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loops_main.cc File Reference

loop building tools More...

#include <protocols/loops/loops_main.hh>
#include <protocols/loops/loop_closure/ccd/ccd_closure.hh>
#include <protocols/loops/Loop.hh>
#include <protocols/loops/Loops.hh>
#include <core/types.hh>
#include <core/chemical/VariantType.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/conformation/util.hh>
#include <core/chemical/ResidueSelector.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/id/TorsionID.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/MoveMap.hh>
#include <basic/options/option.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/pose/util.tmpl.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/TenANeighborGraph.hh>
#include <core/fragment/ConstantLengthFragSet.hh>
#include <core/fragment/util.hh>
#include <core/fragment/FragmentIO.hh>
#include <core/fragment/BBTorsionSRFD.hh>
#include <core/pose/symmetry/util.hh>
#include <core/conformation/symmetry/util.hh>
#include <numeric/model_quality/rms.hh>
#include <core/id/SequenceMapping.hh>
#include <basic/Tracer.hh>
#include <numeric/random/random.hh>
#include <utility/io/izstream.hh>
#include <ObjexxFCL/string.functions.hh>
#include <iostream>
#include <map>
#include <string>
#include <basic/options/keys/loops.OptionKeys.gen.hh>
#include <core/fragment/FragData.hh>
#include <core/import_pose/import_pose.hh>
#include <utility/vector1.hh>
#include <ObjexxFCL/format.hh>
#include <core/conformation/Conformation.hh>

Namespaces

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

Constant Groups

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

Functions

basic::Tracer protocols::loops::tt ("protocols.loops.loops_main")
 
static
numeric::random::RandomGenerator 
protocols::loops::RG (31413)
 
void protocols::loops::read_loop_fragments (std::vector< core::fragment::FragSetOP > &frag_libs)
 
void protocols::loops::read_loop_fragments (utility::vector1< core::fragment::FragSetOP > &frag_libs)
 
void protocols::loops::fold_tree_from_loops (core::pose::Pose const &pose, Loops const &loops, core::kinematics::FoldTree &f, bool terminal_cutpoint=false)
 the main function for perform loop modeling More...
 
void protocols::loops::set_single_loop_fold_tree (core::pose::Pose &pose, Loop const &loop)
 
void protocols::loops::set_loop_cutpoint_in_pose_fold_tree (Size const new_cutpoint, pose::Pose &pose, Size const loop_begin, Size const loop_end)
 
void protocols::loops::remove_cutpoint_variants (core::pose::Pose &pose, bool force)
 
void protocols::loops::add_cutpoint_variants (core::pose::Pose &pose)
 
void protocols::loops::add_single_cutpoint_variant (core::pose::Pose &pose, const Loop &loop)
 
void protocols::loops::loops_set_move_map (core::pose::Pose &pose, Loops const &loops, bool const fix_template_sc, core::kinematics::MoveMap &mm, core::Real neighbor_dist=10.0)
 create a MoveMap for use of minimization based on loop definition (wrapper) More...
 
void protocols::loops::loops_set_move_map (Loops const &loops, utility::vector1< bool > const &allow_sc_move, core::kinematics::MoveMap &mm)
 create a MoveMap for use of minimization based on loop definition More...
 
void protocols::loops::set_move_map_for_centroid_loop (Loop const &loop, core::kinematics::MoveMap &mm)
 
void protocols::loops::add_loop_flank_residues_bb_to_movemap (Loops const &loops, core::kinematics::MoveMap &mm, core::Size flank_size=2)
 add flank stem residues to the loop movemap More...
 
void protocols::loops::ccd_close_loops (core::pose::Pose &pose, Loops const &loops, core::kinematics::MoveMap const &mm)
 close loops by the CCD mechanism More...
 
void protocols::loops::get_tenA_neighbor_residues (core::pose::Pose const &pose, utility::vector1< bool > &residue_positions)
 get neighbor residues within 10 A CB distance cutoff More...
 
void protocols::loops::select_loop_residues (core::pose::Pose const &pose, Loops const &loops, bool const include_neighbors, utility::vector1< bool > &map, core::Real neighbor_dist=10.0)
 mark loop residues and its neighbors as necessary in a sequence map. More...
 
void protocols::loops::select_loop_residues (pose::Pose const &pose, Loop const &loop, bool const include_neighbors, utility::vector1< bool > &map, Real neighbor_dist)
 
void protocols::loops::filter_loop_neighbors_by_distance (core::pose::Pose const &pose, utility::vector1< bool > &map, Loops const &loops, core::Real &dist_cutoff)
 filter set of loop neighbors to a certain CB distance More...
 
void protocols::loops::extend_sequence_mapping (pose::Pose const &pose, id::SequenceMapping &mapping, std::string &source_seq, std::string &target_seq)
 
void protocols::loops::apply_sequence_mapping (pose::Pose &pose, std::string const &target_seq, id::SequenceMapping const &start_mapping)
 
void protocols::loops::trim_back_sequence_mapping (core::id::SequenceMapping &mapping, std::string const &source_seq, std::string const &target_seq, core::Size const min_loop_size)
 
bool protocols::loops::set_secstruct_from_psipred_ss2 (core::pose::Pose &pose)
 helper function to set secondary structure of a Pose from an external file. More...
 
bool protocols::loops::set_secstruct_from_dssp (core::pose::Pose &pose, std::string const &filename)
 another helper function to set secondary structure of a Pose from an external file. More...
 
void protocols::loops::idealize_loop (core::pose::Pose &pose, Loop const &loop)
 
void protocols::loops::set_extended_torsions (core::pose::Pose &pose, Loop const &loop)
 
void protocols::loops::remove_missing_density (core::pose::Pose &pose, Loop const &loop)
 
core::Real protocols::loops::native_loop_core_CA_rmsd (const core::pose::Pose &native_pose, const core::pose::Pose &pose, loops::Loops loops, int &corelength)
 
Real protocols::loops::loop_rmsd_with_superimpose (core::pose::Pose const &pose1, core::pose::Pose const &pose2, Loops const &loops, bool CA_only=false, bool bb_only=true)
 As above but actuall superimposes the non-loop part. More...
 
Real protocols::loops::loop_rmsd_with_superimpose_core (core::pose::Pose const &pose1, core::pose::Pose const &pose2, Loops const &loops, Loops const &core, bool CA_only=false, bool bb_only=true)
 As above but actually superimposes only the core part (in case there are multiple loops...) More...
 
Real protocols::loops::loop_rmsd (core::pose::Pose const &pose1, core::pose::Pose const &pose2, Loops const &loops, bool CA_only=false, bool bb_only=true)
 calculate rmsd of loop residues with repect to native (template aligned) More...
 
Real protocols::loops::loop_local_rmsd (core::pose::Pose const &pose1, core::pose::Pose const &pose2, Loops const &loops)
 calculate rmsd of loop residues with repect to native (loop fit) More...
 

Detailed Description

loop building tools

Author
Mike Tyka
Chu Wang
Daniel J. Mandell