basic::options::OptionKeys::frags Namespace Reference

Namespaces
	ABEGO
	contacts
	nonlocal
	picking
	scoring

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

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	score_output_silent

Function Documentation

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

(

"frags:allowed_pdb"

)

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

(

"frags:annotate"

)

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

(

"frags:bounded_protocol"

)

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

(

"frags:denied_pdb"

)

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

(

"frags:depth"

)

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

(

"frags:describe_fragments"

)

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

(

"frags:filter_JC"

)

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

(

"frags:frag_sizes"

)

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

(

"frags:fragment_contacts"

)

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

(

"frags"

)

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

(

"frags:j"

)

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

(

"frags:keep_all_protocol"

)

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

(

"frags:n_candidates"

)

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

(

"frags:n_frags"

)

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

(

"frags:nonlocal_pairs"

)

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

(

"frags:nr_large_copies"

)

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

(

"frags:output_silent"

)

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

(

"frags:p_value_selection"

)

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

(

"frags:picking_old_max_score"

)

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

(

"frags:quota_protocol"

)

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

(

"frags:rama_B"

)

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

(

"frags:rama_C"

)

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

(

"frags:rama_norm"

)

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

(

"frags:score_output_silent"

)

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

(

"frags:seqsim_E"

)

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

(

"frags:seqsim_H"

)

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

(

"frags:seqsim_L"

)

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

(

"frags:sigmoid_cs_A"

)

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

(

"frags:sigmoid_cs_B"

)

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

(

"frags:spine_x"

)

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

(

"frags:ss_pred"

)

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

(

"frags:write_ca_coordinates"

)

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

(

"frags:write_rama_tables"

)

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

(

"frags:write_scores"

)

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

(

"frags:write_sequence_only"

)

Variable Documentation

FileOptionKey const basic::options::OptionKeys::frags::allowed_pdb("frags:allowed_pdb")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::frags::annotate("frags:annotate")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::frags::bounded_protocol("frags:bounded_protocol")

Referenced by add_rosetta_options_0().

FileOptionKey const basic::options::OptionKeys::frags::denied_pdb("frags:denied_pdb")

Referenced by add_rosetta_options_0().

FileOptionKey const basic::options::OptionKeys::frags::depth("frags:depth")

Referenced by add_rosetta_options_0(), numeric::geometry::hashing::SixDOffsetTree::insert(), and numeric::geometry::hashing::SixDOffsetTree::lookup().

StringOptionKey const basic::options::OptionKeys::frags::describe_fragments("frags:describe_fragments")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::frags::filter_JC("frags:filter_JC")

Referenced by add_rosetta_options_0().

IntegerVectorOptionKey const basic::options::OptionKeys::frags::frag_sizes("frags:frag_sizes")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::frags::fragment_contacts("frags:fragment_contacts")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::frags::frags("frags")

Referenced by add_rosetta_options_0().

IntegerOptionKey const basic::options::OptionKeys::frags::j("frags:j")

Referenced by numeric::model_quality::RmsData::add_rms(), add_rosetta_options_0(), utility::BitVector< B >::BitVector(), numeric::kinematic_closure::radians::bridge_objects(), numeric::kinematic_closure::bridgeObjects(), numeric::kinematic_closure::build_sin_and_cos(), numeric::model_quality::calc_rms_fast(), numeric::kinematic_closure::chainTORS(), numeric::kinematic_closure::radians::chainTORS(), numeric::kinematic_closure::chainXYZ(), numeric::kinematic_closure::radians::chainXYZ(), numeric::model_quality::RmsData::clear_rms(), 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(), 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(), numeric::model_quality::findUU(), SVC_Q::get_Q(), ONE_CLASS_Q::get_Q(), SVR_Q::get_Q(), utility::graph::RingDetection< Graph >::GetRings(), utility::options::ScalarOption_T_< PathOptionKey, file::PathName >::has_any_of_characters(), utility::options::VectorOption_T_< BooleanVectorOptionKey, bool >::has_any_of_characters(), numeric::geometry::hashing::SixDOffsetTree::init(), numeric::random::mt19937_RG::init_by_array(), numeric::MathMatrix< Real >::inverse_square_matrix(), numeric::MathMatrix< Real >::inverse_tridiagonal_matrix(), numeric::MathMatrix< Real >::is_diagonal(), numeric::MathMatrix< Real >::is_tri_diagonal(), numeric::jacobi(), numeric::kinematic_closure::kic_jac(), 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(), basic::database::make_compound_statement(), numeric::model_quality::MatrixMult(), numeric::model_quality::maxsub(), numeric::kinematic_closure::modp(), multiclass_probability(), numeric::kinematic_closure::multMatrix(), numeric::kinematic_closure::multTransMatrix(), numeric::operator*(), numeric::MathMatrix< Real >::operator*=(), numeric::random::mt19937_RG::period_certification(), numeric::principal_components_and_eigenvalues(), numeric::kinematic_closure::printMatrix(), numeric::kinematic_closure::printTranspose(), numeric::product(), numeric::linear_algebra::qzhes(), numeric::linear_algebra::qzit(), numeric::linear_algebra::qzval(), numeric::linear_algebra::qzvec(), numeric::geometry::hashing::SixDCoordinateBinner::radial_bin_index(), numeric::IntervalSet< double >::random_point(), numeric::linear_algebra::GeneralizedEigenSolver< _MatrixType >::real_eigenvectors(), Solver::reconstruct_gradient(), utility::signals::BufferedSignalHub< ReturnType, Signal >::release_buffer(), numeric::model_quality::rms_wrapper_slow_and_correct(), numeric::model_quality::rmsfitca2(), numeric::model_quality::rmsfitca3(), numeric::model_quality::rsym_rotation(), basic::svd::SVD_Solver::run_score_svd_on_matrix(), basic::svd::SVD_Solver::run_score_svd_without_solving(), Solver::select_working_set(), Solver_NU::select_working_set(), basic::svd::SVD_Solver::set_matrix_A(), Solver::Solve(), basic::options::start_files(), utility::string_split(), utility::string_split_multi_delim(), basic::svd::SVD_Solver::svbksb(), 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(), 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_kic_jac(), numeric::kinematic_closure::test_rotateX(), numeric::MathMatrix< Real >::transpose(), numeric::kinematic_closure::triaxialCoefficients(), and numeric::kinematic_closure::radians::triaxialCoefficients().

BooleanOptionKey const basic::options::OptionKeys::frags::keep_all_protocol("frags:keep_all_protocol")

Referenced by add_rosetta_options_0().

IntegerOptionKey const basic::options::OptionKeys::frags::n_candidates("frags:n_candidates")

Referenced by add_rosetta_options_0().

IntegerOptionKey const basic::options::OptionKeys::frags::n_frags("frags:n_frags")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::frags::nonlocal_pairs("frags:nonlocal_pairs")

Referenced by add_rosetta_options_0().

IntegerOptionKey const basic::options::OptionKeys::frags::nr_large_copies("frags:nr_large_copies")

Referenced by add_rosetta_options_0(), and add_rosetta_options_1().

BooleanOptionKey const basic::options::OptionKeys::frags::output_silent("frags:output_silent")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::frags::p_value_selection("frags:p_value_selection")

Referenced by add_rosetta_options_0().

RealOptionKey const basic::options::OptionKeys::frags::picking_old_max_score("frags:picking_old_max_score")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::frags::quota_protocol("frags:quota_protocol")

Referenced by add_rosetta_options_0().

RealOptionKey const basic::options::OptionKeys::frags::rama_B("frags:rama_B")

Referenced by add_rosetta_options_0().

RealOptionKey const basic::options::OptionKeys::frags::rama_C("frags:rama_C")

Referenced by add_rosetta_options_0().

RealOptionKey const basic::options::OptionKeys::frags::rama_norm("frags:rama_norm")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::frags::score_output_silent("frags:score_output_silent")

Referenced by add_rosetta_options_0().

RealOptionKey const basic::options::OptionKeys::frags::seqsim_E("frags:seqsim_E")

Referenced by add_rosetta_options_0().

RealOptionKey const basic::options::OptionKeys::frags::seqsim_H("frags:seqsim_H")

Referenced by add_rosetta_options_0().

RealOptionKey const basic::options::OptionKeys::frags::seqsim_L("frags:seqsim_L")

Referenced by add_rosetta_options_0().

RealOptionKey const basic::options::OptionKeys::frags::sigmoid_cs_A("frags:sigmoid_cs_A")

Referenced by add_rosetta_options_0().

RealOptionKey const basic::options::OptionKeys::frags::sigmoid_cs_B("frags:sigmoid_cs_B")

Referenced by add_rosetta_options_0().

FileOptionKey const basic::options::OptionKeys::frags::spine_x("frags:spine_x")

Referenced by add_rosetta_options_0().

StringVectorOptionKey const basic::options::OptionKeys::frags::ss_pred("frags:ss_pred")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::frags::write_ca_coordinates("frags:write_ca_coordinates")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::frags::write_rama_tables("frags:write_rama_tables")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::frags::write_scores("frags:write_scores")

Referenced by add_rosetta_options_0().

BooleanOptionKey const basic::options::OptionKeys::frags::write_sequence_only("frags:write_sequence_only")

Referenced by add_rosetta_options_0().