protocols::stepwise::sampling::rna::sugar::SugarModeling Class Reference

#include <SugarModeling.hh>

Public Member Functions
	SugarModeling (core::Size const input_moving_res, core::Size const input_reference_res)
	SugarModeling ()
	~SugarModeling ()
void	check_compatibility (core::Size const nres) const
void	set_base_and_pucker_state (core::pose::Pose const &pose, StepWiseRNA_JobParametersCOP const &JP)
SugarModeling &	operator= (SugarModeling const &src)

Public Attributes
bool	sample_sugar
core::Size	moving_res
core::Size	reference_res
bool	is_prepend
core::Size	bulge_res
core::Size	bulge_suite
core::Size	five_prime_chain_break
PuckerState	moving_res_pucker_state
PuckerState	bulge_res_pucker_state
ChiState	moving_res_base_state
ChiState	bulge_res_base_state
utility::vector1 < core::pose::PoseOP >	pose_list

Constructor & Destructor Documentation

protocols::stepwise::sampling::rna::sugar::SugarModeling::SugarModeling	(	core::Size const	input_moving_res,
		core::Size const	input_reference_res
	)

References bulge_res, bulge_suite, five_prime_chain_break, is_prepend, moving_res, pose_list, and reference_res.

protocols::stepwise::sampling::rna::sugar::SugarModeling::SugarModeling

(

)

References ANY_CHI, ANY_PUCKER, bulge_res, and pose_list.

protocols::stepwise::sampling::rna::sugar::SugarModeling::~SugarModeling

(

)

Member Function Documentation

void protocols::stepwise::sampling::rna::sugar::SugarModeling::check_compatibility

(

core::Size const

nres

)

const

References moving_res, reference_res, and runtime_assert.

Referenced by protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::apply().

SugarModeling & protocols::stepwise::sampling::rna::sugar::SugarModeling::operator=

(

SugarModeling const &

src

)

References bulge_res, bulge_res_base_state, bulge_res_pucker_state, bulge_suite, five_prime_chain_break, is_prepend, moving_res, moving_res_base_state, moving_res_pucker_state, pose_list, reference_res, and sample_sugar.

void protocols::stepwise::sampling::rna::sugar::SugarModeling::set_base_and_pucker_state	(	core::pose::Pose const &	pose,
		StepWiseRNA_JobParametersCOP const &	JP
	)

References ANTI, ANY_CHI, ANY_PUCKER, bulge_res, bulge_res_base_state, bulge_res_pucker_state, bulge_suite, five_prime_chain_break, has_value(), is_prepend, core::chemical::rna::is_purine(), moving_res, moving_res_base_state, moving_res_pucker_state, NORTH, protocols::stepwise::sampling::rna::output_boolean(), protocols::stepwise::sampling::rna::print_base_state(), protocols::stepwise::sampling::rna::print_sugar_pucker_state(), reference_res, core::pose::Pose::residue(), SOUTH, SYN, and protocols::TR.

Referenced by protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSamplerFromStringList::apply().

Member Data Documentation

core::Size protocols::stepwise::sampling::rna::sugar::SugarModeling::bulge_res

Referenced by protocols::stepwise::screener::AnchorSugarScreener::add_mover(), protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::apply(), protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::bulge_chain_closure_complete(), protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::bulge_chain_closure_legacy(), protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::bulge_chain_minimize_legacy(), protocols::stepwise::sampling::rna::sugar::get_res_map(), protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::initialize_pose_variants_for_chain_closure(), protocols::stepwise::sampling::rna::sugar::minimize_all_sampled_floating_bases(), operator=(), protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::restore_pose_variants_after_chain_closure(), set_base_and_pucker_state(), protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::setup_sugar_modeling(), protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::setup_sugar_modeling(), protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::setup_VDW_bin_checker(), and SugarModeling().

ChiState protocols::stepwise::sampling::rna::sugar::SugarModeling::bulge_res_base_state

Referenced by operator=(), and set_base_and_pucker_state().

PuckerState protocols::stepwise::sampling::rna::sugar::SugarModeling::bulge_res_pucker_state

Referenced by operator=(), and set_base_and_pucker_state().

core::Size protocols::stepwise::sampling::rna::sugar::SugarModeling::bulge_suite

Referenced by protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::bulge_chain_closure_legacy(), operator=(), set_base_and_pucker_state(), protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::setup_sugar_modeling(), protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::setup_sugar_modeling(), and SugarModeling().

core::Size protocols::stepwise::sampling::rna::sugar::SugarModeling::five_prime_chain_break

Referenced by protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::bulge_chain_closure_legacy(), protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::initialize_pose_variants_for_chain_closure(), operator=(), protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::restore_pose_variants_after_chain_closure(), set_base_and_pucker_state(), protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::setup_sugar_conformations(), and SugarModeling().

bool protocols::stepwise::sampling::rna::sugar::SugarModeling::is_prepend

Referenced by protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::bulge_chain_closure_legacy(), operator=(), set_base_and_pucker_state(), protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::setup_sugar_conformations(), protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::setup_VDW_bin_checker(), and SugarModeling().

core::Size protocols::stepwise::sampling::rna::sugar::SugarModeling::moving_res

Referenced by protocols::stepwise::screener::AnchorSugarScreener::add_mover(), protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::apply(), protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::bulge_chain_closure_legacy(), check_compatibility(), protocols::stepwise::sampling::rna::sugar::convert_sugar_modeling_to_residue_alternative_set(), protocols::stepwise::sampling::rna::sugar::copy_bulge_res_and_sugar_torsion(), protocols::stepwise::sampling::rna::sugar::get_res_map(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::initialize_rigid_body_sampler(), protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::minimize_sugar(), operator=(), protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::reinstantiate_distal_partition(), protocols::stepwise::sampling::rna::sugar::sampling_starting_pose_data_list(), set_base_and_pucker_state(), protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::setup_sugar_conformations(), protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::setup_sugar_modeling(), protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::setup_sugar_modeling(), protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::setup_VDW_bin_checker(), SugarModeling(), and protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::virtualize_distal_partition().

ChiState protocols::stepwise::sampling::rna::sugar::SugarModeling::moving_res_base_state

Referenced by operator=(), set_base_and_pucker_state(), protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::setup_sugar_conformations(), protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::setup_sugar_modeling(), and protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::setup_sugar_modeling().

PuckerState protocols::stepwise::sampling::rna::sugar::SugarModeling::moving_res_pucker_state

Referenced by operator=(), set_base_and_pucker_state(), and protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::setup_sugar_conformations().

utility::vector1< core::pose::PoseOP > protocols::stepwise::sampling::rna::sugar::SugarModeling::pose_list

Referenced by protocols::stepwise::screener::AnchorSugarScreener::add_mover(), protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSamplerFromStringList::apply(), protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::apply(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::apply(), protocols::stepwise::screener::AnchorSugarScreener::check_screen(), protocols::stepwise::sampling::rna::sugar::convert_sugar_modeling_to_residue_alternative_set(), protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::do_sugar_sampling(), protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::do_sugar_sampling(), protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::do_the_sampling(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::initialize_poses_and_stubs_and_checkers(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::initialize_poses_and_stubs_and_checkers(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::initialize_residue_level_screeners(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::initialize_rigid_body_sampler(), protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::instantiate_sugar(), protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::instantiate_sugar(), operator=(), protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::prepare_from_prior_sampled_sugar_jobs(), protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::prepare_from_prior_sampled_sugar_jobs_for_chain_break(), protocols::stepwise::sampling::rna::sugar::sampling_starting_pose_data_list(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::screen_anchor_sugar_conformation(), and SugarModeling().

core::Size protocols::stepwise::sampling::rna::sugar::SugarModeling::reference_res

Referenced by protocols::stepwise::screener::AnchorSugarScreener::add_mover(), protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::apply(), check_compatibility(), protocols::stepwise::sampling::rna::sugar::get_res_map(), operator=(), set_base_and_pucker_state(), protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::setup_sugar_conformations(), protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::setup_sugar_modeling(), protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarJustInTimeInstantiator::setup_sugar_modeling(), protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::setup_VDW_bin_checker(), SugarModeling(), and protocols::stepwise::sampling::rna::sugar::StepWiseRNA_VirtualSugarSampler::virtualize_distal_partition().

bool protocols::stepwise::sampling::rna::sugar::SugarModeling::sample_sugar

Referenced by protocols::stepwise::screener::AnchorSugarScreener::add_mover(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::apply(), protocols::stepwise::screener::AnchorSugarScreener::check_screen(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::initialize_residue_level_screeners(), protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodySampler::initialize_rigid_body_sampler(), operator=(), protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::sampling_sugar(), protocols::stepwise::sampling::rna::sugar::legacy::StepWiseRNA_VirtualSugarJustInTimeInstantiatorOLD::sampling_sugar_at_chain_break(), and protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::screen_anchor_sugar_conformation().

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The documentation for this class was generated from the following files:

• symlinks/rosetta/src/protocols/stepwise/sampling/rna/sugar/SugarModeling.hh
• symlinks/rosetta/src/protocols/stepwise/sampling/rna/sugar/SugarModeling.cc