#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

#define INF HUGE_VAL

Referenced by Solver::calculate_rho(), Solver_NU::calculate_rho(), Solver::do_shrinking(), Solver_NU::do_shrinking(), Solver::select_working_set(), and Solver_NU::select_working_set().

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

Referenced by multiclass_probability(), sigmoid_train(), svm_binary_svc_probability(), svm_check_parameter(), svm_cross_validation(), svm_group_classes(), svm_load_model(), svm_predict(), svm_predict_probability(), svm_predict_values(), svm_svr_probability(), svm_train(), and svm_train_one().

#define TAU 1e-12

Referenced by Solver::select_working_set(), Solver_NU::select_working_set(), and Solver::Solve().

Typedef Documentation

using Qfloat = float

using schar = signed char

Function Documentation

template<class S , class T >

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

inlinestatic

Referenced by HDmakerMover::fresh_instance(), ExposedStrandMover::fresh_instance(), Kernel::Kernel(), Solver::Solve(), and SVC_Q::SVC_Q().

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

static

Referenced by Solver::do_shrinking(), numeric::nls::lm_lmdif(), multiclass_probability(), utility::json_spirit::read_range_or_throw(), Solver::reconstruct_gradient(), sample_torsions(), sigmoid_train(), Solver::Solve(), solve_c_svc(), solve_epsilon_svr(), solve_nu_svc(), solve_nu_svr(), svm_check_parameter(), svm_group_classes(), svm_svr_probability(), svm_train(), and svm_train_one().

template<class T >

static T max	(	T	x,
		T	y
	)

inlinestatic

References numeric::crick_equations::y().

Referenced by pyrosetta.EnergyMethod::__call__(), PyMOL-RosettaServer.Matrix::__init__(), numeric::xyzTransform< numeric::Real >::align(), ExposedStrandMover::apply(), ObjexxFCL::format::bite(), numeric::boltzmann_accept_probability(), utility::io::ozstream::buffer_size(), Cache::Cache(), Solver::calculate_rho(), Solver_NU::calculate_rho(), ObjexxFCL::DimensionExpressionMax::clone(), numeric::coordinate_fitting::FlatLookup< Real *, numeric::Size, Real >::closest_match(), numeric::coordinate_fitting::FlatLookup< Real *, numeric::Size, Real >::closest_match_subset(), numeric::fourier::SO3coeffs::coefLoc(), pyrosetta.numeric.alignment.rmsd_calc::coordinate_array_rmsd(), correct_rama(), numeric::deriv::dihedral_deriv_second(), Solver_NU::do_shrinking(), ObjexxFCL::format::E(), numeric::kdtree::HyperRectangle::extend(), ObjexxFCL::format::F(), ObjexxFCL::FArray1D< double >::FArray1D(), ObjexxFCL::FArray2D< double >::FArray2D(), ObjexxFCL::FArray3D< typename >::FArray3D(), ObjexxFCL::FArray4D< typename >::FArray4D(), ObjexxFCL::FArray5D< typename >::FArray5D(), ObjexxFCL::FArray6D< typename >::FArray6D(), mutant_modeler::figure_out_WT_seq(), numeric::coordinate_fitting::FlatLookup< Real *, numeric::Size, Real >::first_match(), fmt::BasicFormatter< CharType, ArgFormatter >::format(), full_length_rmsd_over_reside_list_general(), gen_pep_bb_sequential(), numeric::fourier::SO3coeffs::genWigner_ds(), PyMOL-RosettaServer::get_ends(), numeric::kdtree::get_percentile_bounds(), arls_impl::get_procs_per_case(), utility::get_undefined_real(), utility::get_undefined_size(), numeric::VoxelGrid< typename >::GetIndex(), harvest_scores(), ObjexxFCL::format::I(), ObjexxFCL::KeyFArray1D< typename >::KeyFArray1D(), ObjexxFCL::KeyFArray2D< typename >::KeyFArray2D(), ObjexxFCL::KeyFArray3D< typename >::KeyFArray3D(), ObjexxFCL::KeyFArray4D< typename >::KeyFArray4D(), ObjexxFCL::KeyFArray5D< typename >::KeyFArray5D(), ObjexxFCL::KeyFArray6D< typename >::KeyFArray6D(), numeric::fourier::kiss_fftndr(), numeric::fourier::kiss_fftndri(), utility::graph::RingDetection< Graph >::LengthOfSmallestCycleWithVertex(), utility::tag::XMLErrorHandler::lines_near_error(), main(), utility::max(), ObjexxFCL::max(), numeric::max(), ObjexxFCL::Chunk< T >::max_size(), ObjexxFCL::ChunkVector< typename >::max_size(), numeric::xyzVector< core::Real >::maximum_value(), multiclass_probability(), numeric::interpolation::multilinear_interpolation(), pyrosetta.io.silent_file_map::open_compressed(), ObjexxFCL::DimensionExpressionMax::operator()(), numeric::expression_parser::MaxExpression::operator()(), numeric::deriv::p1_theta_deriv(), fmt::internal::parse_nonnegative_int(), DockFragmentsMover::process_fragfile(), numeric::proj_angl(), ObjexxFCL::format::repeat(), numeric::fourier::kiss_fftndr_state::resize(), numeric::xyzTransform< numeric::Real >::rotation_axis(), numeric::model_quality::rsym_eigenval(), ConsensusFragmentMover::run(), Solver_NU::select_working_set(), numeric::VoxelGrid< typename >::SetObjects(), numeric::VoxelGrid< typename >::SetupGrid(), ObjexxFCL::format::skip(), utility::io::skip(), numeric::fourier::SHT::so3CombineCoef(), Solver::Solve(), ObjexxFCL::format::space(), numeric::linear_algebra::svdcmp(), basic::svd::SVD_Solver::svdcmp(), svm_predict_probability(), pyrosetta.utility.array::to_structured_array(), numeric::kdtree::transform_percentile(), ObjexxFCL::Fstring::trimmed_whitespace_range(), ObjexxFCL::DimensionExpressionMax::value(), numeric::fourier::SO3coeffs::wignerSynthesis(), numeric::fourier::SO3coeffs::wignerSynthesisDiffSign(), numeric::fourier::SO3coeffs::wignerSynthesisSameSign(), ObjexxFCL::format::X(), numeric::deriv::x_and_dtheta_dx(), and numeric::HomogeneousTransform< double >::xform_magnitude().

template<class T >

static T min	(	T	x,
		T	y
	)

inlinestatic

References numeric::crick_equations::y().

Referenced by PyMOL-RosettaServer.Matrix::__init__(), numeric::xyzTransform< numeric::Real >::align(), ExposedStrandMover::apply(), zlib_stream::basic_zip_streambuf< Elem, Tr, ElemA, ByteT, ByteAT >::basic_zip_streambuf(), numeric::boltzmann_accept_probability(), calc_rama_scores(), calc_scores(), Solver::calculate_rho(), Solver_NU::calculate_rho(), ObjexxFCL::DimensionExpressionMin::clone(), DockFragmentsMover::cluster_frags(), ObjexxFCL::Fstring::copy(), correct_dunbrack(), correct_rama(), numeric::deriv::dihedral_deriv_second(), pyrosetta.bindings.pose::display_secstruct(), ObjexxFCL::format::E(), numeric::kdtree::HyperRectangle::extend(), ObjexxFCL::format::F(), ObjexxFCL::FArray1D< double >::FArray1D(), ObjexxFCL::FArray2D< double >::FArray2D(), ObjexxFCL::FArray3D< typename >::FArray3D(), ObjexxFCL::FArray4D< typename >::FArray4D(), ObjexxFCL::FArray5D< typename >::FArray5D(), ObjexxFCL::FArray6D< typename >::FArray6D(), mutant_modeler::figure_out_WT_seq(), numeric::fourier::SO3coeffs::genWigner_ds(), PyMOL-RosettaServer::get_ends(), DRRAFTER::get_n_cycles(), numeric::kdtree::get_percentile_bounds(), numeric::VoxelGrid< typename >::GetIndex(), options_class::getMarkdownPage(), go_main(), harvest_scores(), ObjexxFCL::format::I(), ObjexxFCL::KeyFArray1D< typename >::KeyFArray1D(), ObjexxFCL::KeyFArray2D< typename >::KeyFArray2D(), ObjexxFCL::KeyFArray3D< typename >::KeyFArray3D(), ObjexxFCL::KeyFArray4D< typename >::KeyFArray4D(), ObjexxFCL::KeyFArray5D< typename >::KeyFArray5D(), ObjexxFCL::KeyFArray6D< typename >::KeyFArray6D(), utility::graph::RingDetection< Graph >::LengthOfSmallestCycleWithVertex(), utility::tag::XMLErrorHandler::lines_near_error(), get_lowest_scoring_relaxed_models::main(), best_ifaceE::main(), main(), make_fragments(), utility::options::OptionCollection::merged(), utility::min(), ObjexxFCL::min(), numeric::min(), numeric::xyzVector< core::Real >::minimum_value(), numeric::interpolation::multilinear_interpolation(), utility::options::OptionCollection::n_part_prefix_match(), numeric::kdtree::nearest_neighbor(), numeric::kdtree::nearest_neighbors(), ObjexxFCL::DimensionExpressionMin::operator()(), numeric::expression_parser::MinExpression::operator()(), ObjexxFCL::operator<(), ObjexxFCL::operator<=(), ObjexxFCL::operator==(), ObjexxFCL::Fstring::overlay(), numeric::deriv::p1_theta_deriv(), DockFragmentsMover::process_fragfile(), numeric::proj_angl(), numeric::random::reservoir_sample_accept_prob(), ObjexxFCL::ChunkVector< typename >::reshape(), ObjexxFCL::Chunk< T >::resize(), numeric::xyzTransform< numeric::Real >::rotation_axis(), FragmentAssemblyMover::run(), numeric::VoxelGrid< typename >::SetObjects(), numeric::VoxelGrid< typename >::SetupGrid(), utility::options::OptionCollection::show_option_help(), Solver::Solve(), solve_nu_svc(), solve_nu_svr(), binder::split_in_two(), numeric::linear_algebra::svdcmp(), basic::svd::SVD_Solver::svdcmp(), svm_check_parameter(), svm_predict_probability(), pyrosetta.utility.array::to_structured_array(), numeric::kdtree::transform_percentile(), ObjexxFCL::DimensionExpressionMin::value(), numeric::kdtree::KDPointList::worst_distance(), utility::options::OptionCollection::wrapped(), and numeric::deriv::x_and_dtheta_dx().

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

static

References erraser_analysis::diff, free(), info(), basic::options::OptionKeys::frags::j, Malloc, max(), and basic::options::OptionKeys::in::file::t.

Referenced by svm_predict_probability().

static double powi	(	double	base,
		int	times
	)

inlinestatic

References basic::options::OptionKeys::in::file::t.

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

static void print_string_stdout ( const char * s )

static

Referenced by svm_set_print_string_function().

static char* readline ( FILE * input )

static

References ObjexxFCL::len(), and line.

Referenced by svm_load_model().

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

static

Referenced by svm_predict_probability().

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

static

References test.T009_Exceptions::e, free(), info(), basic::options::OptionKeys::in::file::l, numeric::log(), Malloc, basic::options::OptionKeys::score::fiber_diffraction::p, erraser_analysis::sigma, and basic::options::OptionKeys::in::file::t.

Referenced by svm_binary_svc_probability().

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

static

References svm_parameter::eps, info(), svm_problem::l, basic::options::OptionKeys::in::file::l, basic::options::OptionKeys::in::file::s, svm_parameter::shrinking, Solver::Solve(), svm_problem::y, and numeric::crick_equations::y().

Referenced by svm_train_one().

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

static

References svm_parameter::C, svm_parameter::eps, info(), svm_problem::l, basic::options::OptionKeys::in::file::l, svm_parameter::p, basic::options::OptionKeys::in::file::s, svm_parameter::shrinking, Solver::Solve(), svm_problem::y, and numeric::crick_equations::y().

Referenced by svm_train_one().

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

static

References svm_parameter::eps, info(), svm_problem::l, basic::options::OptionKeys::in::file::l, min(), svm_parameter::nu, Solver::SolutionInfo::obj, Solver::SolutionInfo::r, Solver::SolutionInfo::rho, basic::options::OptionKeys::in::file::s, svm_parameter::shrinking, Solver_NU::Solve(), Solver::SolutionInfo::upper_bound_n, Solver::SolutionInfo::upper_bound_p, svm_problem::y, and numeric::crick_equations::y().

Referenced by svm_train_one().

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

static

References C, svm_parameter::C, svm_parameter::eps, info(), svm_problem::l, basic::options::OptionKeys::in::file::l, min(), svm_parameter::nu, Solver::SolutionInfo::r, basic::options::OptionKeys::in::file::s, svm_parameter::shrinking, Solver_NU::Solve(), sum(), svm_problem::y, and numeric::crick_equations::y().

Referenced by svm_train_one().

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

static

References svm_parameter::eps, svm_problem::l, basic::options::OptionKeys::in::file::l, svm_parameter::nu, basic::options::OptionKeys::in::file::s, svm_parameter::shrinking, and Solver::Solve().

Referenced by svm_train_one().

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

static

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

int svm_check_probability_model ( const svm_model * model )

References C_SVC, EPSILON_SVR, NU_SVC, NU_SVR, svm_model::param, svm_model::probA, svm_model::probB, and svm_parameter::svm_type.

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

void svm_destroy_param ( svm_parameter * param )

References free(), svm_parameter::weight, and svm_parameter::weight_label.

Referenced by svm_binary_svc_probability().

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().

void svm_free_model_content ( svm_model * model_ptr )

References free(), svm_model::free_sv, 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().

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

References svm_model::label, and svm_model::nr_class.

int svm_get_nr_class ( const svm_model * model )

References svm_model::nr_class.

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

int svm_get_nr_sv ( const svm_model * model )

References svm_model::l.

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

References svm_model::l, and svm_model::sv_indices.

int svm_get_svm_type ( const svm_model * model )

References svm_model::param, and svm_parameter::svm_type.

double svm_get_svr_probability ( const svm_model * model )

References EPSILON_SVR, NU_SVR, svm_model::param, svm_model::probA, and svm_parameter::svm_type.

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 clean_pdb_keep_ligand::count, free(), info(), basic::options::OptionKeys::frags::j, svm_problem::l, basic::options::OptionKeys::in::file::l, svm_model::label, Malloc, svm_model::nr_class, basic::options::OptionKeys::cutoutdomain::start, and svm_problem::y.

Referenced by svm_cross_validation(), and svm_train().

svm_model* svm_load_model ( const char * model_file_name )

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

References EPSILON_SVR, free(), Malloc, svm_model::nr_class, NU_SVR, ONE_CLASS, svm_model::param, svm_predict_values(), and svm_parameter::svm_type.

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

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

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

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

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

References print_string_stdout(), and svm_print_string.

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

static

References clean_pdb_keep_ligand::count, free(), info(), svm_problem::l, Malloc, svm_model::param, svm_parameter::probability, svm_cross_validation(), and svm_problem::y.

Referenced by svm_train().

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

References decision_function::alpha, svm_parameter::C, clean_pdb_keep_ligand::count, EPSILON_SVR, demo.D060_Folding::f, free(), info(), basic::options::OptionKeys::frags::j, svm_problem::l, basic::options::OptionKeys::in::file::l, svm_model::label, Malloc, svm_model::nr_class, svm_parameter::nr_weight, svm_model::nSV, NU_SVR, ONE_CLASS, basic::options::OptionKeys::score::fiber_diffraction::p, svm_model::param, svm_model::probA, svm_parameter::probability, svm_model::probB, decision_function::rho, basic::options::OptionKeys::cutoutdomain::start, svm_binary_svc_probability(), svm_group_classes(), svm_svr_probability(), svm_train_one(), svm_parameter::svm_type, svm_parameter::weight, svm_parameter::weight_label, svm_problem::x, numeric::crick_equations::x(), and svm_problem::y.

Referenced by svm_binary_svc_probability(), and svm_cross_validation().

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

static

template<class T >

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

inlinestatic

References basic::options::OptionKeys::in::file::t, numeric::crick_equations::x(), and numeric::crick_equations::y().

Variable Documentation

const char* kernel_type_table[]

static

Initial value:

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

Referenced by svm_load_model(), and svm_save_model().

int libsvm_version = LIBSVM_VERSION

char* line = nullptr

static

Referenced by utility::file_contents(), utility::io::get_lines_from_file_data(), apps::pilot::frankdt::import_motifs(), load_loops_from_file(), utility::options::OptionCollection::load_options_from_stream(), basic::resource_manager::locator::FileListResourceLocator::locate_resource_stream(), main(), apps::pilot::frankdt::main(), basic::sampling::orientations::QuaternionGrid::QuaternionGrid(), binder::Config::read(), numeric::interpolation::Histogram< typename, typename >::read_from_db(), read_rama_map_file(), readline(), rhiju_pdbstats(), run_pep_prep(), numeric::interpolation::spline_from_file(), binder::split(), statistics(), and svm_load_model().

int max_line_len

static

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

static

Referenced by svm_set_print_string_function().

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

Typedef Documentation

Function Documentation

Variable Documentation