#include <cmath>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include <cstdarg>
#include <climits>
#include <clocale>
#include <iostream>
#include <cassert>
#include "Svm.hh"

Classes
class	Cache

struct	Cache::head_t

class	QMatrix

class	Kernel

class	Solver

struct	Solver::SolutionInfo

class	Solver_NU

class	SVC_Q

class	ONE_CLASS_Q

class	SVR_Q

struct	decision_function

Macros
#define	INF HUGE_VAL

#define	TAU 1e-12

#define	Malloc(type, n) (type )malloc((n)sizeof(type))

Typedefs
using	Qfloat = float

using	schar = signed char

Functions
template<class T >
static T	min (T x, T y)

template<class T >
static T	max (T x, T y)

template<class T >
static void	swap (T &x, T &y)

template<class S , class T >
static void	clone (T &dst, S src, int n)

static double	powi (double base, int times)

static void	print_string_stdout (const char *s)

static void	info (const char *fmt,...)

static void	solve_c_svc (const svm_problem prob, const svm_parameter param, double alpha, Solver::SolutionInfo si, double Cp, double Cn)

static void	solve_nu_svc (const svm_problem prob, const svm_parameter param, double alpha, Solver::SolutionInfo si)

static void	solve_one_class (const svm_problem prob, const svm_parameter param, double alpha, Solver::SolutionInfo si)

static void	solve_epsilon_svr (const svm_problem prob, const svm_parameter param, double alpha, Solver::SolutionInfo si)

static void	solve_nu_svr (const svm_problem prob, const svm_parameter param, double alpha, Solver::SolutionInfo si)

static decision_function	svm_train_one (const svm_problem prob, const svm_parameter param, double Cp, double Cn)

static void	sigmoid_train (int l, const double dec_values, const double labels, double &A, double &B)

static double	sigmoid_predict (double decision_value, double A, double B)

static void	multiclass_probability (int k, double *r, double p)

static void	svm_binary_svc_probability (const svm_problem prob, const svm_parameter param, double Cp, double Cn, double &probA, double &probB)

static double	svm_svr_probability (const svm_problem prob, const svm_parameter param)

static void	svm_group_classes (const svm_problem prob, int nr_class_ret, int label_ret, int start_ret, int *count_ret, int perm)

svm_model *	svm_train (const svm_problem prob, const svm_parameter param)

void	svm_cross_validation (const svm_problem prob, const svm_parameter param, int nr_fold, double *target)

int	svm_get_svm_type (const svm_model *model)

int	svm_get_nr_class (const svm_model *model)

void	svm_get_labels (const svm_model model, int label)

void	svm_get_sv_indices (const svm_model model, int indices)

int	svm_get_nr_sv (const svm_model *model)

double	svm_get_svr_probability (const svm_model *model)

double	svm_predict_values (const svm_model model, const svm_node x, double *dec_values)

double	svm_predict (const svm_model model, const svm_node x)

double	svm_predict_probability (const svm_model model, const svm_node x, double *prob_estimates)

int	svm_save_model (const char model_file_name, const svm_model model)

static char *	readline (FILE *input)

svm_model *	svm_load_model (const char *model_file_name)

void	svm_free_model_content (svm_model *model_ptr)

void	svm_free_and_destroy_model (svm_model **model_ptr_ptr)

void	svm_destroy_param (svm_parameter *param)

const char *	svm_check_parameter (const svm_problem prob, const svm_parameter param)

int	svm_check_probability_model (const svm_model *model)

void	svm_set_print_string_function (void(print_func)(const char ))

Variables
int	libsvm_version = LIBSVM_VERSION

static void(*	svm_print_string )(const char *) = &print_string_stdout

static const char *	svm_type_table []

static const char *	kernel_type_table []

static char *	line = nullptr

static int	max_line_len

Macro Definition Documentation

◆ INF

#define INF HUGE_VAL

◆ Malloc

#define Malloc	(	type,
		n
	)	(type )malloc((n)sizeof(type))

◆ TAU

#define TAU 1e-12

Typedef Documentation

◆ Qfloat

using Qfloat = float

◆ schar

using schar = signed char

Function Documentation

◆ clone()

template<class S , class T >

static void clone	(	T *&	dst,
		S *	src,
		int	n
	)

inlinestatic

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::n.

Referenced by PeptoidDihedralGrabber::fresh_instance(), PeptoidRotamerRecoverer::fresh_instance(), PepMinMover::fresh_instance(), CalcsTestMover::fresh_instance(), ExposedStrandMover::fresh_instance(), HDmakerMover::fresh_instance(), Kernel::Kernel(), main(), Solver::Solve(), and SVC_Q::SVC_Q().

◆ info()

static void info	(	const char *	fmt,
			...
	)

static

◆ max()

template<class T >

static T max	(	T	x,
		T	y
	)

inlinestatic

References x, and predPRE::y.

◆ min()

template<class T >

static T min	(	T	x,
		T	y
	)

inlinestatic

References x, and predPRE::y.

Referenced by TCDock::__dock_base__(), PyMOL-Rosetta-relay-client.Matrix::__init__(), PyMOL-RosettaServer.Matrix::__init__(), add_scores(), add_symm_zns(), numeric::xyzTransform< T >::align(), Tet4HMatchAligner::align_rot(), align_sf4(), align_zns(), GetURLHandler::AppendDataBytes(), CovalentPeptidomimeticDockDesign::apply(), B3AADihedralGrabber::apply(), HotspotPlacementMover::apply(), LoopHashRelax_Sampler::apply(), ExposedStrandMover::apply(), CrystFFTDock::apply(), balls_pdb(), zlib_stream::basic_zip_streambuf< Elem, Tr, ElemA, ByteT, ByteAT >::basic_zip_streambuf(), bin2string(), numeric::boltzmann_accept_probability(), brute_mindis(), cal_score(), calc_ddg(), calc_min(), calc_rama_scores(), calc_rmsd_and_clash_score(), calc_scores(), Solver::calculate_rho(), Solver_NU::calculate_rho(), numeric::ccd_angle(), check_protein_rna_clash(), choose_centroids(), ClashCheck::clash_check(), MatchSet::clash_check(), clash_score(), ObjexxFCL::DimensionExpressionMin::clone(), ClosabilityScore::closability_score(), DockFragmentsMover::cluster_frags(), compute_intrinsic_deviation(), compute_num_bins(), ObjexxFCL::Fstring::copy(), protocols::abinitio::Application::copy_native_structure(), protocols::abinitio::JumpSpecificAbrelax::copy_structure(), protocols::abinitio::ApplicationContext::copyStructure(), correct_dunbrack(), correct_rama(), utility::decode6bit(), design(), design_1comp(), numeric::deriv::dihedral_deriv_second(), pyrosetta.bindings.pose::display_secstruct(), basic::thread_manager::RosettaThreadManager::do_multistage_work_vector_in_threads(), PerturbStruct::do_mutate(), do_tmscore(), basic::thread_manager::RosettaThreadManager::do_work_vector_in_threads(), basic::thread_manager::RosettaThreadManager::do_work_vector_in_threads_no_locking(), dock(), doit(), job_manager.CommandRunner::dump(), dump_bundle_pose(), dump_pair_pose(), ObjexxFCL::format::E(), numeric::kdtree::HyperRectangle::extend(), ObjexxFCL::format::F(), ObjexxFCL::FArray1D< T >::FArray1D(), ObjexxFCL::FArray2D< T >::FArray2D(), ObjexxFCL::FArray3D< T >::FArray3D(), ObjexxFCL::FArray4D< T >::FArray4D(), ObjexxFCL::FArray5D< T >::FArray5D(), ObjexxFCL::FArray6D< T >::FArray6D(), auto-DRRAFTER_setup_next_round::figure_out_next_round(), mutant_modeler::figure_out_WT_seq(), gaussian-sampling::final_accept(), CapriTotalEnergy::finalize_total_energy(), detail::int_checker< true >::fits_in_int(), for(), TCDock::gather_hits(), generalize_gaussian_chain_func_test(), generate_disulfide_conformations(), numeric::fourier::SO3coeffs::genWigner_ds(), PyMOL-Rosetta-relay-client::get_ends(), PyMOL-RosettaServer::get_ends(), pyrosetta.PyMOLRosettaServer::get_ends(), get_gap_size(), get_interface_score(), get_localreso(), DRRAFTER::get_n_cycles(), numeric::kdtree::get_percentile_bounds(), get_radius(), ui::task::get_retry_interval(), numeric::VoxelGrid< T >::GetIndex(), options_class::getMarkdownPage(), go_main(), gradual_minimization(), harvest_scores(), ObjexxFCL::format::I(), TCDock::init(), ui::network::IntegerArgument::init(), ui::network::FloatArgument::init(), gaussian-sampling::initial_accept(), intersect(), IsctFast::IsctFast(), isctfast(), TCDock::justone(), ObjexxFCL::KeyFArray1D< T >::KeyFArray1D(), ObjexxFCL::KeyFArray2D< T >::KeyFArray2D(), ObjexxFCL::KeyFArray3D< T >::KeyFArray3D(), ObjexxFCL::KeyFArray4D< T >::KeyFArray4D(), ObjexxFCL::KeyFArray5D< T >::KeyFArray5D(), ObjexxFCL::KeyFArray6D< T >::KeyFArray6D(), utility::graph::RingDetection< Graph >::LengthOfSmallestCycleWithVertex(), utility::tag::XMLErrorHandler::lines_near_error(), safe_duration_cast::lossless_integral_conversion(), get_lowest_scoring_relaxed_models::main(), best_ifaceE::main(), main(), make_fragments(), MC_run(), utility::options::OptionCollection::merged(), numeric::min(), ObjexxFCL::min(), utility::min(), min_index(), TCDock::min_termini_dis(), TCDock::min_termini_proj(), numeric::xyzVector< T >::minimum_value(), protocols::abinitio::JumpSpecificAbrelax::multi_fast_relax(), numeric::interpolation::multilinear_interpolation(), multimodel_gdt(), utility::options::OptionCollection::n_part_prefix_match(), numeric::kdtree::nearest_neighbor(), numeric::kdtree::nearest_neighbors(), nearlyEqual(), on_segment(), numeric::expression_parser::MinExpression::operator()(), ObjexxFCL::DimensionExpressionMin::operator()(), optimize_weights(), overlap_score(), ObjexxFCL::Fstring::overlay(), numeric::deriv::p1_theta_deriv(), KinFunGroupTK::place_c(), job_manager.CommandRunner::poll(), populate_database_with_dummy_data(), pose2bin(), print_verbose_ddgs(), process_for_motifs(), DockFragmentsMover::process_fragfile(), numeric::proj_angl(), CL::q2d(), CL::q3d(), read_sphere(), refine(), repack_iface(), repackmin(), myspace::report_data(), numeric::random::reservoir_sample_accept_prob(), ObjexxFCL::ChunkVector< T >::reshape(), ObjexxFCL::Chunk< T >::resize(), DisulfEposDatabase::rms(), rna_design_test(), rna_protein_pdbstats_test(), numeric::xyzTransform< T >::rotation_axis(), run(), TCDock::run(), FragmentAssemblyMover::run(), FragMonteCarlo::run(), run_3bpy(), run_parallel_docking(), safe_duration_cast::safe_duration_cast(), RMS_ScoringScheme::score(), CapriTotalEnergy::score_experimental_constraints(), set_basic_dock_options(), MinTestMover::set_foldtree_for_variable_movement(), numeric::VoxelGrid< T >::SetObjects(), numeric::VoxelGrid< T >::SetupGrid(), shift_center_and_PCA(), pointGroupHit::show(), ConstraintConfig::show_cst_grids(), utility::options::OptionCollection::show_option_help(), sic_fast_x(), sicdock_thread_num(), sicfast(), soft_overlap_score(), Solver::Solve(), solve_nu_svc(), solve_nu_svr(), binder::split_in_two(), basic::svd::SVD_Solver::svdcmp(), numeric::linear_algebra::svdcmp(), svm_check_parameter(), svm_predict_probability(), TCDock::TCDock(), TEST(), test(), test_gradient(), test_pack14(), test_refold(), test_suck_res(), pyrosetta.utility.array::to_structured_array(), traceCAs(), numeric::kdtree::transform_percentile(), ObjexxFCL::DimensionExpressionMin::value(), visualize(), numeric::kdtree::KDPointList::worst_distance(), utility::options::OptionCollection::wrapped(), numeric::deriv::x_and_dtheta_dx(), and CL::zero_gpu_mem().

◆ multiclass_probability()

static void multiclass_probability	(	int	k,
		double **	r,
		double *	p
	)

static

References erraser_analysis::diff, eps, closure_error::error, free(), info(), create_a3b_hbs::j, create_a3b_hbs::k, Malloc, max(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, docking::Q, create_a3b_hbs::r, and predPRE::t.

Referenced by svm_predict_probability().

◆ powi()

static double powi	(	double	base,
		int	times
	)

inlinestatic

References test.T005_Bindings::base, and predPRE::t.

Referenced by Kernel::k_function(), and Kernel::kernel_poly().

◆ print_string_stdout()

static void print_string_stdout ( const char * s )

static

References detail::fputs(), docking::s, and build::stdout.

Referenced by svm_set_print_string_function().

◆ readline()

static char* readline ( FILE * input )

static

References gaussian-sampling::input, enumerate_junctions::int, ObjexxFCL::len(), line, max_line_len, and val2thr::newline.

Referenced by svm_load_model().

◆ sigmoid_predict()

static double sigmoid_predict	(	double	decision_value,
		double	A,
		double	B
	)

static

Referenced by svm_predict_probability().

◆ sigmoid_train()

static void sigmoid_train	(	int	l,
		const double *	dec_values,
		const double *	labels,
		double &	A,
		double &	B
	)

static

References test.T009_Exceptions::e, eps, free(), create_a3b_hbs::i, info(), extract_by_sidechain_sasa_score::l, numeric::log(), Malloc, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, enumerate_junctions::q, spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::sigma, and predPRE::t.

Referenced by svm_binary_svc_probability().

◆ solve_c_svc()

static void solve_c_svc	(	const svm_problem *	prob,
		const svm_parameter *	param,
		double *	alpha,
		Solver::SolutionInfo *	si,
		double	Cp,
		double	Cn
	)

static

References compute_difference::alpha, create_a3b_hbs::i, info(), extract_by_sidechain_sasa_score::l, PREcst::param, spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::prob, docking::s, and predPRE::y.

Referenced by svm_train_one().

◆ solve_epsilon_svr()

static void solve_epsilon_svr	(	const svm_problem *	prob,
		const svm_parameter *	param,
		double *	alpha,
		Solver::SolutionInfo *	si
	)

static

References compute_difference::alpha, create_a3b_hbs::i, info(), extract_by_sidechain_sasa_score::l, PREcst::param, spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::prob, docking::s, and predPRE::y.

Referenced by svm_train_one().

◆ solve_nu_svc()

static void solve_nu_svc	(	const svm_problem *	prob,
		const svm_parameter *	param,
		double *	alpha,
		Solver::SolutionInfo *	si
	)

static

References compute_difference::alpha, create_a3b_hbs::i, info(), extract_by_sidechain_sasa_score::l, min(), Solver::SolutionInfo::obj, PREcst::param, spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::prob, create_a3b_hbs::r, Solver::SolutionInfo::r, Solver::SolutionInfo::rho, docking::s, Solver::SolutionInfo::upper_bound_n, Solver::SolutionInfo::upper_bound_p, predPRE::y, and zeros().

Referenced by svm_train_one().

◆ solve_nu_svr()

static void solve_nu_svr	(	const svm_problem *	prob,
		const svm_parameter *	param,
		double *	alpha,
		Solver::SolutionInfo *	si
	)

static

References compute_difference::alpha, C, create_a3b_hbs::i, info(), extract_by_sidechain_sasa_score::l, min(), PREcst::param, spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::prob, Solver::SolutionInfo::r, docking::s, sum(), and predPRE::y.

Referenced by svm_train_one().

◆ solve_one_class()

static void solve_one_class	(	const svm_problem *	prob,
		const svm_parameter *	param,
		double *	alpha,
		Solver::SolutionInfo *	si
	)

static

References compute_difference::alpha, create_a3b_hbs::i, enumerate_junctions::int, extract_by_sidechain_sasa_score::l, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, PREcst::param, spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::prob, docking::s, and zeros().

Referenced by svm_train_one().

◆ svm_binary_svc_probability()

static void svm_binary_svc_probability	(	const svm_problem *	prob,
		const svm_parameter *	param,
		double	Cp,
		double	Cn,
		double &	probA,
		double &	probB
	)

static

◆ svm_check_parameter()

const char* svm_check_parameter	(	const svm_problem *	prob,
		const svm_parameter *	param
	)

◆ svm_check_probability_model()

int svm_check_probability_model ( const svm_model * model )

References C_SVC, EPSILON_SVR, closure_error::model, NU_SVC, and NU_SVR.

◆ svm_cross_validation()

void svm_cross_validation	(	const svm_problem *	prob,
		const svm_parameter *	param,
		int	nr_fold,
		double *	target
	)

◆ svm_destroy_param()

void svm_destroy_param ( svm_parameter * param )

References free(), and PREcst::param.

Referenced by svm_binary_svc_probability().

◆ svm_free_and_destroy_model()

void svm_free_and_destroy_model ( svm_model ** model_ptr_ptr )

References free(), and svm_free_model_content().

Referenced by svm_binary_svc_probability(), and svm_cross_validation().

◆ svm_free_model_content()

void svm_free_model_content ( svm_model * model_ptr )

References free(), svm_model::free_sv, create_a3b_hbs::i, svm_model::l, svm_model::label, svm_model::nr_class, svm_model::nSV, svm_model::probA, svm_model::probB, svm_model::rho, svm_model::SV, and svm_model::sv_coef.

Referenced by svm_free_and_destroy_model(), and utility::libsvm::Svm_rosetta::~Svm_rosetta().

◆ svm_get_labels()

void svm_get_labels	(	const svm_model *	model,
		int *	label
	)

References create_a3b_hbs::i, predPRE::label, and closure_error::model.

◆ svm_get_nr_class()

int svm_get_nr_class ( const svm_model * model )

References closure_error::model.

Referenced by utility::libsvm::Svm_rosetta::get_nr_class(), utility::libsvm::Svm_rosetta::predict_probability(), and svm_cross_validation().

◆ svm_get_nr_sv()

int svm_get_nr_sv ( const svm_model * model )

References closure_error::model.

◆ svm_get_sv_indices()

void svm_get_sv_indices	(	const svm_model *	model,
		int *	indices
	)

References create_a3b_hbs::i, internal_coordinates::indices, and closure_error::model.

◆ svm_get_svm_type()

int svm_get_svm_type ( const svm_model * model )

References closure_error::model.

◆ svm_get_svr_probability()

double svm_get_svr_probability ( const svm_model * model )

References EPSILON_SVR, fprintf(), closure_error::model, and NU_SVR.

◆ svm_group_classes()

static void svm_group_classes	(	const svm_problem *	prob,
		int *	nr_class_ret,
		int **	label_ret,
		int **	start_ret,
		int **	count_ret,
		int *	perm
	)

static

References count, for(), free(), create_a3b_hbs::i, info(), enumerate_junctions::int, create_a3b_hbs::j, extract_by_sidechain_sasa_score::l, predPRE::label, Malloc, svm_model::nr_class, spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::prob, and basic::options::OptionKeys::cutoutdomain::start.

Referenced by svm_cross_validation(), and svm_train().

◆ svm_load_model()

svm_model* svm_load_model ( const char * model_file_name )

◆ svm_predict()

double svm_predict	(	const svm_model *	model,
		const svm_node *	x
	)

References EPSILON_SVR, free(), Malloc, closure_error::model, svm_model::nr_class, NU_SVR, ONE_CLASS, svm_predict_values(), and x.

Referenced by utility::libsvm::Svm_rosetta::predict(), svm_cross_validation(), and svm_predict_probability().

◆ svm_predict_probability()

double svm_predict_probability	(	const svm_model *	model,
		const svm_node *	x,
		double *	prob_estimates
	)

References C_SVC, test.T009_Exceptions::e, free(), create_a3b_hbs::i, create_a3b_hbs::j, create_a3b_hbs::k, Malloc, max(), min(), closure_error::model, multiclass_probability(), svm_model::nr_class, NU_SVC, sigmoid_predict(), svm_predict(), svm_predict_values(), and x.

Referenced by utility::libsvm::Svm_rosetta::predict_probability(), and svm_cross_validation().

◆ svm_predict_values()

double svm_predict_values	(	const svm_model *	model,
		const svm_node *	x,
		double *	dec_values
	)

◆ svm_save_model()

int svm_save_model	(	const char *	model_file_name,
		const svm_model *	model
	)

◆ svm_set_print_string_function()

void svm_set_print_string_function ( void(*)(const char *) print_func )

References print_string_stdout(), and svm_print_string.

◆ svm_svr_probability()

static double svm_svr_probability	(	const svm_problem *	prob,
		const svm_parameter *	param
	)

static

References count, free(), create_a3b_hbs::i, info(), Malloc, PREcst::param, spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::prob, svm_parameter::probability, and svm_cross_validation().

Referenced by svm_train().

◆ svm_train()

svm_model* svm_train	(	const svm_problem *	prob,
		const svm_parameter *	param
	)

◆ svm_train_one()

static decision_function svm_train_one	(	const svm_problem *	prob,
		const svm_parameter *	param,
		double	Cp,
		double	Cn
	)

static

◆ swap()

template<class T >

static void swap	(	T &	x,
		T &	y
	)

inlinestatic

References predPRE::t, x, and predPRE::y.

Referenced by Cache::get_data(), svm_binary_svc_probability(), svm_cross_validation(), Cache::swap_index(), Solver::swap_index(), Kernel::swap_index(), SVC_Q::swap_index(), ONE_CLASS_Q::swap_index(), and SVR_Q::swap_index().

Variable Documentation

◆ kernel_type_table

const char* kernel_type_table[]

static

Initial value:

=
{
"linear","polynomial","rbf","sigmoid","precomputed",nullptr
}

Referenced by svm_load_model(), and svm_save_model().

◆ libsvm_version

int libsvm_version = LIBSVM_VERSION

◆ line

char* line = nullptr

static

Referenced by add_constraints(), InterfaceStrandFinderMover::apply(), CrystCluster::apply(), detail::assert_fail(), blosum_score_alignment(), calculate_hydrophobic_accessible_surface_area(), compute_intrinsic_deviation(), utility::cond_exit(), protocols::surface_docking::AntibodyInfoRMLoader::create_resource(), create_starting_template(), design_test(), utility::exit(), utility::exit_handler(), utility::exit_with_user_fixable_issue(), utility::file_contents(), InterfaceDDGBindJobInputter::fill_jobs(), fillPoseAndDataList(), filter_frags(), generateRankedAlignments(), utility::io::get_lines_from_file_data(), get_native_pdb_names(), SequenceProfileDB::get_next_profile(), get_pair_keys_from_list(), get_sc(), get_sequence_and_secstruct_from_dssp(), utility::io::icstream::getline(), utility::io::izstream::getline(), pdbline::getline(), utility::io::getline(), handle_assert_failure(), utility::tag::XMLErrorHandler::handle_xml_error(), utility::tag::XMLErrorHandler::handle_xml_warning(), apps::pilot::frankdt::import_motifs(), initialize_sequence_mask(), is_nonempty_input_silent_file(), utility::tag::XMLErrorHandler::lines_near_error(), load_checkpoint(), HBondReporter::load_job_data(), load_loops_from_file(), TNM::load_normal_modes(), utility::options::OptionCollection::load_options_from_stream(), basic::resource_manager::locator::FileListResourceLocator::locate_resource_stream(), main(), apps::pilot::frankdt::main(), VallReader::make_fragment_lines(), VallReader::make_nmer_profile(), mg_pdbstats_test(), motif_scan(), name2elt(), basic::citation_manager::Citation::parse_authors(), ui::viewers::parse_score_file(), basic::citation_manager::Citation::parse_string_entry(), basic::citation_manager::Citation::parse_year(), parsefilelist(), pdbline::pdbline(), polar_pdbstats_test(), basic::citation_manager::CitationManager::populate_doi_rosetta_citation_map(), processChildren(), processChildrenIntensification(), project_line(), basic::sampling::orientations::QuaternionGrid::QuaternionGrid(), RBSegmentRelax_test(), binder::Config::read(), read_alignment_fasta_file(), read_B_vals(), read_complex_type(), read_covalent_connections_file(), CapriTotalEnergy::read_datafile(), read_distances(), read_embeddings(), read_equivalent_position_file(), read_ERMS(), read_FileVector(), read_fold_tree_from_file(), numeric::interpolation::Histogram< X, Y >::read_from_db(), read_in_cl_data(), myspace::read_input(), VallReader::read_lines(), read_list_file(), read_list_pose_range(), read_master_pose_range(), read_membrane(), read_NACCESS_asa_file(), read_parameters(), read_patchdock_entry(), read_penalties(), read_rama_map_file(), read_RDC_file(), read_soft_segment_file(), readline(), PickSSE::readSSE(), recover_clustered_frags(), utility::io::remove_inline_comments(), rhiju_pdbstats(), rna_backbone_rebuild_test(), run_pep_prep(), utility::save_crash_report(), utility::save_crash_report_to_file(), set_secstruct_from_psipred_ss2(), setup_activity_table(), setup_capri_data(), DomainAssemblerNDocker::setup_cen_domains(), setup_rna_base_pair_constraints(), setup_secstruct(), simple_opte_test(), SpacegroupHit::SpacegroupHit(), numeric::interpolation::spline_from_file(), binder::split(), statistics(), svm_load_model(), symmetrize_map(), tf_specificity_test(), write_cluster_frags(), and zf_test().

◆ max_line_len

int max_line_len

static

Referenced by readline(), and svm_load_model().

◆ svm_print_string

void(* svm_print_string) (const char *) ( const char * ) = &print_string_stdout

static

Referenced by svm_set_print_string_function().

◆ svm_type_table

const char* svm_type_table[]

static

Initial value:

=
{
"c_svc","nu_svc","one_class","epsilon_svr","nu_svr",nullptr
}

Referenced by svm_load_model(), and svm_save_model().

Classes

Macros

Typedefs

Functions

Variables

Macro Definition Documentation

◆ INF

◆ Malloc

◆ TAU

Typedef Documentation

◆ Qfloat

◆ schar

Function Documentation

◆ clone()

◆ info()

◆ max()

◆ min()

◆ multiclass_probability()

◆ powi()

◆ print_string_stdout()

◆ readline()

◆ sigmoid_predict()

◆ sigmoid_train()

◆ solve_c_svc()

◆ solve_epsilon_svr()

◆ solve_nu_svc()

◆ solve_nu_svr()

◆ solve_one_class()

◆ svm_binary_svc_probability()

◆ svm_check_parameter()

◆ svm_check_probability_model()

◆ svm_cross_validation()

◆ svm_destroy_param()

◆ svm_free_and_destroy_model()

◆ svm_free_model_content()

◆ svm_get_labels()

◆ svm_get_nr_class()

◆ svm_get_nr_sv()

◆ svm_get_sv_indices()

◆ svm_get_svm_type()

◆ svm_get_svr_probability()

◆ svm_group_classes()

◆ svm_load_model()

◆ svm_predict()

◆ svm_predict_probability()

◆ svm_predict_values()

◆ svm_save_model()

◆ svm_set_print_string_function()

◆ svm_svr_probability()

◆ svm_train()

◆ svm_train_one()

◆ swap()

Variable Documentation

◆ kernel_type_table

◆ libsvm_version

◆ line

◆ max_line_len

◆ svm_print_string

◆ svm_type_table