util.cc File Reference

#include <protocols/mpi_refinement/util.hh>
#include <basic/options/keys/lh.OptionKeys.gen.hh>
#include <basic/options/option.hh>
#include <core/types.hh>
#include <core/id/AtomID.hh>
#include <core/pose/selection.hh>
#include <core/pose/Pose.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreType.hh>
#include <core/conformation/Residue.hh>
#include <core/io/silent/SilentStruct.hh>
#include <protocols/wum/SilentStructStore.hh>
#include <core/pose/PDBInfo.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/optimization/CartesianMinimizer.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <core/pack/task/PackerTask.fwd.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <protocols/minimization_packing/PackRotamersMover.hh>
#include <core/scoring/constraints/CoordinateConstraint.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/BoundConstraint.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/scoring/rms_util.hh>
#include <cmath>
#include <cstdlib>
#include <algorithm>
#include <fstream>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <basic/Tracer.hh>
#include <numeric/random/random.hh>
#include <utility/vector1.hh>
#include <utility/string_util.hh>

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

Functions
static basic::Tracer	TR ("MPI.LHR.util")
utility::vector1< std::pair< core::Size, core::Size > >	protocols::mpi_refinement::get_loop_info_full (core::io::silent::SilentStructOP ss, utility::vector1< bool > &is_terminus, std::string const &mode)
void	protocols::mpi_refinement::get_loop_info (core::io::silent::SilentStructOP ss, core::Size &res1, core::Size &res2, bool &is_terminus)
void	protocols::mpi_refinement::constrain_residue (core::pose::Pose &pose, core::Size const resno, utility::vector1< core::Size > exclres, std::string const &cst_type, core::Real const stdev)
utility::vector1< core::Size >	protocols::mpi_refinement::get_touched_res (core::pose::Pose const pose, utility::vector1< core::Size > const loopres, core::Real dist_cut)
protocols::minimization_packing::PackRotamersMoverOP	protocols::mpi_refinement::setup_packer (core::pose::Pose const &pose, core::kinematics::MoveMap const mm, core::scoring::ScoreFunctionCOP sfxn)
void	protocols::mpi_refinement::add_movemap_from_loopres (core::kinematics::MoveMap &mm, core::pose::Pose const &pose, utility::vector1< core::Size > const loopres, bool const nonideal)
void	protocols::mpi_refinement::ramp_minpack_loop (core::pose::Pose &pose, utility::vector1< core::Size > const loopres, core::scoring::ScoreFunctionCOP sfxn, bool const nonideal, bool const ramp, bool const efficient, bool const envmin)
void	protocols::mpi_refinement::ramp_minpack_pose (core::pose::Pose &pose, core::scoring::ScoreFunctionCOP sfxn, bool const nonideal, bool const ramp)
void	protocols::mpi_refinement::add_poseinfo_to_ss (core::io::silent::SilentStruct &ss, core::pose::Pose const &ref_pose, std::string const &suffix)
core::Real	protocols::mpi_refinement::Zscore_to_library (core::Real const score, core::Real const mean, core::Real const stdev, core::Real const maxval, core::Real const minval)
utility::vector1< core::Size >	protocols::mpi_refinement::loopstring_to_loopvector (std::string const &loopstr, core::Size const ext)
utility::vector1< utility::vector1< core::Size > >	protocols::mpi_refinement::loopstring_to_loopregions (std::string const &loopstr)
void	protocols::mpi_refinement::copy_pose_crd (core::pose::Pose const pose_frame, core::pose::Pose &pose_work, utility::vector1< utility::vector1< core::Size > > const loopregions)
void	protocols::mpi_refinement::mean_and_stdev (utility::vector1< core::Real > values, core::Real const frac, core::Real &shave_cut, core::Real &mean, core::Real &stdev)
void	protocols::mpi_refinement::superimpose_all (core::io::silent::SilentStructCOP ss_ref, protocols::wum::SilentStructStore &structs, utility::vector1< std::string > const columns_copy)
core::Real	protocols::mpi_refinement::CA_Sscore (core::io::silent::SilentStructOP ss1, core::io::silent::SilentStructOP ss2, core::Real &rmsd, utility::vector1< core::Size > const &loopres, bool const superimpose, core::Real const dbase)
core::Real	protocols::mpi_refinement::CA_Sscore (core::io::silent::SilentStructOP ss1, core::io::silent::SilentStructOP ss2, core::Real &rmsd, bool const superimpose, core::Real const dbase)
core::Real	protocols::mpi_refinement::distance (core::io::silent::SilentStructOP ss1, core::io::silent::SilentStructOP ss2, std::string const &similarity_measure, bool const superimpose)
void	protocols::mpi_refinement::add_init_dev_penalty (core::io::silent::SilentStructOP ss, ObjexxFCL::FArray2D< core::Real > const init_xyz, std::string const &mode, core::Real const iha_cut, core::Real const iha_penalty_slope)
void	protocols::mpi_refinement::add_init_dev_penalty (core::io::silent::SilentStructOP ss, core::pose::Pose pose0, std::string const &mode, core::Real const iha_cut, core::Real const iha_penalty_slope)
void	protocols::mpi_refinement::add_init_dev_penalty (protocols::wum::SilentStructStore &structs, core::pose::Pose const pose0, std::string const &mode, core::Real const iha_cut, core::Real const iha_penalty_slope)
std::map< core::Size, utility::vector1< core::Real > >	protocols::mpi_refinement::read_ss2 (std::string ssfile)

Function Documentation

TR()

static basic::Tracer TR ( "MPI.LHR.util"  )

static