protocols::rotamer_sampler::rna Namespace Reference

Classes
class	RNA_ChiRotamer
class	RNA_KicSampler
class	RNA_KinematicCloser
	The RNA de novo structure modeling protocol. More...
class	RNA_McMultiSuite
class	RNA_McSugar
class	RNA_McSuite
class	RNA_NucleosideRotamer
class	RNA_SugarRotamer
class	RNA_SuiteRotamer

Typedefs
typedef utility::pointer::owning_ptr < RNA_ChiRotamer >	RNA_ChiRotamerOP
typedef utility::pointer::owning_ptr < RNA_KicSampler >	RNA_KicSamplerOP
typedef utility::pointer::owning_ptr < RNA_KinematicCloser >	RNA_KinematicCloserOP
typedef utility::pointer::owning_ptr < RNA_McMultiSuite >	RNA_McMultiSuiteOP
typedef utility::pointer::owning_ptr < RNA_McSugar >	RNA_McSugarOP
typedef utility::pointer::access_ptr < RNA_McSugar >	RNA_McSugarAP
typedef utility::pointer::owning_ptr < RNA_McSuite >	RNA_McSuiteOP
typedef utility::pointer::owning_ptr < RNA_NucleosideRotamer >	RNA_NucleosideRotamerOP
typedef utility::pointer::owning_ptr < RNA_RotamerSamplerUtil >	RNA_RotamerSamplerUtilOP
typedef utility::pointer::owning_ptr < RNA_RotamerSamplerUtil const >	RNA_RotamerSamplerUtilCOP
typedef utility::pointer::owning_ptr < RNA_SugarRotamer >	RNA_SugarRotamerOP
typedef utility::pointer::owning_ptr < RNA_SuiteRotamer >	RNA_SuiteRotamerOP

Functions
RotamerBaseOP	setup_rotamer_sampler (pose::Pose const &pose, StepWiseRNA_ModelerOptionsCOP options, StepWiseRNA_JobParametersCOP job_parameters, bool const build_pose_from_scratch, bool const kic_sampling, bool const close_chain)
bool	sampling_sugar_at_five_prime (pose::Pose const &pose, Size const moving_suite)
bool	sampling_sugar_at_three_prime (pose::Pose const &pose, Size const moving_suite)

Variables
static basic::Tracer	TR ("protocols.rotamer_sampler.rna.RNA_SugarRotamer")

Typedef Documentation

typedef utility::pointer::owning_ptr< RNA_ChiRotamer > protocols::rotamer_sampler::rna::RNA_ChiRotamerOP

typedef utility::pointer::owning_ptr< RNA_KicSampler > protocols::rotamer_sampler::rna::RNA_KicSamplerOP

typedef utility::pointer::owning_ptr< RNA_KinematicCloser > protocols::rotamer_sampler::rna::RNA_KinematicCloserOP

typedef utility::pointer::owning_ptr< RNA_McMultiSuite > protocols::rotamer_sampler::rna::RNA_McMultiSuiteOP

typedef utility::pointer::access_ptr< RNA_McSugar > protocols::rotamer_sampler::rna::RNA_McSugarAP

typedef utility::pointer::owning_ptr< RNA_McSugar > protocols::rotamer_sampler::rna::RNA_McSugarOP

typedef utility::pointer::owning_ptr< RNA_McSuite > protocols::rotamer_sampler::rna::RNA_McSuiteOP

typedef utility::pointer::owning_ptr< RNA_NucleosideRotamer > protocols::rotamer_sampler::rna::RNA_NucleosideRotamerOP

typedef utility::pointer::owning_ptr< RNA_RotamerSamplerUtil const > protocols::rotamer_sampler::rna::RNA_RotamerSamplerUtilCOP

typedef utility::pointer::owning_ptr< RNA_RotamerSamplerUtil > protocols::rotamer_sampler::rna::RNA_RotamerSamplerUtilOP

typedef utility::pointer::owning_ptr< RNA_SugarRotamer > protocols::rotamer_sampler::rna::RNA_SugarRotamerOP

typedef utility::pointer::owning_ptr< RNA_SuiteRotamer > protocols::rotamer_sampler::rna::RNA_SuiteRotamerOP

Function Documentation

bool protocols::rotamer_sampler::rna::sampling_sugar_at_five_prime	(	pose::Pose const &	pose,
		Size const	moving_suite
	)

References core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), core::chemical::ResidueType::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), and core::pose::Pose::residue_type().

Referenced by protocols::stepwise::sampling::rna::figure_out_sample_both_sugar_base_rotamer(), protocols::stepwise::sampling::rna::checker::AtrRepChecker::get_base_atr_rep_score(), and setup_rotamer_sampler().

bool protocols::rotamer_sampler::rna::sampling_sugar_at_three_prime	(	pose::Pose const &	pose,
		Size const	moving_suite
	)

References core::chemical::CUTPOINT_LOWER, core::pose::Pose::fold_tree(), core::chemical::ResidueType::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), core::pose::Pose::residue_type(), and core::pose::Pose::total_residue().

Referenced by protocols::stepwise::sampling::rna::figure_out_sample_both_sugar_base_rotamer(), protocols::stepwise::sampling::rna::checker::AtrRepChecker::get_base_atr_rep_score(), and setup_rotamer_sampler().

rotamer_sampler::RotamerBaseOP protocols::rotamer_sampler::rna::setup_rotamer_sampler	(	pose::Pose const &	pose,
		StepWiseRNA_ModelerOptionsCOP	options,
		StepWiseRNA_JobParametersCOP	job_parameters,
		bool const	build_pose_from_scratch,
		bool const	kic_sampling,
		bool const	close_chain
	)

References ANTI, ANY_CHI, ANY_PUCKER, assign_pucker(), is_purine(), NO_CHI, NO_PUCKER, NORTH, core::pose::Pose::residue(), runtime_assert, sampling_sugar_at_five_prime(), sampling_sugar_at_three_prime(), SOUTH, and SYN.

Referenced by protocols::stepwise::sampling::rna::connection::StepWiseRNA_ConnectionSampler::get_full_bond_sampler(), and protocols::stepwise::sampling::rna::legacy::suite::StepWiseRNA_ClassicResidueSampler::initialize_poses_and_checkers().

Variable Documentation

basic::Tracer protocols::rotamer_sampler::rna::TR("protocols.rotamer_sampler.rna.RNA_SugarRotamer")

static

Referenced by protocols::rotamer_sampler::rna::RNA_KicSampler::apply(), protocols::rotamer_sampler::rna::RNA_KinematicCloser::figure_out_offset(), protocols::rotamer_sampler::rna::RNA_KinematicCloser::init(), protocols::rotamer_sampler::rna::RNA_KicSampler::operator++(), and protocols::rotamer_sampler::rna::RNA_KinematicCloser::output_chainTORS().