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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...
 
class  ResHashMap
 
struct  ResPred
 checks whether two rotamer hashes match - if the rounded values of their chi angles match More...
 
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< booljagged_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 >
max (jagged_array< T > const &input)
 Find the largest value in a jagged_array. More...
 
template<class 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 >
add (T const &operand_from_ja, T const &other_operand)
 implements add function using operator += More...
 
template<class T >
subtract (T const &operand_from_ja, T const &other_operand)
 implements subtract function using operator -= More...
 
template<class T >
multiply (T const &operand_from_ja, T const &other_operand)
 implements multiply function using operator *= More...
 
template<class T >
divide (T const &operand_from_ja, T const &other_operand)
 implements divide function using operator /= More...
 
template<class T , class T_2 >
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

typedef utility::pointer::shared_ptr< AAMatrix const > protocols::mean_field::AAMatrixCOP
typedef utility::pointer::shared_ptr< AAMatrix > protocols::mean_field::AAMatrixOP
typedef utility::pointer::shared_ptr< DesignMeanField const > protocols::mean_field::DesignMeanFieldCOP
typedef utility::pointer::shared_ptr< DesignMeanField > protocols::mean_field::DesignMeanFieldOP
typedef utility::pointer::shared_ptr<FlexBBDesignMeanField const> protocols::mean_field::FlexBBDesignMeanFieldCOP
typedef utility::pointer::shared_ptr<FlexBBMeanField const> protocols::mean_field::FlexBBMeanFieldCOP
typedef utility::pointer::shared_ptr<FlexBBMeanField> protocols::mean_field::FlexBBMeanFieldOP
typedef utility::pointer::shared_ptr< GenMeanFieldMover const > protocols::mean_field::GenMeanFieldMoverCOP
typedef utility::pointer::shared_ptr< GenMeanFieldMover > protocols::mean_field::GenMeanFieldMoverOP
typedef utility::pointer::shared_ptr< MeanField const > protocols::mean_field::MeanFieldCOP
typedef utility::pointer::shared_ptr< MeanField > protocols::mean_field::MeanFieldOP
typedef utility::pointer::shared_ptr<ResHashMap const> protocols::mean_field::ResHashMapCOP
typedef utility::pointer::shared_ptr<ResHashMap> protocols::mean_field::ResHashMapOP
typedef utility::pointer::shared_ptr< RotMatrix const > protocols::mean_field::RotMatrixCOP
typedef utility::pointer::shared_ptr< RotMatrix > protocols::mean_field::RotMatrixOP

Function Documentation

template<class T >
T protocols::mean_field::add ( T const &  operand_from_ja,
T const &  other_operand 
)
inline
template<class T >
jagged_array< T >::Size protocols::mean_field::arg_max ( jagged_array< T > const &  input)
template<class T >
jagged_array< T >::Size protocols::mean_field::arg_min ( jagged_array< T > const &  input)
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/=().

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)

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(), core::io::silent::SilentStruct::add_energy(), protocols::loops::Loops::add_loop(), protocols::sewing::data_storage::HashedSmartAssembly::add_segment(), protocols::sewing::data_storage::SmartAssembly::add_segment(), core::io::silent::SilentStruct::add_string_value(), 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::epr_deer::DEERDistanceDistribution::append(), core::scoring::hbonds::HBondSet::append_hbond(), protocols::simple_moves::PSSM2BfactorMover::apply(), protocols::protein_interface_design::movers::SetAtomTree::apply(), protocols::ligand_docking::RigidSearchMover::apply(), protocols::abinitio::ResolutionSwitcher::apply(), protocols::dna::SeparateDnaFromNonDna::apply(), protocols::task_operations::SelectResiduesWithinChainOperation::apply(), protocols::rbsegment_relax::OptimizeThreadingMover::apply(), protocols::cyclic_peptide::PeptideStubMover::apply(), protocols::analysis::LoopAnalyzerMover::apply(), protocols::hybridization::CartesianSampler::apply(), protocols::recces::scratch::ThermalSamplingMover::apply(), protocols::hybridization::CartesianHybridize::apply(), protocols::ncbb::ResidueReplacementRebuildMover::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::cryst::SetCrystWeightMover::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::loops::loop_closure::jacobi::JacobiLoopClosureMover::apply(), protocols::docking::membrane::MPFindInterfaceMover::apply(), protocols::fold_from_loops::movers::SplitAndMixPoseMover::apply(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::apply(), protocols::antibody_legacy::LoopRlxMover::apply(), protocols::rbsegment_relax::SequenceShiftMover::apply(), protocols::cryst::MakeLatticeMover::apply(), protocols::rigid::RigidBodyDofPerturbMover::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::monte_carlo::GenericMonteCarloMover::boltzmann(), protocols::moves::MonteCarlo::boltzmann(), protocols::forge::remodel::RemodelLoopMover::boost_closure_stage(), core::scoring::epr_deer::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::epr_deer::Simulated4PDEERTrace::calc_4pdeer(), 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::score_filters::GeometryFilter::compute(), protocols::simple_filters::LeastNativeLike9merFilter::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_atomwise::ElectronDensityAtomwise::computeCrystParams(), core::scoring::electron_density::ElectronDensity::computeCrystParams(), core::scoring::electron_density::ElectronDensity::computeStats(), core::scoring::power_diagram::PowerDiagram::construct_from_pose(), core::scoring::packstat::Octree2D::contains(), core::membrane::convex_hull(), 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::scoring::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::MakeLayerMover::detect_connecting_subunits(), protocols::cryst::MakeLatticeMover::detect_connecting_subunits(), 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::scoring::methods::PairEnergy::eval_residue_pair_derivatives(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_pair_deriv(), core::scoring::CenRotEnvPairPotential::evaluate_cen_rot_pair_score(), 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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(), 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::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::scoring::methods::IntermolEnergy::get_num_chains_frozen(), protocols::canonical_sampling::mc_convergence_checks::HPool_RMSD::get_pair_dist(), protocols::electron_density::DockIntoDensityMover::get_radius(), protocols::electron_density::get_rot_angle(), core::scoring::epr_deer::DEERDistanceBounds::get_score(), core::scoring::epr_deer::DEERDistanceDistribution::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(), 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(), 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::loop_graph::evaluator::GaussianChainFuncPotentialEvaluator::initialize(), protocols::recces::RECCES_Mover::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::scoring::methods::LinearBranchEnergy::LinearBranchEnergy(), core::scoring::methods::LinearChainbreakEnergy::LinearChainbreakEnergy(), core::scoring::lkball::LK_BallEnergy::LK_BallEnergy(), 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::PocketGrid::mark(), protocols::pockets::ComparisonGrid::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::pockets::max_values_versus_cluster(), protocols::noesy_assign::CrossPeak::max_volume_contribution(), core::scoring::dssp::StrandPairing::merge(), protocols::helical_bundle_predict::HBPHelixAssignments::merge_helices(), core::optimization::BrentLineMinimization::MNBRAK(), core::scoring::epr_deer::DEERDecayData::mod_depth_bounds(), core::scoring::epr_deer::DEERDecayData::mod_distr(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_KIC::model_loop(), protocols::loop_build::LoopMover_SlidingWindow::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::model_loop(), protocols::forge::build::SegmentRebuild::modify_impl(), protocols::forge::build::SegmentInsert::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::scoring::epr_deer::EPRSpinLabel::normalize_distribution(), core::optimization::symmetry::numerical_derivative_check(), core::optimization::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(), protocols::recon_design::FitnessFilter::parse_my_tag(), protocols::monte_carlo::GenericMonteCarloMover::parse_my_tag(), protocols::motif_grafting::movers::MotifGraftMover::parse_my_tag(), core::kinematics::FoldTree::partition_by_residue(), core::pose::symmetry::partition_by_symm_jumps(), protocols::canonical_sampling::SidechainMetropolisHastingsMover::pass_metropolis(), protocols::simple_moves::sidechain_moves::SidechainMCMover::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(), 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::recon_design::FitnessFilter::provide_xml_schema(), protocols::motif_grafting::movers::MotifGraftMover::provide_xml_schema(), core::scoring::epr_deer::DEERIO::read_dist_lines(), core::fragment::MinimalFragSet::read_fragment_stream(), core::fragment::ConstantLengthFragSet::read_fragment_stream(), core::scoring::epr_deer::DEERIO::read_gauss_lines(), 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< core::Real >::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::WidthFirstSlidingWindowLoopClosure::sample_loops(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::sample_loops(), 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::lkball::LK_BallEnergy::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::scoring::membrane::FaMPEnvEnergy::setup_for_fullatom(), core::scoring::membrane::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::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::protein_interface_design::movers::PlaceStubMover::StubMinimize(), protocols::match::Bool3DGrid::subtract(), protocols::stepwise::modeler::rna::suite_rmsd(), protocols::splice::RBOutMover::superimpose_source_on_pose(), core::scoring::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::PCluster::testNeighbor(), protocols::pockets::CCluster::testNeighbor(), core::scoring::trie::trie_vs_trie(), core::scoring::motif::uint16_to_real(), core::scoring::motif::uint8_to_real(), protocols::jobdist::universal_main(), protocols::hybridization::HybridizeFoldtreeDynamic::update(), core::pack::task::ResidueLevelTask_::update_commutative(), core::pack::task::PackerTask_::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().

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(), core::scoring::epr_deer::DEERDistanceDistribution::append(), protocols::ligand_docking::LigandDockProtocol::append_ligand_docking_scores(), protocols::simple_moves::PSSM2BfactorMover::apply(), protocols::protein_interface_design::movers::PatchdockTransform::apply(), protocols::protein_interface_design::movers::SetAtomTree::apply(), protocols::ligand_docking::RigidSearchMover::apply(), protocols::dna::SeparateDnaFromNonDna::apply(), protocols::task_operations::RestrictToAlignedSegmentsOperation::apply(), protocols::rbsegment_relax::OptimizeThreadingMover::apply(), protocols::abinitio::AbrelaxMover::apply(), protocols::simple_filters::ChiWellRmsdEvaluator::apply(), protocols::fold_from_loops::constraint_generator::AutomaticSheetConstraintGenerator::apply(), protocols::hybridization::CartesianSampler::apply(), protocols::recces::scratch::ThermalSamplingMover::apply(), protocols::hybridization::CartesianHybridize::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub::apply(), protocols::ncbb::ResidueReplacementRebuildMover::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::switches::GraftSwitchMover::apply(), protocols::loops::loop_closure::ccd::LoopClosure::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::apply(), protocols::splice::Splice::apply(), protocols::simple_moves::SimpleThreadingMover::apply(), protocols::abinitio::KinematicAbinitio::apply(), protocols::rbsegment_relax::SequenceShiftMover::apply(), protocols::rigid::RigidBodyDofPerturbMover::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::monte_carlo::GenericMonteCarloMover::boltzmann(), protocols::moves::MonteCarlo::boltzmann(), protocols::forge::remodel::RemodelLoopMover::boost_closure_stage(), core::scoring::epr_deer::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::epr_deer::Simulated4PDEERTrace::calc_4pdeer(), core::scoring::electron_density::ElectronDensity::calcRhoC(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::calculate_ccd_angle(), core::scoring::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::score_filters::GeometryFilter::compute(), protocols::fldsgn::filters::HelixBendFilter::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(), core::scoring::packstat::compute_sasa(), core::scoring::nmr::pcs::PCSMultiSet::compute_score(), core::scoring::electron_density_atomwise::ElectronDensityAtomwise::computeCrystParams(), core::scoring::electron_density::ElectronDensity::computeCrystParams(), core::scoring::electron_density::ElectronDensity::computeStats(), core::scoring::power_diagram::PowerDiagram::construct_from_pose(), core::scoring::packstat::Octree2D::contains(), 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::DockIntoDensityMover::density_grid_search(), 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_atomwise::ElectronDensityAtomwise::expandToUnitCell(), core::scoring::electron_density::ElectronDensity::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(), core::scoring::epr_deer::DEERDataCache::fetch_and_organize_data(), 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::SoedingFunc::func(), core::scoring::func::MixtureFunc::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::scoring::methods::GoapEnergy::get_angle_score(), 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::antibody::clusters::CDRClusterMatcher::get_closest_cluster(), core::scoring::PolymerBondedEnergyContainer::get_computed(), core::pose::full_model_info::get_connection_domains(), 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::DEERDistanceDistribution::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(), core::scoring::epr_deer::EPRSpinLabel::get_weight(), 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(), 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(), protocols::recces::RECCES_Mover::initialize(), protocols::abinitio::abscript::RigidChunkCM::initialize(), core::chemical::gasteiger::GasteigerAtomTypeData::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(), protocols::pockets::PocketGrid::linkExemplarsThroughSolvent(), 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::PocketGrid::mark(), protocols::pockets::ComparisonGrid::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(), protocols::electron_density::DensitySymmInfo::min_symm_dist2(), protocols::pockets::min_values_versus_cluster(), core::scoring::epr_deer::DEERDecayData::mod_depth_bounds(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves::model_loop(), 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::loop_grower::LoopGrower::modifieddensity(), protocols::forge::build::SegmentRebuild::modify_impl(), protocols::forge::build::ConnectRight::modify_impl(), protocols::forge::build::SegmentInsert::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::ligand_docking::ga_ligand_dock::GAOptimizer::next_generation(), protocols::abinitio::noe_stage(), core::optimization::symmetry::numerical_derivative_check(), core::optimization::numerical_derivative_check(), core::optimization::StrongWolfeLineMinimization::operator()(), protocols::pack_daemon::VMin::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::kinematics::FoldTree::partition_by_residue(), core::pose::symmetry::partition_by_symm_jumps(), protocols::canonical_sampling::SidechainMetropolisHastingsMover::pass_metropolis(), protocols::simple_moves::sidechain_moves::SidechainMCMover::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(), core::scoring::epr_deer::DEERIO::read_dist_lines(), core::scoring::epr_deer::DEERIO::read_gauss_lines(), 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::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::FACTSPotential::res_res_burial_for_scoring(), core::scoring::electron_density::resample(), core::grid::CartGrid< core::Real >::reset_boundaries(), core::scoring::methods::SymmetricLigandEnergy::residue_energy(), core::scoring::magnesium::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::WidthFirstSlidingWindowLoopClosure::sample_loops(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::sample_loops(), core::scoring::electron_density::ElectronDensity::scaleIntensities(), protocols::sic_dock::XfoxmScore::score(), protocols::fldsgn::potentials::sspot::HSPairPotential::score(), core::pose::symmetry::sealed_symmetric_fold_tree(), protocols::LoopRebuild::select_one_loop(), protocols::electron_density::DockIntoDensityMover::select_points(), 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::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::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::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::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::protein_interface_design::movers::PlaceStubMover::StubMinimize(), protocols::match::Bool3DGrid::subtract(), protocols::abinitio::PairingStatistics::suggest_topology(), protocols::splice::RBOutMover::superimpose_source_on_pose(), core::scoring::methods::ResidualDipolarCouplingEnergy_Rohl::svdcmp(), core::conformation::symmetry::symmetrize_fold_tree(), protocols::canonical_sampling::SimulatedTempering::temperature_move(), protocols::pockets::PCluster::testNeighbor(), protocols::pockets::CCluster::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(), core::chemical::ElectronConfiguration::unpaired_valence_electrons_sp(), protocols::hybridization::HybridizeFoldtreeDynamic::update(), core::pack::task::ResidueLevelTask_::update_commutative(), core::pack::task::PackerTask_::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(), protocols::abinitio::abscript::RigidChunkCM::yield_claims(), protocols::loops::loop_mover::LoopCM::yield_claims(), and core::optimization::StrongWolfeLineMinimization::zoom().

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*=().

template<class T >
jagged_array< T >::Size protocols::mean_field::num_elements ( jagged_array< T > const &  input)
inline
template<class T >
jagged_array< T > protocols::mean_field::operator* ( jagged_array< T > const &  input,
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 *

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 *

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 *

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

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().

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().

template<class T >
jagged_array< T > protocols::mean_field::operator+ ( jagged_array< T > const &  input,
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 +

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 +

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 +

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().

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().

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().

template<class T >
jagged_array< T > protocols::mean_field::operator- ( jagged_array< T > const &  input,
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 -

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 -

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 -

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

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().

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().

template<class T >
jagged_array< T > protocols::mean_field::operator/ ( jagged_array< T > const &  input,
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 /

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 /

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 /

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

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().

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().

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().

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().

std::ostream& protocols::mean_field::operator<< ( std::ostream &  output,
ResHashMap const &  object_to_output 
)
std::ostream& protocols::mean_field::operator<< ( std::ostream &  output,
DesignMeanField const &  object_to_output 
)
std::ostream& protocols::mean_field::operator<< ( std::ostream &  output,
AAProb const &  object_to_output 
)
std::ostream& protocols::mean_field::operator<< ( std::ostream &  output,
RotProb const &  object_to_output 
)
std::ostream& protocols::mean_field::operator<< ( std::ostream &  output,
FlexBBDesignMeanField const &  object_to_output 
)
std::ostream& protocols::mean_field::operator<< ( std::ostream &  output,
RotMatrix const &  object_to_output 
)
std::ostream& protocols::mean_field::operator<< ( std::ostream &  output,
FlexBBMeanField const &  object_to_output 
)
std::ostream& protocols::mean_field::operator<< ( std::ostream &  output,
MeanField const &  object_to_output 
)
std::ostream& protocols::mean_field::operator<< ( std::ostream &  output,
AAMatrix const &  object_to_output 
)
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(), and operator-=().

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