StepWiseRNA_VirtualRiboseSampler.cc File Reference

#include <protocols/swa/rna/StepWiseRNA_Util.hh>
#include <protocols/swa/rna/StepWiseRNA_OutputData.hh>
#include <protocols/swa/rna/StepWiseRNA_VirtualRiboseSampler.hh>
#include <protocols/swa/rna/StepWiseRNA_RotamerGenerator_Wrapper.hh>
#include <protocols/swa/rna/StepWiseRNA_RotamerGenerator_Wrapper.fwd.hh>
#include <protocols/swa/rna/StepWiseRNA_Base_Sugar_Rotamer.hh>
#include <protocols/swa/rna/StepWiseRNA_Base_Sugar_Rotamer.fwd.hh>
#include <core/scoring/rna/RNA_FittedTorsionInfo.hh>
#include <core/scoring/rna/RNA_Util.hh>
#include <protocols/rna/RNA_LoopCloser.hh>
#include <protocols/swa/rna/StepWiseRNA_JobParameters.hh>
#include <protocols/swa/rna/StepWiseRNA_VDW_Bin_Screener.hh>
#include <protocols/swa/rna/StepWiseRNA_VDW_Bin_Screener.fwd.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <core/id/TorsionID.hh>
#include <core/pose/util.hh>
#include <basic/Tracer.hh>
#include <core/types.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/chemical/util.hh>
#include <core/chemical/VariantType.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/AtomType.hh>
#include <core/conformation/Conformation.fwd.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/pose/Pose.hh>
#include <core/io/pdb/pose_io.hh>
#include <core/io/silent/SilentFileData.fwd.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/io/silent/BinaryRNASilentStruct.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/pack/rotamer_trials.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/rna/RNA_TorsionPotential.hh>
#include <core/scoring/rms_util.tmpl.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/constraints/ConstraintSet.fwd.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/AngleConstraint.hh>
#include <core/scoring/constraints/util.hh>
#include <set>
#include <numeric/conversions.hh>
#include <iostream>
#include <fstream>
#include <sstream>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/EnergyMap.hh>
#include <core/scoring/EnergyMap.fwd.hh>

Go to the source code of this file.

Namespaces
	protocols
	The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
	protocols::swa
	protocols::swa::rna

Constant Groups
	protocols
	The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
	protocols::swa
	protocols::swa::rna

Functions
static basic::Tracer	TR ("protocols.swa.stepwise_rna_virtual_ribose_sampler")
bool	protocols::swa::rna::fast_full_atom_VDW_repulsion_screen (core::pose::Pose const &pose, core::Size const res_1, core::Size const res_2, bool const Is_prepend)
bool	protocols::swa::rna::floating_base_full_atom_van_der_Waals_screening (core::pose::Pose &current_pose_screen, core::Real const &base_rep_score, core::scoring::ScoreFunctionOP const &atr_rep_screening_scorefxn, SillyCountStruct &count_data, bool const verbose)
bool	protocols::swa::rna::floating_base_chain_break_screening (core::pose::Pose &chain_break_screening_pose, core::scoring::ScoreFunctionOP const &chainbreak_scorefxn, SillyCountStruct &count_data, core::Size const &five_prime_res, std::string const &tag, bool const verbose)
utility::vector1< FB_Pose_Data >	protocols::swa::rna::floating_base_chain_closure_setup (utility::vector1< pose_data_struct2 > const &input_pose_data_list, FloatingBaseChainClosureJobParameter const &FB_job_params, core::scoring::ScoreFunctionOP const &atr_rep_screening_scorefxn, core::scoring::ScoreFunctionOP const &full_scorefxn, pose::Pose &viewer_pose, bool const do_minimize)
void	protocols::swa::rna::floating_base_chain_closure_sampling (utility::vector1< FB_Pose_Data > &pose_data_list, core::pose::Pose &viewer_pose, FloatingBaseChainClosureJobParameter const &FB_job_params, core::scoring::ScoreFunctionOP const &chainbreak_scorefxn, core::scoring::ScoreFunctionOP const &atr_rep_screening_scorefxn, StepWiseRNA_VDW_Bin_ScreenerOP const &VDW_bin_screener, bool const CCD_grid_index_screen)
utility::vector1 < pose_data_struct2 >	protocols::swa::rna::floating_base_chain_closure_post_process (utility::vector1< FB_Pose_Data > &pose_data_list, core::pose::Pose &viewer_pose, core::scoring::ScoreFunctionOP const &sampling_scorefxn, FloatingBaseChainClosureJobParameter const &FB_job_params, bool const rm_chain_break_jump_point)
void	protocols::swa::rna::minimize_all_sampled_floating_bases (core::pose::Pose &viewer_pose, utility::vector1< FloatingBaseChainClosureJobParameter > const &FB_JP_list, utility::vector1< pose_data_struct2 > &pose_data_list, core::scoring::ScoreFunctionOP const &sampling_scorefxn, StepWiseRNA_JobParametersCOP const &job_parameters, bool const virtual_ribose_is_from_prior_step)
bool	protocols::swa::rna::Is_ribose_virtual (core::pose::Pose const &pose, core::Size const ribose_res, core::Size const bulge_res)
void	protocols::swa::rna::copy_bulge_res_and_ribose_torsion (FloatingBaseChainClosureJobParameter const &FB_job_params, core::pose::Pose &pose, core::pose::Pose const &template_pose)
bool	protocols::swa::rna::sort_pose_data_by_score (pose_data_struct2 pose_data_1, pose_data_struct2 pose_data_2)
utility::vector1 < pose_data_struct2 >	protocols::swa::rna::sample_virtual_ribose_and_bulge_and_close_chain (pose::Pose &viewer_pose, FloatingBaseChainClosureJobParameter const &FB_job_params, std::string const name, core::scoring::ScoreFunctionOP const &scorefxn, core::scoring::ScoreFunctionOP const &sampling_scorefxn, core::scoring::ScoreFunctionOP const &atr_rep_screening_scorefxn, core::scoring::ScoreFunctionOP const &chainbreak_scorefxn, StepWiseRNA_JobParametersCOP &job_parameters, bool const virtual_ribose_is_from_prior_step)
void	protocols::swa::rna::enumerate_starting_pose_data_list (utility::vector1< pose_data_struct2 > &starting_pose_data_list, utility::vector1< FloatingBaseChainClosureJobParameter > const &FB_CC_JP_list, core::pose::Pose const &pose)
utility::vector1 < FloatingBaseChainClosureJobParameter >	protocols::swa::rna::setup_FB_CC_JP_list (pose::Pose const &pose, utility::vector1< std::string > const &sample_virtual_ribose_string_list, StepWiseRNA_JobParametersCOP &job_parameters)
void	protocols::swa::rna::sample_user_specified_virtual_riboses (pose::Pose &pose, utility::vector1< std::string > const &sample_virtual_ribose_string_list, StepWiseRNA_JobParametersCOP &job_parameters, core::scoring::ScoreFunctionOP const &scorefxn, std::string const silent_file_out, std::string const input_tag)

Function Documentation

static basic::Tracer TR ( "protocols.swa.stepwise_rna_virtual_ribose_sampler"  )

static