protocols::grafting Namespace Reference

Classes
class	AnchoredGraftMover
	Grafting class adapted from Steven Lewis' pose_into_pose algorithm. Basic, and quick, but with many options. More...
class	GraftMoverBase
	Base class for GraftMovers. Created for simplicity and control for C++ programmer, as well as PyRosetta user. More...

Typedefs
typedef utility::pointer::owning_ptr < AnchoredGraftMover >	AnchoredGraftMoverOP
typedef utility::pointer::owning_ptr < AnchoredGraftMover const >	AnchoredGraftMoverCOP
typedef utility::pointer::access_ptr < AnchoredGraftMover >	AnchoredGraftMoverAP
typedef utility::pointer::access_ptr < AnchoredGraftMover const >	AnchoredGraftMoverCAP
typedef utility::pointer::owning_ptr < GraftMoverBase >	GraftMoverBaseOP
typedef utility::pointer::owning_ptr < GraftMoverBase const >	GraftMoverBaseCOP

Functions
void	delete_region (Pose &pose, Size const start, Size const end)
	Deletes a region of the pose. Starting from and including 'start' and 'end' residue. More...
Pose	return_region (Pose &pose, Size const start, 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 (Pose const &from_pose, Pose const &to_pose, Size const from_pose_start_residue, Size const to_pose_start_residue, Size const insertion_length)
	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 (Pose const &scaffold_pose, Pose const &insert_pose, Size const insert_point, Size const insert_point_end)
	inserts one pose into another pose, returning the product as a new value. More...

Typedef Documentation

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

Definition at line 33 of file AnchoredGraftMover.fwd.hh.

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

Definition at line 34 of file AnchoredGraftMover.fwd.hh.

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

Definition at line 31 of file AnchoredGraftMover.fwd.hh.

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

Definition at line 27 of file AnchoredGraftMover.fwd.hh.

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

Definition at line 27 of file GraftMoverBase.fwd.hh.

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

Definition at line 24 of file GraftMoverBase.fwd.hh.

Function Documentation

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

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

Definition at line 45 of file util.cc.

References core::pose::Pose::conformation(), core::conformation::Conformation::delete_residue_slow(), and protocols::TR().

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

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
	)

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

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

Begins insertion AFTER insert point.

Definition at line 102 of file util.cc.

References core::kinematics::FoldTree::clear(), core::pose::Pose::fold_tree(), protocols::simple_moves::insert, core::pose::Pose::insert_residue_by_jump(), core::chemical::LOWER_TERMINUS, core::kinematics::remodel_fold_tree_to_account_for_insertion(), core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), protocols::TR(), and core::chemical::UPPER_TERMINUS.

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

Pose protocols::grafting::replace_region	(	Pose const &	to_pose,
		Pose const &	from_pose,
		Size const	from_pose_start_residue,
		Size const	to_pose_start_residue,
		Size const	insertion_length
	)

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

Definition at line 85 of file util.cc.

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

Pose protocols::grafting::return_region	(	Pose &	pose,
		Size const	start,
		Size const	end
	)

Returns a region of the pose including start and end as a new pose. Has a simple foldtree.

Definition at line 60 of file util.cc.

References core::kinematics::FoldTree::clear(), core::pose::create_subpose(), core::sequence::end, core::kinematics::FoldTree::simple_tree(), and protocols::TR().