#include <PeakAssignmentParameters.hh>

Public Member Functions
void	show (std::ostream &) const

void	show_on_tracer () const

Static Public Member Functions
static void	register_options ()

static void	set_cycle (core::Size)

static PeakAssignmentParameters const *	get_instance ()
	static function to get the instance of ( pointer to) this singleton class More...

static PeakAssignmentParameters *	get_nonconst_instance ()

static void	reset ()

Public Attributes
core::Real	chemshift_overlap_weight_

bool	ignore_resonancefile_tolerances_

bool	ignore_resonancefile_intensities_

core::Real	vmin_

core::Real	vmax_

core::Real	nmax_

core::Real	nr_conformers_violatable_

core::Real	network_reswise_high_

core::Real	centroid_mapping_distance_padding_

core::Real	symmetry_compliance_weight_

core::Real	covalent_compliance_weight_

core::Real	min_contribution_symmetric_peaks_

core::Real	smax_

core::Real	dcut_

core::Real	dcalibrate_

bool	use_local_distviol_

core::Real	local_distviol_range_

core::Real	local_distviol_global_buffer_

core::Real	local_distviol_global_factor_

core::Real	local_distviol_cutoff_

core::Real	local_distviol_cutoff_buffer_

core::Real	network_reswise_min_

core::Real	network_atom_min_

core::Real	calibration_target_

bool	calibration_ignore_eliminated_peaks_

bool	atom_dependent_calibration_

core::Real	min_volume_

core::Real	cst_strength_

bool	no_network_

bool	network_use_all_covalent_atoms_

bool	network_include_reverse_dir_

bool	network_allow_same_residue_connect_

std::string	network_mode_

bool	map_to_cen_atom_

core::Real	calibration_convergence_

core::Real	calibration_max_noe_dist_

core::Real	calibration_stop_nudging_

core::Real	calibration_start_nudging_

core::Real	calibration_max_nudging_

bool	calibration_eliminate_

bool	calibration_use_median_

core::Size	calibration_cycles_

utility::vector1< core::Real >	prob_sigmoid_tau_

utility::vector1< core::Real >	prob_sigmoid_m_

utility::vector1< core::Real >	prob_sigmoid_w_

utility::vector1< core::Real >	prob_level_

Private Member Functions
	PeakAssignmentParameters ()

void	set_options_from_cmdline (core::Size cycle=0)

Static Private Member Functions
static PeakAssignmentParameters *	create_singleton_instance ()
	private singleton creation function to be used with utility::thread::threadsafe_singleton More...

Private Attributes
core::Size	cycle_selector_

Static Private Attributes
static bool	options_registered_

static PeakAssignmentParameters *	instance_

Constructor & Destructor Documentation

protocols::noesy_assign::PeakAssignmentParameters::PeakAssignmentParameters ( )

inlineprivate

Referenced by create_singleton_instance(), get_nonconst_instance(), and set_cycle().

Member Function Documentation

PeakAssignmentParameters * protocols::noesy_assign::PeakAssignmentParameters::create_singleton_instance ( )

staticprivate

private singleton creation function to be used with utility::thread::threadsafe_singleton

References PeakAssignmentParameters(), and set_options_from_cmdline().

Referenced by get_instance().

PeakAssignmentParameters const * protocols::noesy_assign::PeakAssignmentParameters::get_instance ( )

static

static function to get the instance of ( pointer to) this singleton class

References create_singleton_instance(), instance_, and utility::thread::safely_create_singleton().

PeakAssignmentParameters * protocols::noesy_assign::PeakAssignmentParameters::get_nonconst_instance ( )

static

DANGER DANGER DANGER! NOT IN ANY WAY THREADSAFE!!!

References instance_, PeakAssignmentParameters(), and set_options_from_cmdline().

Referenced by protocols::noesy_assign::PeakCalibrator::interpolate_on_statistics(), and protocols::abinitio::IterativeBase::reassign_noesy_data().

void protocols::noesy_assign::PeakAssignmentParameters::register_options ( )

static

References NEW_OPT, NEW_OPT2, NEW_OPT5, NEW_OPT7, options_registered_, and protocols::sic_dock::range().

void protocols::noesy_assign::PeakAssignmentParameters::reset ( void )

static

DANGER DANGER DANGER! NOT IN ANY WAY THREADSAFE!!!

References instance_.

Referenced by protocols::abinitio::IterativeBase::reassign_noesy_data().

void protocols::noesy_assign::PeakAssignmentParameters::set_cycle ( core::Size cycle )

static

References instance_, PeakAssignmentParameters(), and set_options_from_cmdline().

Referenced by protocols::abinitio::IterativeBase::reassign_noesy_data().

void protocols::noesy_assign::PeakAssignmentParameters::set_options_from_cmdline ( core::Size cycle = 0 )

private

References atom_dependent_calibration_, calibration_convergence_, calibration_cycles_, calibration_eliminate_, calibration_ignore_eliminated_peaks_, calibration_max_noe_dist_, calibration_max_nudging_, calibration_start_nudging_, calibration_stop_nudging_, calibration_target_, calibration_use_median_, centroid_mapping_distance_padding_, chemshift_overlap_weight_, covalent_compliance_weight_, cst_strength_, cycle_selector_, dcalibrate_, dcut_, ignore_resonancefile_intensities_, ignore_resonancefile_tolerances_, local_distviol_cutoff_, local_distviol_cutoff_buffer_, local_distviol_global_buffer_, local_distviol_global_factor_, local_distviol_range_, map_to_cen_atom_, min_contribution_symmetric_peaks_, min_volume_, network_allow_same_residue_connect_, network_atom_min_, network_include_reverse_dir_, network_mode_, network_reswise_high_, network_reswise_min_, network_use_all_covalent_atoms_, nmax_, no_network_, nr_conformers_violatable_, opt_read_out_macro, opt_read_out_macro2, option, options_registered_, prob_level_, prob_sigmoid_m_, prob_sigmoid_tau_, prob_sigmoid_w_, protocols::sic_dock::range(), runtime_assert, show_on_tracer(), smax_, symmetry, symmetry_compliance_weight_, use_local_distviol_, utility_exit_with_message, vmax_, and vmin_.

Referenced by create_singleton_instance(), get_nonconst_instance(), and set_cycle().

void protocols::noesy_assign::PeakAssignmentParameters::show ( std::ostream & os ) const

void protocols::noesy_assign::PeakAssignmentParameters::show_on_tracer ( ) const

References show(), and protocols::noesy_assign::tr.

Referenced by protocols::abinitio::IterativeBase::reassign_noesy_data(), and set_options_from_cmdline().

Member Data Documentation

bool protocols::noesy_assign::PeakAssignmentParameters::atom_dependent_calibration_

Referenced by protocols::noesy_assign::PeakCalibrator::atom_type(), protocols::noesy_assign::PeakCalibrator::PeakCalibrator(), set_options_from_cmdline(), and show().

core::Real protocols::noesy_assign::PeakAssignmentParameters::calibration_convergence_

Referenced by protocols::noesy_assign::StructureDependentPeakCalibrator::collect_upperbound_statistics(), and set_options_from_cmdline().

core::Size protocols::noesy_assign::PeakAssignmentParameters::calibration_cycles_

Referenced by protocols::noesy_assign::CrossPeakList::calibrate(), and set_options_from_cmdline().

bool protocols::noesy_assign::PeakAssignmentParameters::calibration_eliminate_

Referenced by protocols::noesy_assign::CrossPeakList::calibrate(), and set_options_from_cmdline().

bool protocols::noesy_assign::PeakAssignmentParameters::calibration_ignore_eliminated_peaks_

Referenced by protocols::noesy_assign::StructureDependentPeakCalibrator::collect_upperbound_statistics(), and set_options_from_cmdline().

core::Real protocols::noesy_assign::PeakAssignmentParameters::calibration_max_noe_dist_

Referenced by protocols::noesy_assign::PeakFileFormat::read_header(), and set_options_from_cmdline().

core::Real protocols::noesy_assign::PeakAssignmentParameters::calibration_max_nudging_

Referenced by protocols::noesy_assign::StructureDependentPeakCalibrator::eliminate_violated_constraints(), and set_options_from_cmdline().

core::Real protocols::noesy_assign::PeakAssignmentParameters::calibration_start_nudging_

Referenced by protocols::noesy_assign::StructureDependentPeakCalibrator::eliminate_violated_constraints(), and set_options_from_cmdline().

core::Real protocols::noesy_assign::PeakAssignmentParameters::calibration_stop_nudging_

Referenced by protocols::noesy_assign::StructureDependentPeakCalibrator::eliminate_violated_constraints(), and set_options_from_cmdline().

core::Real protocols::noesy_assign::PeakAssignmentParameters::calibration_target_

Referenced by protocols::noesy_assign::CrossPeakList::calibrate(), and set_options_from_cmdline().

bool protocols::noesy_assign::PeakAssignmentParameters::calibration_use_median_

Referenced by protocols::noesy_assign::PeakCalibrator::interpolate_on_statistics(), and set_options_from_cmdline().

core::Real protocols::noesy_assign::PeakAssignmentParameters::centroid_mapping_distance_padding_

Referenced by protocols::noesy_assign::CrossPeak::create_fa_and_cen_constraint(), set_options_from_cmdline(), and show().

core::Real protocols::noesy_assign::PeakAssignmentParameters::chemshift_overlap_weight_

Referenced by set_options_from_cmdline(), show(), and protocols::noesy_assign::PeakAssignment::update_chemshiftscore_from_peak().

core::Real protocols::noesy_assign::PeakAssignmentParameters::covalent_compliance_weight_

Referenced by protocols::noesy_assign::PeakAssignment::dump_weights(), protocols::noesy_assign::PeakAssignment::peak_volume(), set_options_from_cmdline(), and show().

core::Real protocols::noesy_assign::PeakAssignmentParameters::cst_strength_

Referenced by protocols::noesy_assign::CrossPeak::create_fa_and_cen_constraint(), set_options_from_cmdline(), and show().

core::Size protocols::noesy_assign::PeakAssignmentParameters::cycle_selector_

private

Referenced by set_options_from_cmdline(), and show().

core::Real protocols::noesy_assign::PeakAssignmentParameters::dcalibrate_

Referenced by protocols::noesy_assign::CrossPeakList::calibrate(), set_options_from_cmdline(), and show().

core::Real protocols::noesy_assign::PeakAssignmentParameters::dcut_

Referenced by protocols::noesy_assign::StructureDependentPeakCalibrator::eliminate_violated_constraints(), protocols::abinitio::IterativeBase::reassign_noesy_data(), set_options_from_cmdline(), show(), and protocols::noesy_assign::CrossPeakList::update_decoy_compatibility_score().

bool protocols::noesy_assign::PeakAssignmentParameters::ignore_resonancefile_intensities_

Referenced by protocols::noesy_assign::ResonanceList::read_from_stream(), and set_options_from_cmdline().

bool protocols::noesy_assign::PeakAssignmentParameters::ignore_resonancefile_tolerances_

Referenced by protocols::noesy_assign::ResonanceList::read_from_stream(), and set_options_from_cmdline().

PeakAssignmentParameters * protocols::noesy_assign::PeakAssignmentParameters::instance_

staticprivate

Referenced by get_instance(), get_nonconst_instance(), reset(), and set_cycle().

core::Real protocols::noesy_assign::PeakAssignmentParameters::local_distviol_cutoff_

Referenced by protocols::noesy_assign::StructureDependentPeakCalibrator::eliminate_violated_constraints(), and set_options_from_cmdline().

core::Real protocols::noesy_assign::PeakAssignmentParameters::local_distviol_cutoff_buffer_

Referenced by protocols::noesy_assign::StructureDependentPeakCalibrator::eliminate_violated_constraints(), and set_options_from_cmdline().

core::Real protocols::noesy_assign::PeakAssignmentParameters::local_distviol_global_buffer_

Referenced by protocols::noesy_assign::StructureDependentPeakCalibrator::eliminate_violated_constraints(), set_options_from_cmdline(), and show().

core::Real protocols::noesy_assign::PeakAssignmentParameters::local_distviol_global_factor_

Referenced by protocols::noesy_assign::StructureDependentPeakCalibrator::eliminate_violated_constraints(), set_options_from_cmdline(), and show().

core::Real protocols::noesy_assign::PeakAssignmentParameters::local_distviol_range_

Referenced by protocols::noesy_assign::StructureDependentPeakCalibrator::eliminate_violated_constraints(), set_options_from_cmdline(), and show().

bool protocols::noesy_assign::PeakAssignmentParameters::map_to_cen_atom_

Referenced by protocols::noesy_assign::CrossPeak::create_fa_and_cen_constraint(), and set_options_from_cmdline().

core::Real protocols::noesy_assign::PeakAssignmentParameters::min_contribution_symmetric_peaks_

Referenced by protocols::noesy_assign::NoesyModule::assign(), set_options_from_cmdline(), and protocols::noesy_assign::CrossPeakList::update_symmetry_score().

core::Real protocols::noesy_assign::PeakAssignmentParameters::min_volume_

Referenced by protocols::noesy_assign::DistanceScoreMover::apply(), protocols::noesy_assign::CrossPeak::calibrate(), protocols::noesy_assign::CrossPeak::create_fa_and_cen_constraint(), protocols::noesy_assign::CrossPeak::eliminated(), protocols::noesy_assign::CrossPeak::n_Vmin_assignments(), set_options_from_cmdline(), and show().

bool protocols::noesy_assign::PeakAssignmentParameters::network_allow_same_residue_connect_

Referenced by set_options_from_cmdline(), and show().

core::Real protocols::noesy_assign::PeakAssignmentParameters::network_atom_min_

Referenced by protocols::noesy_assign::CrossPeak::eliminated(), set_options_from_cmdline(), and show().

bool protocols::noesy_assign::PeakAssignmentParameters::network_include_reverse_dir_

Referenced by set_options_from_cmdline(), and show().

std::string protocols::noesy_assign::PeakAssignmentParameters::network_mode_

Referenced by protocols::noesy_assign::CrossPeakList::network_analysis(), and set_options_from_cmdline().

core::Real protocols::noesy_assign::PeakAssignmentParameters::network_reswise_high_

Referenced by protocols::noesy_assign::CrossPeak::eliminated(), set_options_from_cmdline(), and show().

core::Real protocols::noesy_assign::PeakAssignmentParameters::network_reswise_min_

Referenced by protocols::noesy_assign::CrossPeak::eliminated(), set_options_from_cmdline(), and show().

bool protocols::noesy_assign::PeakAssignmentParameters::network_use_all_covalent_atoms_

Referenced by set_options_from_cmdline(), show(), and protocols::noesy_assign::CrossPeakList::update_assignment_list().

core::Real protocols::noesy_assign::PeakAssignmentParameters::nmax_

Referenced by protocols::noesy_assign::CrossPeak::eliminated(), set_options_from_cmdline(), and show().

bool protocols::noesy_assign::PeakAssignmentParameters::no_network_

Referenced by protocols::noesy_assign::NoesyModule::assign(), set_options_from_cmdline(), and show().

core::Real protocols::noesy_assign::PeakAssignmentParameters::nr_conformers_violatable_

Referenced by protocols::noesy_assign::StructureDependentPeakCalibrator::eliminate_violated_constraints(), set_options_from_cmdline(), and show().

bool protocols::noesy_assign::PeakAssignmentParameters::options_registered_

staticprivate

Referenced by register_options(), and set_options_from_cmdline().

utility::vector1<core::Real> protocols::noesy_assign::PeakAssignmentParameters::prob_level_

Referenced by protocols::noesy_assign::CrossPeak::quality_class(), and set_options_from_cmdline().

utility::vector1<core::Real> protocols::noesy_assign::PeakAssignmentParameters::prob_sigmoid_m_

Referenced by protocols::noesy_assign::CrossPeak::probability(), and set_options_from_cmdline().

utility::vector1<core::Real> protocols::noesy_assign::PeakAssignmentParameters::prob_sigmoid_tau_

Referenced by protocols::noesy_assign::CrossPeak::probability(), and set_options_from_cmdline().

utility::vector1<core::Real> protocols::noesy_assign::PeakAssignmentParameters::prob_sigmoid_w_

Referenced by protocols::noesy_assign::CrossPeak::probability(), and set_options_from_cmdline().

core::Real protocols::noesy_assign::PeakAssignmentParameters::smax_

Referenced by protocols::noesy_assign::PeakAssignment::peak_volume(), set_options_from_cmdline(), and show().

core::Real protocols::noesy_assign::PeakAssignmentParameters::symmetry_compliance_weight_

Referenced by protocols::noesy_assign::PeakAssignment::dump_weights(), protocols::noesy_assign::PeakAssignment::peak_volume(), set_options_from_cmdline(), and show().

bool protocols::noesy_assign::PeakAssignmentParameters::use_local_distviol_

Referenced by protocols::noesy_assign::StructureDependentPeakCalibrator::eliminate_violated_constraints(), protocols::abinitio::IterativeBase::reassign_noesy_data(), set_options_from_cmdline(), and show().

core::Real protocols::noesy_assign::PeakAssignmentParameters::vmax_

Referenced by protocols::noesy_assign::PeakAssignmentResidueMap::compute_Nk(), protocols::noesy_assign::PeakAssignmentResidueMap::network_analysis2(), set_options_from_cmdline(), and show().

core::Real protocols::noesy_assign::PeakAssignmentParameters::vmin_

Referenced by protocols::noesy_assign::PeakAssignmentResidueMap::compute_Nk(), protocols::noesy_assign::PeakAssignmentResidueMap::network_analysis2(), set_options_from_cmdline(), and show().

The documentation for this class was generated from the following files:

src/protocols/noesy_assign/PeakAssignmentParameters.hh
src/protocols/noesy_assign/PeakAssignmentParameters.cc

Public Member Functions

Static Public Member Functions

Public Attributes

Private Member Functions

Static Private Member Functions

Private Attributes

Static Private Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation