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Namespaces | Variables
basic::options::OptionKeys::frags Namespace Reference

Namespaces

 ABEGO
 
 contacts
 
 nonlocal
 
 picking
 
 scoring
 

Variables

BooleanOptionKey const frags
 
IntegerOptionKey const j
 
BooleanOptionKey const filter_JC
 
BooleanOptionKey const bounded_protocol
 
BooleanOptionKey const keep_all_protocol
 
BooleanOptionKey const quota_protocol
 
BooleanOptionKey const nonlocal_pairs
 
BooleanOptionKey const fragment_contacts
 
BooleanOptionKey const p_value_selection
 
IntegerOptionKey const n_frags
 
FileOptionKey const allowed_pdb
 
StringVectorOptionKey const ss_pred
 
FileOptionKey const spine_x
 
FileOptionKey const depth
 
FileOptionKey const denied_pdb
 
IntegerVectorOptionKey const frag_sizes
 
BooleanOptionKey const write_ca_coordinates
 
BooleanOptionKey const write_scores
 
BooleanOptionKey const annotate
 
IntegerOptionKey const nr_large_copies
 
IntegerOptionKey const n_candidates
 
BooleanOptionKey const write_rama_tables
 
RealOptionKey const rama_C
 
RealOptionKey const rama_B
 
RealOptionKey const sigmoid_cs_A
 
RealOptionKey const sigmoid_cs_B
 
RealOptionKey const seqsim_H
 
RealOptionKey const seqsim_E
 
RealOptionKey const seqsim_L
 
RealOptionKey const rama_norm
 
StringOptionKey const describe_fragments
 
RealOptionKey const picking_old_max_score
 
BooleanOptionKey const write_sequence_only
 
BooleanOptionKey const output_silent
 
BooleanOptionKey const output_index
 
BooleanOptionKey const score_output_silent
 

Variable Documentation

FileOptionKey const basic::options::OptionKeys::frags::allowed_pdb

Referenced by add_rosetta_options_8().

BooleanOptionKey const basic::options::OptionKeys::frags::annotate

Referenced by add_rosetta_options_8().

BooleanOptionKey const basic::options::OptionKeys::frags::bounded_protocol

Referenced by add_rosetta_options_8().

FileOptionKey const basic::options::OptionKeys::frags::denied_pdb

Referenced by add_rosetta_options_8().

FileOptionKey const basic::options::OptionKeys::frags::depth
StringOptionKey const basic::options::OptionKeys::frags::describe_fragments

Referenced by add_rosetta_options_9().

BooleanOptionKey const basic::options::OptionKeys::frags::filter_JC

Referenced by add_rosetta_options_8().

IntegerVectorOptionKey const basic::options::OptionKeys::frags::frag_sizes

Referenced by add_rosetta_options_8(), and Prepare().

BooleanOptionKey const basic::options::OptionKeys::frags::fragment_contacts

Referenced by add_rosetta_options_8().

BooleanOptionKey const basic::options::OptionKeys::frags::frags
IntegerOptionKey const basic::options::OptionKeys::frags::j

Referenced by numeric::model_quality::RmsData::add_rms(), add_rosetta_options_8(), AnchorFinderMover::apply(), PeptoidDesignMover::apply(), MPDomainAssembly::apply(), DougsDockDesignMinimizeMagicMover::apply(), ObjexxFCL::ChunkVector< typename >::assign(), IAMover::assign_IA_mover(), average_score_components(), supercharge::AvNAPSA_values(), numeric::AxisRotationSampler::AxisRotationSampler(), utility::io::base64_decode(), utility::io::base64_encode(), HDmakerMover::bb_score(), ExposedStrandMover::bb_score(), utility::BitVector< B >::BitVector(), numeric::kinematic_closure::radians::bridge_objects(), numeric::kinematic_closure::bridgeObjects(), numeric::kinematic_closure::bridgeObjects_nonredundant(), numeric::kinematic_closure::build_sin_and_cos(), caculate_order_scores(), calc_rama_scores(), numeric::model_quality::calc_rms_fast(), calculate_average_residue_scores(), calculate_burial(), calculate_res_map(), numeric::kinematic_closure::chainTORS(), numeric::kinematic_closure::radians::chainTORS(), numeric::kinematic_closure::chainXYZ(), numeric::kinematic_closure::radians::chainXYZ(), ObjexxFCL::ChunkVector< typename >::ChunkVector(), ScoreFragmentSetMover::clash_score(), numeric::model_quality::RmsData::clear_rms(), ObjexxFCL::Cstring::compress(), ObjexxFCL::Fstring::compress(), compute_folding_energies(), numeric::alignment::coordinate_array_broadcast_rmsd(), numeric::alignment::coordinate_array_rmsd(), correct_dunbrack(), correct_rama(), create_bp_jump_database_test(), DockFragmentsMover::cut_from_map(), define_interface(), numeric::interpolation::spline::TricubicSpline::dFdx(), numeric::interpolation::spline::BicubicSpline::dFdx(), numeric::interpolation::spline::TricubicSpline::dFdy(), numeric::interpolation::spline::BicubicSpline::dFdy(), numeric::interpolation::spline::TricubicSpline::dFdz(), numeric::kinematic_closure::dixon_sturm(), do_color_by_score(), drrafter_error_estimation(), dump_table(), numeric::eigenvalue_jacobi(), numeric::eigenvector_jacobi(), numeric::linear_algebra::GeneralizedEigenSolver< _MatrixType >::extract_eigenvectors(), numeric::interpolation::spline::TricubicSpline::F(), numeric::interpolation::spline::BicubicSpline::F(), numeric::interpolation::spline::BicubicSpline::FdF(), zinc2_homodimer_setup::filter_metal_geom(), ObjexxFCL::Fstring::find_first_not_of(), ObjexxFCL::Fstring::find_first_of(), ObjexxFCL::Fstring::find_last_not_of(), ObjexxFCL::Fstring::find_last_of(), find_neighbors(), find_neighbors_directional(), find_residues_around_mutation(), numeric::model_quality::findUU(), numeric::fourier::SHT::forwardS2(), utility::fractional_rank(), numeric::UniformRotationSampler::generateIcosahedralSamples(), numeric::fourier::SO3coeffs::genWigner_ds(), get_clash_pairs(), numeric::MathNTensor< double, 2 >::get_mathmatrix(), get_median_structure(), get_n_pep_nbrs(), get_obligated_rna_pairings(), SVC_Q::get_Q(), ONE_CLASS_Q::get_Q(), SVR_Q::get_Q(), go_main(), ObjexxFCL::Cstring::has_any_of(), ObjexxFCL::Fstring::has_any_of(), utility::options::ScalarOption_T_< PathOptionKey, file::PathName >::has_any_of_characters(), utility::options::VectorOption_T_< BooleanVectorOptionKey, bool >::has_any_of_characters(), has_clash(), numeric::alignment::indexed_coordinate_array_broadcast_rmsd(), numeric::geometry::hashing::SixDOffsetTree::init(), numeric::random::mt19937_RG::init_by_array(), UBQ_GTPase_disulfide_Mover::init_on_new_input(), UBQ_E2Mover::init_on_new_input(), interface_rmsd(), numeric::MathMatrix< float >::inverse_square_matrix(), numeric::MathMatrix< float >::inverse_tridiagonal_matrix(), numeric::fourier::SHT::inverseSo3(), numeric::fourier::SO3coeffs::InvLegendre(), is_deletable(), numeric::MathMatrix< float >::is_diagonal(), ObjexxFCL::FArray2< T >::is_identity(), numeric::MathMatrix< float >::is_tri_diagonal(), numeric::fourier::SO3coeffs::Legendre(), ObjexxFCL::ChunkVector< typename >::length(), ObjexxFCL::ChunkVector< typename >::length_squared(), ligand_rmsd(), numeric::nls::lm_lmdif(), numeric::nls::lm_lmpar(), numeric::nls::lm_qrfac(), numeric::nls::lm_qrsolv(), numeric::nls::lmmin(), utility::options::OptionCollection::load_options_from_stream(), numeric::geometry::hashing::SixDOffsetTree::lookup(), main(), make_1mer_frags(), basic::database::make_compound_statement(), make_fragments(), make_frags(), numeric::model_quality::MatrixMult(), numeric::model_quality::maxsub(), numeric::linear_algebra::minimum_bounding_ellipse(), numeric::kinematic_closure::modp(), multiclass_probability(), numeric::kinematic_closure::multMatrix(), numeric::kinematic_closure::multTransMatrix(), nucleobase_probe_score_test(), numeric::interpolation::InterpolatedPotential< N >::operator()(), numeric::operator*(), ObjexxFCL::FArray2< T >::operator*=(), numeric::MathMatrix< float >::operator*=(), ObjexxFCL::ChunkVector< typename >::operator+=(), ObjexxFCL::ChunkVector< typename >::operator-=(), ObjexxFCL::ChunkVector< typename >::operator=(), output_canonical_base_pair_steps(), output_general_base_pair_steps(), output_packstat(), output_packstat_pdb(), ScoreFragmentSetMover::overlap_score(), numeric::random::mt19937_RG::period_certification(), Prepare(), numeric::principal_components_and_eigenvalues(), numeric::principal_components_and_eigenvalues_ndimensions(), numeric::kinematic_closure::printTranspose(), numeric::product(), numeric::linear_algebra::qzhes(), numeric::linear_algebra::qzit(), numeric::linear_algebra::qzval(), numeric::linear_algebra::qzvec(), numeric::IntervalSet< double >::random_point(), read_rama_map_file(), numeric::linear_algebra::GeneralizedEigenSolver< _MatrixType >::real_eigenvectors(), Solver::reconstruct_gradient(), numeric::UniformRotationSampler::remove_redundant(), repack_test(), ObjexxFCL::FArray2< T >::right_multiply_by_transpose(), numeric::model_quality::rms_fit(), numeric::model_quality::rms_wrapper_slow_and_correct(), numeric::model_quality::rmsfitca2(), numeric::model_quality::rmsfitca3(), rna_suitename(), numeric::model_quality::rsym_rotation(), numeric::xyzTransform< numeric::Real >::rt6(), DockFragmentsMover::run(), ConsensusFragmentMover::run(), basic::svd::SVD_Solver::run_score_svd_on_matrix(), basic::svd::SVD_Solver::run_score_svd_without_solving(), RunPepSpec(), FragmentAssemblyMover::score(), Solver::select_working_set(), Solver_NU::select_working_set(), ObjexxFCL::FArray2< T >::set_diagonal(), basic::svd::SVD_Solver::set_matrix_A(), supercharge::set_resfile(), supercharge::set_resfile_AvNAPSA(), supercharge::set_surface(), setup_ca_constraints(), numeric::fourier::SHT::setup_Pmls(), setup_rmsd_atom_map(), numeric::fourier::SHT::setup_Weights(), slice_ellipsoid_envelope(), Solver::Solve(), numeric::kinematic_closure::solve_sturm(), numeric::fourier::SHT::sph_standardize(), basic::options::start_files(), store_energies(), utility::string_split(), utility::string_split_multi_delim(), utility::string_split_simple(), basic::svd::SVD_Solver::svbksb(), numeric::linear_algebra::svdcmp(), basic::svd::SVD_Solver::svdcmp(), svm_binary_svc_probability(), svm_check_parameter(), svm_cross_validation(), svm_group_classes(), svm_load_model(), svm_predict_probability(), svm_predict_values(), svm_save_model(), svm_train(), Kernel::swap_index(), ObjexxFCL::FArray2< T >::symmetric(), numeric::kinematic_closure::test_chainParams(), numeric::kinematic_closure::test_chainTORS(), numeric::kinematic_closure::test_chainXYZ(), numeric::kinematic_closure::test_dixon(), numeric::kinematic_closure::test_frame(), numeric::kinematic_closure::test_rotateX(), ObjexxFCL::FArray2< T >::to_diag(), ObjexxFCL::FArray2< T >::to_identity(), numeric::MathMatrix< float >::transpose(), ObjexxFCL::FArray2< T >::transpose(), ObjexxFCL::transposed(), numeric::kinematic_closure::triaxialCoefficients(), numeric::kinematic_closure::radians::triaxialCoefficients(), numeric::UniformRotationSampler::UniformRotationSampler(), numeric::fourier::SO3coeffs::wignerSynthesis(), numeric::fourier::SO3coeffs::wignerSynthesisDiffSign(), and numeric::fourier::SO3coeffs::wignerSynthesisSameSign().

BooleanOptionKey const basic::options::OptionKeys::frags::keep_all_protocol

Referenced by add_rosetta_options_8().

IntegerOptionKey const basic::options::OptionKeys::frags::n_candidates

Referenced by add_rosetta_options_8().

IntegerOptionKey const basic::options::OptionKeys::frags::n_frags

Referenced by add_rosetta_options_8(), and run().

BooleanOptionKey const basic::options::OptionKeys::frags::nonlocal_pairs

Referenced by add_rosetta_options_8().

IntegerOptionKey const basic::options::OptionKeys::frags::nr_large_copies

Referenced by add_rosetta_options_8().

BooleanOptionKey const basic::options::OptionKeys::frags::output_index

Referenced by add_rosetta_options_9().

BooleanOptionKey const basic::options::OptionKeys::frags::output_silent

Referenced by add_rosetta_options_9().

BooleanOptionKey const basic::options::OptionKeys::frags::p_value_selection

Referenced by add_rosetta_options_8().

RealOptionKey const basic::options::OptionKeys::frags::picking_old_max_score

Referenced by add_rosetta_options_9().

BooleanOptionKey const basic::options::OptionKeys::frags::quota_protocol

Referenced by add_rosetta_options_8().

RealOptionKey const basic::options::OptionKeys::frags::rama_B

Referenced by add_rosetta_options_9().

RealOptionKey const basic::options::OptionKeys::frags::rama_C

Referenced by add_rosetta_options_9().

RealOptionKey const basic::options::OptionKeys::frags::rama_norm

Referenced by add_rosetta_options_9().

BooleanOptionKey const basic::options::OptionKeys::frags::score_output_silent

Referenced by add_rosetta_options_9().

RealOptionKey const basic::options::OptionKeys::frags::seqsim_E

Referenced by add_rosetta_options_9().

RealOptionKey const basic::options::OptionKeys::frags::seqsim_H

Referenced by add_rosetta_options_9().

RealOptionKey const basic::options::OptionKeys::frags::seqsim_L

Referenced by add_rosetta_options_9().

RealOptionKey const basic::options::OptionKeys::frags::sigmoid_cs_A

Referenced by add_rosetta_options_9().

RealOptionKey const basic::options::OptionKeys::frags::sigmoid_cs_B

Referenced by add_rosetta_options_9().

FileOptionKey const basic::options::OptionKeys::frags::spine_x

Referenced by add_rosetta_options_8().

StringVectorOptionKey const basic::options::OptionKeys::frags::ss_pred

Referenced by add_rosetta_options_8().

BooleanOptionKey const basic::options::OptionKeys::frags::write_ca_coordinates

Referenced by add_rosetta_options_8().

BooleanOptionKey const basic::options::OptionKeys::frags::write_rama_tables

Referenced by add_rosetta_options_9().

BooleanOptionKey const basic::options::OptionKeys::frags::write_scores

Referenced by add_rosetta_options_8().

BooleanOptionKey const basic::options::OptionKeys::frags::write_sequence_only

Referenced by add_rosetta_options_9().