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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.hh>
#include <core/chemical/ResidueTypeSet.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/file_data.hh>
#include <core/io/pdb/pdb_dynamic_reader.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/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/vector1.hh>
#include <utility/io/izstream.hh>
#include <algorithm>
#include <set>
#include <sstream>

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 defining atom parameters, known as atom_types.
 
 core::import_pose
 
 core::import_pose::atom_tree_diffs
 

Constant Groups

 core
 A class for defining atom parameters, known as atom_types.
 
 core::import_pose
 
 core::import_pose::atom_tree_diffs
 

Macros

#define foreach   BOOST_FOREACH
 

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...
 
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...
 

Macro Definition Documentation

#define foreach   BOOST_FOREACH