util.cc File Reference

#include <core/fragment/util.hh>
#include <core/fragment/BBTorsionSRFD.hh>
#include <core/fragment/JumpSRFD.hh>
#include <core/fragment/FragID_Iterator.hh>
#include <core/fragment/FragmentIO.hh>
#include <core/fragment/FrameIterator.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/pose/Pose.hh>
#include <core/pose/extra_pose_info_util.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/annotated_sequence.hh>
#include <core/conformation/util.hh>
#include <core/types.hh>
#include <ObjexxFCL/format.hh>
#include <basic/Tracer.hh>
#include <numeric/random/random.hh>
#include <numeric/random/random_permutation.hh>
#include <numeric/xyz.functions.hh>
#include <utility/io/ozstream.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/abinitio.OptionKeys.gen.hh>
#include <basic/options/keys/frags.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <core/scoring/ScoreFunction.hh>
#include <string>
#include <fstream>
#include <core/fragment/ConstantLengthFragSet.hh>
#include <core/fragment/FragData.hh>
#include <core/import_pose/import_pose.hh>
#include <utility/vector1.hh>
#include <core/conformation/Conformation.hh>
#include <core/fragment/Frame.hh>
#include <core/io/pdb/pdb_writer.hh>

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

Functions
static basic::Tracer	core::fragment::tr ("core.fragment")
void	core::fragment::retain_top (core::Size k, FragSetOP fragments)
	Removes all but the top <k> fragments from <fragments> More...
void	core::fragment::steal_constant_length_frag_set_from_pose (pose::Pose const &pose_in, ConstantLengthFragSet &fragset)
void	core::fragment::steal_frag_set_from_pose (pose::Pose const &pose_in, FragSet &fragset, core::fragment::FragDataCOP frag_type)
void	core::fragment::steal_frag_set_from_pose (pose::Pose const &pose_in, Size const begin, Size const end, FragSet &fragset, core::fragment::FragDataCOP frag_type)
void	core::fragment::steal_frag_set_from_pose (pose::Pose const &pose_in, FragSet &fragset, core::fragment::FragDataCOP frag_type, std::set< core::Size > const &selected_residues)
void	core::fragment::chop_fragments (core::fragment::FragSet &source, core::fragment::FragSet &dest)
	Function for chopping the X-sized fragments in source into fragments that go into N-sized fragments in dest. Sizes are encoded by the value of max_frag_length() in both source and dest. More...
void	core::fragment::compute_per_residue_coverage (core::fragment::FragSet const &_frags, utility::vector1< core::Size > &nr_frags)
void	core::fragment::flatten_list (FrameList &frames, FragID_List &frag_ids)
FragSetOP	core::fragment::merge_frags (FragSet const &good_frags, FragSet const &filling, Size min_nr_frags, bool bRandom)
void	core::fragment::apply_best_scoring_fragdata (pose::Pose &pose, Frame const &frame, scoring::ScoreFunction const &sfxn)
	goes through all frag_data in the frame and puts the best scoring one into the pose, i.e. quenches the frame More...
void	core::fragment::dump_frames_as_pdb (pose::Pose const &pose, utility::vector1< FrameOP > const &frames, std::string const &filename, core::Size start_frag=1)
	writes FragData in multimodel pdb format start_tag can be used to only write a subset of the contained frag data More...
bool	core::fragment::fill_template_frames_from_pdb (pose::Pose const &pose, utility::vector1< FrameOP > const &template_frames, std::string const &filename)
	filling a frameset from a multimodel pdb file More...
void	core::fragment::read_std_frags_from_cmd (FragSetOP &fragset_large, FragSetOP &fragset_small)
void	core::fragment::make_simple_fold_tree_from_jump_frame (Frame const &frame, Size total_residue, kinematics::FoldTree &new_fold_tree)
	given a JumpFrame with Up and DownJumpSRFDs as LAST SRFDs this will make a fold-tree compatible with the Frame... this is NOT GOOD for sampling, since it introduces cut-points outside of fragments later for sampling: one could probably write a routine that looks if it can move existing Jumps in Fold-tree to fit the FRAME ... if not it returns failure... More...
void	core::fragment::fragment_set_slice (ConstantLengthFragSetOP &fragset, Size const &min_res, Size const &max_res)
void	core::fragment::fragment_set_slice (core::fragment::ConstantLengthFragSetOP &fragset, utility::vector1< core::Size > const &slice_res)
void	core::fragment::FindBoundaries (const core::kinematics::FoldTree &tree, core::Size pos, core::Size *left, core::Size *right)
	Finds the fold tree boundaries to the left and right of <pos>. More...
core::kinematics::Stub	core::fragment::getxform (numeric::xyzVector< core::Real > m1, numeric::xyzVector< core::Real > m2, numeric::xyzVector< core::Real > m3, numeric::xyzVector< core::Real > f1, numeric::xyzVector< core::Real > f2, numeric::xyzVector< core::Real > f3)
void	core::fragment::xform_pose (core::pose::Pose &pose, const core::kinematics::Stub &s, core::Size sres, core::Size eres)
void	core::fragment::make_pose_from_frags (pose::Pose &pose, std::string sequence, utility::vector1< FragDataCOP > frags, bool chains)