Module _protocols_grafting_

add_cutpoint_variants_for_ccd( (Pose)pose, (Loops)loops) -> None :
    Adds cutpoint varients above and below cutpoint
    

    C++ signature :
        void add_cutpoint_variants_for_ccd(core::pose::Pose {lvalue},protocols::loops::Loops)

combine_movemaps_post_insertion( (MoveMap)scaffold_mm, (MoveMap)insert_mm, (int)start, (int)original_end, (int)insertion_length [, (int)cter_overhang_start=0]) -> MoveMap :
    combines the two main movemaps to use after the insertion.
    Start + End denote residue number before and after the insert.
    original_end denotes the end residue number before insertion occurred
    

    C++ signature :
        boost::shared_ptr<core::kinematics::MoveMap> combine_movemaps_post_insertion(boost::shared_ptr<core::kinematics::MoveMap const>,boost::shared_ptr<core::kinematics::MoveMap const>,unsigned long,unsigned long,unsigned long [,unsigned long=0])

delete_overhang_residues( (Pose)piece, (int)Nter_overhang_len, (int)Cter_overhang_length_len) -> None :
    deletes overhang residues of the pose piece.
    Recommended use is within apply method
    

    C++ signature :
        void delete_overhang_residues(core::pose::Pose {lvalue},unsigned long,unsigned long)

delete_region( (Pose)pose, (int)start, (int)end) -> None :
    Deletes a region of the pose. Starting from and including 'start' and 'end' residue.
    

    C++ signature :
        void delete_region(core::pose::Pose {lvalue},unsigned long,unsigned long)

graft_closed( (Pose)pose, (Loops)loops) -> bool :
    Uses has_severe_peptide_bond_issues with stringent geometry values to
    determine graft closure at cutpoint.
    

    C++ signature :
        bool graft_closed(core::pose::Pose {lvalue},protocols::loops::Loops {lvalue})

idealize_combined_pose( (Pose)combined, (MoveMap)movemap, (int)start, (int)insert_start, (int)insert_end, (int)Nter_loop_start, (int)Cter_loop_end [, (bool)idealize_insert=False]) -> None :
    Idealize loop residues and residues in movemap.
    

    C++ signature :
        void idealize_combined_pose(core::pose::Pose {lvalue},boost::shared_ptr<core::kinematics::MoveMap>,unsigned long,unsigned long,unsigned long,unsigned long,unsigned long [,bool=False])

insert_pose_into_pose( (Pose)scaffold_pose, (Pose)insert_pose, (int)insert_point [, (bool)copy_pdbinfo=False]) -> Pose :
    inserts one pose into another pose, returning the product as a new value.
    Nter->Cter. Coordinates and dihedrals of insert are unchanged.
    Begins insertion AFTER insert point. insert_point_end is assumed to be insert_point+1.
    

    C++ signature :
        core::pose::Pose insert_pose_into_pose(core::pose::Pose,core::pose::Pose,unsigned long [,bool=False])

insert_pose_into_pose( (Pose)scaffold_pose, (Pose)insert_pose, (int)insert_point, (int)insert_point_end [, (bool)copy_pdbinfo=False]) -> Pose :
    Steven Lewis smlewi@gmail.com, Jared Adolf-Bryfogle
    inserts one pose into another pose, returning the product as a new value.
    Nter->Cter. Coordinates and dihedrals of insert are unchanged.
    Begins insertion AFTER insert point.
    

    C++ signature :
        core::pose::Pose insert_pose_into_pose(core::pose::Pose,core::pose::Pose,unsigned long,unsigned long [,bool=False])

perturb_backbone_for_test( (Pose)pose, (MoveMap)mm) -> float :
    Uses a small mover at high KT to perturb residues in the movemap for testing.
     Returns bb_RMS_including_o
    

    C++ signature :
        double perturb_backbone_for_test(core::pose::Pose {lvalue},boost::shared_ptr<core::kinematics::MoveMap>)

remove_cutpoint_variants_for_ccd( (Pose)pose, (Loops)loops) -> None :
    Removes cutpoint variants above and below cutpoint
    

    C++ signature :
        void remove_cutpoint_variants_for_ccd(core::pose::Pose {lvalue},protocols::loops::Loops)

repack_connection_and_residues_in_movemap( (Pose)pose, (__CPP_ScoreFunction__)fa_scorefxn, (int)start, (int)end, (MoveMap)movemap) -> None :
    /////////////////////////////
     convenience function for AFTER apply method.
     flexible Nter and Cter residues plus the first and last residue of the insert.
    

    C++ signature :
        void repack_connection_and_residues_in_movemap(core::pose::Pose {lvalue},boost::shared_ptr<core::scoring::ScoreFunction const>,unsigned long,unsigned long,boost::shared_ptr<core::kinematics::MoveMap const>)

repack_connection_and_residues_in_movemap_and_piece( (Pose)pose, (__CPP_ScoreFunction__)fa_scorefxn, (int)start, (int)end, (MoveMap)movemap) -> None :
    convenience function for AFTER apply method.
    flexible Nter and Cter residues plus the entire insert.
    

    C++ signature :
        void repack_connection_and_residues_in_movemap_and_piece(core::pose::Pose {lvalue},boost::shared_ptr<core::scoring::ScoreFunction const>,unsigned long,unsigned long,boost::shared_ptr<core::kinematics::MoveMap const>)

repack_connection_and_residues_in_movemap_and_piece_and_neighbors( (Pose)pose, (__CPP_ScoreFunction__)fa_scorefxn, (int)start, (int)end, (MoveMap)movemap [, (float)neighbor_dis=4.0]) -> None :
    convenience function for AFTER apply method.
    flexible Nter and Cter residues plus the entire insert and neighbors.
    

    C++ signature :
        void repack_connection_and_residues_in_movemap_and_piece_and_neighbors(core::pose::Pose {lvalue},boost::shared_ptr<core::scoring::ScoreFunction const>,unsigned long,unsigned long,boost::shared_ptr<core::kinematics::MoveMap const> [,double=4.0])

replace_region( (Pose)from_pose, (Pose)to_pose, (int)from_pose_start_residue, (int)to_pose_start_residue, (int)insertion_length [, (bool)copy_pdbinfo=False]) -> Pose :
    replaces residues from from_pose to to_pose into pose where insertion region is defined. Returns product as a new value.
    

    C++ signature :
        core::pose::Pose replace_region(core::pose::Pose,core::pose::Pose,unsigned long,unsigned long,unsigned long [,bool=False])

return_region( (Pose)pose, (int)start, (int)end) -> Pose :
    Returns a region of the pose including start and end as a new pose. Has a simple foldtree.
    

    C++ signature :
        core::pose::Pose return_region(core::pose::Pose {lvalue},unsigned long,unsigned long)

setup_single_loop_double_arm_remodeling_foldtree( (Pose)pose, (int)Nter_loop_start, (int)Cter_loop_end, (int)end [, (bool)loop_modeling=False]) -> None :
    ///////////////////////////////////////////////////////////////
     ****Nter_loop_start---->Piece | <----Nter_loop_end****
     Insert will move in cartesian space
     s lower_cutpoint for CCD and loops is end_-1
    
    

    C++ signature :
        void setup_single_loop_double_arm_remodeling_foldtree(core::pose::Pose {lvalue},unsigned long,unsigned long,unsigned long [,bool=False])

setup_single_loop_single_arm_remodeling_foldtree( (Pose)pose, (int)Nter_loop_start, (int)Cter_loop_end [, (bool)loop_modeling=False]) -> None :
    /////////////////////////////////////////////////////////////////////////////
    /////////////////////////////////////////////////////////////////////////////
    //////////////////////////////////////////////////////////////
     ****Nter_loop_start---->Piece----> | Cter_loop_end****
      Default FoldTree used by AnchoredGraftMover.
     s lower_cutpoint for CCD and loops is Cter_loop_end-1
    
    

    C++ signature :
        void setup_single_loop_single_arm_remodeling_foldtree(core::pose::Pose {lvalue},unsigned long,unsigned long [,bool=False])

superimpose_overhangs_heavy( (Pose)pose, (Pose)piece, (bool)ca_only, (int)start, (int)end [, (int)Nter_overhang_len=2 [, (int)Cter_overhang_length_len=2]]) -> None :
    uses rms_util to superimpose overhang residues of piece onto pose.
    Start + End denote residue number before and after the insert will be.
    For example, start = 10, end = 11 for a scaffold where the previous residues are already deleted
    or a scaffold where you are superposimposing a linker between two domains -
    one that ends at start and the other that begins at end
    

    C++ signature :
        void superimpose_overhangs_heavy(core::pose::Pose,core::pose::Pose {lvalue},bool,unsigned long,unsigned long [,unsigned long=2 [,unsigned long=2]])