util.cc File Reference

#include <protocols/stepwise/modeler/rna/sugar/util.hh>
#include <protocols/stepwise/modeler/rna/sugar/VirtualSugarJustInTimeInstantiator.hh>
#include <protocols/stepwise/modeler/working_parameters/StepWiseWorkingParameters.hh>
#include <protocols/stepwise/modeler/options/StepWiseModelerOptions.hh>
#include <protocols/stepwise/modeler/rna/util.hh>
#include <protocols/stepwise/modeler/rna/sugar/SugarModeling.hh>
#include <protocols/stepwise/sampler/copy_dofs/ResidueAlternativeSet.hh>
#include <core/id/TorsionID.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoreType.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/copydofs/util.hh>
#include <core/pose/variant_util.hh>
#include <core/pose/extra_pose_info_util.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <utility/stream_util.hh>
#include <basic/Tracer.hh>

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

Macros
#define	viewer_pose   ( *pose_data_list[n] )

Functions
static basic::Tracer	TR ("protocols.stepwise.modeler.rna.sugar.util")
void	protocols::stepwise::modeler::rna::sugar::minimize_all_sampled_floating_bases (core::pose::Pose &, utility::vector1< SugarModeling > const &modeling_list, utility::vector1< PoseOP > &pose_data_list, core::scoring::ScoreFunctionCOP const &scorefxn, working_parameters::StepWiseWorkingParametersCOP const &working_parameters_, bool const virtual_sugar_is_from_prior_step_)
bool	protocols::stepwise::modeler::rna::sugar::is_sugar_virtual (core::pose::Pose const &pose, core::Size const sugar_res, core::Size const bulge_res)
bool	protocols::stepwise::modeler::rna::sugar::is_sugar_virtual (core::pose::Pose const &pose, core::Size const sugar_res, core::Size const bulge_res, utility::vector1< core::Size > &bulge_residues_to_virtualize)
void	protocols::stepwise::modeler::rna::sugar::modeler_starting_pose_data_list (utility::vector1< PoseOP > &starting_pose_data_list, utility::vector1< SugarModeling > const &sugar_modeling_list, core::pose::Pose const &pose)
std::map< core::Size, core::Size >	protocols::stepwise::modeler::rna::sugar::get_res_map (SugarModeling const &sugar_modeling)
void	protocols::stepwise::modeler::rna::sugar::copy_bulge_res_and_sugar_torsion (SugarModeling const &sugar_modeling, core::pose::Pose &pose, core::pose::Pose const &template_pose, bool instantiate_sugar)
std::map< core::Size, core::Size > const	protocols::stepwise::modeler::rna::sugar::get_reference_res_for_each_virtual_sugar (pose::Pose const &pose, bool const check_for_non_jump, core::Size const moving_suite)
std::map< core::Size, core::Size > const	protocols::stepwise::modeler::rna::sugar::get_reference_res_for_each_virtual_sugar_without_fold_tree (pose::Pose const &pose, core::Size const moving_suite)
Size	protocols::stepwise::modeler::rna::sugar::look_for_non_jump_reference_to_previous (core::Size const virtual_sugar_res, pose::Pose const &pose, core::Size const moving_suite)
Size	protocols::stepwise::modeler::rna::sugar::look_for_non_jump_reference_to_next (core::Size const virtual_sugar_res, pose::Pose const &pose, core::Size const moving_suite)
utility::vector1< core::Size >	protocols::stepwise::modeler::rna::sugar::get_possible_reference_res_list_from_pose_without_fold_tree (core::Size const virtual_sugar_res, pose::Pose const &pose, core::Size const moving_suite)
std::map< core::Size, core::Size > const	protocols::stepwise::modeler::rna::sugar::get_reference_res_for_each_virtual_sugar_based_on_fold_tree (pose::Pose const &pose)
Size	protocols::stepwise::modeler::rna::sugar::get_reference_res_for_virtual_sugar_based_on_fold_tree (pose::Pose const &pose, core::Size const n)
Size	protocols::stepwise::modeler::rna::sugar::look_for_jumps (core::Size const n, pose::Pose const &pose, bool const force_upstream)
Size	protocols::stepwise::modeler::rna::sugar::look_for_jumps_to_previous (core::Size const virtual_sugar_res, pose::Pose const &pose, bool const force_upstream)
Size	protocols::stepwise::modeler::rna::sugar::look_for_jumps_to_next (core::Size const virtual_sugar_res, pose::Pose const &pose, bool const force_upstream)
sampler::copy_dofs::ResidueAlternativeSetOP	protocols::stepwise::modeler::rna::sugar::convert_sugar_modeling_to_residue_alternative_set (SugarModeling const &sugar_modeling)
VirtualSugarJustInTimeInstantiatorOP	protocols::stepwise::modeler::rna::sugar::instantiate_any_virtual_sugars (pose::Pose &pose, working_parameters::StepWiseWorkingParametersCOP working_parameters, core::scoring::ScoreFunctionCOP scorefxn, options::StepWiseModelerOptionsCOP options)

Macro Definition Documentation

#define viewer_pose   ( *pose_data_list[n] )

Referenced by protocols::stepwise::modeler::packer::SideChainCopier::apply(), protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::apply(), protocols::stepwise::modeler::rna::sugar::minimize_all_sampled_floating_bases(), protocols::stepwise::monte_carlo::mover::TransientCutpointHandler::put_in_cutpoints(), protocols::stepwise::monte_carlo::mover::TransientCutpointHandler::take_out_cutpoints(), and protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::virtualize_distal_partition().

Function Documentation

static basic::Tracer TR ( "protocols.stepwise.modeler.rna.sugar.util"  )

static