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protocols::noesy_assign::PeakAssignmentParameters Class Reference

#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 PeakAssignmentParametersget_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_
 
bool calibration_eliminate_
 
bool calibration_use_median_
 
core::Size calibration_cycles_
 
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_
 
utility::vector1< core::Realprob_sigmoid_tau_
 
utility::vector1< core::Realprob_sigmoid_m_
 
utility::vector1< core::Realprob_sigmoid_w_
 
utility::vector1< core::Realprob_level_
 

Private Member Functions

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

Static Private Member Functions

static PeakAssignmentParameterscreate_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 PeakAssignmentParametersinstance_
 Singleton instance pointer. More...
 

Constructor & Destructor Documentation

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

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().

Referenced by get_instance().

PeakAssignmentParameters const * protocols::noesy_assign::PeakAssignmentParameters::get_instance ( )
static
PeakAssignmentParameters * protocols::noesy_assign::PeakAssignmentParameters::get_nonconst_instance ( )
static
void protocols::noesy_assign::PeakAssignmentParameters::register_options ( )
static
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

DANGER DANGER DNAGER: Completely thread unsafe.

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

Member Data Documentation

bool protocols::noesy_assign::PeakAssignmentParameters::atom_dependent_calibration_
core::Real protocols::noesy_assign::PeakAssignmentParameters::calibration_convergence_
core::Size protocols::noesy_assign::PeakAssignmentParameters::calibration_cycles_
bool protocols::noesy_assign::PeakAssignmentParameters::calibration_eliminate_
bool protocols::noesy_assign::PeakAssignmentParameters::calibration_ignore_eliminated_peaks_
core::Real protocols::noesy_assign::PeakAssignmentParameters::calibration_max_noe_dist_
core::Real protocols::noesy_assign::PeakAssignmentParameters::calibration_max_nudging_
core::Real protocols::noesy_assign::PeakAssignmentParameters::calibration_start_nudging_
core::Real protocols::noesy_assign::PeakAssignmentParameters::calibration_stop_nudging_
core::Real protocols::noesy_assign::PeakAssignmentParameters::calibration_target_
bool protocols::noesy_assign::PeakAssignmentParameters::calibration_use_median_
core::Real protocols::noesy_assign::PeakAssignmentParameters::centroid_mapping_distance_padding_
core::Real protocols::noesy_assign::PeakAssignmentParameters::chemshift_overlap_weight_
core::Real protocols::noesy_assign::PeakAssignmentParameters::covalent_compliance_weight_
core::Real protocols::noesy_assign::PeakAssignmentParameters::cst_strength_
core::Size protocols::noesy_assign::PeakAssignmentParameters::cycle_selector_
private

Referenced by set_options_from_cmdline(), and show().

core::Real protocols::noesy_assign::PeakAssignmentParameters::dcalibrate_
core::Real protocols::noesy_assign::PeakAssignmentParameters::dcut_
bool protocols::noesy_assign::PeakAssignmentParameters::ignore_resonancefile_intensities_
bool protocols::noesy_assign::PeakAssignmentParameters::ignore_resonancefile_tolerances_
PeakAssignmentParameters * protocols::noesy_assign::PeakAssignmentParameters::instance_
staticprivate

Singleton instance pointer.

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

core::Real protocols::noesy_assign::PeakAssignmentParameters::local_distviol_cutoff_
core::Real protocols::noesy_assign::PeakAssignmentParameters::local_distviol_cutoff_buffer_
core::Real protocols::noesy_assign::PeakAssignmentParameters::local_distviol_global_buffer_
core::Real protocols::noesy_assign::PeakAssignmentParameters::local_distviol_global_factor_
core::Real protocols::noesy_assign::PeakAssignmentParameters::local_distviol_range_
bool protocols::noesy_assign::PeakAssignmentParameters::map_to_cen_atom_
core::Real protocols::noesy_assign::PeakAssignmentParameters::min_contribution_symmetric_peaks_
core::Real protocols::noesy_assign::PeakAssignmentParameters::min_volume_
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_
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_
core::Real protocols::noesy_assign::PeakAssignmentParameters::network_reswise_high_
core::Real protocols::noesy_assign::PeakAssignmentParameters::network_reswise_min_
bool protocols::noesy_assign::PeakAssignmentParameters::network_use_all_covalent_atoms_
core::Real protocols::noesy_assign::PeakAssignmentParameters::nmax_
bool protocols::noesy_assign::PeakAssignmentParameters::no_network_
core::Real protocols::noesy_assign::PeakAssignmentParameters::nr_conformers_violatable_
bool protocols::noesy_assign::PeakAssignmentParameters::options_registered_
staticprivate
utility::vector1<core::Real> protocols::noesy_assign::PeakAssignmentParameters::prob_level_
utility::vector1<core::Real> protocols::noesy_assign::PeakAssignmentParameters::prob_sigmoid_m_
utility::vector1<core::Real> protocols::noesy_assign::PeakAssignmentParameters::prob_sigmoid_tau_
utility::vector1<core::Real> protocols::noesy_assign::PeakAssignmentParameters::prob_sigmoid_w_
core::Real protocols::noesy_assign::PeakAssignmentParameters::smax_
core::Real protocols::noesy_assign::PeakAssignmentParameters::symmetry_compliance_weight_
bool protocols::noesy_assign::PeakAssignmentParameters::use_local_distviol_
core::Real protocols::noesy_assign::PeakAssignmentParameters::vmax_
core::Real protocols::noesy_assign::PeakAssignmentParameters::vmin_

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