#include <PeakAssignmentParameters.hh>

Collaboration diagram for protocols::noesy_assign::PeakAssignmentParameters:

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 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)

Private Attributes
core::Size	cycle_selector_

Static Private Attributes
static bool	options_registered_

static PeakAssignmentParameters *	instance_

Detailed Description

Definition at line 31 of file PeakAssignmentParameters.hh.

Constructor & Destructor Documentation

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

inlineprivate

Definition at line 35 of file PeakAssignmentParameters.hh.

Referenced by get_instance().

Member Function Documentation

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

static

Definition at line 49 of file PeakAssignmentParameters.cc.

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

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

static

Definition at line 63 of file PeakAssignmentParameters.cc.

References 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

Definition at line 76 of file PeakAssignmentParameters.cc.

References protocols::evaluation::options_registered_, and protocols::sic_dock::range().

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

static

Definition at line 57 of file PeakAssignmentParameters.cc.

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

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

static

Definition at line 70 of file PeakAssignmentParameters.cc.

References 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

Definition at line 159 of file PeakAssignmentParameters.cc.

References opt_read_out_macro, protocols::evaluation::options_registered_, and protocols::sic_dock::range().

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

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

Definition at line 247 of file PeakAssignmentParameters.cc.

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

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

Definition at line 292 of file PeakAssignmentParameters.cc.

References tr().

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

Member Data Documentation

bool protocols::noesy_assign::PeakAssignmentParameters::atom_dependent_calibration_

Definition at line 91 of file PeakAssignmentParameters.hh.

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

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

Definition at line 103 of file PeakAssignmentParameters.hh.

Referenced by protocols::noesy_assign::StructureDependentPeakCalibrator::collect_upperbound_statistics().

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

Definition at line 110 of file PeakAssignmentParameters.hh.

Referenced by protocols::noesy_assign::CrossPeakList::calibrate().

bool protocols::noesy_assign::PeakAssignmentParameters::calibration_eliminate_

Definition at line 108 of file PeakAssignmentParameters.hh.

Referenced by protocols::noesy_assign::CrossPeakList::calibrate().

bool protocols::noesy_assign::PeakAssignmentParameters::calibration_ignore_eliminated_peaks_

Definition at line 90 of file PeakAssignmentParameters.hh.

Referenced by protocols::noesy_assign::StructureDependentPeakCalibrator::collect_upperbound_statistics().

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

Definition at line 104 of file PeakAssignmentParameters.hh.

Referenced by protocols::noesy_assign::PeakFileFormat::read_header().

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

Definition at line 107 of file PeakAssignmentParameters.hh.

Referenced by protocols::noesy_assign::StructureDependentPeakCalibrator::eliminate_violated_constraints().

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

Definition at line 106 of file PeakAssignmentParameters.hh.

Referenced by protocols::noesy_assign::StructureDependentPeakCalibrator::eliminate_violated_constraints().

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

Definition at line 105 of file PeakAssignmentParameters.hh.

Referenced by protocols::noesy_assign::StructureDependentPeakCalibrator::eliminate_violated_constraints().

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

Definition at line 89 of file PeakAssignmentParameters.hh.

Referenced by protocols::noesy_assign::CrossPeakList::calibrate().

bool protocols::noesy_assign::PeakAssignmentParameters::calibration_use_median_

Definition at line 109 of file PeakAssignmentParameters.hh.

Referenced by protocols::noesy_assign::PeakCalibrator::interpolate_on_statistics().

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

Definition at line 69 of file PeakAssignmentParameters.hh.

Referenced by protocols::noesy_assign::CrossPeak::create_fa_and_cen_constraint().

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

Definition at line 60 of file PeakAssignmentParameters.hh.

Referenced by protocols::noesy_assign::PeakAssignment::update_chemshiftscore_from_peak().

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

Definition at line 72 of file PeakAssignmentParameters.hh.

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

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

Definition at line 94 of file PeakAssignmentParameters.hh.

Referenced by protocols::noesy_assign::CrossPeak::create_fa_and_cen_constraint().

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

private

Definition at line 48 of file PeakAssignmentParameters.hh.

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

Definition at line 78 of file PeakAssignmentParameters.hh.

Referenced by protocols::noesy_assign::CrossPeakList::calibrate().

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

Definition at line 77 of file PeakAssignmentParameters.hh.

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

bool protocols::noesy_assign::PeakAssignmentParameters::ignore_resonancefile_intensities_

Definition at line 62 of file PeakAssignmentParameters.hh.

Referenced by protocols::noesy_assign::ResonanceList::read_from_stream().

bool protocols::noesy_assign::PeakAssignmentParameters::ignore_resonancefile_tolerances_

Definition at line 61 of file PeakAssignmentParameters.hh.

Referenced by protocols::noesy_assign::ResonanceList::read_from_stream().

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

staticprivate

Definition at line 47 of file PeakAssignmentParameters.hh.

Referenced by get_instance().

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

Definition at line 84 of file PeakAssignmentParameters.hh.

Referenced by protocols::noesy_assign::StructureDependentPeakCalibrator::eliminate_violated_constraints().

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

Definition at line 85 of file PeakAssignmentParameters.hh.

Referenced by protocols::noesy_assign::StructureDependentPeakCalibrator::eliminate_violated_constraints().

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

Definition at line 82 of file PeakAssignmentParameters.hh.

Referenced by protocols::noesy_assign::StructureDependentPeakCalibrator::eliminate_violated_constraints().

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

Definition at line 83 of file PeakAssignmentParameters.hh.

Referenced by protocols::noesy_assign::StructureDependentPeakCalibrator::eliminate_violated_constraints().

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

Definition at line 81 of file PeakAssignmentParameters.hh.

Referenced by protocols::noesy_assign::StructureDependentPeakCalibrator::eliminate_violated_constraints().

bool protocols::noesy_assign::PeakAssignmentParameters::map_to_cen_atom_

Definition at line 101 of file PeakAssignmentParameters.hh.

Referenced by protocols::noesy_assign::CrossPeak::create_fa_and_cen_constraint().

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

Definition at line 75 of file PeakAssignmentParameters.hh.

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

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

Definition at line 92 of file PeakAssignmentParameters.hh.

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(), and protocols::noesy_assign::CrossPeak::n_Vmin_assignments().

bool protocols::noesy_assign::PeakAssignmentParameters::network_allow_same_residue_connect_

Definition at line 99 of file PeakAssignmentParameters.hh.

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

Definition at line 88 of file PeakAssignmentParameters.hh.

Referenced by protocols::noesy_assign::CrossPeak::eliminated().

bool protocols::noesy_assign::PeakAssignmentParameters::network_include_reverse_dir_

Definition at line 98 of file PeakAssignmentParameters.hh.

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

Definition at line 100 of file PeakAssignmentParameters.hh.

Referenced by protocols::noesy_assign::CrossPeakList::network_analysis().

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

Definition at line 68 of file PeakAssignmentParameters.hh.

Referenced by protocols::noesy_assign::CrossPeak::eliminated().

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

Definition at line 87 of file PeakAssignmentParameters.hh.

Referenced by protocols::noesy_assign::CrossPeak::eliminated().

bool protocols::noesy_assign::PeakAssignmentParameters::network_use_all_covalent_atoms_

Definition at line 97 of file PeakAssignmentParameters.hh.

Referenced by protocols::noesy_assign::CrossPeakList::update_assignment_list().

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

Definition at line 66 of file PeakAssignmentParameters.hh.

Referenced by protocols::noesy_assign::CrossPeak::eliminated().

bool protocols::noesy_assign::PeakAssignmentParameters::no_network_

Definition at line 96 of file PeakAssignmentParameters.hh.

Referenced by protocols::noesy_assign::NoesyModule::assign().

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

Definition at line 67 of file PeakAssignmentParameters.hh.

Referenced by protocols::noesy_assign::StructureDependentPeakCalibrator::eliminate_violated_constraints().

bool protocols::noesy_assign::PeakAssignmentParameters::options_registered_

staticprivate

Definition at line 34 of file PeakAssignmentParameters.hh.

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

Definition at line 115 of file PeakAssignmentParameters.hh.

Referenced by protocols::noesy_assign::CrossPeak::quality_class().

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

Definition at line 113 of file PeakAssignmentParameters.hh.

Referenced by protocols::noesy_assign::CrossPeak::probability().

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

Definition at line 112 of file PeakAssignmentParameters.hh.

Referenced by protocols::noesy_assign::CrossPeak::probability().

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

Definition at line 114 of file PeakAssignmentParameters.hh.

Referenced by protocols::noesy_assign::CrossPeak::probability().

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

Definition at line 76 of file PeakAssignmentParameters.hh.

Referenced by protocols::noesy_assign::PeakAssignment::peak_volume().

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

Definition at line 71 of file PeakAssignmentParameters.hh.

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

bool protocols::noesy_assign::PeakAssignmentParameters::use_local_distviol_

Definition at line 80 of file PeakAssignmentParameters.hh.

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

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

Definition at line 65 of file PeakAssignmentParameters.hh.

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

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

Definition at line 64 of file PeakAssignmentParameters.hh.

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

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

Private Attributes

Static Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation