protocols::swa::rna::FloatingBaseChainClosureJobParameter Class Reference

#include <StepWiseRNA_VirtualRiboseSampler.hh>

Collaboration diagram for protocols::swa::rna::FloatingBaseChainClosureJobParameter:

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

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
BaseState	moving_res_base_state
BaseState	bulge_res_base_state
utility::vector1 < pose_data_struct2 >	PDL

Detailed Description

Definition at line 83 of file StepWiseRNA_VirtualRiboseSampler.hh.

Constructor & Destructor Documentation

protocols::swa::rna::FloatingBaseChainClosureJobParameter::FloatingBaseChainClosureJobParameter ( core::Size const  input_moving_res, core::Size const  input_reference_res  )

inline

Definition at line 88 of file StepWiseRNA_VirtualRiboseSampler.hh.

References bulge_res, bulge_suite, five_prime_chain_break, Is_prepend, moving_res, PDL, and reference_res.

protocols::swa::rna::FloatingBaseChainClosureJobParameter::FloatingBaseChainClosureJobParameter ( )

inline

Definition at line 119 of file StepWiseRNA_VirtualRiboseSampler.hh.

References PDL.

protocols::swa::rna::FloatingBaseChainClosureJobParameter::~FloatingBaseChainClosureJobParameter ( )

inline

Definition at line 125 of file StepWiseRNA_VirtualRiboseSampler.hh.

Member Function Documentation

void protocols::swa::rna::FloatingBaseChainClosureJobParameter::check_compatibility ( core::Size const  nres) const

inline

Definition at line 129 of file StepWiseRNA_VirtualRiboseSampler.hh.

References bulge_res, moving_res, and reference_res.

Referenced by protocols::swa::rna::sample_virtual_ribose_and_bulge_and_close_chain().

void protocols::swa::rna::FloatingBaseChainClosureJobParameter::set_base_and_pucker_state ( core::pose::Pose const &  pose, StepWiseRNA_JobParametersCOP const &  JP  )

inline

Definition at line 140 of file StepWiseRNA_VirtualRiboseSampler.hh.

References protocols::swa::rna::ALL, protocols::swa::rna::ANTI, protocols::swa::rna::BOTH, bulge_res, bulge_res_base_state, bulge_res_pucker_state, bulge_suite, protocols::swa::rna::Contain_seq_num(), five_prime_chain_break, Is_prepend, core::scoring::rna::is_purine(), moving_res, moving_res_base_state, moving_res_pucker_state, protocols::swa::rna::NORTH, protocols::swa::rna::Output_boolean(), protocols::swa::rna::print_base_state(), protocols::swa::rna::print_ribose_pucker_state(), reference_res, core::pose::Pose::residue(), protocols::swa::rna::SOUTH, and protocols::swa::rna::SYN.

Referenced by protocols::swa::rna::sample_user_specified_virtual_riboses().

Member Data Documentation

core::Size protocols::swa::rna::FloatingBaseChainClosureJobParameter::bulge_res

Definition at line 179 of file StepWiseRNA_VirtualRiboseSampler.hh.

Referenced by check_compatibility(), protocols::swa::rna::copy_bulge_res_and_ribose_torsion(), protocols::swa::rna::floating_base_chain_closure_post_process(), protocols::swa::rna::floating_base_chain_closure_sampling(), protocols::swa::rna::floating_base_chain_closure_setup(), FloatingBaseChainClosureJobParameter(), protocols::swa::rna::minimize_all_sampled_floating_bases(), protocols::swa::rna::sample_virtual_ribose_and_bulge_and_close_chain(), and set_base_and_pucker_state().

BaseState protocols::swa::rna::FloatingBaseChainClosureJobParameter::bulge_res_base_state

Definition at line 185 of file StepWiseRNA_VirtualRiboseSampler.hh.

Referenced by protocols::swa::rna::floating_base_chain_closure_sampling(), and set_base_and_pucker_state().

PuckerState protocols::swa::rna::FloatingBaseChainClosureJobParameter::bulge_res_pucker_state

Definition at line 183 of file StepWiseRNA_VirtualRiboseSampler.hh.

Referenced by protocols::swa::rna::floating_base_chain_closure_sampling(), and set_base_and_pucker_state().

core::Size protocols::swa::rna::FloatingBaseChainClosureJobParameter::bulge_suite

Definition at line 180 of file StepWiseRNA_VirtualRiboseSampler.hh.

Referenced by protocols::swa::rna::floating_base_chain_closure_sampling(), FloatingBaseChainClosureJobParameter(), and set_base_and_pucker_state().

core::Size protocols::swa::rna::FloatingBaseChainClosureJobParameter::five_prime_chain_break

Definition at line 181 of file StepWiseRNA_VirtualRiboseSampler.hh.

Referenced by protocols::swa::rna::floating_base_chain_closure_post_process(), protocols::swa::rna::floating_base_chain_closure_sampling(), protocols::swa::rna::floating_base_chain_closure_setup(), FloatingBaseChainClosureJobParameter(), and set_base_and_pucker_state().

bool protocols::swa::rna::FloatingBaseChainClosureJobParameter::Is_prepend

Definition at line 178 of file StepWiseRNA_VirtualRiboseSampler.hh.

Referenced by protocols::swa::rna::floating_base_chain_closure_sampling(), protocols::swa::rna::floating_base_chain_closure_setup(), FloatingBaseChainClosureJobParameter(), protocols::swa::rna::sample_virtual_ribose_and_bulge_and_close_chain(), and set_base_and_pucker_state().

core::Size protocols::swa::rna::FloatingBaseChainClosureJobParameter::moving_res

Definition at line 176 of file StepWiseRNA_VirtualRiboseSampler.hh.

Referenced by check_compatibility(), protocols::swa::rna::copy_bulge_res_and_ribose_torsion(), protocols::swa::rna::floating_base_chain_closure_sampling(), protocols::swa::rna::floating_base_chain_closure_setup(), protocols::swa::rna::StepWiseRNA_ResidueSampler::floating_base_sampling(), FloatingBaseChainClosureJobParameter(), protocols::swa::rna::sample_virtual_ribose_and_bulge_and_close_chain(), and set_base_and_pucker_state().

BaseState protocols::swa::rna::FloatingBaseChainClosureJobParameter::moving_res_base_state

Definition at line 184 of file StepWiseRNA_VirtualRiboseSampler.hh.

Referenced by protocols::swa::rna::floating_base_chain_closure_setup(), and set_base_and_pucker_state().

PuckerState protocols::swa::rna::FloatingBaseChainClosureJobParameter::moving_res_pucker_state

Definition at line 182 of file StepWiseRNA_VirtualRiboseSampler.hh.

Referenced by protocols::swa::rna::floating_base_chain_closure_setup(), and set_base_and_pucker_state().

utility::vector1< pose_data_struct2 > protocols::swa::rna::FloatingBaseChainClosureJobParameter::PDL

Definition at line 186 of file StepWiseRNA_VirtualRiboseSampler.hh.

Referenced by protocols::swa::rna::enumerate_starting_pose_data_list(), protocols::swa::rna::StepWiseRNA_ResidueSampler::floating_base_sampling(), FloatingBaseChainClosureJobParameter(), protocols::swa::rna::sample_user_specified_virtual_riboses(), and protocols::swa::rna::StepWiseRNA_ResidueSampler::standard_sampling_WRAPPER().

core::Size protocols::swa::rna::FloatingBaseChainClosureJobParameter::reference_res

Definition at line 177 of file StepWiseRNA_VirtualRiboseSampler.hh.

Referenced by check_compatibility(), protocols::swa::rna::copy_bulge_res_and_ribose_torsion(), protocols::swa::rna::floating_base_chain_closure_setup(), FloatingBaseChainClosureJobParameter(), protocols::swa::rna::sample_virtual_ribose_and_bulge_and_close_chain(), and set_base_and_pucker_state().

bool protocols::swa::rna::FloatingBaseChainClosureJobParameter::sample_sugar

Definition at line 175 of file StepWiseRNA_VirtualRiboseSampler.hh.

Referenced by protocols::swa::rna::StepWiseRNA_ResidueSampler::floating_base_sampling(), and protocols::swa::rna::StepWiseRNA_ResidueSampler::standard_sampling_WRAPPER().

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

• src/protocols/swa/rna/StepWiseRNA_VirtualRiboseSampler.hh