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protocols::recces::scratch Namespace Reference

Classes

class  ThermalMinimizer
 Use a simulated tempering simulation to refine a pose. More...
 
class  ThermalMinimizerCreator
 
class  ThermalSamplingMover
 Use a simulated tempering simulation to refine a pose. More...
 
class  ThermalSamplingMoverCreator
 

Typedefs

typedef
utility::pointer::shared_ptr
< ThermalMinimizer
ThermalMinimizerOP
 
typedef
utility::pointer::shared_ptr
< ThermalMinimizer const > 
ThermalMinimizerCOP
 
typedef
utility::pointer::shared_ptr
< ThermalSamplingMover
ThermalSamplingMoverOP
 
typedef
utility::pointer::shared_ptr
< ThermalSamplingMover const > 
ThermalSamplingMoverCOP
 

Functions

utility::vector1< core::Realget_torsions (utility::vector1< core::id::TorsionID > &torsion_ids, const Pose &pose)
 
void set_gaussian_stdevs (utility::vector1< protocols::recces::sampler::rna::MC_RNA_KIC_SamplerOP > &internal_bb_sampler, utility::vector1< protocols::recces::sampler::MC_OneTorsionOP > &chi_sampler, sampler::rna::MC_RNA_MultiSuite &standard_bb_sampler, moves::SimulatedTempering const &tempering, core::Size const &total_rsd, core::Size const &sampled_rsd, utility::vector1< bool > is_free)
 
void set_gaussian_stdevs (utility::vector1< MC_RNA_KIC_SamplerOP > &internal_bb_sampler, utility::vector1< MC_OneTorsionOP > &chi_sampler, Real const temp, core::Size const )
 
void set_gaussian_stdevs (utility::vector1< MC_RNA_KIC_SamplerOP > &internal_bb_sampler, utility::vector1< MC_OneTorsionOP > &chi_sampler, MC_RNA_MultiSuite &standard_bb_sampler, Real const temp, core::Size const total_sampled)
 
bool mm_compatible_with_kic (core::kinematics::MoveMapOP mm, core::Size const ii)
 
std::ostream & operator<< (std::ostream &os, ThermalMinimizer const &mover)
 
Size find_likely_first_chain_ending (Pose const &pose)
 at least in the helix-strand case, will successfully distinguish a bad bond length from actual breaks More...
 
std::ostream & operator<< (std::ostream &os, ThermalSamplingMover const &mover)
 

Typedef Documentation

typedef utility::pointer::shared_ptr< ThermalMinimizer const > protocols::recces::scratch::ThermalMinimizerCOP
typedef utility::pointer::shared_ptr< ThermalMinimizer > protocols::recces::scratch::ThermalMinimizerOP
typedef utility::pointer::shared_ptr< ThermalSamplingMover const > protocols::recces::scratch::ThermalSamplingMoverCOP

Function Documentation

Size protocols::recces::scratch::find_likely_first_chain_ending ( Pose const &  pose)

at least in the helix-strand case, will successfully distinguish a bad bond length from actual breaks

References core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

Referenced by protocols::recces::scratch::ThermalSamplingMover::apply().

utility::vector1< core::Real > protocols::recces::scratch::get_torsions ( utility::vector1< core::id::TorsionID > &  torsion_ids,
const Pose pose 
)
bool protocols::recces::scratch::mm_compatible_with_kic ( core::kinematics::MoveMapOP  mm,
core::Size const  ii 
)
std::ostream & protocols::recces::scratch::operator<< ( std::ostream &  os,
ThermalMinimizer const &  mover 
)
std::ostream & protocols::recces::scratch::operator<< ( std::ostream &  os,
ThermalSamplingMover const &  mover 
)
void protocols::recces::scratch::set_gaussian_stdevs ( utility::vector1< MC_RNA_KIC_SamplerOP > &  internal_bb_sampler,
utility::vector1< MC_OneTorsionOP > &  chi_sampler,
Real const  temp,
core::Size  const 
)

References core::id::BB.

void protocols::recces::scratch::set_gaussian_stdevs ( utility::vector1< protocols::recces::sampler::rna::MC_RNA_KIC_SamplerOP > &  internal_bb_sampler,
utility::vector1< protocols::recces::sampler::MC_OneTorsionOP > &  chi_sampler,
sampler::rna::MC_RNA_MultiSuite standard_bb_sampler,
moves::SimulatedTempering const &  tempering,
core::Size const &  total_rsd,
core::Size const &  sampled_rsd,
utility::vector1< bool is_free 
)
void protocols::recces::scratch::set_gaussian_stdevs ( utility::vector1< MC_RNA_KIC_SamplerOP > &  internal_bb_sampler,
utility::vector1< MC_OneTorsionOP > &  chi_sampler,
MC_RNA_MultiSuite standard_bb_sampler,
Real const  temp,
core::Size const  total_sampled 
)