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loops_main.hh File Reference
#include <core/types.hh>
#include <core/kinematics/FoldTree.fwd.hh>
#include <core/kinematics/MoveMap.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <protocols/loops/Loop.fwd.hh>
#include <protocols/loops/Loops.fwd.hh>
#include <core/id/SequenceMapping.fwd.hh>
#include <core/fragment/FragSet.fwd.hh>
#include <utility/vector1.fwd.hh>
#include <vector>
#include <utility/vector1.hh>

Namespaces

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

Functions

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::remove_cutpoint_variants (core::pose::Pose &pose, bool force)
 
void protocols::loops::add_cutpoint_variants (core::pose::Pose &pose)
 Add cutpoint variants to all the cutpoints in a Pose. More...
 
void protocols::loops::add_single_cutpoint_variant (core::pose::Pose &pose, const Loop &loop)
 Add cutpoint variants around a single cutpoint (defined by a Loop). More...
 
void protocols::loops::add_single_cutpoint_variant (core::pose::Pose &pose, const core::uint cutpoint)
 Add cutpoint variants around a single cutpoint (defined by residue number). More...
 
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, bool const allow_omega_move, bool const allow_takeoff_torsion_move)
 create a MoveMap for use of minimization based on loop definition (wrapper) More...
 
void protocols::loops::loops_set_move_map (pose::Pose &pose, Loops const &loops, bool const fix_template_sc, core::kinematics::MoveMap &mm, Real neighbor_dist)
 
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::loops_set_move_map (Loops const &loops, utility::vector1< bool > const &allow_sc_move, core::kinematics::MoveMap &mm, bool const allow_omega_move, bool const allow_takeoff_torsion_move)
 
core::kinematics::MoveMapOP protocols::loops::move_map_from_loops (core::pose::Pose &pose, Loops const &loops, bool const fix_template_sc, core::Real neighbor_dist=10.0, bool const flanking_residues=false)
 Create a new MoveMapOP for use in minimizing the given loop. More...
 
core::kinematics::MoveMapOP protocols::loops::move_map_from_loop (core::pose::Pose &pose, Loop const &loop, bool const fix_template_sc, core::Real neighbor_dist=10.0, bool const flanking_residues=false)
 Create a new MoveMapOP for use in minimizing the given loop. 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::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...
 
utility::vector1< boolprotocols::loops::select_loop_residues (core::pose::Pose const &pose, Loops const &loops, bool const include_neighbors, 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 (core::pose::Pose const &pose, Loop const &loop, bool const include_neighbors, utility::vector1< bool > &map, core::Real neighbor_dist=10.0)
 mark loop residues and its neighbors as necessary for one loop. More...
 
utility::vector1< boolprotocols::loops::select_loop_residues (core::pose::Pose const &pose, Loop const &loop, bool const include_neighbors, core::Real neighbor_dist=10.0)
 mark loop residues and its neighbors as necessary for one loop. More...
 
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 Takes distance from selection to neighbors to trim neighbors. More...
 
bool protocols::loops::set_secstruct_from_psipred_ss2 (core::pose::Pose &pose, std::string const &filename=std::string())
 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::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::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 (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_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_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...
 
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)
 Given a sequence mapping which may have simple indels, trim back around those indels so that the loops can plausibly be closed. 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::set_loop_cutpoint_in_pose_fold_tree (core::Size const new_cutpoint, pose::Pose &pose, core::Size const loop_begin, core::Size const loop_end)
 
void protocols::loops::apply_sequence_mapping (pose::Pose &pose, std::string const &target_seq, id::SequenceMapping const &start_mapping)
 

Detailed Description

Author
Chu Wang