protocols::idealize Namespace Reference

Classes
class	IdealizeMover
	Mover class for transforming a Pose to ideal bonds of the given Pose. The idea is that this Mover stochastically picks a move-able position, forces that position into ideal geometry, and tries to use minimization to bring the coordinates back to very near their starting points. More...
class	IdealizeMoverCreator

Typedefs
typedef utility::pointer::shared_ptr< IdealizeMover >	IdealizeMoverOP
typedef utility::pointer::shared_ptr< IdealizeMover const >	IdealizeMoverCOP

Functions
static basic::Tracer	TR ("protocols.idealize")
void	dihedral_distance (pose::Pose const &pose1, pose::Pose const &pose2, utility::vector1< bool > const &use_pos, Real &avg_bb_angle_dev, Real &max_bb_angle_dev, Real &avg_chi_angle_dev, Real &max_chi_angle_dev)
	helper More...
void	basic_idealize (pose::Pose &pose, utility::vector1< core::Size > pos_list, scoring::ScoreFunction const &scorefxn, bool const fast, bool const chainbreaks, bool const cis_omega)
static basic::Tracer	TR ("protocols.idealize.IdealizeMover")

Typedef Documentation

IdealizeMoverCOP

typedef utility::pointer::shared_ptr< IdealizeMover const > protocols::idealize::IdealizeMoverCOP

IdealizeMoverOP

typedef utility::pointer::shared_ptr< IdealizeMover > protocols::idealize::IdealizeMoverOP

Function Documentation

basic_idealize()

void protocols::idealize::basic_idealize	(	pose::Pose &	pose,
		utility::vector1< core::Size >	pos_list,
		scoring::ScoreFunction const &	scorefxn,
		bool const	fast,
		bool const	chainbreaks,
		bool const	cis_omega
	)

References core::conformation::Residue::aa(), core::chemical::aa_pro, core::chemical::aa_vrt, core::pose::add_variant_type_to_pose_residue(), core::scoring::all_atom_rmsd(), core::conformation::Residue::atom(), core::id::BB, core::pose::Pose::conformation(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, dihedral_distance(), core::chemical::element::F, core::pose::Pose::fold_tree(), core::chemical::element::I, core::conformation::idealize_position(), core::kinematics::FoldTree::is_cutpoint(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_polymer(), core::conformation::Residue::is_protein(), core::pose::symmetry::is_symmetric(), core::conformation::Residue::is_upper_terminus(), core::conformation::Residue::lower_connect_atom(), core::pose::symmetry::make_symmetric_movemap(), core::conformation::Residue::name1(), core::kinematics::FoldTree::new_jump(), core::pose::Pose::num_jump(), core::pose::Pose::omega(), core::pose::Pose::pdb_info(), core::id::phi_torsion(), core::pose::Pose::residue(), core::scoring::rg, core::kinematics::MoveMap::set(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), core::kinematics::MoveMap::set_jump(), core::pose::Pose::set_omega(), core::scoring::ScoreFunction::show(), core::conformation::Conformation::size(), core::pose::Pose::size(), TR(), core::conformation::Residue::upper_connect_atom(), core::kinematics::FoldTree::upstream_jump_residue(), and core::conformation::Atom::xyz().

Referenced by protocols::idealize::IdealizeMover::apply().

dihedral_distance()

void protocols::idealize::dihedral_distance	(	pose::Pose const &	pose1,
		pose::Pose const &	pose2,
		utility::vector1< bool > const &	use_pos,
		Real &	avg_bb_angle_dev,
		Real &	max_bb_angle_dev,
		Real &	avg_chi_angle_dev,
		Real &	max_chi_angle_dev
	)

helper

References core::conformation::Residue::chi(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_polymer(), core::conformation::Residue::is_upper_terminus(), core::conformation::Residue::mainchain_torsion(), protocols::mean_field::max(), core::conformation::Residue::n_mainchain_atoms(), core::conformation::Residue::nchi(), core::pose::Pose::residue(), core::pose::Pose::size(), and TR().

Referenced by basic_idealize().

TR() [1/2]

static basic::Tracer protocols::idealize::TR ( "protocols.idealize"  )

static

Referenced by protocols::idealize::IdealizeMover::apply(), basic_idealize(), dihedral_distance(), protocols::idealize::IdealizeMover::parse_my_tag(), and protocols::idealize::IdealizeMover::setup_idealize_constraints().

TR() [2/2]

static basic::Tracer protocols::idealize::TR ( "protocols.idealize.IdealizeMover"  )

static