Svm.cc File Reference

#include <math.h>
#include <cstdio>
#include <stdlib.h>
#include <string.h>
#include <stdarg.h>
#include <limits.h>
#include <locale.h>
#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
typedef float	Qfloat
typedef signed char	schar

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 = NULL
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

typedef float Qfloat

typedef signed char schar

Function Documentation

template<class S , class T >

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

inlinestatic

References test.T007_TracerIO::T.

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 y().

Referenced by pyrosetta.EnergyMethod::__call__(), src.EnergyMethod::__call__(), src.PyMolLink.PyMOLMover::_scale_list(), app.pyrosetta_toolkit.modules.prettytable.prettytable.PrettyTable::_stringify_row(), calccontacts::addMax_radius(), ExposedStrandMover::apply(), ObjexxFCL::format::bite(), numeric::boltzmann_accept_probability(), utility::io::ozstream::buffer_size(), BuildBindings::BuildRosettaOnWindows(), Cache::Cache(), Solver::calculate_rho(), Solver_NU::calculate_rho(), BuildBindings::calculate_source_modification_date(), 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(), 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(), numeric::coordinate_fitting::FlatLookup< Real *, numeric::Size, Real >::first_match(), full_length_rmsd_over_reside_list_general(), gen_pep_bb_sequential(), numeric::fourier::SO3coeffs::genWigner_ds(), PyMOLPyRosettaServer::get_ends(), numeric::kdtree::get_percentile_bounds(), arls_impl::get_procs_per_case(), utility::get_undefined_size(), fmt::internal::MemoryBuffer< T, SIZE, Allocator >::grow(), 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(), MC_run(), multiclass_probability(), ObjexxFCL::DimensionExpressionMax::operator()(), numeric::expression_parser::MaxExpression::operator()(), boost_adaptbx::python::streambuf::overflow(), numeric::deriv::p1_theta_deriv(), 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(), yaml.scanner.Scanner::scan_block_scalar(), boost_adaptbx::python::streambuf::seekoff_without_calling_python(), Solver_NU::select_working_set(), src.PyMolLink.PyMOLMover::send_foldtree(), src.PyMolLink.PyMOLMover::send_hbonds(), ObjexxFCL::format::skip(), utility::io::skip(), BuildBindings::Sleep(), BuildBindings::SleepPrecise(), numeric::fourier::SHT::so3CombineCoef(), Solver::Solve(), ObjexxFCL::format::space(), numeric::linear_algebra::svdcmp(), basic::svd::SVD_Solver::svdcmp(), svm_predict_probability(), boost_adaptbx::python::streambuf::sync(), numeric::kdtree::transform_percentile(), ObjexxFCL::Fstring::trimmed_whitespace_range(), ObjexxFCL::DimensionExpressionMax::value(), numeric::fourier::SO3coeffs::wignerSynthesis(), numeric::fourier::SO3coeffs::wignerSynthesisDiffSign(), numeric::fourier::SO3coeffs::wignerSynthesisSameSign(), BuildBindings::windows_buildOneNamespace(), fmt::BasicWriter< Char >::write_double(), ObjexxFCL::format::X(), and numeric::deriv::x_and_dtheta_dx().

template<class T >

static T min ( T  x, T  y  )

inlinestatic

References y().

Referenced by src.PyMolLink.PyMOLMover::_scale_list(), app.pyrosetta_toolkit.modules.prettytable.prettytable.PrettyTable::_stringify_row(), app.surface_docking.append_data::append_constraints(), ExposedStrandMover::apply(), zlib_stream::basic_zip_streambuf< Elem, Tr, ElemA, ByteT, ByteAT >::basic_zip_streambuf(), numeric::boltzmann_accept_probability(), Solver::calculate_rho(), Solver_NU::calculate_rho(), ObjexxFCL::DimensionExpressionMin::clone(), DockFragmentsMover::cluster_frags(), fmt::BasicStringRef< Char >::compare(), PlotSurfaceContactMap::ContactList(), ObjexxFCL::Fstring::copy(), correct_dunbrack(), numeric::deriv::dihedral_deriv_second(), 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(), numeric::fourier::SO3coeffs::genWigner_ds(), PyMOLPyRosettaServer::get_ends(), numeric::kdtree::get_percentile_bounds(), options_class::getMarkdownPage(), go_main(), Histogram::Histogram(), 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(), best_ifaceE::main(), main(), make_fragments(), MC_run(), utility::options::OptionCollection::merged(), utility::min(), ObjexxFCL::min(), numeric::min(), numeric::xyzVector< core::Real >::minimum_value(), 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(), PhiPsi::SecondaryStructure(), src.PyMolLink.PyMOLMover::send_hbonds(), 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(), 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 basic::options::OptionKeys::optE::free, info(), basic::options::OptionKeys::mp::mutate_relax::iter, 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 basic::options::OptionKeys::optE::free, info(), basic::options::OptionKeys::mp::mutate_relax::iter, basic::options::OptionKeys::in::file::l, numeric::log(), Malloc, basic::options::OptionKeys::score::fiber_diffraction::p, 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 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 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 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 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

References begin, svm_parameter::C, basic::options::OptionKeys::cutoutdomain::end, basic::options::OptionKeys::optE::free, basic::options::OptionKeys::frags::j, svm_problem::l, svm_model::label, Malloc, svm_parameter::nr_weight, svm_parameter::probability, sigmoid_train(), svm_destroy_param(), svm_free_and_destroy_model(), svm_predict_values(), svm_train(), swap(), svm_parameter::weight, svm_parameter::weight_label, svm_problem::x, and svm_problem::y.

Referenced by svm_train().

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

References svm_parameter::C, C_SVC, svm_parameter::cache_size, clean_pdb_keep_ligand::count, svm_parameter::degree, svm_parameter::eps, EPSILON_SVR, basic::options::OptionKeys::optE::free, svm_parameter::gamma, info(), basic::options::OptionKeys::frags::j, svm_parameter::kernel_type, svm_problem::l, basic::options::OptionKeys::in::file::l, svm_model::label, LINEAR, Malloc, min(), svm_model::nr_class, svm_parameter::nu, NU_SVC, NU_SVR, ONE_CLASS, svm_parameter::p, POLY, PRECOMPUTED, svm_parameter::probability, RBF, svm_parameter::shrinking, SIGMOID, svm_parameter::svm_type, and svm_problem::y.

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
	)

References begin, C_SVC, clean_pdb_keep_ligand::count, basic::options::OptionKeys::cutoutdomain::end, basic::options::OptionKeys::optE::free, ObjexxFCL::index(), basic::options::OptionKeys::frags::j, svm_problem::l, basic::options::OptionKeys::in::file::l, svm_model::label, Malloc, svm_model::nr_class, NU_SVC, svm_parameter::probability, basic::options::OptionKeys::cutoutdomain::start, svm_free_and_destroy_model(), svm_get_nr_class(), svm_group_classes(), svm_predict(), svm_predict_probability(), svm_train(), svm_parameter::svm_type, swap(), svm_problem::x, and svm_problem::y.

Referenced by svm_svr_probability().

void svm_destroy_param

(

svm_parameter *

param

)

References basic::options::OptionKeys::optE::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 basic::options::OptionKeys::optE::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 basic::options::OptionKeys::optE::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, fmt::fprintf(), 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, basic::options::OptionKeys::optE::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

)

References PlotSurfaceContactMap::cmd, svm_parameter::coef0, utility::io::oc::cout, svm_parameter::degree, fmt::fprintf(), basic::options::OptionKeys::optE::free, svm_model::free_sv, svm_parameter::gamma, svm_node::index, basic::options::OptionKeys::frags::j, svm_parameter::kernel_type, kernel_type_table, svm_model::l, basic::options::OptionKeys::in::file::l, svm_model::label, line, Malloc, svm_model::nr_class, svm_model::nSV, basic::options::OptionKeys::score::fiber_diffraction::p, svm_model::param, make_symmdef_file_denovo::pos, svm_model::probA, svm_model::probB, readline(), svm_model::rho, svm_model::SV, svm_model::sv_coef, svm_parameter::svm_type, svm_type_table, and svm_node::value.

Referenced by utility::libsvm::Svm_rosetta::Svm_rosetta().

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

References EPSILON_SVR, basic::options::OptionKeys::optE::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
	)

References C_SVC, basic::options::OptionKeys::optE::free, basic::options::OptionKeys::frags::j, svm_model::label, Malloc, max(), min(), multiclass_probability(), svm_model::nr_class, NU_SVC, svm_model::param, svm_model::probA, svm_model::probB, sigmoid_predict(), svm_predict(), svm_predict_values(), and svm_parameter::svm_type.

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

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

References EPSILON_SVR, basic::options::OptionKeys::optE::free, basic::options::OptionKeys::frags::j, Kernel::k_function(), svm_model::l, basic::options::OptionKeys::in::file::l, svm_model::label, Malloc, svm_model::nr_class, svm_model::nSV, NU_SVR, ONE_CLASS, basic::options::OptionKeys::score::fiber_diffraction::p, svm_model::param, svm_model::rho, basic::options::OptionKeys::cutoutdomain::start, sum(), svm_model::SV, svm_model::sv_coef, and svm_parameter::svm_type.

Referenced by svm_binary_svc_probability(), svm_predict(), and svm_predict_probability().

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

References svm_parameter::coef0, svm_parameter::degree, fmt::fprintf(), basic::options::OptionKeys::optE::free, svm_parameter::gamma, svm_node::index, basic::options::OptionKeys::frags::j, svm_parameter::kernel_type, kernel_type_table, svm_model::l, basic::options::OptionKeys::in::file::l, svm_model::label, svm_model::nr_class, svm_model::nSV, basic::options::OptionKeys::score::fiber_diffraction::p, svm_model::param, POLY, PRECOMPUTED, svm_model::probA, svm_model::probB, RBF, svm_model::rho, SIGMOID, svm_model::SV, svm_model::sv_coef, svm_parameter::svm_type, svm_type_table, and svm_node::value.

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, basic::options::OptionKeys::optE::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, fmt::fprintf(), basic::options::OptionKeys::optE::free, svm_model::free_sv, info(), basic::options::OptionKeys::frags::j, svm_problem::l, svm_model::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, svm_model::rho, decision_function::rho, basic::options::OptionKeys::cutoutdomain::start, svm_model::SV, svm_model::sv_coef, svm_model::sv_indices, 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, 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

References decision_function::alpha, C_SVC, EPSILON_SVR, demo.D060_Folding::f, info(), svm_problem::l, Malloc, NU_SVC, NU_SVR, Solver::SolutionInfo::obj, ONE_CLASS, Solver::SolutionInfo::rho, decision_function::rho, solve_c_svc(), solve_epsilon_svr(), solve_nu_svc(), solve_nu_svr(), solve_one_class(), svm_parameter::svm_type, Solver::SolutionInfo::upper_bound_n, Solver::SolutionInfo::upper_bound_p, and svm_problem::y.

Referenced by svm_train().

template<class T >

static void swap ( T &  x, T &  y  )

inlinestatic

References test.T007_TracerIO::T, basic::options::OptionKeys::in::file::t, x(), and y().

Referenced by Cache::get_data(), utility::insert_middle(), utility::json_spirit::Value_impl< Config >::operator=(), tools.CppParser.GccXML::parse(), tools.CppParser::sortObjects(), svm_binary_svc_probability(), svm_cross_validation(), utility::keys::SmallKeyMap< K, T >::swap(), utility::keys::SmallKeyVector< PathVectorOptionKey, PathVectorOption >::swap(), ObjexxFCL::Cstring::swap(), ObjexxFCL::Dimension::swap(), ObjexxFCL::CArray< typename >::swap(), utility::vectorL< L, bool, A >::swap(), ObjexxFCL::Chunk< T >::swap(), utility::keys::swap(), utility::vectorL< 1, std::string, A >::swap(), ObjexxFCL::IndexRange::swap(), ObjexxFCL::FArray1D< double >::swap(), ObjexxFCL::KeyFArray1D< typename >::swap(), ObjexxFCL::CArrayP< typename >::swap(), ObjexxFCL::FArray2D< double >::swap(), ObjexxFCL::KeyFArray2D< typename >::swap(), ObjexxFCL::FArray3D< typename >::swap(), ObjexxFCL::KeyFArray3D< typename >::swap(), ObjexxFCL::FArray4D< typename >::swap(), ObjexxFCL::KeyFArray4D< typename >::swap(), ObjexxFCL::FArray5D< typename >::swap(), ObjexxFCL::KeyFArray5D< typename >::swap(), ObjexxFCL::FArray6D< typename >::swap(), ObjexxFCL::swap(), ObjexxFCL::KeyFArray6D< typename >::swap(), ObjexxFCL::DynamicIndexRange::swap(), ObjexxFCL::ChunkVector< typename >::swap(), ObjexxFCL::FArray2< T >::swap2DB(), ObjexxFCL::FArray3< T >::swap3DB(), ObjexxFCL::FArray4< T >::swap4DB(), ObjexxFCL::FArray5< T >::swap5DB(), ObjexxFCL::FArray6< T >::swap6DB(), numeric::MathMatrix< Real >::swap_cols(), Cache::swap_index(), Kernel::swap_index(), Solver::swap_index(), SVC_Q::swap_index(), ONE_CLASS_Q::swap_index(), SVR_Q::swap_index(), ObjexxFCL::Dimension::swap_no_notify(), ObjexxFCL::DynamicIndexRange::swap_no_notify(), numeric::MathMatrix< Real >::swap_rows(), ObjexxFCL::FArray< T >::swapB(), and binder::vector_binder< T, Allocator >::vector_binder().

Variable Documentation

const char* kernel_type_table[]

static

Initial value:

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

Referenced by svm_load_model(), and svm_save_model().

int libsvm_version = LIBSVM_VERSION

char* line = NULL

static

Referenced by utility::file_contents(), utility::io::get_lines_from_file_data(), load_loops_from_file(), utility::options::OptionCollection::load_options_from_stream(), basic::resource_manager::locator::FileListResourceLocator::locate_resource_stream(), main(), basic::sampling::orientations::QuaternionGrid::QuaternionGrid(), binder::Config::read(), numeric::interpolation::Histogram< typename, typename >::read_from_db(), readline(), rhiju_pdbstats(), run_pep_prep(), utility::slurp(), 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",NULL
}

Referenced by svm_load_model(), and svm_save_model().