protocols::fibril Namespace Reference

Classes
class	SetupForFibrilMover

Typedefs
typedef utility::pointer::shared_ptr< SetupForFibrilMover >	SetupForFibrilMoverOP
typedef utility::pointer::shared_ptr< SetupForFibrilMover const >	SetupForFibrilMoverCOP

Functions
static basic::Tracer	TR ("protocols.moves.symmetry.fibril_util")
bool	set_xyz_coord (Vector const &origin, Vector const &x, Vector const &y, Vector &z, bool check_angle)
void	reorient_extended_fibril (Conformation &src_conformation, SymmData &symmdata)
void	make_symmetric_fibril (pose::Pose &pose)
void	superimpose_pose_on_subset_bb (pose::Pose &pose, pose::Pose &ref_pose, protocols::loops::Loops core, protocols::loops::Loops ref_core)
static basic::Tracer	TR ("protocols.moves.symmetry.SetupForFibrilMover")

Typedef Documentation

SetupForFibrilMoverCOP

typedef utility::pointer::shared_ptr< SetupForFibrilMover const > protocols::fibril::SetupForFibrilMoverCOP

SetupForFibrilMoverOP

typedef utility::pointer::shared_ptr< SetupForFibrilMover > protocols::fibril::SetupForFibrilMoverOP

Function Documentation

make_symmetric_fibril()

void protocols::fibril::make_symmetric_fibril

(

pose::Pose &

pose

)

References core::scoring::alignment, core::pose::Pose::conformation(), core::pose::Pose::fold_tree(), core::pose::symmetry::make_symmetric_pose(), core::pose::Pose::num_jump(), core::import_pose::PDB_file, core::import_pose::pose_from_file(), protocols::loops::Loops::push_back(), core::conformation::symmetry::SymmData::read_symmetry_data_from_file(), reorient_extended_fibril(), core::pose::Pose::size(), and superimpose_pose_on_subset_bb().

Referenced by protocols::fibril::SetupForFibrilMover::apply().

reorient_extended_fibril()

void protocols::fibril::reorient_extended_fibril	(	Conformation &	src_conformation,
		SymmData &	symmdata
	)

References core::chemical::ResidueType::atom_index(), core::conformation::Conformation::fold_tree(), core::conformation::symmetry::SymmData::get_anchor_residue(), core::kinematics::Stub::global2local(), core::kinematics::Stub::local2global(), core::conformation::Conformation::residue_type(), core::conformation::Conformation::set_xyz(), set_xyz_coord(), core::conformation::Conformation::size(), and core::conformation::Conformation::xyz().

Referenced by make_symmetric_fibril().

set_xyz_coord()

bool protocols::fibril::set_xyz_coord	(	Vector const &	origin,
		Vector const &	x,
		Vector const &	y,
		Vector &	z,
		bool	check_angle
	)

Referenced by reorient_extended_fibril().

superimpose_pose_on_subset_bb()

void protocols::fibril::superimpose_pose_on_subset_bb	(	pose::Pose &	pose,
		pose::Pose &	ref_pose,
		protocols::loops::Loops	core,
		protocols::loops::Loops	ref_core
	)

References core::conformation::Residue::atom_index(), core::id::AtomID::BOGUS_ATOM_ID(), core::pose::initialize_atomid_map(), core::pose::Pose::residue(), core::id::AtomID_Map< T >::set(), and core::scoring::superimpose_pose().

Referenced by protocols::fibril::SetupForFibrilMover::align(), and make_symmetric_fibril().

TR() [1/2]

static basic::Tracer protocols::fibril::TR ( "protocols.moves.symmetry.fibril_util"  )

static

TR() [2/2]

static basic::Tracer protocols::fibril::TR ( "protocols.moves.symmetry.SetupForFibrilMover"  )

static