protocols::grafting Namespace Reference

Namespaces
	simple_movers

Classes
class	AnchoredGraftMover
	Grafting class adapted from Steven Lewis' pose_into_pose algorithm. More...
class	AnchoredGraftMoverCreator
class	CCDEndsGraftMover
	General purpose Grafting class which: 1) superimposes the insert onto the scaffold using any overhang residues, 2) Inserts the pose piece into the scaffold pose, deleting any overhang residues or residues in the region the isertion will occur between. 3) Cycles of: a) SmallMover for sampling (Can be disabled)) b) CCDs both terminal ends of the scaffold using flexibility settings or movemap To close the graft. c) MinMover to help close the graft through chainbreak terms d) Closure check - will return if closed (Can be disabled) d) MonteCarlo Boltzmann criterion. More...
class	CCDEndsGraftMoverCreator
class	GraftMoverBase
	Fairly abstract base class for GraftMover classes. More...

Typedefs
typedef utility::pointer::shared_ptr< AnchoredGraftMover >	AnchoredGraftMoverOP
typedef utility::pointer::shared_ptr< AnchoredGraftMover const >	AnchoredGraftMoverCOP
typedef utility::pointer::weak_ptr< AnchoredGraftMover >	AnchoredGraftMoverAP
typedef utility::pointer::weak_ptr< AnchoredGraftMover const >	AnchoredGraftMoverCAP
typedef utility::pointer::shared_ptr< CCDEndsGraftMover >	CCDEndsGraftMoverOP
typedef utility::pointer::shared_ptr< CCDEndsGraftMover const >	CCDEndsGraftMoverCOP
typedef utility::pointer::shared_ptr< GraftMoverBase >	GraftMoverBaseOP
typedef utility::pointer::shared_ptr< GraftMoverBase const >	GraftMoverBaseCOP
typedef utility::pointer::shared_ptr< DeleteRegionMover >	DeleteRegionMoverOP
typedef utility::pointer::shared_ptr< DeleteRegionMover const >	DeleteRegionMoverCOP
typedef utility::pointer::shared_ptr< InsertPoseIntoPoseMover >	InsertPoseIntoPoseMoverOP
typedef utility::pointer::shared_ptr< InsertPoseIntoPoseMover const >	InsertPoseIntoPoseMoverCOP
typedef utility::pointer::shared_ptr< ReplaceRegionMover >	ReplaceRegionMoverOP
typedef utility::pointer::shared_ptr< ReplaceRegionMover const >	ReplaceRegionMoverCOP

Functions
void	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...
Pose	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	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	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...
Pose	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...
void	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	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	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	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	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	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	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	add_cutpoint_variants_for_ccd (core::pose::Pose &pose, protocols::loops::Loops const &loops)
	Adds cutpoint varients above and below cutpoint. More...
void	remove_cutpoint_variants_for_ccd (core::pose::Pose &pose, protocols::loops::Loops const &loops)
	Removes cutpoint variants above and below cutpoint. More...
bool	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	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	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...
void	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...

Typedef Documentation

AnchoredGraftMoverAP

typedef utility::pointer::weak_ptr< AnchoredGraftMover > protocols::grafting::AnchoredGraftMoverAP

AnchoredGraftMoverCAP

typedef utility::pointer::weak_ptr< AnchoredGraftMover const > protocols::grafting::AnchoredGraftMoverCAP

AnchoredGraftMoverCOP

typedef utility::pointer::shared_ptr< AnchoredGraftMover const > protocols::grafting::AnchoredGraftMoverCOP

AnchoredGraftMoverOP

typedef utility::pointer::shared_ptr< AnchoredGraftMover > protocols::grafting::AnchoredGraftMoverOP

CCDEndsGraftMoverCOP

typedef utility::pointer::shared_ptr<CCDEndsGraftMover const> protocols::grafting::CCDEndsGraftMoverCOP

CCDEndsGraftMoverOP

typedef utility::pointer::shared_ptr<CCDEndsGraftMover> protocols::grafting::CCDEndsGraftMoverOP

DeleteRegionMoverCOP

typedef utility::pointer::shared_ptr<DeleteRegionMover const> protocols::grafting::DeleteRegionMoverCOP

DeleteRegionMoverOP

typedef utility::pointer::shared_ptr<DeleteRegionMover> protocols::grafting::DeleteRegionMoverOP

GraftMoverBaseCOP

typedef utility::pointer::shared_ptr<GraftMoverBase const> protocols::grafting::GraftMoverBaseCOP

GraftMoverBaseOP

typedef utility::pointer::shared_ptr<GraftMoverBase> protocols::grafting::GraftMoverBaseOP

InsertPoseIntoPoseMoverCOP

typedef utility::pointer::shared_ptr<InsertPoseIntoPoseMover const> protocols::grafting::InsertPoseIntoPoseMoverCOP

InsertPoseIntoPoseMoverOP

typedef utility::pointer::shared_ptr<InsertPoseIntoPoseMover> protocols::grafting::InsertPoseIntoPoseMoverOP

ReplaceRegionMoverCOP

typedef utility::pointer::shared_ptr<ReplaceRegionMover const> protocols::grafting::ReplaceRegionMoverCOP

ReplaceRegionMoverOP

typedef utility::pointer::shared_ptr<ReplaceRegionMover> protocols::grafting::ReplaceRegionMoverOP

Function Documentation

add_cutpoint_variants_for_ccd()

void protocols::grafting::add_cutpoint_variants_for_ccd	(	Pose &	pose,
		Loops const &	loops
	)

Adds cutpoint varients above and below cutpoint.

References core::pose::add_variant_type_to_pose_residue(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, and protocols::TR().

Referenced by protocols::grafting::AnchoredGraftMover::apply(), and protocols::grafting::CCDEndsGraftMover::apply().

combine_movemaps_post_insertion()

core::kinematics::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.

Start + End denote residue number before and after the insert. original_end denotes the end residue number before insertion occurred

References protocols::denovo_design::movers::new_id(), protocols::loops::start, and protocols::TR().

Referenced by protocols::grafting::AnchoredGraftMover::setup_movemap_and_regions().

delete_overhang_residues()

void protocols::grafting::delete_overhang_residues	(	Pose &	piece,
		core::Size	Nter_overhang,
		core::Size	Cter_overhang
	)

deletes overhang residues of the pose piece. Recommended use is within apply method

References core::pose::Pose::conformation(), core::conformation::Conformation::delete_residue_slow(), core::pose::Pose::pdb_info(), and core::pose::Pose::size().

Referenced by protocols::grafting::GraftMoverBase::insert_piece().

delete_region()

void protocols::grafting::delete_region	(	Pose &	pose,
		core::Size const	start,
		core::Size const	end,
		bool	detect_disulfides
	)

Deletes a region of the pose. Starting from and including 'start' and 'end' residue.

References core::pose::Pose::conformation(), core::pose::Pose::delete_residue_range_slow(), core::conformation::Conformation::detect_disulfides(), core::sequence::end, core::pose::Pose::pdb_info(), protocols::loops::start, and protocols::TR().

Referenced by protocols::grafting::simple_movers::DeleteRegionMover::apply(), protocols::antibody::design::insert_cdr_into_antibody(), and protocols::grafting::GraftMoverBase::insert_piece().

graft_closed()

bool protocols::grafting::graft_closed	(	Pose &	pose,
		Loops &	loops
	)

Uses has_severe_peptide_bond_issues with stringent geometry values to determine graft closure at cutpoint.

References protocols::loops::has_severe_pep_bond_geom_issues().

Referenced by protocols::grafting::AnchoredGraftMover::apply(), protocols::grafting::CCDEndsGraftMover::apply(), and protocols::antibody::design::AntibodyDesignMover::setup_random_start_pose().

idealize_combined_pose()

void protocols::grafting::idealize_combined_pose	(	Pose &	combined,
		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
	)

Idealize loop residues and residues in movemap.

References core::pose::Pose::conformation(), core::conformation::Conformation::insert_ideal_geometry_at_polymer_bond(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), protocols::loops::start, and protocols::TR().

Referenced by protocols::grafting::AnchoredGraftMover::apply(), and protocols::grafting::CCDEndsGraftMover::apply().

insert_pose_into_pose() [1/2]

core::pose::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.

Nter->Cter. Coordinates and dihedrals of insert are unchanged.

Begins insertion AFTER insert point. insert_point_end is assumed to be insert_point+1.

Referenced by protocols::grafting::simple_movers::InsertPoseIntoPoseMover::apply(), protocols::antibody::design::insert_cdr_into_antibody(), and protocols::grafting::GraftMoverBase::insert_piece().

insert_pose_into_pose() [2/2]

core::pose::Pose protocols::grafting::insert_pose_into_pose	(	Pose const &	scaffold_pose,
		Pose const &	insert_pose,
		core::Size const	insert_point,
		core::Size const	insert_point_end,
		bool	copy_pdbinfo
	)

inserts one pose into another pose, returning the product as a new value.

Author

Steven Lewis smlew.nosp@m.i@gm.nosp@m.ail.c.nosp@m.om

brief inserts one pose into another pose, returning the product as a new value. The insert pose will be added immediately after insert_point and before insert_point_end.

Author

Steven Lewis smlew.nosp@m.i@gm.nosp@m.ail.c.nosp@m.om, Jared Adolf-Bryfogle

Nter->Cter. Coordinates and dihedrals of insert are unchanged.

Begins insertion AFTER insert point.

References core::kinematics::FoldTree::add_edge(), core::kinematics::FoldTree::clear(), core::pose::Pose::conformation(), core::conformation::Conformation::declare_chemical_bond(), core::conformation::disulfide_bonds(), core::pose::Pose::fold_tree(), core::pose::Pose::insert_residue_by_jump(), core::chemical::LOWER_TERMINUS_VARIANT, core::pose::Pose::pdb_info(), core::kinematics::Edge::PEPTIDE, core::pose::remove_variant_type_from_pose_residue(), core::kinematics::FoldTree::reorder(), core::pose::Pose::residue(), core::pose::set_reasonable_fold_tree(), core::pose::Pose::size(), protocols::TR(), and core::chemical::UPPER_TERMINUS_VARIANT.

perturb_backbone_for_test()

core::Real protocols::grafting::perturb_backbone_for_test	(	Pose &	pose,
		MoveMapOP	mm
	)

Uses a small mover at high KT to perturb residues in the movemap for testing. Returns bb_RMS_including_o.

References core::scoring::bb_rmsd_including_O(), and protocols::TR().

Referenced by protocols::grafting::AnchoredGraftMover::apply(), and protocols::grafting::CCDEndsGraftMover::apply().

remove_cutpoint_variants_for_ccd()

void protocols::grafting::remove_cutpoint_variants_for_ccd	(	Pose &	pose,
		Loops const &	loops
	)

Removes cutpoint variants above and below cutpoint.

References core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, and core::pose::remove_variant_type_from_pose_residue().

Referenced by protocols::grafting::AnchoredGraftMover::apply(), and protocols::grafting::CCDEndsGraftMover::apply().

repack_connection_and_residues_in_movemap()

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.

flexible Nter and Cter residues plus the first and last residue of the insert.

References core::sequence::end, and protocols::loops::start.

repack_connection_and_residues_in_movemap_and_piece()

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.

flexible Nter and Cter residues plus the entire insert.

References core::sequence::end, and protocols::loops::start.

repack_connection_and_residues_in_movemap_and_piece_and_neighbors()

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.

flexible Nter and Cter residues plus the entire insert and neighbors.

References core::sequence::end, and protocols::loops::start.

Referenced by protocols::grafting::AnchoredGraftMover::apply(), and protocols::grafting::CCDEndsGraftMover::apply().

replace_region()

core::pose::Pose protocols::grafting::replace_region	(	Pose const &	from_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
	)

replaces residues from from_pose to to_pose into pose where insertion region is defined. Returns product as a new value.

References core::pose::Pose::conformation(), core::conformation::Conformation::detect_disulfides(), core::pose::Pose::pdb_info(), core::conformation::Conformation::replace_residue(), and core::pose::Pose::residue().

Referenced by protocols::grafting::simple_movers::ReplaceRegionMover::apply().

return_region()

core::pose::Pose protocols::grafting::return_region	(	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.

References core::kinematics::FoldTree::clear(), core::pose::Pose::conformation(), core::pose::create_subpose(), core::conformation::Conformation::detect_disulfides(), core::sequence::end, core::pose::Pose::pdb_info(), core::kinematics::FoldTree::simple_tree(), core::pose::Pose::size(), protocols::loops::start, and protocols::TR().

Referenced by protocols::grafting::simple_movers::KeepRegionMover::apply(), protocols::tcr::graft_cdr(), and protocols::tcr::graft_framework().

setup_single_loop_double_arm_remodeling_foldtree()

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

References core::kinematics::FoldTree::add_edge(), core::kinematics::FoldTree::clear(), core::sequence::end, core::pose::Pose::fold_tree(), core::kinematics::Edge::PEPTIDE, core::kinematics::FoldTree::reorder(), core::pose::Pose::size(), and protocols::TR().

setup_single_loop_single_arm_remodeling_foldtree()

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

****Nter_loop_start-—>Piece-—> | Cter_loop_end**** Default FoldTree used by AnchoredGraftMover. @params lower_cutpoint for CCD and loops is Cter_loop_end-1

FOLDTREE SETUP. options depending on how you want your graft algorithm to work! —Indicates Flexible regions, | indicates cutpoint. Arrows are direction of ARMs used to close the loop in conjunction with algorithm. (CCD, KIC)

References core::kinematics::FoldTree::add_edge(), core::kinematics::FoldTree::clear(), core::pose::Pose::fold_tree(), core::kinematics::Edge::PEPTIDE, core::kinematics::FoldTree::reorder(), core::pose::Pose::size(), and protocols::TR().

Referenced by protocols::grafting::AnchoredGraftMover::apply().

superimpose_overhangs_heavy()

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.

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

References core::conformation::Residue::atom_index(), core::id::AtomID::BOGUS_ATOM_ID(), core::sequence::end, core::pose::initialize_atomid_map(), core::pose::remove_lower_terminus_type_from_pose_residue(), core::pose::remove_upper_terminus_type_from_pose_residue(), core::pose::Pose::residue(), core::scoring::rms, core::pose::Pose::size(), protocols::loops::start, core::scoring::superimpose_pose(), and protocols::TR().

Referenced by protocols::grafting::CCDEndsGraftMover::apply().