ErraserMinimizerMover.cc File Reference

#include <protocols/rna/movers/ErraserMinimizerMover.hh>
#include <protocols/rna/movers/ErraserMinimizerMoverCreator.hh>
#include <protocols/stepwise/modeler/rna/util.hh>
#include <protocols/stepwise/modeler/output_util.hh>
#include <core/types.hh>
#include <core/chemical/AA.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/conformation/Residue.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <core/optimization/CartesianMinimizer.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <basic/Tracer.hh>
#include <protocols/viewer/viewers.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/pose/full_model_info/FullModelInfo.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreType.hh>
#include <core/pose/rna/util.hh>
#include <core/chemical/rna/util.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/AtomTree.hh>
#include <core/kinematics/MoveMap.hh>
#include <protocols/moves/Mover.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/constraints/CoordinateConstraint.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <basic/options/keys/rna.OptionKeys.gen.hh>
#include <basic/options/keys/full_model.OptionKeys.gen.hh>
#include <core/pose/PDBInfo.hh>
#include <utility/vector1.hh>
#include <utility/tag/Tag.hh>
#include <utility/pointer/owning_ptr.hh>
#include <utility/io/izstream.hh>
#include <utility/file/file_sys_util.hh>
#include <utility/options/OptionCollection.hh>
#include <numeric/conversions.hh>
#include <numeric/random/random_permutation.hh>
#include <fstream>
#include <algorithm>
#include <utility/tag/XMLSchemaGeneration.hh>
#include <protocols/moves/mover_schemas.hh>
#include <core/import_pose/pose_stream/SilentFilePoseInputStream.hh>
#include <protocols/stepwise/monte_carlo/util.hh>
#include <numeric>
#include <ObjexxFCL/FArray2D.hh>
#include <core/pose/full_model_info/FullModelParameters.hh>
#include <utility/stream_util.hh>

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

Typedefs
using	protocols::rna::movers::ErraserMinimizerMoverOP = utility::pointer::shared_ptr< ErraserMinimizerMover >
using	protocols::rna::movers::ErraserMinimizerMoverCOP = utility::pointer::shared_ptr< const ErraserMinimizerMover >

Functions
static basic::Tracer	TR ("protocols.rna.movers.ErraserMinimizerMover")
utility::vector1< core::Size >	protocols::rna::movers::string_to_size_vector (std::string const &sv)
template<typename T >
void	protocols::rna::movers::remove_set1_elements_from_set2 (std::set< T > const &set1, std::set< T > &set2)
void	protocols::rna::movers::fill_gaps_and_remove_isolated_res (std::set< core::Size > &res_list, core::Size const total_res, std::set< core::Size > &res_remove)
std::set< core::Size >	protocols::rna::movers::find_nearby_res (Pose const &pose, std::set< core::Size > res_list_current, Real const dist_cutoff)
void	protocols::rna::movers::erase_if_in_any_slice (utility::vector1< std::set< core::Size > > const &res_list_sliced, core::Size const res, std::set< core::Size > &res_list_new)
void	protocols::rna::movers::clean_res_list (std::set< core::Size > &res_list_new, utility::vector1< std::set< core::Size > > const &res_list_sliced)
void	protocols::rna::movers::identify_chunks (Pose const &pose, utility::vector1< std::set< core::Size > > &sliced_list_final, core::Size const virtual_res_pos, core::Size const nproc)
core::Vector	protocols::rna::movers::com_of_true_residues (kinematics::MoveMap const &mm, Pose const &pose)
std::string	protocols::rna::movers::min_checkpoint_namer (core::Size const nstruct)
std::string	protocols::rna::movers::min_log_namer (core::Size const nstruct)
void	protocols::rna::movers::read_checkpoint_log (utility::vector1< core::Size > &chunk_indices, core::Size &start_idx, core::Size const nstruct)
void	protocols::rna::movers::write_checkpoint (utility::vector1< core::Size > const &chunk_indices, core::Size const cur_idx, core::Size const nstruct, Pose const &pose)
void	protocols::rna::movers::load_checkpoint (core::Size const nstruct, utility::vector1< core::Size > &chunk_indices, Pose &pose, core::Size &first_chunk)

Detailed Description

Author

Andy Watkins, amw57.nosp@m.9@st.nosp@m.anfor.nosp@m.d.ed.nosp@m.u

Function Documentation

TR()

static basic::Tracer TR ( "protocols.rna.movers.ErraserMinimizerMover"  )

static