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Namespaces | Functions
util.hh File Reference

Header for grafting utility functions. More...

#include <core/pose/Pose.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/kinematics/MoveMap.fwd.hh>
#include <protocols/loops/Loops.hh>

Namespaces

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

Functions

void protocols::grafting::delete_region (core::pose::Pose &pose, core::Size const start, core::Size const end)
 Deletes a region of the pose. Starting from and including 'start' and 'end' residue. More...
 
Pose protocols::grafting::return_region (core::pose::Pose &pose, core::Size const start, core::Size const end)
 Returns a region of the pose including start and end as a new pose. Has a simple foldtree. More...
 
Pose protocols::grafting::replace_region (core::pose::Pose const &from_pose, core::pose::Pose const &to_pose, core::Size const from_pose_start_residue, core::Size const to_pose_start_residue, core::Size const insertion_length, bool copy_pdbinfo=false)
 replaces residues from from_pose to to_pose into pose where insertion region is defined. Returns product as a new value. More...
 
Pose protocols::grafting::insert_pose_into_pose (core::pose::Pose const &scaffold_pose, core::pose::Pose const &insert_pose, core::Size const insert_point, core::Size const insert_point_end, bool copy_pdbinfo=false)
 inserts one pose into another pose, returning the product as a new value. More...
 
Pose protocols::grafting::insert_pose_into_pose (core::pose::Pose const &scaffold_pose, core::pose::Pose const &insert_pose, core::Size const insert_point, bool copy_pdbinfo=false)
 inserts one pose into another pose, returning the product as a new value. More...
 
void protocols::grafting::repack_connection_and_residues_in_movemap (core::pose::Pose &pose, core::scoring::ScoreFunctionCOP fa_scorefxn, core::Size const start, core::Size const end, core::kinematics::MoveMapCOP movemap)
 convenience function for AFTER apply method. More...
 
void protocols::grafting::repack_connection_and_residues_in_movemap_and_piece (core::pose::Pose &pose, core::scoring::ScoreFunctionCOP fa_scorefxn, core::Size const start, core::Size const end, core::kinematics::MoveMapCOP movemap)
 convenience function for AFTER apply method. More...
 
void protocols::grafting::repack_connection_and_residues_in_movemap_and_piece_and_neighbors (core::pose::Pose &pose, core::scoring::ScoreFunctionCOP fa_scorefxn, core::Size const start, core::Size const end, core::kinematics::MoveMapCOP movemap, core::Real neighbor_dis=4.0)
 convenience function for AFTER apply method. More...
 
void protocols::grafting::superimpose_overhangs_heavy (core::pose::Pose const &pose, core::pose::Pose &piece, bool ca_only, core::Size start, core::Size end, core::Size Nter_overhang_len=2, core::Size Cter_overhang_length_len=2)
 uses rms_util to superimpose overhang residues of piece onto pose. More...
 
void protocols::grafting::delete_overhang_residues (core::pose::Pose &piece, core::Size Nter_overhang_len, core::Size Cter_overhang_length_len)
 deletes overhang residues of the pose piece. Recommended use is within apply method More...
 
MoveMapOP protocols::grafting::combine_movemaps_post_insertion (core::kinematics::MoveMapCOP scaffold_mm, core::kinematics::MoveMapCOP insert_mm, core::Size start, core::Size original_end, core::Size insertion_length, core::Size cter_overhang_start=0)
 combines the two main movemaps to use after the insertion. More...
 
core::Real protocols::grafting::perturb_backbone_for_test (core::pose::Pose &pose, core::kinematics::MoveMapOP mm)
 Uses a small mover at high KT to perturb residues in the movemap for testing. Returns bb_RMS_including_o. More...
 
void protocols::grafting::idealize_combined_pose (core::pose::Pose &combined, core::kinematics::MoveMapOP movemap, core::Size start, core::Size insert_start, core::Size insert_end, core::Size Nter_loop_start, core::Size Cter_loop_end, bool idealize_insert=false)
 Idealize loop residues and residues in movemap. More...
 
void protocols::grafting::add_cutpoint_variants_for_ccd (core::pose::Pose &pose, protocols::loops::Loops const &loops)
 Adds cutpoint varients above and below cutpoint. More...
 
void protocols::grafting::remove_cutpoint_variants_for_ccd (core::pose::Pose &pose, protocols::loops::Loops const &loops)
 Removes cutpoint variants above and below cutpoint. More...
 
bool protocols::grafting::graft_closed (core::pose::Pose &pose, protocols::loops::Loops &loops)
 Uses has_severe_peptide_bond_issues with stringent geometry values to determine graft closure at cutpoint. More...
 
void protocols::grafting::setup_single_loop_single_arm_remodeling_foldtree (Pose &pose, core::Size const Nter_loop_start, core::Size const Cter_loop_end, bool loop_modeling)
 ****Nter_loop_start-—>Piece-—> | Cter_loop_end**** Insert will move in cartesian space lower_cutpoint for CCD and loops is Cter_loop_end-1 More...
 
void protocols::grafting::setup_single_loop_double_arm_remodeling_foldtree (Pose &pose, core::Size const Nter_loop_start, core::Size const Cter_loop_end, core::Size end, bool loop_modeling)
 ****Nter_loop_start-—>Piece | <-—Nter_loop_end**** Insert will move in cartesian space lower_cutpoint for CCD and loops is end_-1 More...
 

Detailed Description

Header for grafting utility functions.

Author
Jared Adolf-Bryfogle (jadol.nosp@m.fbr@.nosp@m.gmail.nosp@m..com)
Steven Lewis (smlew.nosp@m.i@gm.nosp@m.ail.c.nosp@m.om)