protocols::cluster::calibur Namespace Reference

Classes
class	AdjacentList
class	Stru
class	Clustering
class	PreloadedPDB
class	SimPDB

Typedefs
typedef unsigned short	LIST_TYPE
typedef utility::pointer::shared_ptr< AdjacentList >	AdjacentListOP
typedef utility::pointer::shared_ptr< Stru >	StruOP
using	StringVec = std::vector< std::string >
using	StringVecOP = utility::pointer::shared_ptr< StringVec >
typedef utility::pointer::shared_ptr< PreloadedPDB >	PreloadedPDBOP
typedef utility::pointer::shared_ptr< SimPDB >	SimPDBOP

Enumerations
enum	ADJ_LIST_MODE { MATRIX , LIST , LITE }
enum	EST_THRESHOLD_MODE {   PERCENT_EDGES , MIN_AVG_DIST_BASED , MOST_FREQ_BASED , ROSETTA ,   SAMPLED_ROSETTA , USER_SPECIFIED }
enum	INPUT_FILE_TYPE { UNKNOWN =-1 , SILENT_FILE , PDB_LIST }

Functions
static int	__cmp (const void *a, const void *b)
void	cubic_roots1 (core::Real a2, core::Real a1, core::Real a0, core::Real *z)
void	cubic_roots2 (core::Real a2, core::Real a1, core::Real a0, core::Real *z)
core::Real	__timeval_difference (struct timeval *x, struct timeval *y)
core::Real	_get_elapsed (int set_start)
template<class T >
void	ROTATE (T &a, int x1, int y1, int x2, int y2, core::Real s, core::Real tau)
bool	jacobi3 (core::Real a[3][3], core::Real d[3], core::Real v[3][3])
void	print_matrix (core::Real a[3][3])
int	toInt (std::string const &aString)
core::Real	toFloat (std::string const &aString)
void	center_residues (std::vector< core::Real > &calpha_vector, int num_residue_)
INPUT_FILE_TYPE	filetype (std::string const &filename)
unsigned int	num_lines_in_file (std::string const &filename)
core::Real	RMSD (std::vector< core::Real > &coords1, std::vector< core::Real > &coords2, int n, core::Real R[3][3])
core::Real	RMSD (std::vector< core::Real > &coords1, std::vector< core::Real > &coords2, int n)
void	rotate (std::vector< core::Real > &coords, int n, core::Real R[3][3], core::Real *result)
core::Real	fast_rmsd (std::vector< core::Real > &coords1, std::vector< core::Real > &coords2, int n)

Variables
char	aa [][4]
char	slc []

Typedef Documentation

AdjacentListOP

typedef utility::pointer::shared_ptr< AdjacentList > protocols::cluster::calibur::AdjacentListOP

LIST_TYPE

typedef unsigned short protocols::cluster::calibur::LIST_TYPE

PreloadedPDBOP

typedef utility::pointer::shared_ptr< PreloadedPDB > protocols::cluster::calibur::PreloadedPDBOP

SimPDBOP

typedef utility::pointer::shared_ptr< SimPDB > protocols::cluster::calibur::SimPDBOP

StringVec

typedef std::vector< std::string > protocols::cluster::calibur::StringVec

StringVecOP

typedef utility::pointer::shared_ptr< StringVec > protocols::cluster::calibur::StringVecOP

StruOP

typedef utility::pointer::shared_ptr< Stru > protocols::cluster::calibur::StruOP

Enumeration Type Documentation

ADJ_LIST_MODE

enum protocols::cluster::calibur::ADJ_LIST_MODE

Enumerator
MATRIX
LIST
LITE

EST_THRESHOLD_MODE

enum protocols::cluster::calibur::EST_THRESHOLD_MODE

Enumerator
PERCENT_EDGES
MIN_AVG_DIST_BASED
MOST_FREQ_BASED
ROSETTA
SAMPLED_ROSETTA
USER_SPECIFIED

INPUT_FILE_TYPE

enum protocols::cluster::calibur::INPUT_FILE_TYPE

Enumerator
UNKNOWN
SILENT_FILE
PDB_LIST

Function Documentation

__cmp()

static int protocols::cluster::calibur::__cmp ( const void *  a, const void *  b  )

static

References core::pose::motif::a(), and protocols::match::upstream::b.

Referenced by protocols::cluster::calibur::Clustering::estimateDist().

__timeval_difference()

core::Real protocols::cluster::calibur::__timeval_difference	(	struct timeval *	x,
		struct timeval *	y
	)

Referenced by _get_elapsed().

_get_elapsed()

core::Real protocols::cluster::calibur::_get_elapsed

(

int

set_start

)

References __timeval_difference().

Referenced by protocols::cluster::calibur::Clustering::cluster().

center_residues()

void protocols::cluster::calibur::center_residues	(	std::vector< core::Real > &	calpha_vector,
		int	num_residue_
	)

Referenced by protocols::cluster::calibur::PreloadedPDB::loadSilentFile(), and protocols::cluster::calibur::SimPDB::read().

cubic_roots1()

void protocols::cluster::calibur::cubic_roots1	(	core::Real	a2,
		core::Real	a1,
		core::Real	a0,
		core::Real *	z
	)

References core::chemical::element::C, and PI.

cubic_roots2()

void protocols::cluster::calibur::cubic_roots2	(	core::Real	a2,
		core::Real	a1,
		core::Real	a0,
		core::Real *	z
	)

This is faster but leaves no option for obtaining imaginary roots. (After "-O" in GCC, the speed gain is not much, only ~4%)

References PI.

fast_rmsd()

core::Real protocols::cluster::calibur::fast_rmsd	(	std::vector< core::Real > &	coords1,
		std::vector< core::Real > &	coords2,
		int	n
	)

References core::chemical::element::C, cubic_roots, protocols::ddg::min_index(), and core::scoring::omega.

Referenced by protocols::cluster::calibur::Clustering::trueD().

filetype()

INPUT_FILE_TYPE protocols::cluster::calibur::filetype

(

std::string const &

filename

)

References protocols::abinitio::filename(), PDB_LIST, SILENT_FILE, and UNKNOWN.

Referenced by core::import_pose::extension_from_filetype(), protocols::cluster::calibur::Clustering::readDecoyNames(), protocols::simple_moves::SaveProbabilitiesMetricMover::set_filetype(), and core::scoring::mhc_epitope_energy::MHCEpitopeEnergySetup::setup_predictor().

jacobi3()

bool protocols::cluster::calibur::jacobi3	(	core::Real	a[3][3],
		core::Real	d[3],
		core::Real	v[3][3]
	)

Computes the eigenvalues and (normalized) eigenvectors of a real symmetric matrix a[3][3] in d[3] and v[3][3] respectively.

Only the upper-right triangle of a[3][3] is referenced and over-written.

(The method follows closely the discussions in "Numerical Recipes in C".)

References core::pose::motif::a(), NUM_ITER, ROTATE(), SMALL_NUM_ITER, and protocols::hybridization::t.

Referenced by RMSD().

num_lines_in_file()

unsigned int protocols::cluster::calibur::num_lines_in_file

(

std::string const &

filename

)

References protocols::abinitio::filename().

Referenced by protocols::cluster::calibur::Clustering::readDecoyNames().

print_matrix()

void protocols::cluster::calibur::print_matrix

(

core::Real

a[3][3]

)

References core::pose::motif::a().

RMSD() [1/2]

core::Real protocols::cluster::calibur::RMSD	(	std::vector< core::Real > &	coords1,
		std::vector< core::Real > &	coords2,
		int	n
	)

References core::chemical::element::C, and jacobi3().

RMSD() [2/2]

core::Real protocols::cluster::calibur::RMSD	(	std::vector< core::Real > &	coords1,
		std::vector< core::Real > &	coords2,
		int	n,
		core::Real	R[3][3]
	)

References core::chemical::element::C, and jacobi3().

Referenced by protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::create_large_cluster_centers_member_list(), protocols::protein_interface_design::filters::RmsdSimpleFilter::dist_bb(), protocols::motif_grafting::movers::MotifGraftMover::get_bb_alignment_and_transformation(), protocols::motif_grafting::movers::MotifGraftMover::get_bb_alignment_and_transformation_wTipsExtraInfo(), protocols::motif_grafting::movers::MotifGraftMover::get_bb_distance(), protocols::motif_grafting::movers::MotifGraftMover::get_motif_scaffold_superposition_and_RMSD(), protocols::protein_interface_design::filters::RmsdSimpleFilter::rmsd_bb(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_Clusterer::setup_fail_triangle_inequailty_list(), and protocols::cluster::calibur::Clustering::superimposeAndReplace().

rotate()

void protocols::cluster::calibur::rotate	(	std::vector< core::Real > &	coords,
		int	n,
		core::Real	R[3][3],
		core::Real *	result
	)

References protocols::simple_filters::coords().

Referenced by protocols::membrane::RandomPositionRotationMover::apply(), protocols::membrane::TranslationRotationMover::apply(), protocols::membrane_benchmark::MembraneEnergyLandscapeSampler::apply(), protocols::membrane_benchmark::PeptideOrientationMover::apply(), protocols::rna::denovo::movers::RNA_HelixMover::apply(), protocols::splice::AlignEndsMover::apply(), core::scoring::MultipoleElecPotential::build_frame_and_rotate(), core::chemical::read_topology_file(), and protocols::cluster::calibur::Clustering::superimposeAndReplace().

ROTATE()

template<class T >

void protocols::cluster::calibur::ROTATE	(	T &	a,
		int	x1,
		int	y1,
		int	x2,
		int	y2,
		core::Real	s,
		core::Real	tau
	)

References core::pose::motif::a().

Referenced by jacobi3().

toFloat()

core::Real protocols::cluster::calibur::toFloat

(

std::string const &

aString

)

References protocols::loops::start.

Referenced by protocols::cluster::calibur::PreloadedPDB::loadSilentFile(), and protocols::cluster::calibur::SimPDB::read().

toInt()

int protocols::cluster::calibur::toInt

(

std::string const &

aString

)

References protocols::loops::start.

Referenced by protocols::cluster::calibur::PreloadedPDB::loadSilentFile(), and protocols::cluster::calibur::SimPDB::read().

Variable Documentation

aa

char protocols::cluster::calibur::aa[][4]

Initial value:

= {"BCK","GLY","ALA","SER","CYS","VAL","THR","ILE",
"PRO","MET","ASP","ASN","LEU",
"LYS","GLU","GLN","ARG",
"HIS","PHE","TYR","TRP","CYX", "MSE"}

Referenced by core::energy_methods::aa2idx(), core::chemical::NucleotideTools::aa2randomCodon(), protocols::mean_field::AAProb::aa_ind(), protocols::task_operations::SeqprofConsensusOperation::aa_occurrence_filter(), protocols::task_operations::SeqprofConsensusOperation::aa_probability_filter(), core::fragment::picking_old::vall::eval::IdentityEval::aa_str(), core::scoring::motif::aa_trustworthiness(), core::scoring::abego3aa_to_index(), core::io::raw_data::ScoreMap::add_arbitrary_string_data_from_pose(), core::pack::dunbrack::cenrot::CenrotLibrary::add_cenrot_residue_library(), protocols::relax::add_coordinate_constraint_func_atoms(), protocols::protein_interface_design::movers::add_coordinate_constraints(), protocols::simple_moves::StructProfileMover::add_MSAcst_to_pose(), core::io::PositionDdGInfo::PositionDdGInfo::add_mutation_ddG(), core::scoring::methods::NMerSVMEnergy::add_pssm_features(), core::pack::dunbrack::RotamerLibrary::add_residue_library(), core::chemical::ResidueTypeSetCache::all_types_with_variants_aa_already_cached(), protocols::seeded_abinitio::GrowPeptides::append_residues_cterminally(), protocols::seeded_abinitio::GrowPeptides::append_residues_nterminally(), protocols::ligand_docking::AddHydrogen::apply(), protocols::task_operations::ThreadSequenceOperation::apply(), protocols::protein_interface_design::filters::FilterScanFilter::apply(), protocols::task_operations::ResidueProbDesignOperation::apply(), protocols::protein_interface_design::movers::SecretionOptimizationMover::apply(), protocols::flxbb::FilterStructs_TotalCharge::apply(), protocols::task_operations::JointSequenceOperation::apply(), protocols::task_operations::SeqprofConsensusOperation::apply(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::apply_coord_cst_to_sctip(), core::scoring::ScoreFunctionFactory::apply_user_defined_reweighting_(), core::kinematics::inverse::assert_atoms_are_downstream_of_jump(), core::kinematics::inverse::assert_atoms_are_upstream_of_jump(), protocols::noesy_assign::PeakCalibrator::atom_type(), protocols::mean_field::AAMatrix::ave_abs_diff(), core::pack::interaction_graph::SurfaceNode< V, E, G >::average_residue_hASA(), core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >::average_residue_hASA(), protocols::indexed_structure_store::bind_StructureStore(), core::chemical::ResidueTypeSetCache::cache_all_types_with_variants_aa(), protocols::mean_field::FlexBBMeanField::calc_bb_boltz_probs(), core::energy_methods::MembraneEnvSmoothEnergy::calc_energy(), core::energy_methods::FaMPEnvSmoothEnergy::calc_energy(), core::energy_methods::EnvSmoothEnergy::calc_energy(), protocols::mean_field::FlexBBDesignMeanField::calc_exp_value_aa_matrix(), protocols::analysis::simple_metrics::SequenceRecoveryMetric::calculate(), core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::calculate_alt_state_hpatch_score(), core::pack::interaction_graph::SurfaceNode< V, E, G >::calculate_amount_total_hydrophobic_ASA(), core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >::calculate_amount_total_hydrophobic_ASA(), core::pack::guidance_scoreterms::sap::SapConstraintHelper::calculate_energy(), protocols::simple_moves::SampleSequenceFromProbabilities::calculate_position_diffs(), core::scoring::Ramachandran::cdf_for_aa(), core::scoring::Ramachandran::cdf_for_aa_for_torsion_bin(), protocols::forge::components::VarLengthBuild::centroid_build(), core::scoring::rna::RNA_LowResolutionPotential::check_atom_numbers_for_backbone_oxygens(), core::chemical::sdf::MolWriter::compose_naming(), core::simple_metrics::metrics::AverageProbabilitiesMetric::compute_average(), core::simple_metrics::composite_metrics::BestMutationsFromProbabilitiesMetric::compute_deltas(), core::energy_methods::MPEnvEnergy::compute_mpenv_score(), core::pack::interaction_graph::OnTheFlyNode::compute_rotamer_pair_energy(), core::pack::interaction_graph::SymmOnTheFlyNode::compute_rotamer_pair_energy(), protocols::task_operations::ConservativeDesignOperation::conserved_mutations(), protocols::simple_moves::SampleSequenceFromProbabilities::construct_modified_sequence(), protocols::toolbox::pose_manipulation::construct_poly_XXX_pose(), protocols::simple_moves::SaveProbabilitiesMetricMover::convert_probabilities_to_logits(), core::pack::dunbrack::cenrot::SingleResidueCenrotLibraryCreator::create(), core::pack::dunbrack::SingleResidueDunbrackLibraryCreator::create(), core::scoring::ScoringManager::create_nmer_pssm(), core::scoring::ScoringManager::create_nmer_svm_aa_matrix(), core::chemical::SetAACreator::create_operation(), core::scoring::P_AA::defines_p_aa_pp_energy_for_res(), protocols::forge::components::BDR::design_refine(), protocols::protein_interface_design::movers::SecretionOptimizationMover::DesignAroundApply(), core::io::silent::SilentStruct::detect_fullatom(), core::scoring::dna::DirectReadoutPotential::DirectReadoutPotential(), protocols::task_operations::RestrictAAsFromProbabilities::disable_AAs(), core::scoring::constraints::SequenceProfileConstraint::dist(), protocols::mean_field::AAMatrix::dump_transfac(), protocols::pockets::EggshellGrid::EggshellGrid(), core::scoring::methods::NMerSVMEnergy::encode_aa_string(), core::scoring::methods::NMerSVMEnergy::encode_wtd_avg_aa_string(), core::scoring::EnvPairPotential::EnvPairPotential(), core::scoring::OmegaTether::eval_omega_score_residue(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::eval_rotameric_energy(), core::scoring::rna::RNP_LowResPotential::evaluate_rnp_aa_rna_backbone_score(), core::scoring::rna::RNP_LowResPotential::evaluate_rnp_base_pair_score(), core::scoring::rna::RNP_LowResPotential::evaluate_rnp_pair_score(), core::scoring::rna::RNP_LowResStackData::evaluate_rnp_stack_xy_score(), core::energy_methods::FaMPAsymEzCBEnergy::FaMPAsymEzCBEnergy(), core::energy_methods::FaMPAsymEzCGEnergy::FaMPAsymEzCGEnergy(), core::energy_methods::FaMPEnvSmoothEnergy::FaMPEnvSmoothEnergy(), core::scoring::rna::RNA_LowResolutionPotential::fill_atom_numbers_for_backbone_oxygens(), core::energy_methods::MHCEpitopeEnergy::finalize_total_energy(), core::energy_methods::FreeDOF_Energy::finalize_total_energy(), core::energy_methods::DNA_EnvPairEnergy::finalize_total_energy(), core::energy_methods::AspartimidePenaltyEnergy::first_res_types(), protocols::denovo_design::task_operations::AAFrequencies::frequency(), protocols::denovo_design::task_operations::ConsensusLoopDatabase::frequency(), protocols::mean_field::AAMatrix::frob_distance(), core::chemical::full_name_from_aa(), protocols::jd3::JobGenealogist::garbage_collection(), core::chemical::Patch::generates_aa(), core::scoring::P_AA::get_aa_to_use(), core::chemical::ResidueTypeSet::get_all_types_with_variants_aa(), core::chemical::GlobalResidueTypeSet::get_all_types_with_variants_aa(), core::chemical::ResidueTypeSet::get_base_types_aa(), core::pack::dunbrack::cenrot::CenrotLibrary::get_cenrot_library_by_aa(), protocols::simple_moves::StructProfileMover::get_closest_sequence_at_res(), core::chemical::get_D_equivalent(), protocols::struct_fragment::StructFragmentMover::get_fragset(), core::scoring::hbonds::get_hb_acc_chem_type(), core::scoring::hbonds::get_hb_don_chem_type(), protocols::pockets::GenPharmacophore::get_ideal_hydrogenBond_atoms(), core::chemical::get_L_equivalent(), core::pack::dunbrack::RotamerLibrary::get_library_by_aa(), protocols::stepwise::modeler::rna::rigid_body::get_max_centroid_to_atom_distance(), protocols::optimize_weights::IterativeOptEDriver::get_nat_aa_opte_data(), core::scoring::P_AA::get_Paa_pp_deriv(), core::scoring::get_pairwise_atom_energies(), core::chemical::ResidueTypeSet::get_representative_type_aa(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_rotamer_from_chi_static(), protocols::optimize_weights::PNatAAOptEPositionData::get_score(), core::scoring::get_single_atom_energies(), protocols::sparta::Sparta::SpartaLib::getANN_PredError(), protocols::frag_picker::FragmentPicker::getFragSet(), protocols::forge::remodel::RemodelData::getLoopsToBuildFromBlueprint(), core::pose::carbohydrates::glycosylate_pose(), protocols::denovo_design::task_operations::AAFrequencies::has_frequency(), protocols::denovo_design::task_operations::ConsensusLoopDatabase::has_frequency(), protocols::sasa_scores::help_load_data(), protocols::simple_moves::Hit::Hit(), core::pack::guidance_scoreterms::sap::SapDatabase::hydrophobic_weight(), protocols::pockets::NonPlaidFingerprint::include_eggshell_points_based_on_known_ligand(), core::scoring::motif::MotifHashManager::init(), protocols::sparta::Sparta::SpartaLib::init(), core::scoring::motif::ResPairMotifQuery::init(), protocols::mean_field::RotMatrix::init(), protocols::mean_field::AAMatrix::init(), core::energy_methods::BurialEnergy::init_from_file(), protocols::dna::DnaInterfaceMultiStateDesign::initialize(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::initialize(), protocols::simple_filters::InterfaceHbondsFilter::initialize_charged_residue_map(), protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::initialize_filter(), protocols::match::Matcher::initialize_from_file(), core::pack::task::PIKAA::initialize_from_tokens(), core::pack::task::NOTAA::initialize_from_tokens(), core::sequence::ProfSimScoringScheme::initialize_parameters(), core::scoring::rna::RNP_LowResPotential::initialize_rnp_aa_rna_backbone(), core::scoring::rna::RNP_LowResPotential::initialize_rnp_base_pair(), core::scoring::rna::RNP_LowResPotential::initialize_rnp_pair(), core::scoring::rna::RNP_LowResPairDistPotential::initialize_rnp_pair_dist(), core::scoring::rna::RNP_LowResStackData::initialize_rnp_stack_xy(), protocols::ligand_docking::ga_ligand_dock::GAOptimizer::initialize_rotamer_set_and_scores(), protocols::design_opt::insert_point_mut_filter_vals(), protocols::matdes::insert_point_mut_filter_vals(), core::import_pose::libraries::ChunkSet::insert_protein_chunk_into_pose(), protocols::scoring::InterchainPotential::InterchainPotential(), protocols::simple_moves::SampleSequenceFromProbabilities::is_aa_allowed_by_task(), core::energy_methods::ArgCationPiEnergy::is_arg(), core::scoring::constraints::is_aromatic(), core::chemical::is_canonical_beta3_aa(), core::chemical::is_canonical_D_aa(), core::chemical::is_canonical_L_aa_excluding_gly(), core::chemical::is_canonical_L_aa_or_gly(), core::energy_methods::ArgCationPiEnergy::is_his(), protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::is_isopeptide_forming_carbonyl_type(), core::energy_methods::ArgCationPiEnergy::is_phe(), core::energy_methods::ArgCationPiEnergy::is_trp(), core::energy_methods::ArgCationPiEnergy::is_tyr(), protocols::noesy_assign::label_atom_name(), protocols::noesy_assign::CrossPeakInfo::label_atom_name(), core::pack::guidance_scoreterms::sap::SapConstraintHelper::lightning_1b_lookup(), protocols::multistate_design::list_amino_acid_options(), protocols::indexed_structure_store::FragmentStoreManager::load_and_hash_fragmentStore(), protocols::noesy_assign::MethylNameLibrary::load_database_table(), core::scoring::mhc_epitope_energy::MHCEpitopePredictorMatrix::load_matrix(), core::scoring::membrane::MembraneData::load_menv_info(), protocols::protein_interface_design::ReportPSSMDifferences::load_pssm_data(), protocols::optimize_weights::IterativeOptEDriver::load_pssm_data(), core::scoring::dna::DNA_EnvPairPotential::load_score_tables(), protocols::motifs::make_base_pair_mutation(), core::io::mmtf::make_current_group(), core::fragment::make_pose_from_sequence_(), protocols::tcr::match_template_and_target_sequence(), core::pack::guidance_scoreterms::sap::SapDatabase::max_sasa(), core::energy_methods::MembraneEnvSmoothEnergy::MembraneEnvSmoothEnergy(), core::scoring::MembranePotential::MembranePotential(), core::pack::guidance_scoreterms::sap::SapConstraintHelper::my_hydrophobic_weight(), core::chemical::name_from_aa(), protocols::protein_interface_design::movers::nearest_atom_for_constraint(), core::chemical::oneletter_code_from_aa(), core::chemical::GraphvizPropertyWriter::operator()(), core::chemical::operator<<(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::operator==(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::operator==(), protocols::frags::operator>>(), core::chemical::operator>>(), protocols::noesy_assign::MethylNameLibrary::operator[](), protocols::optimize_weights::IterativeOptEDriver::output_weighted_unfolded_energies(), core::scoring::P_AA_ABEGO3::P_AA_ABEGO3_energy(), core::scoring::P_AA::P_AA_energy(), core::scoring::P_AA::P_AA_pp_energy(), core::scoring::P_AA_ss::P_AA_ss_energy(), core::chemical::sdf::CtabV2000Parser::parse(), protocols::mean_field::AAMatrix::parse_aa_matrix_line(), protocols::flxbb::LayerDesignOperation::parse_layer_secstruct_tag(), protocols::calc_taskop_filters::RotamerBoltzmannWeight::parse_my_tag(), core::scoring::constraints::parse_NMR_name(), core::scoring::constraints::parse_NMR_name_old(), protocols::ligand_docking::StartFrom::parse_pdb_file(), core::pose::parse_sequence(), core::pack::task::operation::DesignRestrictions::parse_tag(), core::io::pose_from_sfr::PoseFromSFRBuilder::pass_2_quick_and_dirty_resolve_residue_types(), core::scoring::Ramachandran::phipsi_in_allowed_rama(), core::scoring::Ramachandran::phipsi_in_forbidden_rama(), core::fragment::picking_old::vall::pick_fragments(), core::fragment::picking_old::vall::pick_fragments_by_ss_plus_aa(), protocols::protein_interface_design::movers::LoopRemodel::pick_loop_frags(), protocols::drug_design::place_new_restype_rotamer_align(), core::scoring::motif::Xfres::place_sidechain_in_pose(), core::pack::interaction_graph::SurfaceNode< V, E, G >::print(), protocols::optimize_weights::PNatAAOptEPositionData::print_score(), protocols::forge::components::BDR::process_insert_design_string(), protocols::forge::remodel::RemodelMover::process_insert_design_string(), protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::process_score(), core::scoring::methods::NMerPSSMEnergy::pssm_energy_at_frame_seqpos(), core::scoring::Ramachandran::rama_probability(), protocols::frag_picker::LAMBEGO_IO::read(), protocols::frag_picker::TorsionBinIO::read(), protocols::frag_picker::CSTalosIO::read(), protocols::frag_picker::PhiPsiTalosIO::read(), protocols::frag_picker::CS2ndShift::read_adjust_table(), protocols::parser::BluePrint::read_blueprint_stream(), core::sequence::MatrixScoringScheme::read_data(), protocols::denovo_design::task_operations::ConsensusLoopDatabase::read_db(), protocols::simple_filters::ResidueDepthFilter::read_db(), core::energy_methods::SequenceDependentRefEnergy::read_energy_weight_table(), protocols::frags::TorsionFragmentLibrary::read_file(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::read_file(), core::fragment::MinimalFragSet::read_fragment_stream(), core::fragment::ConstantLengthFragSet::read_fragment_stream(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::read_from_binary(), core::sequence::SequenceProfile::read_from_checkpoint(), core::sequence::ChemicalShiftSequence::read_from_file(), core::sequence::SequenceProfile::read_from_file(), protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::read_from_file(), protocols::optimize_weights::PNatAAOptEPositionData::read_from_file(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::read_from_file(), protocols::noesy_assign::ResonanceList::read_from_stream(), core::scoring::P_AA::read_P_AA(), core::scoring::P_AA::read_P_AA_n(), core::scoring::P_AA::read_P_AA_pp(), core::scoring::P_AA_ss::read_P_AA_ss(), core::scoring::PointWaterPotential::read_pointwater_tables(), core::fragment::SecondaryStructure::read_psipred_ss2(), core::pose::read_psipred_ss2_file(), core::scoring::Ramachandran::read_rama_map_file_shapovalov(), core::chemical::ResidueDatabaseIO::read_residue_type(), protocols::frag_picker::CS2ndShift::read_sslimit_table(), core::fragment::SecondaryStructure::read_talos_ss(), protocols::pockets::NonPlaidFingerprint::remove_duplicate_phi_psi(), core::energy_methods::EnvSmoothEnergy::representative_atom_name(), core::energy_methods::MembraneEnvSmoothEnergy::representative_atom_name(), core::energy_methods::FaMPAsymEzCBEnergy::representative_atom_name(), core::energy_methods::FaMPAsymEzCGEnergy::representative_atom_name(), core::energy_methods::FaMPEnvSmoothEnergy::representative_atom_name(), core::energy_methods::ProQ_Energy::res6(), core::energy_methods::MPEnvEnergy::residue_energy(), core::energy_methods::ReferenceEnergy::residue_energy(), core::energy_methods::SequenceDependentRefEnergy::residue_energy(), core::scoring::methods::NMerPSSMEnergy::residue_energy(), protocols::fldsgn::potentials::AACompositionEnergy::residue_energy(), core::scoring::dna::DNA_EnvPairPotential::residue_env_score(), core::scoring::dna::DNA_EnvPairPotential::residue_pair_score(), core::chemical::residue_selector_single_from_line(), core::pose::residue_types_from_sequence(), core::scoring::constraints::ResidueCouplingConstraint::ResidueCouplingConstraint(), core::scoring::constraints::ResidueTypeLinkingConstraint::ResidueTypeLinkingConstraint(), protocols::task_operations::ThreadSequenceOperation::restrict_aas(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::restrict_sequence_profile(), core::chemical::ResidueTypeSetCache::retrieve_all_types_with_variants_aa(), protocols::mean_field::RotProb::rot_ind(), protocols::frag_picker::sa_faraggi_max(), protocols::match::upstream::DunbrackSCSampler::samples(), protocols::simple_moves::SaveProbabilitiesMetricMover::save_aa_probabilities_to_file(), core::scoring::constraints::SequenceProfileConstraint::score(), protocols::constraints_additional::SequenceCoupling1BDConstraint::score(), core::energy_methods::AspartimidePenaltyEnergy::second_res_types(), protocols::indexed_structure_store::SegmentSequenceProfile::segment_profile(), core::chemical::ResidueTypeSelector::set_aa(), protocols::optimize_weights::IterativeOptEDriver::set_aa_periodicity(), protocols::task_operations::ResidueProbDesignOperation::set_aa_probabilities_from_file(), core::pack::interaction_graph::SparseMatrixIndex::set_aa_type(), core::scoring::methods::EnergyMethodOptions::set_density_sc_scale_byres(), protocols::denovo_design::task_operations::AAFrequencies::set_frequency(), protocols::denovo_design::task_operations::ConsensusLoopDatabase::set_frequency(), core::chemical::sdf::MolFileIOMolecule::set_from_extra_data(), protocols::fldsgn::BluePrintBDR::set_instruction_blueprint(), protocols::fldsgn::potentials::SetAACompositionPotential::set_parameters(), core::simple_metrics::per_residue_metrics::LoadedProbabilitiesMetric::set_probabilities_from_lines(), protocols::simple_moves::MutateResidue::set_res_name(), protocols::task_operations::DsspDesignOperation::set_restrictions_exclude(), protocols::pockets::NonPlaidFingerprint::set_rho_to_zero(), protocols::loops::set_secstruct_from_dssp(), protocols::forge::remodel::RemodelLoopMover::set_starting_sequence(), protocols::electron_density::DockPDBIntoDensityMover::setMultiNative(), core::scoring::fiber_diffraction::setup_centroid_scatter(), core::energy_methods::Abego::setup_for_scoring(), core::scoring::SS_Killhairpins_Info::setup_from_psipred(), core::scoring::constraints::SequenceProfileConstraint::show(), protocols::denovo_design::components::Picker::ss_key(), protocols::hbnet::HBNetStapleInterface::state_is_starting_aa_type(), protocols::noesy_assign::FragsToAtomDist::swap_atoms(), protocols::simple_moves::ResTypeFragmentMover::swap_residue_types(), core::pack::guidance_scoreterms::sap::SapConstraintHelper::symm_calculate_energy(), core::pack::task::ResidueLevelTask_::target_type(), protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::to_sequence_profile(), protocols::vip::VIP_Mover::try_point_mutants(), core::pack::dunbrack::RotamerLibrary::validate_dunbrack_binary(), core::sequence::MatrixScoringScheme::values_for_aa(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::verify_bb_bins(), protocols::noesy_assign::PeakFileFormat_Sparky::write_assignment(), protocols::noesy_assign::PeakFileFormat_xpk::write_assignment(), core::chemical::ResidueDatabaseIO::write_residue_type_table_schema(), protocols::noesy_assign::ResonanceList::write_talos_format(), protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::write_to_file(), protocols::noesy_assign::ResonanceList::write_to_stream(), and core::scoring::motif::Xfres::Xfres().

slc

char protocols::cluster::calibur::slc[]

Initial value:

= {'X','G','A','S','C','V','T','I',
'P','M','D','N','L','K','E','Q','R',
'H','F','Y','W','C', 'm'}