protocols::stepwise::sampler::rna Namespace Reference

Classes
class	RNA_ChiStepWiseSampler
class	RNA_KIC_Sampler
class	RNA_KinematicCloser
	The RNA de novo structure modeling protocol. More...
class	RNA_NucleosideStepWiseSampler
class	RNA_SugarStepWiseSampler
class	RNA_SuiteStepWiseSampler

Typedefs
typedef utility::pointer::shared_ptr < RNA_ChiStepWiseSampler >	RNA_ChiStepWiseSamplerOP
typedef utility::pointer::shared_ptr < RNA_KIC_Sampler >	RNA_KIC_SamplerOP
typedef utility::pointer::shared_ptr < RNA_KinematicCloser >	RNA_KinematicCloserOP
typedef utility::pointer::shared_ptr < RNA_NucleosideStepWiseSampler >	RNA_NucleosideStepWiseSamplerOP
typedef utility::pointer::shared_ptr < RNA_SugarStepWiseSampler >	RNA_SugarStepWiseSamplerOP
typedef utility::pointer::shared_ptr < RNA_SuiteStepWiseSampler >	RNA_SuiteStepWiseSamplerOP

Functions
static basic::Tracer	TR ("protocols.sampler.rna.RNA_SugarStepWiseSampler")
sampler::StepWiseSamplerOP	setup_sampler (pose::Pose const &pose, modeler::options::StepWiseModelerOptionsCOP options, working_parameters::StepWiseWorkingParametersCOP working_parameters, bool const build_pose_from_scratch, bool const kic_modeler, bool const close_chain)
bool	modeler_sugar_at_five_prime (pose::Pose const &pose, core::Size const moving_suite)
bool	modeler_sugar_at_three_prime (pose::Pose const &pose, core::Size const moving_suite)

Typedef Documentation

typedef utility::pointer::shared_ptr< RNA_ChiStepWiseSampler > protocols::stepwise::sampler::rna::RNA_ChiStepWiseSamplerOP

typedef utility::pointer::shared_ptr< RNA_KIC_Sampler > protocols::stepwise::sampler::rna::RNA_KIC_SamplerOP

typedef utility::pointer::shared_ptr< RNA_KinematicCloser > protocols::stepwise::sampler::rna::RNA_KinematicCloserOP

typedef utility::pointer::shared_ptr< RNA_NucleosideStepWiseSampler > protocols::stepwise::sampler::rna::RNA_NucleosideStepWiseSamplerOP

typedef utility::pointer::shared_ptr< RNA_SugarStepWiseSampler > protocols::stepwise::sampler::rna::RNA_SugarStepWiseSamplerOP

typedef utility::pointer::shared_ptr< RNA_SuiteStepWiseSampler > protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSamplerOP

Function Documentation

bool protocols::stepwise::sampler::rna::modeler_sugar_at_five_prime	(	pose::Pose const &	pose,
		core::Size const	moving_suite
	)

References core::pose::full_model_info::const_full_model_info(), core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), core::pose::full_model_info::full_model_info_defined(), core::chemical::ResidueTypeBase::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), core::pose::full_model_info::FullModelInfo::res_list(), core::pose::Pose::residue_type(), core::pose::full_model_info::FullModelInfo::rna_sample_sugar_res(), and core::pose::full_model_info::FullModelInfo::sample_res().

Referenced by protocols::stepwise::modeler::working_parameters::figure_out_sample_both_sugar_base_rotamer(), protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::get_base_atr_rep_score(), and setup_sampler().

bool protocols::stepwise::sampler::rna::modeler_sugar_at_three_prime	(	pose::Pose const &	pose,
		core::Size const	moving_suite
	)

References core::pose::full_model_info::const_full_model_info(), core::chemical::CUTPOINT_LOWER, core::pose::Pose::fold_tree(), core::pose::full_model_info::full_model_info_defined(), core::chemical::ResidueTypeBase::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), core::pose::full_model_info::FullModelInfo::res_list(), core::pose::Pose::residue_type(), core::pose::full_model_info::FullModelInfo::rna_sample_sugar_res(), core::pose::full_model_info::FullModelInfo::sample_res(), and core::pose::Pose::size().

Referenced by protocols::stepwise::modeler::working_parameters::figure_out_sample_both_sugar_base_rotamer(), protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::get_base_atr_rep_score(), and setup_sampler().

sampler::StepWiseSamplerOP protocols::stepwise::sampler::rna::setup_sampler	(	pose::Pose const &	pose,
		modeler::options::StepWiseModelerOptionsCOP	options,
		working_parameters::StepWiseWorkingParametersCOP	working_parameters,
		bool const	build_pose_from_scratch,
		bool const	kic_modeler,
		bool const	close_chain
	)

References core::chemical::rna::ANTI, core::chemical::rna::ANY_CHI, core::chemical::rna::ANY_PUCKER, core::pose::rna::assign_pucker(), core::chemical::ResidueType::is_purine(), core::chemical::ResidueType::is_TNA(), modeler_sugar_at_five_prime(), modeler_sugar_at_three_prime(), core::chemical::rna::NO_CHI, core::chemical::rna::NO_PUCKER, core::chemical::rna::NORTH, core::pose::Pose::residue_type(), core::chemical::rna::SOUTH, and core::chemical::rna::SYN.

Referenced by protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_rna_bond_sampler(), and protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_tna_bond_sampler().

static basic::Tracer protocols::stepwise::sampler::rna::TR ( "protocols.sampler.rna.RNA_SugarStepWiseSampler"  )

static

Referenced by protocols::stepwise::sampler::rna::RNA_KIC_Sampler::apply(), protocols::stepwise::sampler::rna::RNA_KinematicCloser::figure_out_offset(), protocols::stepwise::sampler::rna::RNA_KinematicCloser::init(), protocols::stepwise::sampler::rna::RNA_KIC_Sampler::operator++(), and protocols::stepwise::sampler::rna::RNA_KinematicCloser::output_chainTORS().