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Rosetta
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loop building tools More...
#include <protocols/loops/loops_main.hh>#include <protocols/loops/loop_closure/ccd/CCDLoopClosureMover.hh>#include <protocols/loops/Loop.hh>#include <protocols/loops/Loops.hh>#include <core/chemical/VariantType.hh>#include <core/chemical/ResidueTypeSet.hh>#include <core/conformation/Conformation.hh>#include <core/conformation/ResidueFactory.hh>#include <core/conformation/symmetry/util.hh>#include <core/conformation/util.hh>#include <core/fragment/BBTorsionSRFD.hh>#include <core/fragment/ConstantLengthFragSet.hh>#include <core/fragment/FragData.hh>#include <core/fragment/FragmentIO.hh>#include <core/fragment/util.hh>#include <core/id/SequenceMapping.hh>#include <core/id/TorsionID.hh>#include <core/import_pose/import_pose.hh>#include <core/kinematics/FoldTree.hh>#include <core/kinematics/MoveMap.hh>#include <core/pose/Pose.hh>#include <core/pose/symmetry/util.hh>#include <core/pose/variant_util.hh>#include <core/pose/extra_pose_info_util.hh>#include <core/pose/init_id_map.hh>#include <core/scoring/constraints/ConstraintSet.hh>#include <core/scoring/rms_util.hh>#include <core/select/util.hh>#include <core/types.hh>#include <basic/options/keys/loops.OptionKeys.gen.hh>#include <basic/options/option.hh>#include <basic/Tracer.hh>#include <utility/excn/Exceptions.hh>#include <utility/io/izstream.hh>#include <utility/vector1.hh>#include <numeric/model_quality/rms.hh>#include <numeric/random/random.hh>#include <iostream>#include <string>#include <ObjexxFCL/format.hh>#include <ObjexxFCL/string.functions.hh>#include <ObjexxFCL/FArray2D.hh>Namespaces | |
| protocols | |
| The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP. | |
| protocols::loops | |
Functions | |
| static basic::Tracer | protocols::loops::tt ("protocols.loops.loops_main") |
| 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 (core::Size const new_cutpoint, pose::Pose &pose, core::Size const loop_begin, core::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) |
| 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 (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 (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 (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< bool > | protocols::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< bool > | protocols::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... | |
| 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) |
| Given a sequence mapping which may have simple indels, trim back around those indels so that the loops can plausibly be closed. 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::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... | |
loop building tools
1.9.1