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| static basic::Tracer | TR ("protocols.grafting.util") |
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| void | protocols::grafting::delete_region (core::pose::Pose &pose, core::Size const start, core::Size const end, bool detect_disulfides=true) |
| | Deletes a region of the pose. Starting from and including 'start' and 'end' residue. More...
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| 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...
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| 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...
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| 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...
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| 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...
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| 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...
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| 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...
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| 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...
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| 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...
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| 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...
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| 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...
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| 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...
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| 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...
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| 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...
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| 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...
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| 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...
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| 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 @params lower_cutpoint for CCD and loops is Cter_loop_end-1 More...
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| 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 @params lower_cutpoint for CCD and loops is end_-1 More...
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