protocols::mean_field Namespace Reference

Classes
class	AAMatrix
class	AAProb
class	DesignMeanField
class	EnergiesByTaskCalculator
class	FlexBBDesignMeanField
class	FlexBBMeanField
class	GenMeanFieldMover
class	GenMeanFieldMoverCreator
class	jagged_array
	utility::vector1<utility::vector1>> vector of vectors to create the effect of a jagged array More...
class	MeanField
class	MeanFieldFactory
struct	ResHasher
	uses default boost::hash combine to hash rotamers based on rounded chi angles More...
struct	ResPred
	checks whether two rotamer hashes match - if the rounded values of their chi angles match More...
class	ResHashMap
class	RotMatrix
class	RotProb

Typedefs
typedef utility::pointer::shared_ptr< AAMatrix >	AAMatrixOP
typedef utility::pointer::shared_ptr< AAMatrix const >	AAMatrixCOP
typedef utility::pointer::shared_ptr< DesignMeanField >	DesignMeanFieldOP
typedef utility::pointer::shared_ptr< DesignMeanField const >	DesignMeanFieldCOP
typedef utility::pointer::shared_ptr< EnergiesByTaskCalculator >	EnergiesByTaskCalculatorOP
typedef utility::pointer::shared_ptr< EnergiesByTaskCalculator const >	EnergiesByTaskCalculatorCOP
typedef utility::pointer::shared_ptr< FlexBBDesignMeanField >	FlexBBDesignMeanFieldOP
typedef utility::pointer::shared_ptr< FlexBBDesignMeanField const >	FlexBBDesignMeanFieldCOP
typedef utility::pointer::shared_ptr< FlexBBMeanField >	FlexBBMeanFieldOP
typedef utility::pointer::shared_ptr< FlexBBMeanField const >	FlexBBMeanFieldCOP
typedef utility::pointer::shared_ptr< GenMeanFieldMover >	GenMeanFieldMoverOP
typedef utility::pointer::shared_ptr< GenMeanFieldMover const >	GenMeanFieldMoverCOP
typedef jagged_array< bool >	jagged_array_bool
typedef jagged_array< short int >	jagged_array_short
typedef jagged_array< int >	jagged_array_int
typedef jagged_array< long int >	jagged_array_long
typedef jagged_array< unsigned short int >	jagged_array_ushort
typedef jagged_array< unsigned int >	jagged_array_uint
typedef jagged_array< unsigned long int >	jagged_array_ulong
typedef jagged_array< platform::Size >	jagged_array_size_t
typedef jagged_array< platform::Size >	jagged_array_size
typedef jagged_array< platform::SSize >	jagged_array_ssize_t
typedef jagged_array< platform::SSize >	jagged_array_ssize
typedef jagged_array< float >	jagged_array_float
typedef jagged_array< double >	jagged_array_double
typedef jagged_array< long double >	jagged_array_longdouble
typedef jagged_array< char >	jagged_array_char
typedef jagged_array< unsigned char >	jagged_array_uchar
typedef jagged_array< signed char >	jagged_array_schar
typedef utility::pointer::shared_ptr< MeanField >	MeanFieldOP
typedef utility::pointer::shared_ptr< MeanField const >	MeanFieldCOP
typedef utility::pointer::shared_ptr< ResHashMap >	ResHashMapOP
typedef utility::pointer::shared_ptr< ResHashMap const >	ResHashMapCOP
typedef utility::pointer::shared_ptr< RotMatrix >	RotMatrixOP
typedef utility::pointer::shared_ptr< RotMatrix const >	RotMatrixCOP

Functions
static basic::Tracer	TR ("protocols.mean_field.AAMatrix")
std::ostream &	operator<< (std::ostream &output, AAMatrix const &object_to_output)
std::ostream &	operator<< (std::ostream &output, AAProb const &object_to_output)
std::ostream &	operator<< (std::ostream &output, DesignMeanField const &object_to_output)
std::ostream &	operator<< (std::ostream &output, FlexBBDesignMeanField const &object_to_output)
std::ostream &	operator<< (std::ostream &output, FlexBBMeanField const &object_to_output)
static basic::Tracer	TR ("protocols.mean_field.GenMeanFieldMover")
template<class T >
T	max (jagged_array< T > const &input)
	Find the largest value in a jagged_array. More...
template<class T >
T	min (jagged_array< T > const &input)
	Find the smallest value in a jagged_array. More...
template<class T >
jagged_array< T >::Size	arg_max (jagged_array< T > const &input)
	find the index of the largest value in a jagged_array More...
template<class T >
jagged_array< T >::Size	arg_min (jagged_array< T > const &input)
	find the index of the smallest value in a jagged_array More...
template<class T >
jagged_array< T >::Size	num_elements (jagged_array< T > const &input)
	returns the number of elements in a jagged_array More...
template<class T >
T	add (T const &operand_from_ja, T const &other_operand)
	implements add function using operator += More...
template<class T >
T	subtract (T const &operand_from_ja, T const &other_operand)
	implements subtract function using operator -= More...
template<class T >
T	multiply (T const &operand_from_ja, T const &other_operand)
	implements multiply function using operator *= More...
template<class T >
T	divide (T const &operand_from_ja, T const &other_operand)
	implements divide function using operator /= More...
template<class T , class T_2 >
T	divide (T const &operand_from_ja, T_2 const &other_operand)
	implements add function using operator += More...
template<class T >
void	operator+= (jagged_array< T > &input, T const &operand)
	overload operator += to allow addition of T operand to all elements in jagged_array More...
template<class T >
void	operator+= (jagged_array< T > &input, utility::vector1< T > const &operands)
	overload operator += to allow addition of vector1<T> operands to jagged_array in a column-dependent manner More...
template<class T >
void	operator+= (jagged_array< T > &input, jagged_array< T > const &operands)
	overload operator += to allow addition of jagged_array<T> operands to jagged_array in an element-dependent manner More...
template<class T >
jagged_array< T >	operator+ (jagged_array< T > const &input, T operand)
	overload operator + to allow addition of T operand to all elements in jagged_array More...
template<class T >
jagged_array< T >	operator+ (jagged_array< T > const &input, utility::vector1< T > const &operands)
	overload operator + to allow addition of vector1<T> operands to jagged_array in a column-dependent manner More...
template<class T >
jagged_array< T >	operator+ (jagged_array< T > const &input, jagged_array< T > const &operands)
	overload operator + to allow addition of jagged_array<T> operands to jagged_array in an element-dependent manner More...
template<class T >
void	operator-= (jagged_array< T > &input, T operand)
	overload operator -= to allow subtraction of T operand from all elements in jagged_array More...
template<class T >
void	operator-= (jagged_array< T > &input, utility::vector1< T > const &operands)
	overload operator -= to allow subtraction of vector1<T> operands from jagged_array in a column-dependent manner More...
template<class T >
void	operator-= (jagged_array< T > &input, jagged_array< T > const &operands)
	overload operator -= to allow subtraction of jagged_array<T> operands from jagged_array in an element-dependent manner More...
template<class T >
jagged_array< T >	operator- (jagged_array< T > const &input, T operand)
	overload operator - to allow subtraction of T operand from all elements in jagged_array More...
template<class T >
jagged_array< T >	operator- (jagged_array< T > const &input, utility::vector1< T > const &operands)
	overload operator - to allow subtraction of vector1<T> operands from jagged_array in a column-dependent manner More...
template<class T >
jagged_array< T >	operator- (jagged_array< T > const &input, jagged_array< T > const &operands)
	overload operator - to allow subtraction of jagged_array<T> operands from jagged_array in an element-dependent manner More...
template<class T >
void	operator*= (jagged_array< T > &input, T operand)
	overload operator *= to allow multiplication of all elements in jagged_array by T operand More...
template<class T >
void	operator*= (jagged_array< T > &input, utility::vector1< T > const &operands)
	overload operator *= to allow multiplication of jagged_array by vector1<T> operands in a column-dependent manner More...
template<class T >
void	operator*= (jagged_array< T > &input, jagged_array< T > const &operands)
	overload operator *= to allow multiplication of jagged_array by jagged_array<T> operands in an element-dependent manner More...
template<class T >
jagged_array< T >	operator* (jagged_array< T > const &input, T operand)
	overload operator * to allow multiplication of all elements in jagged_array by T operand More...
template<class T >
jagged_array< T >	operator* (jagged_array< T > const &input, utility::vector1< T > const &operands)
	overload operator * to allow multiplication of jagged_array by vector1<T> operands in a column-dependent manner More...
template<class T >
jagged_array< T >	operator* (jagged_array< T > const &input, jagged_array< T > const &operands)
	overload operator *= to allow multiplication of jagged_array by jagged_array<T> operands in an element-dependent manner More...
template<class T >
void	operator/= (jagged_array< T > &input, T operand)
	overload operator /= to allow division of all elements in jagged_array by T operand More...
template<class T >
void	operator/= (jagged_array< T > &input, utility::vector1< T > const &operands)
	overload operator /= to allow division of jagged_array by vector1<T> operands in a column-dependent manner More...
template<class T , class T_2 >
void	operator/= (jagged_array< T > &input, utility::vector1< T_2 > const &operands)
	overload operator /= to allow division of jagged_array by vector1<T> operands in a column-dependent manner More...
template<class T >
void	operator/= (jagged_array< T > &input, jagged_array< T > const &operands)
	overload operator /= to allow division of jagged_array by jagged_array<T> operands in an element-dependent manner More...
template<class T , class T_2 >
void	operator/= (jagged_array< T > &input, jagged_array< T_2 > const &operands)
	overload operator /= to allow division of jagged_array by jagged_array<T> operands in an element-dependent manner More...
template<class T >
jagged_array< T >	operator/ (jagged_array< T > const &input, T operand)
	overload operator / to allow division of all elements in jagged_array by T operand More...
template<class T >
jagged_array< T >	operator/ (jagged_array< T > const &input, utility::vector1< T > const &operands)
	overload operator / to allow division of jagged_array by vector1<T> operands in a column-dependent manner More...
template<class T >
jagged_array< T >	operator/ (jagged_array< T > const &input, jagged_array< T > const &operands)
	overload operator / to allow division of jagged_array by jagged_array<T> operands in an element-dependent manner More...
std::ostream &	operator<< (std::ostream &output, MeanField const &object_to_output)
std::ostream &	operator<< (std::ostream &output, ResHashMap const &object_to_output)
std::ostream &	operator<< (std::ostream &output, RotMatrix const &object_to_output)
std::ostream &	operator<< (std::ostream &output, RotProb const &object_to_output)

Typedef Documentation

AAMatrixCOP

typedef utility::pointer::shared_ptr< AAMatrix const > protocols::mean_field::AAMatrixCOP

AAMatrixOP

typedef utility::pointer::shared_ptr< AAMatrix > protocols::mean_field::AAMatrixOP

DesignMeanFieldCOP

typedef utility::pointer::shared_ptr< DesignMeanField const > protocols::mean_field::DesignMeanFieldCOP

DesignMeanFieldOP

typedef utility::pointer::shared_ptr< DesignMeanField > protocols::mean_field::DesignMeanFieldOP

EnergiesByTaskCalculatorCOP

typedef utility::pointer::shared_ptr< EnergiesByTaskCalculator const > protocols::mean_field::EnergiesByTaskCalculatorCOP

EnergiesByTaskCalculatorOP

typedef utility::pointer::shared_ptr< EnergiesByTaskCalculator > protocols::mean_field::EnergiesByTaskCalculatorOP

FlexBBDesignMeanFieldCOP

typedef utility::pointer::shared_ptr<FlexBBDesignMeanField const> protocols::mean_field::FlexBBDesignMeanFieldCOP

FlexBBDesignMeanFieldOP

typedef utility::pointer::shared_ptr<FlexBBDesignMeanField> protocols::mean_field::FlexBBDesignMeanFieldOP

FlexBBMeanFieldCOP

typedef utility::pointer::shared_ptr<FlexBBMeanField const> protocols::mean_field::FlexBBMeanFieldCOP

FlexBBMeanFieldOP

typedef utility::pointer::shared_ptr<FlexBBMeanField> protocols::mean_field::FlexBBMeanFieldOP

GenMeanFieldMoverCOP

typedef utility::pointer::shared_ptr< GenMeanFieldMover const > protocols::mean_field::GenMeanFieldMoverCOP

GenMeanFieldMoverOP

typedef utility::pointer::shared_ptr< GenMeanFieldMover > protocols::mean_field::GenMeanFieldMoverOP

jagged_array_bool

typedef jagged_array< bool > protocols::mean_field::jagged_array_bool

jagged_array_char

typedef jagged_array< char > protocols::mean_field::jagged_array_char

jagged_array_double

typedef jagged_array< double > protocols::mean_field::jagged_array_double

jagged_array_float

typedef jagged_array< float > protocols::mean_field::jagged_array_float

jagged_array_int

typedef jagged_array< int > protocols::mean_field::jagged_array_int

jagged_array_long

typedef jagged_array< long int > protocols::mean_field::jagged_array_long

jagged_array_longdouble

typedef jagged_array< long double > protocols::mean_field::jagged_array_longdouble

jagged_array_schar

typedef jagged_array< signed char > protocols::mean_field::jagged_array_schar

jagged_array_short

typedef jagged_array< short int > protocols::mean_field::jagged_array_short

jagged_array_size

typedef jagged_array< platform::Size > protocols::mean_field::jagged_array_size

jagged_array_size_t

typedef jagged_array< platform::Size > protocols::mean_field::jagged_array_size_t

jagged_array_ssize

typedef jagged_array< platform::SSize > protocols::mean_field::jagged_array_ssize

jagged_array_ssize_t

typedef jagged_array< platform::SSize > protocols::mean_field::jagged_array_ssize_t

jagged_array_uchar

typedef jagged_array< unsigned char > protocols::mean_field::jagged_array_uchar

jagged_array_uint

typedef jagged_array< unsigned int > protocols::mean_field::jagged_array_uint

jagged_array_ulong

typedef jagged_array< unsigned long int > protocols::mean_field::jagged_array_ulong

jagged_array_ushort

typedef jagged_array< unsigned short int > protocols::mean_field::jagged_array_ushort

MeanFieldCOP

typedef utility::pointer::shared_ptr< MeanField const > protocols::mean_field::MeanFieldCOP

MeanFieldOP

typedef utility::pointer::shared_ptr< MeanField > protocols::mean_field::MeanFieldOP

ResHashMapCOP

typedef utility::pointer::shared_ptr<ResHashMap const> protocols::mean_field::ResHashMapCOP

ResHashMapOP

typedef utility::pointer::shared_ptr<ResHashMap> protocols::mean_field::ResHashMapOP

RotMatrixCOP

typedef utility::pointer::shared_ptr< RotMatrix const > protocols::mean_field::RotMatrixCOP

RotMatrixOP

typedef utility::pointer::shared_ptr< RotMatrix > protocols::mean_field::RotMatrixOP

Function Documentation

add()

template<class T >

T protocols::mean_field::add ( T const &  operand_from_ja, T const &  other_operand  )

inline

implements add function using operator +=

class T must provide an operator +=

Referenced by protocols::wum::SilentStructStore::add(), protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::add(), core::fragment::FragSet::add(), protocols::multistage_rosetta_scripts::NoFailDataMap::add(), core::scoring::dssp::StrandPairingSet::add_pairing(), core::pack::guidance_scoreterms::sap::SapConstraintHelper::add_remove_rotamer(), core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::add_remove_rotamer(), core::pack::guidance_scoreterms::sap::SapConstraintHelper::add_remove_rotamer_fast(), core::pack::guidance_scoreterms::sap::SapConstraintHelper::add_remove_rotamer_lightning(), protocols::switches::GraftSwitchMover::all_threading_start_combinations(), core::pose::annotated_to_oneletter_sequence(), core::fragment::ConstantLengthFragSet::ConstantLengthFragSet(), protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD::evaluate_and_add(), core::fragment::FragSet::insert_fragID_list(), operator+=(), core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::PackerEnergyAdd(), protocols::anchored_design::AnchoredDesignMover::randomize_input_sequence(), protocols::simple_filters::ResidueDepthFilter::read_db(), core::fragment::MinimalFragSet::read_fragment_stream(), core::fragment::ConstantLengthFragSet::read_fragment_stream(), protocols::wum::SilentStructStore::read_from_cmd_line(), protocols::wum::SilentStructStore::read_from_stream(), core::chemical::ResidueTypeBase::report_adducts(), protocols::grafting::simple_movers::DeleteRegionMover::set_add_jump_on_rechain(), protocols::grafting::simple_movers::DeleteRegionMover::set_add_terminal_types_on_rechain(), and core::pack::guidance_scoreterms::sap::SapConstraintHelper::store_sasa_blocks().

arg_max()

template<class T >

jagged_array< T >::Size protocols::mean_field::arg_max

(

jagged_array< T > const &

input

)

find the index of the largest value in a jagged_array

class T must provide an operator < () and operator = ().

Error if input.size() == 0

References max().

Referenced by protocols::pack_daemon::VMax::active_variables(), protocols::pack_daemon::VMaxBy::active_variables(), core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::calculate_alt_state_hpatch_score(), protocols::toolbox::match_enzdes_util::LigandConformer::create_collcheck_ordering(), protocols::simple_moves::bb_sampler::SugarBBSampler::get_torsion(), and protocols::pack_daemon::VMaxBy::operator()().

arg_min()

template<class T >

jagged_array< T >::Size protocols::mean_field::arg_min

(

jagged_array< T > const &

input

)

find the index of the smallest value in a jagged_array

class T must provide an operator < () and operator = ().

Error if input.size() == 0

References min().

Referenced by protocols::pack_daemon::VMin::active_variables(), protocols::pack_daemon::VMinBy::active_variables(), protocols::constraint_generator::MetalContactsConstraintGenerator::apply(), protocols::make_rot_lib::RotData::get_min_cent_dist(), protocols::pack_daemon::VMinBy::operator()(), protocols::optimize_weights::DDGBindOptEData::process_score(), protocols::optimize_weights::NestedEnergyTermDDGMutationOptEData::process_score(), protocols::optimize_weights::PNatStructureOptEData::process_score(), protocols::optimize_weights::DDGMutationOptEData::process_score(), core::pack::rotamer_trials(), and core::pack::symmetric_rotamer_trials().

divide() [1/2]

template<class T >

T protocols::mean_field::divide ( T const &  operand_from_ja, T const &  other_operand  )

inline

implements divide function using operator /=

class T must provide an operator /=

Referenced by operator/=().

divide() [2/2]

template<class T , class T_2 >

T protocols::mean_field::divide ( T const &  operand_from_ja, T_2 const &  other_operand  )

inline

implements add function using operator +=

class T must provide an operator +=

allows division of class T by a different class T_2 (i.e. AAProb/Real)

max()

template<class T >

T protocols::mean_field::max

(

jagged_array< T > const &

input

)

Find the largest value in a jagged_array.

class T must provide an operator < () and operator = ().

Error if input.size() == 0

Referenced by protocols::noesy_assign::Resonance::_pmatch(), protocols::loops::loop_closure::ccd::RamaCheckBase::accept_new_conformation(), protocols::loops::Loops::add_loop(), protocols::sewing::data_storage::SmartAssembly::add_segment(), protocols::sewing::data_storage::HashedSmartAssembly::add_segment(), core::kinematics::FoldTree::add_vertex(), protocols::matdes::alignaxis(), protocols::sic_dock::alignaxis(), protocols::sic_dock::alignaxis_xform(), protocols::comparative_modeling::AlignmentClustering::AlignmentClustering(), protocols::antibody_legacy::AntibodyModeler::all_cdr_VL_VH_fold_tree(), core::scoring::Membrane_FAEmbed::allocate_appropriate_memory(), protocols::match::Bool3DGrid::and_with(), core::scoring::APBSConfig::APBSConfig(), core::scoring::hbonds::HBondSet::append_hbond(), protocols::abinitio::ResolutionSwitcher::apply(), protocols::analysis::LoopAnalyzerMover::apply(), protocols::cryst::SetCrystWeightMover::apply(), protocols::cryst::MakeLatticeMover::apply(), protocols::dna::SeparateDnaFromNonDna::apply(), protocols::docking::membrane::MPFindInterfaceMover::apply(), protocols::fold_from_loops::movers::SplitAndMixPoseMover::apply(), protocols::hybridization::CartesianHybridize::apply(), protocols::hybridization::CartesianSampler::apply(), protocols::ligand_docking::RigidSearchMover::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::ncbb::ResidueReplacementRebuildMover::apply(), protocols::protein_interface_design::movers::SetAtomTree::apply(), protocols::rbsegment_relax::OptimizeThreadingMover::apply(), protocols::recces::scratch::ThermalSamplingMover::apply(), protocols::relax::loop::LoopRelaxMover::apply(), protocols::rigid::RigidBodyDofPerturbMover::apply(), protocols::simple_moves::PSSM2BfactorMover::apply(), protocols::rbsegment_relax::SequenceShiftMover::apply(), protocols::antibody_legacy::LoopRlxMover::apply(), protocols::task_operations::SelectResiduesWithinChainOperation::apply(), protocols::cyclic_peptide::PeptideStubMover::apply(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::apply(), protocols::fold_from_loops::movers::SplitAndMixPoseMover::apply_without_merge(), protocols::rbsegment_relax::RBSegmentMover::applyTransformation(), protocols::rbsegment_relax::RBSegmentMover::applyTranslation(), arg_max(), core::scoring::MinScoreScoreFunction::assign(), core::scoring::motif::MotifHash::bin_index(), protocols::legacy_sewing::LegacyMonteCarloAssemblyMover::boltzman(), protocols::simple_moves::TorsionDOFMover::boltzmann(), protocols::moves::MonteCarlo::boltzmann(), protocols::monte_carlo::GenericMonteCarloMover::boltzmann(), protocols::forge::remodel::RemodelLoopMover::boost_closure_stage(), core::scoring::epr_deer::metrics::DEERDistanceBounds::bounds(), core::optimization::BrentLineMinimization::BRENT(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::build_Dmtrx(), protocols::LoopRebuild::build_loop_with_ccd_closure(), protocols::jd3::chunk_library::ChunkLibraryJobQueen::build_output_index(), protocols::jd3::standard::StandardJobQueen::build_output_index(), core::kinematics::ShortestPathInFoldTree::build_peptide_table(), protocols::loophash::LoopHashSampler::build_structures(), protocols::moves::ReplicaExchangeMC::build_temperature_list(), core::scoring::calc_per_atom_sasa(), core::scoring::sasa::LeGrandSasa::calculate(), protocols::ligand_docking::ga_ligand_dock::GridScorer::calculate_grid(), core::scoring::etable::Etable::calculate_hydrogen_atom_reach(), protocols::enzdes::EnzdesFlexibleRegion::calculate_rotamer_set_design_targets_partition_sum(), protocols::nmr::pcs::PCSEnergy::calculate_score_and_tensors_with_gridsearch(), protocols::nmr::pcs::PCSEnergy::calculate_score_and_tensors_with_spinlabel(), protocols::nmr::pre::PREEnergy::calculate_total_score(), core::optimization::cart_numerical_derivative_check(), core::scoring::CenRotEnvPairPotential::CenRotEnvPairPotential(), protocols::ub_e2c::ubi_e2c_modeler::centroid_mode_perturbation(), protocols::aa_composition::AddHelixSequenceConstraintsMover::check_lengths_sensible(), protocols::simple_moves::BackboneMover::check_rama(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::check_rama(), protocols::loops::Loop::choose_cutpoint(), core::scoring::nmr::NMRDummySpinlabelEnsemble::clash_check(), protocols::scoring::ImplicitFastClashCheck::clash_count(), protocols::antibody_legacy::CloseOneMover::close_one_loop_stem_helper(), protocols::abinitio::AbrelaxMover::close_with_idealization(), core::scoring::nmr::NMRSpinlabel::cluster_conformers_and_set_weights_and_coordinates(), protocols::environment::collect_dofs(), protocols::enzdes::DesignVsNativeComparison::compare_to_native(), protocols::simple_filters::Worst9merFilter::compute(), protocols::buns::BuriedUnsatHbondFilter2::compute(), protocols::score_filters::GeometryFilter::compute(), protocols::calc_taskop_filters::RotamerBoltzmannWeight::compute_boltz_probability(), core::scoring::packstat::compute_cav_ball_clusters(), protocols::simple_filters::SymmetricMotifFilter::compute_d2(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nls(), core::scoring::packstat::Slice::compute_events(), protocols::calc_taskop_filters::compute_max_probability(), core::scoring::MembranePotential::compute_membrane_embedding(), protocols::enzdes::EnzdesScorefileFilter::compute_metrics_for_residue_subset(), protocols::abinitio::PairingStatistics::compute_model_weights(), protocols::noesy_assign::PeakAssignmentResidueMap::compute_Nk(), core::scoring::nmr::pcs::PCSMultiSet::compute_score(), core::scoring::electron_density::ElectronDensity::computeCrystParams(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::computeCrystParams(), core::scoring::electron_density::ElectronDensity::computeStats(), core::scoring::power_diagram::PowerDiagram::construct_from_pose(), core::scoring::packstat::Octree2D::contains(), protocols::simple_moves::SaveProbabilitiesMetricMover::convert_probabilities_to_logits(), core::membrane::convex_hull(), core::scoring::epr_deer::metrics::DEERData::convolute(), core::scoring::constraints::count_constraint(), protocols::noesy_assign::CrossPeak::create_fa_and_cen_constraint(), protocols::ligand_docking::MinimizeBackbone::create_fold_tree_with_cutpoints(), core::pack::interaction_graph::InteractionGraphFactory::create_interaction_graph(), protocols::jumping::JumpSelector::create_jump_sample(), protocols::jumping::RandomSheetBuilder::create_new_random_topol(), core::pack::create_packer_graph(), core::energy_methods::IdealParametersDatabase::create_parameters_for_restype(), protocols::ligand_docking::Rotate::create_random_rotations(), protocols::mpi_refinement::MPI_Refine_Master::create_WUs(), protocols::cryst::crystRMSfast(), protocols::frag_picker::CS2ndShift::CS2ndShift(), core::optimization::LineMinimizationAlgorithm::cubic_interpolation(), core::kinematics::FoldTree::cut_edge(), core::kinematics::FoldTree::cutpoint_by_jump(), core::import_pose::RNA_DeNovoSetup::de_novo_setup_from_options(), protocols::magnesium::SampleGrid::define_bins(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::define_receptor_phores(), protocols::cryst::MakeLatticeMover::detect_connecting_subunits(), protocols::cryst::MakeLayerMover::detect_connecting_subunits(), core::scoring::lDDT_Calculator::determine_alt_states(), protocols::enzdes::EnzdesFlexBBProtocol::determine_flexible_regions(), protocols::qsar::scoring_grid::SingleGrid::diffuse_ring(), protocols::idealize::dihedral_distance(), protocols::ligand_docking::ga_ligand_dock::GridScorer::do_convolution_and_compute_coeffs(), protocols::abinitio::AbrelaxApplication::do_distributed_rerun(), protocols::jumping::SameStrand::do_same_strand(), protocols::optimize_weights::PNatLigPoseOptEData::do_score(), protocols::cartesian::MolecularDynamics::doMD(), protocols::noesy_assign::PeakAssignment::dump_weights(), core::scoring::epr_deer::DEERDataCache::edge(), core::scoring::electron_density::ElectronDensity::ElectronDensity(), core::io::silent::SilentStruct::energies_from_pose(), protocols::ligand_docking::ga_ligand_dock::RotamerPairEnergies::energy2b(), core::scoring::dna::DNA_BasePotential::eval_base_pair_derivative(), core::scoring::dna::DNA_BasePotential::eval_base_step_derivative(), core::energy_methods::PairEnergy::eval_residue_pair_derivatives(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_pair_deriv(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_pair_score(), core::scoring::SmoothEnvPairPotential::evaluate_pair_and_cenpack_deriv(), core::scoring::SmoothEnvPairPotential::evaluate_pair_and_cenpack_score(), core::scoring::packstat::Event::Event(), protocols::enzdes::EnzdesScorefileFilter::examine_pose(), core::scoring::epr_deer::metrics::DEERDistanceDistribution::expand_hists(), core::scoring::dssp::StrandPairing::extend(), protocols::LoopRebuild::extend_barcode_regions_if_chain_break(), protocols::simple_filters::ExternalEvaluator::ExternalEvaluator(), core::import_pose::figure_out_dock_domain_map(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::figure_out_first_res_in_pose(), core::scoring::rna::RNA_SuitePotential::figure_out_offset(), core::scoring::rna::TNA_SuitePotential::figure_out_offset(), core::scoring::Energies::fill_point_graph(), core::scoring::solid_surface::SurfaceEnergies::fill_point_graph(), core::scoring::symmetry::SymmetricEnergies::fill_point_graph(), protocols::nmr::pcs::PCSLigandTransformMover::find_best_ligand_pose_with_grid_search(), protocols::fold_from_loops::utils::find_cutpoint_from_secondary_structure(), core::membrane::find_farthest(), protocols::ligand_docking::LigandBaseProtocol::find_interface_backbone(), core::conformation::find_neighbors_3dgrid(), core::conformation::find_neighbors_3dgrid_restricted(), core::conformation::find_neighbors_octree(), core::conformation::find_neighbors_octree_restricted(), protocols::pockets::PlaidFingerprint::find_optimal_rotation(), core::scoring::nmr::pre::PREMultiSet::find_para_ion_position_and_compute_pre_score(), protocols::nonlocal::find_regions_with_minimum_size(), protocols::electron_density::findLoopFromDensity(), protocols::pockets::PocketGrid::findPockets(), protocols::pockets::PocketGrid::findPSP(), protocols::pockets::PocketGrid::findSPS(), core::pose::fix_up_residue_type_variants(), protocols::abinitio::AbrelaxApplication::fold(), protocols::stepwise::legacy::modeler::rna::full_length_rmsd_over_residue_list(), protocols::ub_e2c::ubi_e2c_modeler::fullatom_mode_perturbation(), protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::gap_size_to_anchor(), protocols::abinitio::IterativeBase::gen_cen2fullatom(), protocols::abinitio::IterativeBase::gen_cen2fullatom_non_pool_decoys(), protocols::abinitio::IterativeBase::gen_diversity_pool(), protocols::abinitio::IterativeFullatom::gen_resample_core(), protocols::abinitio::IterativeBase::gen_resample_stage2(), protocols::sewing::movers::AssemblyMover::generate_assembly(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::generate_window_list(), protocols::inverse_folding::get_angles(), protocols::sewing::hashing::BasisMapGenerator::get_basis_res_bounds(), protocols::sic_dock::get_bounds_intersection(), core::conformation::symmetry::get_chain2range(), core::pose::full_model_info::get_chain_connections(), core::scoring::PolymerBondedEnergyContainer::get_computed(), core::pose::full_model_info::get_connection_domains(), core::scoring::PolymerBondedEnergyContainer::get_energy(), protocols::fldsgn::potentials::sspot::get_foldtree_seqsep(), core::scoring::SecondaryStructurePotential::get_foldtree_seqsep(), core::kinematics::get_foldtree_which_partitions(), protocols::frags::VallData::get_frags(), core::kinematics::TreeVizBuilder::get_ft_node_bounds(), protocols::magnesium::MgWaterHydrogenPacker::get_heuristic_water_hydrogen_score(), core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid::get_indices_of_voxel_from_coordinates(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_intramolecular_split_move_elements(), protocols::kinematic_closure::ClosureSolution::get_jacobian(), protocols::stepwise::sampler::rna::RNA_KinematicCloser::get_jacobian(), core::conformation::carbohydrates::GlycanTreeSet::get_largest_glycan_tree_layer(), core::conformation::carbohydrates::GlycanTreeSet::get_largest_glycan_tree_length(), core::conformation::carbohydrates::get_largest_glycan_tree_size(), protocols::stepwise::modeler::StepWiseConnectionSampler::get_max_ntries(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::get_movable_scs(), protocols::jd2::FileSystemJobDistributor::get_new_job_id(), protocols::cryst::WallpaperGroup::get_nsubdivisions(), protocols::cryst::Spacegroup::get_nsubdivisions(), core::energy_methods::IntermolEnergy::get_num_chains_frozen(), protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::get_pair_dist(), core::scoring::epr_deer::metrics::DEERDistanceDistribution::get_prs(), protocols::electron_density::DockPDBIntoDensityMover::get_radius(), protocols::electron_density::get_radius(), protocols::electron_density::get_rot_angle(), core::scoring::epr_deer::metrics::DEERChiSqMethod::get_score(), core::scoring::epr_deer::metrics::DEERDistanceBounds::get_score(), core::scoring::epr_deer::metrics::DEERJaccardMethod::get_score(), core::scoring::epr_deer::metrics::DEERMiscMethod::get_score(), core::scoring::epr_deer::metrics::DEEROverlapMethod::get_score(), core::scoring::hbonds::get_ssdep_weight(), core::import_pose::get_tree(), protocols::rbsegment_relax::RBSegmentMover::getCoM(), core::scoring::electron_density::ElectronDensity::getPhaseError(), core::chemical::gasteiger::GetPossibleTypesForAtom(), protocols::loops::Loops::grow_loop(), core::fragment::SecondaryStructure::helix_fraction(), core::scoring::packstat::CavityBall::hetero_atom_line(), protocols::frag_picker::quota::ABEGO_SS_Config::highest_probability(), protocols::recces::Histogram::Histogram(), core::scoring::epr_deer::EPRSpinLabel::histogram(), protocols::seeded_abinitio::SegmentHybridizer::hybridize(), protocols::loops::idealize_loop(), protocols::rna::movers::identify_chunks(), core::scoring::SecondaryStructurePotential::identify_ss(), core::scoring::bin_transitions::BinTransitionData::in_bin(), protocols::forge::remodel::RemodelLoopMover::independent_stage(), protocols::simple_filters::SheetFilter::ingo_proper_sheets(), protocols::antibody::H3RefineCCD::init(), protocols::scoring::ImplicitFastClashCheck::init_clash_check(), protocols::ub_e2c::ubi_e2c_modeler::init_k48r_perturbation(), core::scoring::epr_deer::Simulated4PDEERTraceFactory::initial_search(), protocols::recces::RECCES_Mover::initialize(), core::scoring::loop_graph::evaluator::GaussianChainFuncPotentialEvaluator::initialize(), protocols::abinitio::abscript::RigidChunkCM::initialize(), core::scoring::packing::initialize_AtomID_Map(), protocols::topology_broker::RigidChunkClaimer::initialize_dofs(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::initialize_graph_for_packing(), protocols::ligand_docking::ga_ligand_dock::GAOptimizer::initialize_rotamer_set_and_scores(), protocols::vardist_solaccess::VarSolDistSasaCalculator::initialize_sasa_arrays(), core::id::SequenceMapping::insert_aligned_residue_safe(), protocols::simple_moves::DOFHistogramRecorder::insert_dofs_by_residue(), protocols::features::PdbDataFeatures::insert_residue_pdb_confidence_rows(), core::membrane::inside_boundaries(), core::membrane::intersect(), core::io::mmtf::is_in_bondAtomList(), protocols::ligand_docking::ga_ligand_dock::GridScorer::is_residue_in_grid(), protocols::sewing::data_storage::SmartAssembly::iterate_over_basis_pairs(), protocols::jd3::LarvalJob::job_tag_with_index_suffix(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::just_simple_cycles(), core::scoring::fiber_diffraction::OneGaussianScattering::k(), protocols::loops::Loop::length(), core::energy_methods::LinearBranchEnergy::LinearBranchEnergy(), core::energy_methods::LinearChainbreakEnergy::LinearChainbreakEnergy(), core::scoring::lkball::LK_BallEnergy::LK_BallEnergy(), core::scoring::epr_deer::ln(), protocols::jobdist::load_s_and_l(), core::scoring::dna::DNA_EnvPairPotential::load_score_tables(), protocols::antibody_legacy::CDRH3Modeler::loop_centroid_relax(), protocols::antibody_legacy::CDRH3Modeler::loop_fa_relax(), protocols::frag_picker::scores::MakeFragmentChunkCrms::make(), protocols::sic_dock::XfoxmScore::makebinary(), protocols::loophash::LoopHashRelaxProtocol::manual_call(), protocols::pockets::ComparisonGrid::mark(), protocols::pockets::PocketGrid::mark(), protocols::pockets::ElectrostaticpotentialGrid::mark_atom_espGrid_points(), core::scoring::electron_density::ElectronDensity::matchCentroidPose(), core::scoring::electron_density::ElectronDensity::matchRes(), core::pack::interaction_graph::RotamerDots::max_atom_radius(), protocols::sasa_scores::PPoly::max_degree(), core::sequence::SequenceAlignment::max_gap_percentage(), core::scoring::motif::XformScore::max_score(), protocols::noesy_assign::CrossPeak::max_volume_contribution(), core::scoring::dssp::StrandPairing::merge(), protocols::helical_bundle_predict::HBPHelixAssignments::merge_helices(), core::scoring::epr_deer::min_max(), protocols::simple_moves::DEEROptimizeCoordsMover::minimize(), core::optimization::BrentLineMinimization::MNBRAK(), protocols::loop_build::LoopMover_SlidingWindow::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves::model_loop(), protocols::forge::build::SegmentInsert::modify_impl(), protocols::forge::build::SegmentRebuild::modify_impl(), core::scoring::etable::Etable::modify_pot_one_pair(), protocols::ub_e2c::ubi_e2c_modeler::monoub_centroid_mode_perturbation(), protocols::ub_e2c::ubi_e2c_modeler::monoub_first_perturbation(), protocols::ub_e2c::ubi_e2c_modeler::monoub_fullatom_mode_perturbation(), protocols::frag_picker::quota::ABEGO_SS_Config::most_probable_bin(), protocols::electron_density::BfactorMultifunc::multivec2poseBfacts(), protocols::splice::neighbors_in_vector(), protocols::noesy_assign::PeakAssignmentResidueMap::network_analysis2(), protocols::pockets::PocketGrid::newSearch(), core::optimization::numerical_derivative_check(), core::optimization::symmetry::numerical_derivative_check(), protocols::canonical_sampling::SilentTrajectoryRecorder::observe_after_metropolis(), protocols::pack_daemon::VMax::operator()(), protocols::relax::LocalRelax::optimization_loop(), protocols::ub_e2c::ubi_e2c_modeler::optimize_cov_bond(), protocols::ligand_docking::LigandDockProtocol::optimize_orientation3(), protocols::optimize_weights::IterativeOptEDriver::optimize_weights(), protocols::match::Bool3DGrid::or_with(), protocols::stepwise::StepWiseSampleAndScreen::output_counts(), protocols::rna::denovo::output::RNA_FragmentMonteCarloOutputter::output_jump_information(), core::fragment::ConstantLengthFragSet::overlapping_with_region(), core::scoring::constraints::AngleConstraint::p1_theta_deriv(), protocols::ligand_docking::ga_ligand_dock::GridScorer::packer_loop(), protocols::pdbinfo_manipulations::pad_sequences(), core::scoring::PairEPotential::pair_term_energy(), core::scoring::epr_deer::DEERIO::parse_dist_lines(), protocols::monte_carlo::GenericMonteCarloMover::parse_my_tag(), protocols::motif_grafting::movers::MotifGraftMover::parse_my_tag(), protocols::recon_design::FitnessFilter::parse_my_tag(), core::kinematics::FoldTree::partition_by_residue(), core::pose::symmetry::partition_by_symm_jumps(), protocols::simple_moves::sidechain_moves::SidechainMCMover::pass_metropolis(), protocols::canonical_sampling::SidechainMetropolisHastingsMover::pass_metropolis(), protocols::noesy_assign::PeakAssignment::peak_volume(), core::scoring::ScoreFunction::perturb_weights(), protocols::stepwise::modeler::rna::phosphate_base_phosphate_rmsd(), protocols::kinematic_closure::pivot_pickers::StandardPivots::pick(), protocols::abinitio::Template::pick_large_frags(), protocols::kinmatch::KinFunGroupTK::place_c(), protocols::kinmatch::KinFunGroupTK::place_h(), core::conformation::Residue::polymeric_oriented_sequence_distance(), protocols::ligand_docking::ga_ligand_dock::GridScorer::prepare_grid(), core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::prepare_score_data(), protocols::wum::WorkUnitBase::print(), protocols::make_rot_lib::MakeRotLibMover::print_dunbrack02_rotlib(), protocols::make_rot_lib::MakeRotLibMover::print_dunbrack10_rotlib(), core::io::raw_data::RawStruct::print_header(), protocols::stepwise::modeler::rna::print_heavy_atoms(), core::scoring::motif::XformScore::print_quantiles(), protocols::make_rot_lib::MakeRotLibMover::print_rot_data(), core::io::silent::SilentStruct::print_score_header(), core::io::raw_data::RawStruct::print_scores(), protocols::rna::movers::ErraserMinimizerMover::process_entire_pose(), protocols::optimize_weights::PNatStructureOptEData::process_score(), protocols::motif_grafting::movers::MotifGraftMover::provide_xml_schema(), protocols::recon_design::FitnessFilter::provide_xml_schema(), core::fragment::MinimalFragSet::read_fragment_stream(), core::fragment::ConstantLengthFragSet::read_fragment_stream(), protocols::rna::setup::RNA_CSA_JobDistributor::read_in_silent_file(), core::scoring::Ramachandran::read_rama_map_file(), core::scoring::Ramachandran::read_rama_map_file_shapovalov(), protocols::frag_picker::CS2ndShift::read_sslimit_table(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::readMRCandResize(), core::scoring::electron_density::ElectronDensity::readMRCandResize(), core::scoring::motif::real_to_uint16(), core::scoring::motif::real_to_uint8(), core::kinematics::FoldTree::reorder(), protocols::ligand_docking::LigandBaseProtocol::reorder_foldtree_around_mobile_regions(), core::pose::reorder_root_partition_res(), protocols::features::ModelFeatures::report_features(), protocols::match::BumpGrid::required_separation_distance(), core::scoring::electron_density::resample(), core::scoring::electron_density::ElectronDensity::rescale_fastscoring_temp_bins(), protocols::simple_moves::AtomHash::reset_and_get_clusters(), core::grid::CartGrid< T >::reset_boundaries(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::resize(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::reverse_delete_move(), protocols::stepwise::modeler::rna::rmsd_over_residue_list(), core::optimization::JJH_Minimizer::run(), protocols::jumping::JumpSample::safe_secstruct(), protocols::jumping::safe_secstruct(), core::import_pose::RNA_JumpMover::sample_alternative_chain_connection(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::sample_loops(), protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::sample_loops(), protocols::simple_moves::DEEROptimizeCoordsMover::score(), protocols::enzdes::EnzdesJobOutputter::scorefile(), core::pose::symmetry::sealed_symmetric_fold_tree(), protocols::pockets::PlaidFingerprint::search_random_poses(), core::fragment::SecondaryStructure::secstruct(), protocols::LoopRebuild::select_one_loop(), protocols::moves::PyMOLMover::send_energy(), protocols::features::helixAssembly::HelicalFragment::seq_end(), protocols::frag_picker::scores::sequencealign(), protocols::recces::sampler::MC_OneTorsion::set_angle_range(), protocols::vardist_solaccess::VarSolDistSasaCalculator::set_atom_type_radii(), core::scoring::PolymerBondedEnergyContainer::set_computed(), protocols::rbsegment_relax::set_constraints(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::set_constraints(), protocols::loops::loop_closure::ccd::LoopClosure::set_cycles(), protocols::qsar::scoring_grid::SingleGrid::set_distance_sphere_for_atom(), core::scoring::PolymerBondedEnergyContainer::set_energy(), protocols::loops::loop_mover::LoopMover::set_extended_torsions(), protocols::loops::set_extended_torsions(), protocols::abinitio::KinematicTaskControl::set_extended_torsions_and_idealize_loops(), core::conformation::symmetry::set_fold_tree_from_symm_data(), protocols::hbnet::HBNet::set_max_networks_size(), protocols::hbnet::HBNet::set_max_unsat(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::set_mcfi(), protocols::fold_from_loops::movers::SplitAndMixPoseMover::set_order(), protocols::rbsegment_relax::set_rb_constraints(), protocols::qsar::scoring_grid::SingleGrid::set_ring(), protocols::qsar::scoring_grid::SingleGrid::set_score_sphere_for_atom(), core::pack::interaction_graph::NPDHBSimpleInteractionGraph::set_scorefunction(), protocols::ligand_docking::set_sphere(), protocols::nonlocal::StarTreeBuilder::set_up(), core::scoring::epr_deer::DEERDataCache::set_up_residues(), core::scoring::lkball::LK_BallEnergy::setup_d2_bounds(), core::scoring::lkball::LK_DomeEnergy::setup_d2_bounds(), protocols::rbsegment_relax::setup_disconnected(), core::kinematics::FoldTree::setup_edge_counts(), core::scoring::electron_density::ElectronDensity::setup_fastscoring_first_time(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::setup_fold_tree(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_legacy(), protocols::flexpep_docking::FlexPepDockingProtocol::setup_foldtree(), core::energy_methods::FaMPEnvEnergy::setup_for_fullatom(), core::energy_methods::FaMPSolvEnergy::setup_for_fullatom(), core::pack::annealer::SimAnnealerBase::setup_iterations(), core::import_pose::setup_jumps(), protocols::star::StarAbinitio::setup_kinematics(), protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::setup_obligate_pair(), protocols::rbsegment_relax::setup_pose_rbsegs_keep_loops(), protocols::canonical_sampling::ParallelTempering::shuffle_temperatures(), core::scoring::epr_deer::sigmoid(), core::sequence::simple_mapping_from_file(), core::optimization::simple_numeric_deriv_check(), protocols::forge::remodel::RemodelLoopMover::simultaneous_stage(), protocols::stepwise::modeler::slice(), protocols::sic_dock::SICFast::slide_into_contact(), core::kinematics::FoldTree::slide_jump(), core::scoring::etable::MembEtable::smooth_etables(), core::scoring::etable::Etable::smooth_etables_one_pair(), core::scoring::SmoothEnvPairPotential::SmoothEnvPairPotential(), protocols::minimization_packing::GreenPacker::split_pose_into_groups(), protocols::rbsegment_relax::ConfChangeMover::stage2(), core::scoring::epr_deer::metrics::DEERData::stdev(), protocols::protein_interface_design::movers::PlaceStubMover::StubMinimize(), protocols::match::Bool3DGrid::subtract(), protocols::stepwise::modeler::rna::suite_rmsd(), protocols::splice::RBOutMover::superimpose_source_on_pose(), core::energy_methods::ResidualDipolarCouplingEnergy_Rohl::svdcmp(), core::util::switch_to_centroid_rot_set(), core::conformation::symmetry::symmetrize_fold_tree(), protocols::motif_grafting::movers::MotifGraftMover::test_epigraft_and_contextStructure_clashes(), protocols::optimize_weights::IterativeOptEDriver::test_weight_sensitivity(), protocols::pockets::CCluster::testNeighbor(), protocols::pockets::PCluster::testNeighbor(), core::scoring::trie::trie_vs_trie(), core::scoring::motif::uint16_to_real(), core::scoring::motif::uint8_to_real(), protocols::simple_moves::uniform_dof_distribution(), protocols::jobdist::universal_main(), protocols::hybridization::HybridizeFoldtreeDynamic::update(), core::pack::task::PackerTask_::update_commutative(), core::pack::task::ResidueLevelTask_::update_commutative(), core::conformation::symmetry::SymmetryInfo::update_contiguous_monomers(), core::kinematics::FoldTree::update_cutpoints(), core::import_pose::update_fixed_domain_from_extra_minimize_jump_pairs(), core::pack::task::ResidueLevelTask_::update_intersection(), core::kinematics::FoldTree::update_jump_points(), protocols::mpi_refinement::MultiObjective::update_library_seeds(), core::kinematics::FoldTree::update_nres(), core::kinematics::FoldTree::update_num_jump(), core::pack::task::ResidueLevelTask_::update_union(), core::scoring::DenseNeighborIterator::upper_neighbor_id(), core::scoring::DenseNeighborConstIterator::upper_neighbor_id(), protocols::loops::Loops::verify_against(), protocols::features::StructureFeatures::write_schema_to_db(), protocols::abinitio::abscript::RigidChunkCM::yield_claims(), protocols::loops::loop_mover::LoopCM::yield_claims(), and core::optimization::StrongWolfeLineMinimization::zoom().

min()

template<class T >

T protocols::mean_field::min

(

jagged_array< T > const &

input

)

Find the smallest value in a jagged_array.

class T must provide an operator < () and operator = ().

Error if input.size() == 0

Referenced by core::io::silent::SilentFileData::_read_file(), protocols::mpi_refinement::add_init_dev_penalty(), protocols::loops::Loops::add_loop(), protocols::sewing::hashing::AlignmentFileGeneratorMover::add_pose_segments_to_segment_vector(), protocols::simple_moves::AddCavitiesMover::add_suckers(), core::kinematics::FoldTree::add_vertex(), protocols::matdes::alignaxis(), protocols::sic_dock::alignaxis(), protocols::sic_dock::alignaxis_xform(), protocols::antibody_legacy::AntibodyModeler::all_cdr_VL_VH_fold_tree(), protocols::match::Bool3DGrid::and_with(), core::scoring::motif::angle_distance(), core::scoring::APBSConfig::APBSConfig(), protocols::ligand_docking::LigandDockProtocol::append_ligand_docking_scores(), protocols::simple_filters::ChiWellRmsdEvaluator::apply(), protocols::abinitio::AbrelaxMover::apply(), protocols::abinitio::KinematicAbinitio::apply(), protocols::dna::SeparateDnaFromNonDna::apply(), protocols::hybridization::CartesianHybridize::apply(), protocols::hybridization::CartesianSampler::apply(), protocols::ligand_docking::RigidSearchMover::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::ncbb::ResidueReplacementRebuildMover::apply(), protocols::protein_interface_design::movers::SetAtomTree::apply(), protocols::rbsegment_relax::OptimizeThreadingMover::apply(), protocols::recces::scratch::ThermalSamplingMover::apply(), protocols::rigid::RigidBodyDofPerturbMover::apply(), protocols::simple_moves::PSSM2BfactorMover::apply(), protocols::rbsegment_relax::SequenceShiftMover::apply(), protocols::task_operations::RestrictToAlignedSegmentsOperation::apply(), protocols::loops::loop_closure::ccd::LoopClosure::apply(), protocols::fold_from_loops::constraint_generator::AutomaticSheetConstraintGenerator::apply(), protocols::protein_interface_design::movers::PatchdockTransform::apply(), protocols::splice::Splice::apply(), protocols::switches::GraftSwitchMover::apply(), protocols::hybridization::CartesianHybridize::apply_frag(), protocols::rbsegment_relax::RBSegmentMover::applyTransformation(), protocols::rbsegment_relax::RBSegmentMover::applyTranslation(), arg_min(), protocols::abinitio::abscript::AbscriptLoopCloserCM::attempt_ccd(), core::pack::interaction_graph::auto_use_linmem_ig(), protocols::moves::MonteCarlo::autotemp_reject(), protocols::ddg::ddGMover::average_score_components(), protocols::LoopRebuild::barcode_extend_stems(), protocols::sewing::hashing::LigandBindingResPlacer::best_rotamer_for_residue(), protocols::legacy_sewing::LegacyMonteCarloAssemblyMover::boltzman(), protocols::moves::MonteCarlo::boltzmann(), protocols::monte_carlo::GenericMonteCarloMover::boltzmann(), protocols::forge::remodel::RemodelLoopMover::boost_closure_stage(), core::scoring::epr_deer::metrics::DEERDistanceBounds::bounds(), core::optimization::BrentLineMinimization::BRENT(), protocols::sic_dock::brute_mindis(), protocols::LoopRebuild::build_loop_with_ccd_closure(), core::kinematics::ShortestPathInFoldTree::build_peptide_table(), protocols::LoopRebuild::build_random_loops(), core::scoring::CA_or_equiv_rmsd(), core::scoring::CA_rmsd(), core::scoring::electron_density::ElectronDensity::calcRhoC(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::calculate_ccd_angle(), core::scoring::facts::FACTSPotential::calculate_GBpair_v1trunk(), protocols::abinitio::abscript::AbscriptMover::calculate_iterations(), protocols::enzdes::EnzdesFlexibleRegion::calculate_rotamer_set_design_targets_partition_sum(), protocols::nmr::pcs::PCSEnergy::calculate_score_and_tensors_with_spinlabel(), protocols::noesy_assign::CrossPeak::calibrate(), core::optimization::cart_numerical_derivative_check(), protocols::sic_dock::cb_weight(), core::scoring::CenRotEnvPairPotential::CenRotEnvPairPotential(), protocols::ub_e2c::ubi_e2c_modeler::centroid_mode_perturbation(), protocols::hybridization::HybridizeProtocol::check_and_create_fragments(), protocols::sparta::Sparta::check_pose(), core::scoring::packstat::check_surface_area_leerichards_deriv(), core::scoring::nmr::NMRDummySpinlabelEnsemble::clash_check(), protocols::scoring::ImplicitFastClashCheck::clash_count(), protocols::abinitio::AbrelaxMover::close_with_idealization(), protocols::environment::collect_dofs(), protocols::fldsgn::filters::HelixBendFilter::compute(), protocols::score_filters::GeometryFilter::compute(), core::scoring::packstat::compute_cav_ball_clusters(), protocols::abinitio::IterativeBase::compute_cores(), core::scoring::packstat::Slice::compute_derivatives(), core::scoring::ResidualDipolarCoupling::compute_dipscore(), core::scoring::ResidualDipolarCoupling::compute_dipscore_nls(), core::scoring::packstat::Slice::compute_events(), core::scoring::MembranePotential::compute_membrane_embedding(), protocols::calc_taskop_filters::compute_min_probability(), protocols::esm_perplexity::PseudoPerplexityMetric::compute_perplexity(), core::scoring::packstat::compute_sasa(), core::scoring::nmr::pcs::PCSMultiSet::compute_score(), core::scoring::electron_density::ElectronDensity::computeCrystParams(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::computeCrystParams(), core::scoring::electron_density::ElectronDensity::computeStats(), core::scoring::power_diagram::PowerDiagram::construct_from_pose(), core::scoring::packstat::Octree2D::contains(), protocols::simple_moves::SaveProbabilitiesMetricMover::convert_probabilities_to_logits(), core::membrane::convex_hull(), core::conformation::copy_residue_coordinates_and_rebuild_missing_atoms(), protocols::abinitio::AbrelaxApplication::copy_structure(), protocols::ligand_docking::MinimizeBackbone::create_fold_tree_with_cutpoints(), protocols::abinitio::TemplateJumpSetup::create_jump_sample(), protocols::jumping::JumpSelector::create_jump_sample(), protocols::loophash::MPI_LoopHashRefine_Master::create_loophash_WUs(), protocols::frag_picker::CS2ndShift::CS2ndShift(), core::kinematics::FoldTree::cut_edge(), core::kinematics::FoldTree::cutpoint_by_jump(), core::scoring::electron_density::ElectronDensity::dCCdBs(), protocols::ddG_main(), core::import_pose::RNA_DeNovoSetup::de_novo_setup_from_options(), protocols::magnesium::SampleGrid::define_bins(), protocols::electron_density::density_grid_search(), core::scoring::lDDT_Calculator::determine_alt_states(), protocols::enzdes::EnzdesFlexBBProtocol::determine_flexible_regions(), protocols::electron_density::VoxelSpacingMultifunc::dfunc(), core::scoring::func::MinMultiHarmonicFunc::dfunc(), protocols::qsar::scoring_grid::SingleGrid::diffuse_ring(), protocols::stepwise::modeler::StepWiseMinimizer::do_clustering(), protocols::ligand_docking::ga_ligand_dock::GridScorer::do_convolution_and_compute_coeffs(), protocols::frag_picker::scores::do_one_line(), protocols::rna::denovo::movers::RNA_DeNovoMasterMover::do_random_moves(), protocols::jumping::SameStrand::do_same_strand(), protocols::optimize_weights::PNatLigPoseOptEData::do_score(), protocols::abinitio::FoldConstraints::do_stage1_cycles(), core::scoring::epr_deer::DEERDataCache::edge(), core::scoring::electron_density::ElectronDensity::ElectronDensity(), protocols::ligand_docking::ga_ligand_dock::RotamerPairEnergies::energy2b(), protocols::ligand_docking::ga_ligand_dock::LigandAligner::estimate_nstruct_sample(), core::scoring::dna::DNA_BasePotential::eval_base_pair_derivative(), core::scoring::dna::DNA_BasePotential::eval_base_step_derivative(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_env_and_cbeta_deriv(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_env_and_cbeta_score(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_pair_deriv(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_pair_score(), core::scoring::SmoothEnvPairPotential::evaluate_pair_and_cenpack_deriv(), core::scoring::SmoothEnvPairPotential::evaluate_pair_and_cenpack_score(), core::scoring::packstat::Event::Event(), protocols::jd3::chunk_library::ChunkLibraryJobQueen::expand_job_list(), protocols::jd3::full_model::FullModelJobQueen::expand_job_list(), protocols::jd3::standard::StandardJobQueen::expand_job_list(), core::scoring::electron_density::ElectronDensity::expandToUnitCell(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::expandToUnitCell(), core::scoring::dssp::StrandPairing::extend(), core::pose::symmetry::extract_asymmetric_unit_pdb_info(), protocols::ligand_docking::ga_ligand_dock::GridScorer::fast_get_lk_fractional_contribution(), protocols::ligand_docking::ga_ligand_dock::GridScorer::fast_get_lkbr_fractional_contribution(), protocols::stepwise::modeler::figure_out_root_and_moving_partition_res(), protocols::pockets::PocketGrid::fill(), core::scoring::EnvPairPotential::fill_cenlist(), core::io::silent::BinarySilentStruct::fill_pose(), core::io::silent::ProteinSilentStruct_Template< T >::fill_pose(), core::scoring::fill_rmsd_coordinates(), protocols::pockets::PocketGrid::fillTargetPockets(), core::membrane::find_closest(), protocols::ligand_docking::LigandBaseProtocol::find_interface_backbone(), core::conformation::find_neighbors_3dgrid(), core::conformation::find_neighbors_3dgrid_restricted(), core::conformation::find_neighbors_octree(), core::conformation::find_neighbors_octree_restricted(), protocols::ligand_docking::ga_ligand_dock::Pharmacophore::find_type_matches(), protocols::electron_density::findLoopFromDensity(), core::pose::fix_up_residue_type_variants(), protocols::loops::fix_with_coord_cst(), protocols::abinitio::AbrelaxApplication::fold(), protocols::splice::Splice::fold_tree(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::fragments(), protocols::ub_e2c::ubi_e2c_modeler::fullatom_mode_perturbation(), core::scoring::func::MinMultiHarmonicFunc::func(), core::scoring::func::MixtureFunc::func(), core::scoring::func::SoedingFunc::func(), core::scoring::func::MixtureFunc::func_(), protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters::gap_size_to_anchor(), protocols::enzdes::EnzdesFlexBBProtocol::generate_alc_ensemble_for_region(), protocols::legacy_sewing::LegacyGreedyAssemblyMover::generate_assembly(), protocols::sewing::movers::AssemblyMover::generate_assembly(), protocols::switches::GraftSwitchMover::get_additional_output(), core::energy_methods::GoapEnergy::get_angle_score(), protocols::inverse_folding::get_angles(), protocols::ligand_docking::ga_ligand_dock::get_atomic_contacting_sidechains(), protocols::sewing::hashing::BasisMapGenerator::get_basis_res_bounds(), protocols::sic_dock::get_bounds_intersection(), protocols::vip::VIP_Mover::get_cav_approx(), protocols::antibody::clusters::CDRClusterMatcher::get_cdr_cluster(), core::conformation::symmetry::get_chain2range(), protocols::frags::VallData::get_cheating_frags(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::get_chi_weight(), protocols::antibody::clusters::CDRClusterMatcher::get_closest_cluster(), core::scoring::PolymerBondedEnergyContainer::get_computed(), core::pose::full_model_info::get_connection_domains(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::get_contacting_reslist(), core::scoring::get_damped_scale_factors(), core::scoring::get_damped_scale_factors_with_derivs(), core::scoring::PolymerBondedEnergyContainer::get_energy(), protocols::loops::loop_closure::kinematic_closure::NeighborDependentTabooSamplingKinematicPerturber::get_entries_per_torsion_bin(), core::scoring::dna::DNA_EnvPairPotential::get_env_nbr_bin(), protocols::fldsgn::potentials::sspot::get_foldtree_seqsep(), core::scoring::SecondaryStructurePotential::get_foldtree_seqsep(), core::kinematics::get_foldtree_which_partitions(), protocols::frags::VallData::get_frags(), core::kinematics::TreeVizBuilder::get_ft_node_bounds(), core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid::get_indices_of_voxel_from_coordinates(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::get_intramolecular_split_move_elements(), protocols::vip::VIP_Mover::get_neighbors(), protocols::fold_from_loops::utils::Nub::get_nub_pieces(), protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::get_pair_dist(), protocols::electron_density::get_rot_angle(), core::scoring::epr_deer::metrics::DEERChiSqMethod::get_score(), core::scoring::epr_deer::metrics::DEERJaccardMethod::get_score(), core::scoring::epr_deer::metrics::DEERJSMethod::get_score(), core::scoring::epr_deer::metrics::DEERMiscMethod::get_score(), core::scoring::epr_deer::metrics::DEEROverlapMethod::get_score(), core::conformation::carbohydrates::GlycanTreeSet::get_smallest_glycan_tree_layer(), core::scoring::hbonds::get_ssdep_weight(), core::import_pose::get_tree(), core::pack::interaction_graph::NPDHBondNode< V, E, G >::get_upper_npd_hbond_energy_totals(), core::pack::interaction_graph::NPDHBondBackgroundNode< V, E, G >::get_upper_npd_hbond_energy_totals(), protocols::simple_moves::ExplicitWaterMover::get_water_recovery(), protocols::rbsegment_relax::RBSegmentMover::getCoM(), core::scoring::electron_density::ElectronDensity::getFSC(), core::scoring::electron_density::ElectronDensity::getIntensities(), core::scoring::electron_density::ElectronDensity::getPhaseError(), core::chemical::gasteiger::GetPossibleTypesForAtom(), core::scoring::electron_density::ElectronDensity::getResolutionBins(), protocols::loops::Loops::grow_loop(), protocols::rbsegment_relax::guess_rbsegs_from_pose(), core::scoring::hbonds::hb_energy_deriv_u2(), core::scoring::packstat::CavityBall::hetero_atom_line(), protocols::recces::Histogram::Histogram(), core::scoring::SecondaryStructurePotential::hspair(), protocols::seeded_abinitio::SegmentHybridizer::hybridize(), core::scoring::SecondaryStructurePotential::identify_ss(), core::scoring::bin_transitions::BinTransitionData::in_bin(), protocols::simple_filters::SheetFilter::ingo_ident_sheets(), protocols::toolbox::KMedoid::init(), protocols::scoring::ImplicitFastClashCheck::init_clash_check(), protocols::ub_e2c::ubi_e2c_modeler::init_k48r_perturbation(), protocols::residue_optimization::MetapatchEnumeration::initial_sampling(), core::chemical::gasteiger::GasteigerAtomTypeData::initialize(), protocols::recces::RECCES_Mover::initialize(), protocols::abinitio::abscript::RigidChunkCM::initialize(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::initialize_graph_for_packing(), protocols::simple_moves::DOFHistogramRecorder::insert_dofs_by_residue(), protocols::frags::insert_random_fragments_in_flexible_protein_regions(), protocols::forge::remodel::RemodelLoopMover::insert_random_smallestmer_per_loop(), protocols::features::PdbDataFeatures::insert_residue_pdb_confidence_rows(), core::membrane::inside_boundaries(), core::membrane::intersect(), core::io::mmtf::is_in_bondAtomList(), protocols::ligand_docking::ga_ligand_dock::GridScorer::is_residue_in_grid(), protocols::sewing::hashing::Hasher::iterate_over_basis_pairs(), protocols::sewing::data_storage::SmartAssembly::iterate_over_basis_pairs(), protocols::antibody::kink_RD_Hbond(), core::optimization::Minimizer::lbfgs(), protocols::loops::Loop::length(), IdentifyLigandMotifs::ligand_to_residue_analysis(), protocols::pockets::PocketGrid::linkExemplarsThroughSolvent(), core::scoring::epr_deer::ln(), protocols::hybridization::TMalign::load_pose_allocate_memory(), core::scoring::dna::DNA_EnvPairPotential::load_score_tables(), protocols::loops::loops_around_residues(), core::scoring::DenseNeighborIterator::lower_neighbor_id(), core::scoring::DenseNeighborConstIterator::lower_neighbor_id(), protocols::sic_dock::XfoxmScore::makebinary(), protocols::loophash::LoopHashRelaxProtocol::manual_call(), protocols::pockets::ComparisonGrid::mark(), protocols::pockets::PocketGrid::mark(), protocols::pockets::ElectrostaticpotentialGrid::mark_atom_espGrid_points(), protocols::ligand_docking::ga_ligand_dock::Pharmacophore::match(), core::scoring::electron_density::ElectronDensity::matchRes(), protocols::rotamer_recovery::RRComparerChiDiff::measure_rotamer_recovery(), core::scoring::dssp::StrandPairing::merge(), protocols::helical_bundle_predict::HBPHelixAssignments::merge_helices(), protocols::ddg::min_index(), core::scoring::epr_deer::min_max(), protocols::electron_density::DensitySymmInfo::min_symm_dist2(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves::model_loop(), protocols::loop_grower::LoopGrower::modifieddensity(), protocols::forge::build::SegmentInsert::modify_impl(), protocols::forge::build::SegmentRebuild::modify_impl(), protocols::forge::build::ConnectRight::modify_impl(), protocols::ub_e2c::ubi_e2c_modeler::monoub_centroid_mode_perturbation(), protocols::ub_e2c::ubi_e2c_modeler::monoub_first_perturbation(), protocols::ub_e2c::ubi_e2c_modeler::monoub_fullatom_mode_perturbation(), protocols::jd2::archive::MPIArchiveJobDistributor::MPIArchiveJobDistributor(), protocols::electron_density::BfactorMultifunc::multivec2poseBfacts(), protocols::splice::neighbors_in_vector(), protocols::pockets::PocketGrid::netTargetPocketVolume(), protocols::abinitio::noe_stage(), core::optimization::numerical_derivative_check(), core::optimization::symmetry::numerical_derivative_check(), protocols::pack_daemon::VMin::operator()(), core::optimization::StrongWolfeLineMinimization::operator()(), core::io::pose_from_sfr::GeometricRenameIsomorphismCallback::operator()(), protocols::ub_e2c::ubi_e2c_modeler::optimize_cov_bond(), protocols::optimize_weights::IterativeOptEDriver::optimize_weights(), protocols::match::Bool3DGrid::or_with(), protocols::rna::denovo::output::RNA_FragmentMonteCarloOutputter::output_jump_information(), core::fragment::ConstantLengthFragSet::overlapping_with_region(), core::scoring::constraints::AngleConstraint::p1_theta_deriv(), protocols::ligand_docking::ga_ligand_dock::GridScorer::packer_loop(), core::scoring::epr_deer::DEERIO::parse_dist_lines(), core::kinematics::FoldTree::partition_by_residue(), core::pose::symmetry::partition_by_symm_jumps(), protocols::simple_moves::sidechain_moves::SidechainMCMover::pass_metropolis(), protocols::canonical_sampling::SidechainMetropolisHastingsMover::pass_metropolis(), protocols::noesy_assign::PeakAssignment::peak_volume(), protocols::ligand_docking::ga_ligand_dock::ConstraintInfo::phore_overlaps_with_existing(), protocols::kinematic_closure::pivot_pickers::StandardPivots::pick(), protocols::abinitio::Template::pick_large_frags(), protocols::kinmatch::KinFunGroupTK::place_c(), protocols::splice::SpliceOut::place_cut_site_in_segment(), protocols::kinmatch::KinFunGroupTK::place_h(), protocols::recces::pose_setup_turner(), protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::prepare_foldtree(), core::scoring::motif::XformScore::print_quantiles(), core::io::silent::SilentStruct::print_scores(), protocols::rna::movers::ErraserMinimizerMover::process_entire_pose(), protocols::optimize_weights::PNatStructureOptEData::process_score(), protocols::optimize_weights::DDGMutationOptEData::process_score(), protocols::sic_dock::read_biounit(), protocols::relax::CentroidRelax::read_default_parameters(), protocols::protein_interface_design::PatchdockReader::read_patchdock(), core::scoring::Ramachandran::read_rama_map_file(), core::scoring::Ramachandran::read_rama_map_file_shapovalov(), protocols::frag_picker::CS2ndShift::read_sslimit_table(), core::scoring::motif::real_to_uint16(), core::scoring::motif::real_to_uint8(), protocols::noesy_assign::FragsToAtomDist::DistanceRecord::record(), protocols::noesy_assign::FragsToAtomDist::DistanceRecord::record_inv6(), core::chemical::rdkit::remove_excess_protons(), core::kinematics::FoldTree::reorder(), protocols::ligand_docking::LigandBaseProtocol::reorder_foldtree_around_mobile_regions(), protocols::abinitio::ConstraintFragmentSampler::replace_scorefxn(), protocols::features::ModelFeatures::report_features(), protocols::features::ProteinBondGeometryFeatures::report_interres_angles(), protocols::features::ProteinBondGeometryFeatures::report_interres_lengths(), core::scoring::facts::FACTSPotential::res_res_burial_for_scoring(), core::scoring::electron_density::resample(), core::grid::CartGrid< T >::reset_boundaries(), core::energy_methods::SymmetricLigandEnergy::residue_energy(), core::energy_methods::RNA_MgPointEnergy::residue_pair_energy_one_way(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::resize(), core::fragment::retain_top(), protocols::stepwise::monte_carlo::mover::StepWiseMoveSelector::reverse_delete_move(), protocols::simple_filters::RMSwrapper(), protocols::mpi_refinement::WorkUnit_LoopHash::run(), protocols::jumping::JumpSample::safe_secstruct(), protocols::jumping::safe_secstruct(), core::import_pose::RNA_JumpMover::sample_alternative_chain_connection(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::sample_loops(), protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::sample_loops(), core::scoring::electron_density::ElectronDensity::scaleIntensities(), protocols::fldsgn::potentials::sspot::HSPairPotential::score(), protocols::sic_dock::XfoxmScore::score(), core::pose::symmetry::sealed_symmetric_fold_tree(), protocols::LoopRebuild::select_one_loop(), protocols::moves::PyMOLMover::send_energy(), seq_sep_stage(), protocols::features::helixAssembly::HelicalFragment::seq_start(), protocols::frag_picker::scores::sequencealign(), protocols::recces::sampler::MC_OneTorsion::set_angle_range(), core::scoring::PolymerBondedEnergyContainer::set_computed(), protocols::rbsegment_relax::set_constraints(), protocols::normalmode::NormalModeMultifunc::set_default_modes(), protocols::qsar::scoring_grid::SingleGrid::set_distance_sphere_for_atom(), core::scoring::PolymerBondedEnergyContainer::set_energy(), protocols::loops::loop_mover::LoopMover::set_extended_torsions(), protocols::loops::set_extended_torsions(), protocols::abinitio::KinematicTaskControl::set_extended_torsions_and_idealize_loops(), core::conformation::symmetry::set_fold_tree_from_symm_data(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::set_loop(), protocols::hbnet::HBNet::set_min_networks_size(), protocols::relax::CentroidRelax::set_min_type(), protocols::nmr::pre::PREMover::set_minimize_w_pre_csts(), protocols::rbsegment_relax::set_rb_constraints(), protocols::qsar::scoring_grid::SingleGrid::set_ring(), protocols::qsar::scoring_grid::SingleGrid::set_score_sphere_for_atom(), protocols::ligand_docking::set_sphere(), protocols::nonlocal::StarTreeBuilder::set_up(), core::scoring::epr_deer::DEERDataCache::set_up_residues(), core::pack::scmin::CartSCMinMinimizerMap::setup(), protocols::rbsegment_relax::setup_disconnected(), core::kinematics::FoldTree::setup_edge_counts(), core::scoring::electron_density::ElectronDensity::setup_fastscoring_first_time(), protocols::stepwise::legacy::modeler::rna::StepWiseWorkingParametersSetup::setup_fold_tree(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_legacy(), core::scoring::facts::FACTSPotential::setup_for_derivatives(), core::import_pose::setup_jumps(), protocols::star::StarAbinitio::setup_kinematics(), protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::setup_obligate_pair(), protocols::rbsegment_relax::setup_pose_rbsegs_keep_loops(), protocols::stepwise::modeler::working_parameters::setup_working_parameters_for_swa(), core::scoring::SecondaryStructurePotential::sheets_from_dimers(), protocols::canonical_sampling::ParallelTempering::shuffle_temperatures(), core::scoring::epr_deer::sigmoid(), core::optimization::simple_numeric_deriv_check(), protocols::loop_grower::LoopGrower::single_grow(), protocols::frag_picker::LazySortedVector1< T, StrictWeakOrdering >::size(), protocols::stepwise::modeler::slice(), core::kinematics::FoldTree::slide_jump(), core::scoring::etable::MembEtable::smooth_etables(), core::scoring::etable::Etable::smooth_etables_one_pair(), core::scoring::SmoothEnvPairPotential::SmoothEnvPairPotential(), protocols::rbsegment_relax::ConfChangeMover::stage2(), protocols::protein_interface_design::movers::PlaceStubMover::StubMinimize(), protocols::match::Bool3DGrid::subtract(), protocols::abinitio::PairingStatistics::suggest_topology(), protocols::splice::RBOutMover::superimpose_source_on_pose(), core::energy_methods::ResidualDipolarCouplingEnergy_Rohl::svdcmp(), core::conformation::symmetry::symmetrize_fold_tree(), protocols::canonical_sampling::SimulatedTempering::temperature_move(), protocols::pockets::CCluster::testNeighbor(), protocols::pockets::PCluster::testNeighbor(), protocols::ligand_docking::torsion_constraints_from_rotamers(), protocols::abinitio::ConstraintFragmentSampler::total_res(), protocols::abinitio::FoldConstraints::total_res(), core::pose::transfer_phi_psi(), protocols::loops::Loops::transfer_to_residue_vector(), protocols::loops::trim_back_sequence_mapping(), core::scoring::motif::uint16_to_real(), core::scoring::motif::uint8_to_real(), protocols::simple_moves::uniform_dof_distribution(), core::chemical::ElectronConfiguration::unpaired_valence_electrons_sp(), protocols::hybridization::HybridizeFoldtreeDynamic::update(), core::pack::task::PackerTask_::update_commutative(), core::pack::task::ResidueLevelTask_::update_commutative(), core::conformation::symmetry::SymmetryInfo::update_contiguous_monomers(), core::kinematics::FoldTree::update_cutpoints(), core::pack::task::ResidueLevelTask_::update_intersection(), core::kinematics::FoldTree::update_jump_points(), protocols::abinitio::abscript::AbscriptStageMover::update_max_seq_sep(), protocols::docking::DockingEnsemble::update_pdblist_file(), core::pack::task::ResidueLevelTask_::update_union(), protocols::loops::Loops::verify_against(), protocols::sic_dock::CorrectionVisitor::visit(), core::scoring::epr_deer::EPRSpinLabel::weight(), protocols::abinitio::abscript::RigidChunkCM::yield_claims(), protocols::loops::loop_mover::LoopCM::yield_claims(), and core::optimization::StrongWolfeLineMinimization::zoom().

multiply()

template<class T >

T protocols::mean_field::multiply ( T const &  operand_from_ja, T const &  other_operand  )

inline

implements multiply function using operator *=

class T must provide an operator *=

Referenced by operator*=().

num_elements()

template<class T >

jagged_array< T >::Size protocols::mean_field::num_elements ( jagged_array< T > const &  input )

inline

returns the number of elements in a jagged_array

References protocols::analysis::total.

Referenced by protocols::mean_field::AAMatrix::ave_abs_diff(), protocols::toolbox::match_enzdes_util::EnzdesLoopInfo::generate_ss_strings_from_blueprint(), protocols::cluster::calibur::Clustering::getPDBs(), and core::simple_metrics::metrics::SequenceSimilarityMetric::score().

operator*() [1/3]

template<class T >

jagged_array< T > protocols::mean_field::operator* ( jagged_array< T > const &  input, jagged_array< T > const &  operands  )

inline

overload operator *= to allow multiplication of jagged_array by jagged_array<T> operands in an element-dependent manner

each element in jagged_array is multiplied by each corresponding element in operands

class T must provide an operator *=

since func multiply uses operator *=, no need to provide operator *

operator*() [2/3]

template<class T >

jagged_array< T > protocols::mean_field::operator* ( jagged_array< T > const &  input, T  operand  )

inline

overload operator * to allow multiplication of all elements in jagged_array by T operand

class T must provide an operator *=

since func subtract uses operator *=, no need to provide operator *

operator*() [3/3]

template<class T >

jagged_array< T > protocols::mean_field::operator* ( jagged_array< T > const &  input, utility::vector1< T > const &  operands  )

inline

overload operator * to allow multiplication of jagged_array by vector1<T> operands in a column-dependent manner

each element in jagged_array is multiplied by each element of corresponding column in operands

class T must provide an operator *=

since func multiply uses operator *=, no need to provide operator *

operator*=() [1/3]

template<class T >

void protocols::mean_field::operator*= ( jagged_array< T > &  input, jagged_array< T > const &  operands  )

inline

overload operator *= to allow multiplication of jagged_array by jagged_array<T> operands in an element-dependent manner

each element in jagged_array is multiplied by each corresponding element in operands

class T must provide an operator *=

since func multiply uses operator *=, no need to provide operator *

References protocols::mean_field::jagged_array< T, A >::apply_func_to_each_elem(), and multiply().

operator*=() [2/3]

template<class T >

void protocols::mean_field::operator*= ( jagged_array< T > &  input, T  operand  )

inline

overload operator *= to allow multiplication of all elements in jagged_array by T operand

class T must provide an operator *=

since func multiply uses operator *=, no need to provide operator *

References protocols::mean_field::jagged_array< T, A >::apply_func_to_all(), and multiply().

operator*=() [3/3]

template<class T >

void protocols::mean_field::operator*= ( jagged_array< T > &  input, utility::vector1< T > const &  operands  )

inline

overload operator *= to allow multiplication of jagged_array by vector1<T> operands in a column-dependent manner

each element in jagged_array is multiplied by each element of corresponding column in operands

class T must provide an operator *=

since func multiply uses operator *=, no need to provide operator *

References protocols::mean_field::jagged_array< T, A >::apply_func_to_each_col(), and multiply().

operator+() [1/3]

template<class T >

jagged_array< T > protocols::mean_field::operator+ ( jagged_array< T > const &  input, jagged_array< T > const &  operands  )

inline

overload operator + to allow addition of jagged_array<T> operands to jagged_array in an element-dependent manner

each element in operands is added to each corresponding element in jagged_array

class T must provide an operator +=

since func add uses operator +=, no need to provide operator +

operator+() [2/3]

template<class T >

jagged_array< T > protocols::mean_field::operator+ ( jagged_array< T > const &  input, T  operand  )

inline

overload operator + to allow addition of T operand to all elements in jagged_array

class T must provide an operator +=

since func add uses operator +=, no need to provide operator +

operator+() [3/3]

template<class T >

jagged_array< T > protocols::mean_field::operator+ ( jagged_array< T > const &  input, utility::vector1< T > const &  operands  )

inline

overload operator + to allow addition of vector1<T> operands to jagged_array in a column-dependent manner

each element in operands is added to each element of corresponding column in jagged_array

class T must provide an operator +=

since func add uses operator +=, no need to provide operator +

operator+=() [1/3]

template<class T >

void protocols::mean_field::operator+= ( jagged_array< T > &  input, jagged_array< T > const &  operands  )

inline

overload operator += to allow addition of jagged_array<T> operands to jagged_array in an element-dependent manner

each element in operands is added to each corresponding element in jagged_array

class T must provide an operator +=

since func add uses operator +=, no need to provide operator +

References add(), and protocols::mean_field::jagged_array< T, A >::apply_func_to_each_elem().

operator+=() [2/3]

template<class T >

void protocols::mean_field::operator+= ( jagged_array< T > &  input, T const &  operand  )

inline

overload operator += to allow addition of T operand to all elements in jagged_array

class T must provide an operator +=

since func add uses operator +=, no need to provide operator +

References add(), and protocols::mean_field::jagged_array< T, A >::apply_func_to_all().

operator+=() [3/3]

template<class T >

void protocols::mean_field::operator+= ( jagged_array< T > &  input, utility::vector1< T > const &  operands  )

inline

overload operator += to allow addition of vector1<T> operands to jagged_array in a column-dependent manner

each element in operands is added to each element of corresponding column in jagged_array

class T must provide an operator +=

since func add uses operator +=, no need to provide operator +

References add(), and protocols::mean_field::jagged_array< T, A >::apply_func_to_each_col().

operator-() [1/3]

template<class T >

jagged_array< T > protocols::mean_field::operator- ( jagged_array< T > const &  input, jagged_array< T > const &  operands  )

inline

overload operator - to allow subtraction of jagged_array<T> operands from jagged_array in an element-dependent manner

each element in operands is subtracted from each corresponding element in jagged_array

class T must provide an operator -=

since func subtract uses operator -=, no need to provide operator -

operator-() [2/3]

template<class T >

jagged_array< T > protocols::mean_field::operator- ( jagged_array< T > const &  input, T  operand  )

inline

overload operator - to allow subtraction of T operand from all elements in jagged_array

class T must provide an operator -=

since func subtract uses operator -=, no need to provide operator -

operator-() [3/3]

template<class T >

jagged_array< T > protocols::mean_field::operator- ( jagged_array< T > const &  input, utility::vector1< T > const &  operands  )

inline

overload operator - to allow subtraction of vector1<T> operands from jagged_array in a column-dependent manner

each element in operands is subtracted from each element of corresponding column in jagged_array

class T must provide an operator -=

since func subtract uses operator -=, no need to provide operator -

operator-=() [1/3]

template<class T >

void protocols::mean_field::operator-= ( jagged_array< T > &  input, jagged_array< T > const &  operands  )

inline

overload operator -= to allow subtraction of jagged_array<T> operands from jagged_array in an element-dependent manner

each element in operands is subtracted from each corresponding element in jagged_array

class T must provide an operator -=

since func subtract uses operator -=, no need to provide operator -

References protocols::mean_field::jagged_array< T, A >::apply_func_to_each_elem(), and subtract().

operator-=() [2/3]

template<class T >

void protocols::mean_field::operator-= ( jagged_array< T > &  input, T  operand  )

inline

overload operator -= to allow subtraction of T operand from all elements in jagged_array

class T must provide an operator -=

since func subtract uses operator -=, no need to provide operator -

References protocols::mean_field::jagged_array< T, A >::apply_func_to_all(), and subtract().

operator-=() [3/3]

template<class T >

void protocols::mean_field::operator-= ( jagged_array< T > &  input, utility::vector1< T > const &  operands  )

inline

overload operator -= to allow subtraction of vector1<T> operands from jagged_array in a column-dependent manner

each element in operands is subtracted from each element of corresponding column in jagged_array

class T must provide an operator -=

since func subtract uses operator -=, no need to provide operator -

References protocols::mean_field::jagged_array< T, A >::apply_func_to_each_col(), and subtract().

operator/() [1/3]

template<class T >

jagged_array< T > protocols::mean_field::operator/ ( jagged_array< T > const &  input, jagged_array< T > const &  operands  )

inline

overload operator / to allow division of jagged_array by jagged_array<T> operands in an element-dependent manner

each element in jagged_array is divided by each each corresponding element in operands

class T must provide an operator /=

since func divide uses operator /=, no need to provide operator /

operator/() [2/3]

template<class T >

jagged_array< T > protocols::mean_field::operator/ ( jagged_array< T > const &  input, T  operand  )

inline

overload operator / to allow division of all elements in jagged_array by T operand

class T must provide an operator /=

since func divide uses operator /=, no need to provide operator /

operator/() [3/3]

template<class T >

jagged_array< T > protocols::mean_field::operator/ ( jagged_array< T > const &  input, utility::vector1< T > const &  operands  )

inline

overload operator / to allow division of jagged_array by vector1<T> operands in a column-dependent manner

each element in jagged_array is divided by each element of corresponding column in operands

class T must provide an operator /=

since func divide uses operator /=, no need to provide operator /

operator/=() [1/5]

template<class T >

void protocols::mean_field::operator/= ( jagged_array< T > &  input, jagged_array< T > const &  operands  )

inline

overload operator /= to allow division of jagged_array by jagged_array<T> operands in an element-dependent manner

each element in jagged_array is divided by each each corresponding element in operands

class T must provide an operator /=

since func divide uses operator /=, no need to provide operator /

References protocols::mean_field::jagged_array< T, A >::apply_func_to_each_elem(), and divide().

operator/=() [2/5]

template<class T , class T_2 >

void protocols::mean_field::operator/= ( jagged_array< T > &  input, jagged_array< T_2 > const &  operands  )

inline

overload operator /= to allow division of jagged_array by jagged_array<T> operands in an element-dependent manner

each element in jagged_array is divided by each each corresponding element in operands

class T must provide an operator /=

since func divide uses operator /=, no need to provide operator /

intended to allow for division of a class T by a different class T_2 - used in mean-field method to divide AAProb/Real

References protocols::mean_field::jagged_array< T, A >::apply_func_to_each_elem(), and divide().

operator/=() [3/5]

template<class T >

void protocols::mean_field::operator/= ( jagged_array< T > &  input, T  operand  )

inline

overload operator /= to allow division of all elements in jagged_array by T operand

class T must provide an operator /=

since func divide uses operator /=, no need to provide operator /

References protocols::mean_field::jagged_array< T, A >::apply_func_to_all(), and divide().

operator/=() [4/5]

template<class T >

void protocols::mean_field::operator/= ( jagged_array< T > &  input, utility::vector1< T > const &  operands  )

inline

overload operator /= to allow division of jagged_array by vector1<T> operands in a column-dependent manner

each element in jagged_array is divided by each element of corresponding column in operands

class T must provide an operator /=

since func divide uses operator /=, no need to provide operator /

References protocols::mean_field::jagged_array< T, A >::apply_func_to_each_col(), and divide().

operator/=() [5/5]

template<class T , class T_2 >

void protocols::mean_field::operator/= ( jagged_array< T > &  input, utility::vector1< T_2 > const &  operands  )

inline

overload operator /= to allow division of jagged_array by vector1<T> operands in a column-dependent manner

each element in jagged_array is divided by each element of corresponding column in operands

class T must provide an operator /=

since func divide uses operator /=, no need to provide operator /

intended to allow for division of a class T by a different class T_2 - used in mean-field method to divide AAProb/Real

References protocols::mean_field::jagged_array< T, A >::apply_func_to_each_col(), and divide().

operator<<() [1/9]

std::ostream& protocols::mean_field::operator<<	(	std::ostream &	output,
		AAMatrix const &	object_to_output
	)

operator<<() [2/9]

std::ostream& protocols::mean_field::operator<<	(	std::ostream &	output,
		AAProb const &	object_to_output
	)

operator<<() [3/9]

std::ostream& protocols::mean_field::operator<<	(	std::ostream &	output,
		DesignMeanField const &	object_to_output
	)

operator<<() [4/9]

std::ostream& protocols::mean_field::operator<<	(	std::ostream &	output,
		FlexBBDesignMeanField const &	object_to_output
	)

operator<<() [5/9]

std::ostream& protocols::mean_field::operator<<	(	std::ostream &	output,
		FlexBBMeanField const &	object_to_output
	)

operator<<() [6/9]

std::ostream& protocols::mean_field::operator<<	(	std::ostream &	output,
		MeanField const &	object_to_output
	)

operator<<() [7/9]

std::ostream& protocols::mean_field::operator<<	(	std::ostream &	output,
		ResHashMap const &	object_to_output
	)

operator<<() [8/9]

std::ostream& protocols::mean_field::operator<<	(	std::ostream &	output,
		RotMatrix const &	object_to_output
	)

operator<<() [9/9]

std::ostream& protocols::mean_field::operator<<	(	std::ostream &	output,
		RotProb const &	object_to_output
	)

subtract()

template<class T >

T protocols::mean_field::subtract ( T const &  operand_from_ja, T const &  other_operand  )

inline

implements subtract function using operator -=

class T must provide an operator -=

Referenced by protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::check_base_pair(), operator-=(), and core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::PackerEnergySubtract().

TR() [1/2]

static basic::Tracer protocols::mean_field::TR ( "protocols.mean_field.AAMatrix"  )

static

Referenced by protocols::mean_field::MeanField::build_rot_matrix_for_pose(), protocols::mean_field::MeanField::converge(), protocols::mean_field::AAMatrix::dump_transfac(), protocols::mean_field::AAMatrix::init(), protocols::mean_field::GenMeanFieldMover::parse_my_tag(), protocols::mean_field::GenMeanFieldMover::read_aa_matrix(), protocols::mean_field::GenMeanFieldMover::report_aa_matrix(), protocols::mean_field::GenMeanFieldMover::report_dist(), and protocols::mean_field::GenMeanFieldMover::report_rot_prob().

TR() [2/2]

static basic::Tracer protocols::mean_field::TR ( "protocols.mean_field.GenMeanFieldMover"  )

static