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protocols::cluster::calibur Namespace Reference

Classes

class  AdjacentList
 
class  Clustering
 
class  PreloadedPDB
 
class  SimPDB
 
class  Stru
 

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

typedef utility::pointer::shared_ptr< AdjacentList > protocols::cluster::calibur::AdjacentListOP
typedef utility::pointer::shared_ptr< PreloadedPDB > protocols::cluster::calibur::PreloadedPDBOP
typedef utility::pointer::shared_ptr< SimPDB > protocols::cluster::calibur::SimPDBOP
typedef std::vector< std::string > protocols::cluster::calibur::StringVec
typedef utility::pointer::shared_ptr< StringVec > protocols::cluster::calibur::StringVecOP
typedef utility::pointer::shared_ptr< Stru > protocols::cluster::calibur::StruOP

Enumeration Type Documentation

Enumerator
MATRIX 
LIST 
LITE 
Enumerator
PERCENT_EDGES 
MIN_AVG_DIST_BASED 
MOST_FREQ_BASED 
ROSETTA 
SAMPLED_ROSETTA 
USER_SPECIFIED 
Enumerator
UNKNOWN 
SILENT_FILE 
PDB_LIST 

Function Documentation

static int protocols::cluster::calibur::__cmp ( const void *  a,
const void *  b 
)
static
core::Real protocols::cluster::calibur::__timeval_difference ( struct timeval *  x,
struct timeval *  y 
)

Referenced by _get_elapsed().

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

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.

core::Real protocols::cluster::calibur::fast_rmsd ( std::vector< core::Real > &  coords1,
std::vector< core::Real > &  coords2,
int  n 
)
INPUT_FILE_TYPE protocols::cluster::calibur::filetype ( std::string const &  filename)
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::pack::dunbrack::c, NUM_ITER, ROTATE(), SMALL_NUM_ITER, and protocols::hybridization::t.

Referenced by RMSD().

unsigned int protocols::cluster::calibur::num_lines_in_file ( std::string const &  filename)
void protocols::cluster::calibur::print_matrix ( core::Real  a[3][3])
core::Real protocols::cluster::calibur::RMSD ( std::vector< core::Real > &  coords1,
std::vector< core::Real > &  coords2,
int  n,
core::Real  R[3][3] 
)
core::Real protocols::cluster::calibur::RMSD ( std::vector< core::Real > &  coords1,
std::vector< core::Real > &  coords2,
int  n 
)
template<class T >
void protocols::cluster::calibur::ROTATE ( T &  a,
int  x1,
int  y1,
int  x2,
int  y2,
core::Real  s,
core::Real  tau 
)

Referenced by jacobi3().

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

Variable Documentation

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::scoring::saxs::aa2idx(), core::chemical::NucleotideTools::aa2randomCodon(), protocols::mean_field::AAProb::aa_ind(), core::fragment::picking_old::vall::eval::IdentityEval::aa_str(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::add_aa_virt_rsd_as_root(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::add_aa_virt_rsd_as_root(), 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::relax::add_coordinate_constraints_to_pose(), protocols::loops::add_coordinate_constraints_to_pose(), protocols::backrub::BackrubMover::add_mainchain_segments(), protocols::simple_moves::StructProfileMover::add_MSAcst_to_pose(), core::scoring::methods::NMerSVMEnergy::add_pssm_features(), core::pack::dunbrack::RotamerLibrary::add_residue_library(), protocols::rna::movers::ErraserMinimizerMover::add_virtual_res(), protocols::toolbox::sample_around::add_virtual_res(), core::pose::addVirtualResAsRoot(), protocols::seeded_abinitio::GrowPeptides::append_residues_cterminally(), protocols::seeded_abinitio::GrowPeptides::append_residues_nterminally(), core::pose::full_model_info::append_virtual_residue_to_full_model_info(), protocols::simple_moves::VirtualRootMover::apply(), protocols::ligand_docking::AddHydrogen::apply(), protocols::protein_interface_design::filters::FilterScanFilter::apply(), core::select::residue_selector::NumNeighborsSelector::apply(), protocols::task_operations::ResidueProbDesignOperation::apply(), protocols::task_operations::JointSequenceOperation::apply(), protocols::task_operations::SeqprofConsensusOperation::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::idealize::IdealizeMover::apply(), protocols::rna::movers::RNAThreadAndMinimizeMover::apply(), protocols::flxbb::FilterStructs_TotalCharge::apply(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::apply_coord_cst_to_sctip(), protocols::loophash::BackboneSegment::apply_to_pose(), core::scoring::ScoreFunctionFactory::apply_user_defined_reweighting_(), 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(), protocols::mean_field::FlexBBMeanField::calc_bb_boltz_probs(), core::scoring::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::scoring::Ramachandran::cdf_for_aa(), protocols::forge::components::VarLengthBuild::centroid_build(), core::chemical::sdf::MolWriter::compose_naming(), core::scoring::membrane::MPEnvEnergy::compute_mpenv_score(), core::pack::interaction_graph::OnTheFlyNode::compute_rotamer_pair_energy(), core::pack::interaction_graph::SymmOnTheFlyNode::compute_rotamer_pair_energy(), protocols::toolbox::pose_manipulation::construct_poly_XXX_pose(), core::pack::dunbrack::SingleResidueDunbrackLibraryCreator::create(), core::pack::dunbrack::cenrot::SingleResidueCenrotLibraryCreator::create(), core::scoring::ScoringManager::create_nmer_pssm(), core::scoring::ScoringManager::create_nmer_svm_aa_matrix(), protocols::forge::components::BDR::design_refine(), core::io::silent::SilentStruct::detect_fullatom(), core::scoring::dna::DirectReadoutPotential::DirectReadoutPotential(), 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::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::eval_rotameric_energy_deriv(), 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::scoring::membrane::FaMPEnvSmoothEnergy::FaMPEnvSmoothEnergy(), protocols::residue_optimization::MetapatchEnumeration::final_sampling(), core::scoring::methods::DNA_EnvPairEnergy::finalize_total_energy(), core::scoring::methods::FreeDOF_Energy::finalize_total_energy(), protocols::forge::methods::fold_tree_from_loops(), protocols::loops::fold_tree_from_loops(), protocols::mean_field::AAMatrix::frob_distance(), protocols::jd3::JobGenealogist::garbage_collection(), protocols::relax::AtomCoordinateCstMover::generate_constraints(), core::chemical::Patch::generates_aa(), core::scoring::P_AA::get_aa_to_use(), core::pack::dunbrack::cenrot::CenrotLibrary::get_cenrot_library_by_aa(), protocols::simple_moves::StructProfileMover::get_closest_sequence_at_res(), 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::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(), protocols::simple_filters::ResidueDepthFilter::get_residue_similarity(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::get_rotamer_from_chi_static(), protocols::loophash::get_rt_over_leap(), protocols::loophash::get_rt_over_leap_fast(), protocols::optimize_weights::PNatAAOptEPositionData::get_score(), core::import_pose::RNA_BasePairHandler::get_stem_residues(), protocols::sparta::Sparta::SpartaLib::getANN_PredError(), protocols::frag_picker::FragmentPicker::getFragSet(), protocols::forge::remodel::RemodelData::getLoopsToBuildFromBlueprint(), core::pose::carbohydrates::glycosylate_pose(), protocols::sasa_scores::help_load_data(), protocols::simple_moves::Hit::Hit(), protocols::pockets::NonPlaidFingerprint::include_eggshell_points_based_on_known_ligand(), protocols::sparta::Sparta::SpartaLib::init(), protocols::mean_field::AAMatrix::init(), protocols::mean_field::RotMatrix::init(), core::scoring::motif::ResPairMotifQuery::init(), core::scoring::motif::MotifHashManager::init(), core::scoring::methods::BurialEnergy::init_from_file(), protocols::residue_optimization::MetapatchEnumeration::initial_sampling(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::initialize(), protocols::dna::DnaInterfaceMultiStateDesign::initialize(), protocols::simple_filters::InterfaceHbondsFilter::initialize_charged_residue_map(), 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(), protocols::features::ReportToDB::initialize_pose(), 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::rna::denovo::RNA_DeNovoPoseInitializer::initialize_secstruct(), core::import_pose::libraries::ChunkSet::insert_protein_chunk_into_pose(), protocols::scoring::InterchainPotential::InterchainPotential(), core::scoring::methods::ArgCationPiEnergy::is_arg(), core::scoring::methods::ArgCationPiEnergy::is_his(), core::scoring::RamaPrePro::is_N_substituted(), core::scoring::methods::ArgCationPiEnergy::is_phe(), core::scoring::methods::ArgCationPiEnergy::is_trp(), core::scoring::methods::ArgCationPiEnergy::is_tyr(), protocols::multistate_design::list_amino_acid_options(), 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(), protocols::simple_moves::sidechain_moves::SidechainMover::make_move(), core::fragment::make_pose_from_sequence_(), protocols::tcr::match_template_and_target_sequence(), core::scoring::methods::MembraneEnvSmoothEnergy::MembraneEnvSmoothEnergy(), core::scoring::MembranePotential::MembranePotential(), protocols::forge::build::BuildManager::modify(), 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::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::operator==(), core::pack::dunbrack::SemiRotamericSingleResidueDunbrackLibrary< T, N >::operator==(), protocols::frags::operator>>(), protocols::optimize_weights::IterativeOptEDriver::output_weighted_unfolded_energies(), core::scoring::P_AA::P_AA_energy(), core::scoring::P_AA::P_AA_pp_energy(), core::scoring::P_AA_ss::P_AA_ss_energy(), protocols::fldsgn::filters::ParallelBetaPairingPreferenceFilter::ParallelBetaPairingPreferenceFilter(), 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::chemical::patch_operation_from_patch_file_line(), protocols::protein_interface_design::movers::LoopRemodel::pick_loop_frags(), core::scoring::motif::Xfres::place_sidechain_in_pose(), protocols::constraint_generator::CoordinateConstraintGenerator::prepare_constraint_target_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(), 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::scoring::methods::SequenceDependentRefEnergy::read_energy_weight_table(), protocols::frags::TorsionFragmentLibrary::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(), protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::read_from_file(), core::sequence::ChemicalShiftSequence::read_from_file(), core::sequence::SequenceProfile::read_from_file(), core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary< T, N >::read_from_file(), protocols::optimize_weights::PNatAAOptEPositionData::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::scoring::methods::ProQ_Energy::res6(), core::scoring::methods::SequenceDependentRefEnergy::residue_energy(), core::scoring::methods::ReferenceEnergy::residue_energy(), core::scoring::methods::NMerPSSMEnergy::residue_energy(), core::scoring::membrane::MPEnvEnergy::residue_energy(), protocols::fldsgn::potentials::AACompositionEnergy::residue_energy(), core::scoring::dna::DNA_EnvPairPotential::residue_env_score(), core::scoring::methods::CartesianBondedEnergy::residue_pair_energy_sorted(), 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::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::restrict_sequence_profile(), protocols::stepwise::modeler::revise_root_and_moving_res_list(), protocols::mean_field::RotProb::rot_ind(), protocols::match::upstream::DunbrackSCSampler::samples(), protocols::constraints_additional::SequenceCoupling1BDConstraint::score(), core::scoring::constraints::SequenceProfileConstraint::score(), protocols::indexed_structure_store::SegmentSequenceProfile::segment_profile(), protocols::task_operations::ResidueProbDesignOperation::set_aa_probabilities_from_file(), core::pack::interaction_graph::SparseMatrixIndex::set_aa_type(), protocols::denovo_design::task_operations::AAFrequencies::set_frequency(), core::chemical::sdf::MolFileIOMolecule::set_from_extra_data(), protocols::fldsgn::BluePrintBDR::set_instruction_blueprint(), protocols::fldsgn::potentials::SetAACompositionPotential::set_parameters(), 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::relax::RelaxProtocolBase::set_up_constraints(), core::scoring::fiber_diffraction::setup_centroid_scatter(), protocols::rbsegment_relax::setup_disconnected(), core::scoring::methods::Abego::setup_for_scoring(), core::scoring::SS_Killhairpins_Info::setup_from_psipred(), protocols::rbsegment_relax::setup_pose_rbsegs_keep_loops(), core::scoring::constraints::SequenceProfileConstraint::show(), protocols::hbnet::HBNetStapleInterface::state_is_starting_aa_type(), protocols::noesy_assign::FragsToAtomDist::swap_atoms(), protocols::simple_moves::ResTypeFragmentMover::swap_residue_types(), protocols::calc_taskop_filters::RelativePoseFilter::thread_seq(), protocols::indexed_structure_store::movers::SegmentSequenceProfileMover::to_sequence_profile(), protocols::hybridization::MRMover::trim_target_pose(), 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().

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'}