util.cc File Reference

#include <protocols/loops/util.hh>
#include <protocols/loops/Loop.hh>
#include <protocols/loops/Loops.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/util.tmpl.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/kinematics/MoveMap.hh>
#include <protocols/loops/loops_main.hh>
#include <core/fragment/SecondaryStructure.hh>
#include <core/scoring/constraints/CoordinateConstraint.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/chemical/ResidueType.hh>
#include <core/scoring/constraints/HarmonicFunc.hh>
#include <core/conformation/util.hh>
#include <core/fragment/Frame.hh>
#include <core/fragment/FrameList.hh>
#include <core/fragment/FragSet.hh>
#include <core/pose/util.hh>
#include <core/id/AtomID.hh>
#include <core/scoring/rms_util.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/loops.OptionKeys.gen.hh>
#include <basic/options/keys/evaluation.OptionKeys.gen.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/string.functions.hh>
#include <basic/Tracer.hh>
#include <list>
#include <utility/vector1.hh>
#include <core/id/AtomID_Map.hh>
#include <core/kinematics/FoldTree.hh>
#include <protocols/rosetta_scripts/util.hh>
#include <core/pose/selection.hh>
#include <utility/string_util.hh>
#include <boost/foreach.hpp>

Go to the source code of this file.

Namespaces
	ObjexxFCL
	C++ headers.
	ObjexxFCL::fmt
	protocols
	The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
	protocols::loops

Constant Groups
	ObjexxFCL
	C++ headers.
	ObjexxFCL::fmt
	protocols
	The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
	protocols::loops

Macros
#define	foreach   BOOST_FOREACH

Functions
static basic::Tracer	TR ("protocols.loops.util")
void	protocols::loops::fix_with_coord_cst (Loops const &rigid, core::pose::Pose &pose, bool bCstAllAtom, utility::vector1< core::Real > &weights)
void	protocols::loops::select_loop_frags (loops::Loops const &loops, core::fragment::FragSet &source, core::fragment::FragSet &loop_frags, Size shorten)
	get frags that are fully within the Loop — shorten(=true/false) frags that are close to the end of loops. More...
void	protocols::loops::safe_set_extended_torsions_and_idealize_loops (const protocols::loops::Loops &loops, core::pose::Pose *pose)
	Identical to set_extended_torsions_and_idealize_loops() without the irrational behavior surrounding empty loops. More...
void	protocols::loops::set_extended_torsions_and_idealize_loops (core::pose::Pose &pose, loops::Loops loops)
void	protocols::loops::addScoresForLoopParts (core::pose::Pose &pose, loops::Loops loops, const core::scoring::ScoreFunction &scorefxn, core::pose::Pose &native_pose, core::Size nloops)
loops::Loops	protocols::loops::compute_ss_regions (core::Real max_loop_frac, core::Size min_length, core::fragment::SecondaryStructure const &ss)
core::scoring::ScoreFunctionOP	protocols::loops::get_cen_scorefxn ()
core::scoring::ScoreFunctionOP	protocols::loops::get_fa_scorefxn ()
void	protocols::loops::add_coordinate_constraints_to_pose (core::pose::Pose &pose, const core::pose::Pose &constraint_target_pose, protocols::loops::Loops &exclude_regions)
LoopsOP	protocols::loops::loops_from_string (std::string const loop_str, core::pose::Pose const &pose)
	loop_str has the format: start:end:cut,start:end:cut and can use rosetta or pdb numbering. The return value is an owning pointer to a Loops object encoding that loop More...
void	protocols::loops::define_scorable_core_from_secondary_structure (core::fragment::SecondaryStructure const &ss_def, protocols::loops::Loops &scored_core)
protocols::loops::Loops	protocols::loops::extract_secondary_structure_chunks (core::pose::Pose const &pose, char const extracted_ss_type)
	Extract secondary structure chunks from the secondary structure. More...
protocols::loops::Loops	protocols::loops::split_by_resSeq (core::pose::Pose const &pose)
protocols::loops::Loops	protocols::loops::find_non_protein_chunks (core::pose::Pose const &pose)
protocols::loops::Loops	protocols::loops::split_by_resSeq (core::pose::Pose const &pose, protocols::loops::Loops const &input_chunks)
protocols::loops::Loops	protocols::loops::split_by_ca_ca_dist (core::pose::Pose const &pose, protocols::loops::Loops const &input_chunks, core::Real const CA_CA_distance_cutoff=4)
	Split into separate chunks if CA-CA distance is over the cutoff. More...
protocols::loops::Loops	protocols::loops::remove_small_gaps (protocols::loops::Loops const &input_chunks, core::Size gap_size=1)
	If two chunks are separated by a small gap of size <= <gap_size>, combine them. More...
protocols::loops::Loops	protocols::loops::remove_short_chunks (protocols::loops::Loops const &input_chunks, core::Size min_length=3)
	Remove small chunks. More...
protocols::loops::Loops	protocols::loops::extract_secondary_structure_chunks (core::pose::Pose const &pose, std::string extracted_ss_types="HE", core::Size gap_size=1, core::Size minimum_length_of_chunk_helix=5, core::Size minimum_length_of_chunk_strand=3, core::Real CA_CA_distance_cutoff=4)
	Extract secondary structure chunks from the pose, using multiple secondary structure types this function requires that the pose object already have secstruct information to get this information from structure (DSSP), call protocols::jumping::Dssp dssp_obj( *pose ); dssp_obj.insert_ss_into_pose( *pose ); or from secondary structure prediction (psipred_ss2 file), call core::pose::read_psipred_ss2_file(pose);. More...
protocols::loops::Loops	protocols::loops::extract_continuous_chunks (core::pose::Pose const &pose, core::Size const minimum_size, core::Real const CA_CA_distance_cutoff)

Variables
static const double	protocols::loops::EXT_PHI = -150
static const double	protocols::loops::EXT_PSI = +150
static const double	protocols::loops::EXT_OMG = 180

Macro Definition Documentation

#define foreach   BOOST_FOREACH

Author

Oliver Lange

Mike Tyka

Definition at line 72 of file util.cc.

Function Documentation

static basic::Tracer TR ( "protocols.loops.util"  )

static

Referenced by protocols::loops::add_coordinate_constraints_to_pose(), protocols::loops::select_loop_frags(), and protocols::loops::set_extended_torsions_and_idealize_loops().