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Classes | Typedefs | Functions
protocols::scoring::methods::pcs2 Namespace Reference

Classes

class  GridSearchIteratorCA
 
class  PcsDataCenter
 
class  PcsDataCenterManager
 
class  PcsDataCenterManagerSingleton
 
class  PcsDataLanthanide
 
class  PcsEnergy
 
class  PcsEnergyCreator
 
class  PcsEnergyParameter
 
class  PcsEnergyParameterManager
 
class  PcsGridSearchParameter
 
class  PcsGridSearchParameterManager
 
class  PcsInputCenter
 PcsInputCenter contain all the input information for one paramagnetic center. It can contain multiple data set. More...
 
class  PcsInputCenterManager
 
class  PcsInputFile
 PcsInputFile contain all the information of a .npc file one per lanthanide. More...
 
class  PcsInputLine
 PcsInputLine class: hold a line of the input file information (.npc format) One PcsInputLine per line in the input file. More...
 
class  PcsTensor
 
class  TensorsOptimizer
 
class  TensorsOptimizerFix
 
class  TensorsOptimizerSvd
 

Typedefs

typedef
utility::pointer::shared_ptr
< PcsDataCenter
PcsDataCenterOP
 
typedef
utility::pointer::shared_ptr
< PcsDataCenter const > 
PcsDataCenterCOP
 
typedef
utility::pointer::shared_ptr
< PcsDataCenterManager
PcsDataCenterManagerOP
 
typedef
utility::pointer::shared_ptr
< PcsEnergy
PcsEnergyOP
 
typedef
utility::pointer::shared_ptr
< PcsEnergy const > 
PcsEnergyCOP
 
typedef
utility::pointer::shared_ptr
< PcsInputCenter
PcsInputCenterOP
 
typedef
utility::pointer::shared_ptr
< PcsInputCenter const > 
PcsInputCenterCOP
 

Functions

static basic::Tracer TR_PcsDataCenter ("protocols.scoring.methods.pcs.PcsDataCenter")
 
core::Real fill_A_line_fast (utility::vector1< core::Real > &A_line, core::Real const xM, core::Real const yM, core::Real const zM, core::Real const x, core::Real const y, core::Real const z)
 
void fill_A_line_slow (utility::vector1< core::Real > &A_line, core::Real const xM, core::Real const yM, core::Real const zM, core::Real const x, core::Real const y, core::Real const z)
 
std::ostream & operator<< (std::ostream &out, const PcsDataCenter &me)
 
static basic::Tracer TR_PcsDataCenterManager ("protocols.scoring.methods.pcs.PcsDataCenterManager")
 
std::ostream & operator<< (std::ostream &out, const PcsDataCenterManager &m)
 
static basic::Tracer TR_PcsDataCenterManagerSingleton ("protocols.scoring.methods.pcs.PcsDataCenterManagerSingleton")
 
std::ostream & operator<< (std::ostream &out, const PcsDataCenterManagerSingleton &m)
 
static basic::Tracer TR_PcsDataLanthanide ("protocols.scoring.methods.pcs.PcsDataLanthanide")
 
bool do_I_skip (PcsInputLine &pcs_i_l, core::Size start, core::Size end)
 
core::Size reduced_size (utility::vector1< PcsInputLine > const &pcs_i_l_v, core::Size start, core::Size end)
 
std::ostream & operator<< (std::ostream &out, const PcsDataLanthanide &me)
 
static basic::Tracer TR_PcsEnergy ("protocols.scoring.methods.pcs.PcsEnergy")
 
static basic::Tracer TR_PcsEnergyParameter ("protocols.scoring.methods.pcs.PcsEnergyParameter")
 
std::ostream & operator<< (std::ostream &out, const PcsEnergyParameter &me)
 
static basic::Tracer TR_PcsEnergyParameterManager ("protocols.scoring.methods.pcs.PcsEnergyParameterManager")
 
std::ostream & operator<< (std::ostream &out, const PcsEnergyParameterManager &me)
 
std::ostream & operator<< (std::ostream &out, const PcsGridSearchParameter &me)
 
void output_error_message (core::Size id)
 
bool valide_include_only_stage (core::Size start, core::Size end)
 
static basic::Tracer TR_PcsInputCenter ("protocols.scoring.methods.pcs.PcsInputCenter")
 
std::ostream & operator<< (std::ostream &out, const PcsInputCenter &me)
 
static basic::Tracer TR_PcsInputCenterManager ("protocols.scoring.methods.pcs.PcsInputCenterManager")
 
std::ostream & operator<< (std::ostream &out, const PcsInputCenterManager &me)
 
static basic::Tracer TR_PcsInputFile ("protocols.scoring.methods.pcs.PcsInputFile")
 
std::ostream & operator<< (std::ostream &out, const PcsInputFile &me)
 
static basic::Tracer TR_PcsInputLine ("protocols.scoring.methods.pcs.PcsInputLine")
 
std::ostream & operator<< (std::ostream &out, const PcsInputLine &me)
 
std::ostream & operator<< (std::ostream &out, const PcsTensor &me)
 
static basic::Tracer TR_TensorsOptimizer ("protocols.scoring.methods.pcs.TensorsOptimizer")
 
static basic::Tracer TR_TensorsOptimizerFix ("protocols.scoring.methods.pcs.TensorsOptimizerFix")
 
static basic::Tracer TR_TensorsOptimizerSvd ("protocols.scoring.methods.pcs.TensorsOptimizerSvd")
 

Typedef Documentation

typedef utility::pointer::shared_ptr< PcsDataCenter const > protocols::scoring::methods::pcs2::PcsDataCenterCOP
typedef utility::pointer::shared_ptr< PcsDataCenter > protocols::scoring::methods::pcs2::PcsDataCenterOP
typedef utility::pointer::shared_ptr< PcsEnergy const > protocols::scoring::methods::pcs2::PcsEnergyCOP
typedef utility::pointer::shared_ptr< PcsEnergy > protocols::scoring::methods::pcs2::PcsEnergyOP
typedef utility::pointer::shared_ptr< PcsInputCenter const > protocols::scoring::methods::pcs2::PcsInputCenterCOP

Function Documentation

bool protocols::scoring::methods::pcs2::do_I_skip ( PcsInputLine &  pcs_i_l,
core::Size  start,
core::Size  end 
)
core::Real protocols::scoring::methods::pcs2::fill_A_line_fast ( utility::vector1< core::Real > &  A_line,
core::Real const  xM,
core::Real const  yM,
core::Real const  zM,
core::Real const  x,
core::Real const  y,
core::Real const  z 
)
void protocols::scoring::methods::pcs2::fill_A_line_slow ( utility::vector1< core::Real > &  A_line,
core::Real const  xM,
core::Real const  yM,
core::Real const  zM,
core::Real const  x,
core::Real const  y,
core::Real const  z 
)
std::ostream& protocols::scoring::methods::pcs2::operator<< ( std::ostream &  out,
const PcsInputCenterManager &  me 
)
std::ostream& protocols::scoring::methods::pcs2::operator<< ( std::ostream &  out,
const PcsDataCenterManager &  m 
)
std::ostream& protocols::scoring::methods::pcs2::operator<< ( std::ostream &  out,
const PcsDataCenterManagerSingleton &  m 
)
std::ostream& protocols::scoring::methods::pcs2::operator<< ( std::ostream &  out,
const PcsEnergyParameterManager &  me 
)
std::ostream& protocols::scoring::methods::pcs2::operator<< ( std::ostream &  out,
const PcsInputCenter &  me 
)
std::ostream& protocols::scoring::methods::pcs2::operator<< ( std::ostream &  out,
const PcsEnergyParameter &  me 
)
std::ostream& protocols::scoring::methods::pcs2::operator<< ( std::ostream &  out,
const PcsInputLine &  me 
)
std::ostream& protocols::scoring::methods::pcs2::operator<< ( std::ostream &  out,
const PcsTensor &  me 
)
std::ostream& protocols::scoring::methods::pcs2::operator<< ( std::ostream &  out,
const PcsInputFile &  me 
)
std::ostream& protocols::scoring::methods::pcs2::operator<< ( std::ostream &  out,
const PcsGridSearchParameter &  me 
)

References protocols::scoring::methods::pcs2::PcsGridSearchParameter::filenames_, protocols::scoring::methods::pcs2::PcsGridSearchParameter::include_only_end_stage1_, protocols::scoring::methods::pcs2::PcsGridSearchParameter::include_only_end_stage2_, protocols::scoring::methods::pcs2::PcsGridSearchParameter::include_only_end_stage3_, protocols::scoring::methods::pcs2::PcsGridSearchParameter::include_only_end_stage4_, protocols::scoring::methods::pcs2::PcsGridSearchParameter::include_only_start_stage1_, protocols::scoring::methods::pcs2::PcsGridSearchParameter::include_only_start_stage2_, protocols::scoring::methods::pcs2::PcsGridSearchParameter::include_only_start_stage3_, protocols::scoring::methods::pcs2::PcsGridSearchParameter::include_only_start_stage4_, protocols::scoring::methods::pcs2::PcsGridSearchParameter::individual_scale_stage1_, protocols::scoring::methods::pcs2::PcsGridSearchParameter::individual_scale_stage2_, protocols::scoring::methods::pcs2::PcsGridSearchParameter::individual_scale_stage3_, protocols::scoring::methods::pcs2::PcsGridSearchParameter::individual_scale_stage4_, protocols::scoring::methods::pcs2::PcsGridSearchParameter::individual_weights_, protocols::scoring::methods::pcs2::PcsGridSearchParameter::n_trial_min_stage1_, protocols::scoring::methods::pcs2::PcsGridSearchParameter::n_trial_min_stage2_, protocols::scoring::methods::pcs2::PcsGridSearchParameter::n_trial_min_stage3_, protocols::scoring::methods::pcs2::PcsGridSearchParameter::n_trial_min_stage4_, core::conformation::membrane::out, protocols::scoring::methods::pcs2::PcsGridSearchParameter::pcs_weight_stage1_, protocols::scoring::methods::pcs2::PcsGridSearchParameter::pcs_weight_stage2_, protocols::scoring::methods::pcs2::PcsGridSearchParameter::pcs_weight_stage3_, and protocols::scoring::methods::pcs2::PcsGridSearchParameter::pcs_weight_stage4_.

std::ostream& protocols::scoring::methods::pcs2::operator<< ( std::ostream &  out,
const PcsDataCenter &  me 
)
std::ostream& protocols::scoring::methods::pcs2::operator<< ( std::ostream &  out,
const PcsDataLanthanide &  me 
)
void protocols::scoring::methods::pcs2::output_error_message ( core::Size  id)
core::Size protocols::scoring::methods::pcs2::reduced_size ( utility::vector1< PcsInputLine > const &  pcs_i_l_v,
core::Size  start,
core::Size  end 
)
static basic::Tracer protocols::scoring::methods::pcs2::TR_PcsDataCenter ( "protocols.scoring.methods.pcs.PcsDataCenter"  )
static
static basic::Tracer protocols::scoring::methods::pcs2::TR_PcsDataCenterManager ( "protocols.scoring.methods.pcs.PcsDataCenterManager"  )
static
static basic::Tracer protocols::scoring::methods::pcs2::TR_PcsDataCenterManagerSingleton ( "protocols.scoring.methods.pcs.PcsDataCenterManagerSingleton"  )
static
static basic::Tracer protocols::scoring::methods::pcs2::TR_PcsDataLanthanide ( "protocols.scoring.methods.pcs.PcsDataLanthanide"  )
static
static basic::Tracer protocols::scoring::methods::pcs2::TR_PcsEnergy ( "protocols.scoring.methods.pcs.PcsEnergy"  )
static
static basic::Tracer protocols::scoring::methods::pcs2::TR_PcsEnergyParameter ( "protocols.scoring.methods.pcs.PcsEnergyParameter"  )
static
static basic::Tracer protocols::scoring::methods::pcs2::TR_PcsEnergyParameterManager ( "protocols.scoring.methods.pcs.PcsEnergyParameterManager"  )
static
static basic::Tracer protocols::scoring::methods::pcs2::TR_PcsInputCenter ( "protocols.scoring.methods.pcs.PcsInputCenter"  )
static
static basic::Tracer protocols::scoring::methods::pcs2::TR_PcsInputCenterManager ( "protocols.scoring.methods.pcs.PcsInputCenterManager"  )
static
static basic::Tracer protocols::scoring::methods::pcs2::TR_PcsInputFile ( "protocols.scoring.methods.pcs.PcsInputFile"  )
static
static basic::Tracer protocols::scoring::methods::pcs2::TR_PcsInputLine ( "protocols.scoring.methods.pcs.PcsInputLine"  )
static
static basic::Tracer protocols::scoring::methods::pcs2::TR_TensorsOptimizer ( "protocols.scoring.methods.pcs.TensorsOptimizer"  )
static
static basic::Tracer protocols::scoring::methods::pcs2::TR_TensorsOptimizerFix ( "protocols.scoring.methods.pcs.TensorsOptimizerFix"  )
static
static basic::Tracer protocols::scoring::methods::pcs2::TR_TensorsOptimizerSvd ( "protocols.scoring.methods.pcs.TensorsOptimizerSvd"  )
static
bool protocols::scoring::methods::pcs2::valide_include_only_stage ( core::Size  start,
core::Size  end 
)