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::Real >	get_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

ThermalMinimizerCOP

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

ThermalMinimizerOP

typedef utility::pointer::shared_ptr< ThermalMinimizer > protocols::recces::scratch::ThermalMinimizerOP

ThermalSamplingMoverCOP

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

ThermalSamplingMoverOP

typedef utility::pointer::shared_ptr< ThermalSamplingMover > protocols::recces::scratch::ThermalSamplingMoverOP

Function Documentation

find_likely_first_chain_ending()

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().

get_torsions()

utility::vector1<core::Real> protocols::recces::scratch::get_torsions	(	utility::vector1< core::id::TorsionID > &	torsion_ids,
		const Pose &	pose
	)

References core::pose::Pose::torsion().

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

mm_compatible_with_kic()

bool protocols::recces::scratch::mm_compatible_with_kic	(	core::kinematics::MoveMapOP	mm,
		core::Size const	ii
	)

References core::chemical::rna::ALPHA, core::id::BB, core::chemical::rna::BETA, core::chemical::rna::EPSILON, core::chemical::rna::GAMMA, and core::chemical::rna::ZETA.

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

operator<<() [1/2]

std::ostream & protocols::recces::scratch::operator<<	(	std::ostream &	os,
		ThermalMinimizer const &	mover
	)

References protocols::recces::scratch::ThermalMinimizer::show().

operator<<() [2/2]

std::ostream & protocols::recces::scratch::operator<<	(	std::ostream &	os,
		ThermalSamplingMover const &	mover
	)

References protocols::recces::scratch::ThermalSamplingMover::show().

set_gaussian_stdevs() [1/3]

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
	)

References protocols::recces::sampler::rna::MC_RNA_MultiSuite::set_gaussian_stdev().

set_gaussian_stdevs() [2/3]

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.

set_gaussian_stdevs() [3/3]

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
	)

References protocols::recces::sampler::rna::MC_RNA_MultiSuite::set_gaussian_stdev(), and protocols::moves::SimulatedTempering::temperature().

Referenced by protocols::recces::scratch::ThermalMinimizer::apply(), and protocols::recces::scratch::ThermalSamplingMover::apply().