atom_tree_diff.cc File Reference

#include <core/import_pose/atom_tree_diffs/atom_tree_diff.hh>
#include <core/types.hh>
#include <core/chemical/ChemicalManager.fwd.hh>
#include <core/chemical/ResidueTypeSet.fwd.hh>
#include <core/chemical/util.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/id/AtomID.hh>
#include <core/id/DOF_ID.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/io/pdb/pdb_reader.hh>
#include <core/io/StructFileRep.hh>
#include <core/kinematics/AtomTree.hh>
#include <core/import_pose/import_pose.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/Jump.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/rms_util.tmpl.hh>
#include <core/scoring/ScoreFunction.hh>
#include <basic/Tracer.hh>
#include <numeric/angle.functions.hh>
#include <numeric/random/random.hh>
#include <utility>
#include <utility/vector1.hh>
#include <utility/io/izstream.hh>
#include <algorithm>
#include <set>

Classes
class	core::import_pose::atom_tree_diffs::ScoreLessThanComparator
	Provides a StrictWeakOrdering comparator for sorting elements of a ScoresMap by one particular score type. More...

Namespaces
	core
	A class for reading in the atom type properties.
	core::import_pose
	core::import_pose::atom_tree_diffs

Functions
void	core::import_pose::atom_tree_diffs::dump_score_line (std::ostream &out, std::string const &pose_tag, std::map< std::string, core::Real > const &scores)
	Helper function for writing entries – not usually called by clients. More...
void	core::import_pose::atom_tree_diffs::dump_reference_pose (std::ostream &out, std::string const &pose_tag, Scores const &scores, core::pose::Pose const &pose)
void	core::import_pose::atom_tree_diffs::dump_atom_tree_diff (std::ostream &out, std::string const &pose_tag, std::map< std::string, core::Real > const &scores, core::pose::Pose const &ref_pose_in, core::pose::Pose const &pose, int bb_precision=6, int sc_precision=4, int bondlen_precision=2)
	Encodes pose relative to ref_pose by noting which atom_tree DOFs are different. More...
bool	core::import_pose::atom_tree_diffs::header_from_atom_tree_diff (std::istream &in, std::string &pose_tag_out, Scores &scores_out)
bool	core::import_pose::atom_tree_diffs::pose_from_atom_tree_diff (std::istream &in, core::pose::Pose const &ref_pose, core::pose::Pose &pose)
	Sets pose = ref_pose and then starts modifying DOFs in pose to recreate a saved structure. Call after header_from_atom_tree_diff(). Returns false on error. More...
void	core::import_pose::atom_tree_diffs::map_of_weighted_scores (core::pose::Pose &pose, core::scoring::ScoreFunction const &sfxn, Scores &scores_out)
	Helper for dump_atom_tree_diff(), fills map with weighted score terms. More...
static basic::Tracer	core::import_pose::atom_tree_diffs::TR_rms_error_with_noise ("rms_error_with_noise")
void	core::import_pose::atom_tree_diffs::rms_error_with_noise (core::pose::Pose const &ref_pose, int bb_precision=6, int sc_precision=4)
	For use in deciding how many digits of precision you need when diffing an atom tree. More...
bool	core::import_pose::atom_tree_diffs::file_is_atom_tree_diff (std::string const &filename)
	Test if given file is an atom_tree_diff. More...
bool	core::import_pose::atom_tree_diffs::file_is_atom_tree_diff (std::istream &in)
	Test if given stream is an atom_tree_diff. More...