scoring::ScoreFunctionOP scorefxn_)protocols::jd2::archive::EvaluatedArchive
set_stage(IterationStage setting)protocols::abinitio::IterativeBaseinlineprotected
set_weight(std::string const &column, core::Real weight)protocols::jd2::archive::EvaluatedArchive
set_weights(WeightMap const &setting)protocols::jd2::archive::EvaluatedArchive
setup_autoNOE()protocols::abinitio::IterativeBaseprivate
setup_default_evaluators()protocols::abinitio::IterativeBase
setup_filter_cst(core::Real weight)protocols::abinitio::IterativeBaseprotected
SilentStructs typedefprotocols::jd2::archive::ArchiveBaseprotected
SilentStructVector typedefprotocols::abinitio::IterativeBaseprivate
SOURCE_FILEprotocols::jd2::archive::ArchiveBaseprotectedstatic
stage() const protocols::abinitio::IterativeBaseinlineprotected
STAGE2_RESAMPLING enum valueprotocols::abinitio::IterativeBase
stage_protocols::abinitio::IterativeBaseprivate
start_evaluation_timer() const protocols::jd2::archive::EvaluatedArchive
statistics_valid()protocols::jd2::archive::ArchiveBaseinline
still_interested(jd2::archive::Batch const &batch) const protocols::abinitio::IterativeBasevirtual
super_quick_relax_of_centroids() const protocols::abinitio::IterativeBaseinlineprotected
super_quick_relax_of_centroids_protocols::abinitio::IterativeBaseprivate
TAG_IN_FILEprotocols::jd2::archive::ArchiveBaseprotectedstatic
target_accept_ratio() const protocols::abinitio::IterativeBaseinlineprivate
target_accept_ratio_protocols::abinitio::IterativeBaseprivate
target_sequence() const protocols::abinitio::IterativeBaseinlineprotected
target_sequence_protocols::abinitio::IterativeBaseprivate
test_broker_settings(jd2::archive::Batch const &batch)protocols::abinitio::IterativeBaseprotected
test_for_stage_end()protocols::abinitio::IterativeBase
TOPO_RESAMPLING enum valueprotocols::abinitio::IterativeBase
total_accepts()protocols::jd2::archive::ArchiveBaseinline
total_proposed()protocols::jd2::archive::ArchiveBaseinline
update_noesy_filter_files(std::string const &current, bool fullatom)protocols::abinitio::IterativeBasevirtual
use_dynamic_weights_for_sampling_protocols::abinitio::IterativeBaseprivate
vanilla_options_protocols::abinitio::IterativeBaseprivate
WeightMap typedefprotocols::jd2::archive::EvaluatedArchive
weights() const protocols::jd2::archive::EvaluatedArchiveinline
~AbstractArchiveBase()protocols::jd2::archive::AbstractArchiveBasevirtual
~ArchiveBase()protocols::jd2::archive::ArchiveBase
~EvaluatedArchive()protocols::jd2::archive::EvaluatedArchive
~IterativeBase()protocols::abinitio::IterativeBase
~NormalizedEvaluatedArchive()protocols::jd2::archive::NormalizedEvaluatedArchive
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