protocols::abinitio::IterativeBase Member List

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

AbstractArchiveBase(BaseArchiveManagerAP ptr)	protocols::jd2::archive::AbstractArchiveBase	inline
AbstractArchiveBase()	protocols::jd2::archive::AbstractArchiveBase	inline
accepts_since_last_batch()	protocols::jd2::archive::ArchiveBase	inline
accepts_since_last_batch() const	protocols::jd2::archive::ArchiveBase	inline
add_core_evaluator(loops::Loops const &core, std::string const &core_tag)	protocols::abinitio::IterativeBase	private
add_evaluated_structure(core::io::silent::SilentStructOP from_batch, core::io::silent::SilentStructOP alternative_decoy, Batch const &) override	protocols::jd2::archive::NormalizedEvaluatedArchive	virtual
add_evaluation(evaluation::PoseEvaluatorCOP, core::Real weight=0.0)	protocols::jd2::archive::EvaluatedArchive
add_fullatom_flags(jd2::archive::Batch &batch)	protocols::abinitio::IterativeBase	protected
add_structure(core::io::silent::SilentStructOP new_decoy, core::io::silent::SilentStructOP alternative_decoy, jd2::archive::Batch const &) override	protocols::abinitio::IterativeBase	virtual
add_structure_at_position(SilentStructs::iterator iss, core::io::silent::SilentStructOP new_decoy, core::io::silent::SilentStructOP alternative_decoy)	protocols::jd2::archive::ArchiveBase	protectedvirtual
ArchiveBase(ArchiveManagerAP ptr=nullptr)	protocols::jd2::archive::ArchiveBase
bCombineNoesyCst_	protocols::abinitio::IterativeBase	private
bDoBetaJumping_	protocols::abinitio::IterativeBase	private
bEnumeratedLastTime_	protocols::abinitio::IterativeBase	private
CEN2FULLATOM enum value	protocols::abinitio::IterativeBase
cen_score() const	protocols::abinitio::IterativeBase	inlineprotected
cen_score_	protocols::abinitio::IterativeBase	private
cen_score_patch() const	protocols::abinitio::IterativeBase	inlineprotected
cen_score_patch_	protocols::abinitio::IterativeBase	private
chemshift_column() const	protocols::abinitio::IterativeBase	inlineprotected
chemshift_column_	protocols::abinitio::IterativeBase	private
cluster()	protocols::abinitio::IterativeBase	protected
collect_alternative_decoys(SilentStructs, std::string, SilentStructVector &)	protocols::abinitio::IterativeBase	inlineprotectedvirtual
collect_hedge_structures(core::io::silent::SilentStructOP evaluated_decoy, jd2::archive::Batch const &batch)	protocols::abinitio::IterativeBase	private
collect_hedgeing_decoys_from_batches(jd2::archive::Batch const &batch, core::io::silent::SilentStructOPs &start_decoys, core::Real score_cut_per_batch)	protocols::abinitio::IterativeBase	protected
compute_beta_topology()	protocols::abinitio::IterativeBase	protected
compute_cores()	protocols::abinitio::IterativeBase	protected
const_decoy_iterator typedef	protocols::jd2::archive::ArchiveBase	protected
core(core::Size i)	protocols::abinitio::IterativeBase	inlineprotected
core15_	protocols::abinitio::IterativeBase	private
core2_	protocols::abinitio::IterativeBase	private
core3_	protocols::abinitio::IterativeBase	private
core4_	protocols::abinitio::IterativeBase	private
count_removed_structures(core::Size n_removed)	protocols::jd2::archive::ArchiveBase	protected
count_structure(Batch const &batch, bool accepted)	protocols::jd2::archive::ArchiveBase	protectedvirtual
cst_data_	protocols::abinitio::IterativeBase	mutableprivate
cst_fa_data_	protocols::abinitio::IterativeBase	mutableprivate
current_acceptance_ratio() const	protocols::jd2::archive::ArchiveBase	inline
current_noesy_sampling_file_	protocols::abinitio::IterativeBase	private
decoy_iterator typedef	protocols::jd2::archive::ArchiveBase	protected
decoys() const	protocols::jd2::archive::ArchiveBase	inline
decoys()	protocols::jd2::archive::ArchiveBase	inline
delay_noesy_reassign_	protocols::abinitio::IterativeBase	private
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::IterativeBase	private
ENUMERATION enum value	protocols::abinitio::IterativeBase
erase_decoy(std::string const &tag)	protocols::jd2::archive::ArchiveBase	protectedvirtual
evaluate_local() const	protocols::jd2::archive::EvaluatedArchive	inline
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 typedef	protocols::jd2::archive::EvaluatedArchive
evaluators() const	protocols::jd2::archive::EvaluatedArchive	inline
fa_score() const	protocols::abinitio::IterativeBase	inlineprotected
fa_score_	protocols::abinitio::IterativeBase	private
fa_score_patch() const	protocols::abinitio::IterativeBase	inlineprotected
fa_score_patch_	protocols::abinitio::IterativeBase	private
finish_stage_	protocols::abinitio::IterativeBase	private
FINISHED enum value	protocols::abinitio::IterativeBase
finished() const override	protocols::abinitio::IterativeBase	inlinevirtual
first_batch_this_stage_	protocols::abinitio::IterativeBase	private
first_fullatom_batch_	protocols::abinitio::IterativeBase	private
first_noesy_cst_file_	protocols::abinitio::IterativeBase	private
first_noesy_fa_cst_file_	protocols::abinitio::IterativeBase	private
gen_cen2fullatom(jd2::archive::Batch &batch)	protocols::abinitio::IterativeBase	protected
gen_cen2fullatom_non_pool_decoys(jd2::archive::Batch &batch)	protocols::abinitio::IterativeBase	protected
gen_diversity_pool(jd2::archive::Batch &, bool fullatom=false)	protocols::abinitio::IterativeBase	virtual
gen_dynamic_patches(jd2::archive::Batch &batch)	protocols::abinitio::IterativeBase	virtual
gen_enumerate_pairings(jd2::archive::Batch &batch)	protocols::abinitio::IterativeBase	protected
gen_evaluation_output(jd2::archive::Batch &batch, bool fullatom=false)	protocols::abinitio::IterativeBase	virtual
gen_noe_assignments(jd2::archive::Batch &batch)	protocols::abinitio::IterativeBase	protected
gen_resample_fragments(jd2::archive::Batch &batch)	protocols::abinitio::IterativeBase	protected
gen_resample_stage2(jd2::archive::Batch &batch)	protocols::abinitio::IterativeBase	protected
gen_resample_topologies(jd2::archive::Batch &batch)	protocols::abinitio::IterativeBase	protected
gen_start_structures(jd2::archive::Batch &batch)	protocols::abinitio::IterativeBase	protected
generate_batch() override	protocols::abinitio::IterativeBase	virtual
generate_batch(jd2::archive::Batch &, core::Size repeat_id) override	protocols::abinitio::IterativeBase	virtual
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::IterativeBase	protected
has_evaluator(std::string const &column)	protocols::jd2::archive::EvaluatedArchive
hasher	protocols::abinitio::IterativeBase	private
hedge_archive_	protocols::abinitio::IterativeBase	private
idle() override	protocols::abinitio::IterativeBase	virtual
increment_stage()	protocols::abinitio::IterativeBase	private
init_from_decoy_set(core::io::silent::SilentFileData const &sfd) override	protocols::abinitio::IterativeBase	virtual
init_from_options()	protocols::jd2::archive::NormalizedEvaluatedArchive
initialize() override	protocols::abinitio::IterativeBase	virtual
invalidate_score_variations() override	protocols::jd2::archive::NormalizedEvaluatedArchive	inlineprotectedvirtual
IterationStage enum name	protocols::abinitio::IterativeBase
IterativeBase(std::string name)	protocols::abinitio::IterativeBase
last_accepted_decoys_in_idle_	protocols::abinitio::IterativeBase	private
LAST_CENTROID_START enum value	protocols::abinitio::IterativeBase
load_decoys(std::string const &filename, SilentStructs &decoys)	protocols::jd2::archive::ArchiveBase
manager()	protocols::jd2::archive::AbstractArchiveBase	inline
manager_ptr()	protocols::jd2::archive::AbstractArchiveBase	inlineprotected
max_nstruct()	protocols::jd2::archive::ArchiveBase	inlineprotected
max_nstruct_list_	protocols::abinitio::IterativeBase	private
min_diversity_list_	protocols::abinitio::IterativeBase	private
name() const	protocols::jd2::archive::AbstractArchiveBase	inline
never_switched_noe_filter_	protocols::abinitio::IterativeBase	protected
noesy_assign_float_cycle_	protocols::abinitio::IterativeBase	private
noesy_assign_hash_	protocols::abinitio::IterativeBase	private
noesy_module_	protocols::abinitio::IterativeBase	private
NOESY_PHASEII_S2_RESAMPLING enum value	protocols::abinitio::IterativeBase
NOESY_PHASEII_TOPO enum value	protocols::abinitio::IterativeBase
NormalizedEvaluatedArchive(ArchiveManagerAP ptr)	protocols::jd2::archive::NormalizedEvaluatedArchive
NormalizedEvaluatedArchive()	protocols::jd2::archive::NormalizedEvaluatedArchive
nstruct() const	protocols::jd2::archive::ArchiveBase	inline
options_registered_	protocols::abinitio::IterativeBase	privatestatic
overall_cstfilter_weight() const	protocols::abinitio::IterativeBase	inlineprotected
overall_cstfilter_weight_	protocols::abinitio::IterativeBase	private
Parent typedef	protocols::abinitio::IterativeBase	private
proposed_since_last_batch() const	protocols::jd2::archive::ArchiveBase	inline
PURE_TOPO_RESAMPLING enum value	protocols::abinitio::IterativeBase
rdc_data_	protocols::abinitio::IterativeBase	mutableprivate
read_structures(core::io::silent::SilentFileData &sfd, core::io::silent::SilentFileData &alternative_decoys, jd2::archive::Batch const &batch) override	protocols::abinitio::IterativeBase	virtual
ready_for_batch() const	protocols::abinitio::IterativeBase	inlinevirtual
reassign_noesy_data(jd2::archive::Batch &batch)	protocols::abinitio::IterativeBase	protected
reference_pose_	protocols::abinitio::IterativeBase	private
register_options()	protocols::abinitio::IterativeBase	static
remove_evaluation(std::string const &column)	protocols::jd2::archive::EvaluatedArchive
replace_noesy_filter_constraints()	protocols::abinitio::IterativeBase	private
rescore() override	protocols::abinitio::IterativeBase	virtual
rescore_nonlocal_archive()	protocols::abinitio::IterativeBase	private
reset_accept_counter()	protocols::jd2::archive::ArchiveBase	inline
restore_from_file() override	protocols::jd2::archive::NormalizedEvaluatedArchive	virtual
restore_status(std::istream &) override	protocols::abinitio::IterativeBase	virtual
RIGID_CORE_RESAMPLING enum value	protocols::abinitio::IterativeBase
save_decoys(std::string const &dirname, std::string const &name, SilentStructs const &decoys)	protocols::jd2::archive::ArchiveBase
save_status(std::ostream &) const override	protocols::abinitio::IterativeBase	virtual
save_to_file(std::string suffix="") override	protocols::jd2::archive::NormalizedEvaluatedArchive	virtual
score(core::pose::Pose &pose) const override	protocols::abinitio::IterativeBase	privatevirtual
score_variation(std::string const &col) const override	protocols::jd2::archive::NormalizedEvaluatedArchive	virtual
score_variations() const override	protocols::jd2::archive::NormalizedEvaluatedArchive	virtual
scored_core_	protocols::abinitio::IterativeBase	protected
scorefxn() const	protocols::jd2::archive::EvaluatedArchive
scorefxn_non_const()	protocols::jd2::archive::EvaluatedArchive	protected
select_score(core::io::silent::SilentStructOP evaluated_decoy)	protocols::jd2::archive::EvaluatedArchive
set_evaluate_local(bool setting)	protocols::jd2::archive::EvaluatedArchive	inline
set_evaluators(EvaluatorMap const &, WeightMap const &)	protocols::jd2::archive::EvaluatedArchive
set_finish_stage(IterationStage setting)	protocols::abinitio::IterativeBase	inline
set_manager(BaseArchiveManagerAP manager)	protocols::jd2::archive::AbstractArchiveBase	inlinevirtual
set_max_nstruct(core::Size setting)	protocols::jd2::archive::ArchiveBase	inlineprotected
set_name(std::string const &set)	protocols::jd2::archive::AbstractArchiveBase	inline
set_noesy_assign_float_cycle(core::Real setting)	protocols::abinitio::IterativeBase	inlineprotected
set_nstruct(core::Size set)	protocols::jd2::archive::ArchiveBase	inline
set_overall_cstfilter_weight(core::Real setting)	protocols::abinitio::IterativeBase	inlineprotected
set_scorefxn(core::scoring::ScoreFunctionOP scorefxn_)	protocols::jd2::archive::EvaluatedArchive
set_stage(IterationStage setting)	protocols::abinitio::IterativeBase	inlineprotected
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::IterativeBase	private
setup_default_evaluators()	protocols::abinitio::IterativeBase
setup_filter_cst(core::Real weight)	protocols::abinitio::IterativeBase	protected
SilentStructs typedef	protocols::jd2::archive::ArchiveBase	protected
SilentStructVector typedef	protocols::abinitio::IterativeBase	protected
SOURCE_FILE	protocols::jd2::archive::ArchiveBase	protectedstatic
stage() const	protocols::abinitio::IterativeBase	inlineprotected
STAGE2_RESAMPLING enum value	protocols::abinitio::IterativeBase
stage_	protocols::abinitio::IterativeBase	private
start_evaluation_timer() const	protocols::jd2::archive::EvaluatedArchive
statistics_valid()	protocols::jd2::archive::ArchiveBase	inline
still_interested(jd2::archive::Batch const &batch) const override	protocols::abinitio::IterativeBase	virtual
super_quick_relax_of_centroids() const	protocols::abinitio::IterativeBase	inlineprotected
super_quick_relax_of_centroids_	protocols::abinitio::IterativeBase	private
TAG_IN_FILE	protocols::jd2::archive::ArchiveBase	protectedstatic
target_accept_ratio() const	protocols::abinitio::IterativeBase	inlineprivate
target_accept_ratio_	protocols::abinitio::IterativeBase	private
target_sequence() const	protocols::abinitio::IterativeBase	inlineprotected
target_sequence_	protocols::abinitio::IterativeBase	private
test_broker_settings(jd2::archive::Batch const &batch)	protocols::abinitio::IterativeBase	protected
test_for_stage_end()	protocols::abinitio::IterativeBase
TOPO_RESAMPLING enum value	protocols::abinitio::IterativeBase
total_accepts()	protocols::jd2::archive::ArchiveBase	inline
total_proposed()	protocols::jd2::archive::ArchiveBase	inline
update_noesy_filter_files(std::string const &current, bool fullatom)	protocols::abinitio::IterativeBase	virtual
use_dynamic_weights_for_sampling_	protocols::abinitio::IterativeBase	private
vanilla_options_	protocols::abinitio::IterativeBase	private
WeightMap typedef	protocols::jd2::archive::EvaluatedArchive
weights() const	protocols::jd2::archive::EvaluatedArchive	inline
~AbstractArchiveBase() override	protocols::jd2::archive::AbstractArchiveBase
~ArchiveBase() override	protocols::jd2::archive::ArchiveBase
~EvaluatedArchive() override	protocols::jd2::archive::EvaluatedArchive
~IterativeBase() override	protocols::abinitio::IterativeBase
~NormalizedEvaluatedArchive() override	protocols::jd2::archive::NormalizedEvaluatedArchive