Classes
class	Embedding

class	EmbeddingDef
	Embedding Setup Helper Class. More...

Typedefs
typedef utility::pointer::shared_ptr < Embedding >	EmbeddingOP

typedef utility::pointer::shared_ptr < Embedding const >	EmbeddingCOP

typedef utility::pointer::shared_ptr < EmbeddingDef >	EmbeddingDefOP

typedef utility::pointer::shared_ptr < EmbeddingDef const >	EmbeddingDefCOP

Functions
numeric::xyzVector< core::Real >	center_of_mass (pose::Pose const &pose, core::SSize const start, core::SSize const stop)
	Center of Mass. More...

core::SSize	residue_center_of_mass (pose::Pose const &pose, core::SSize const start, core::SSize const stop)
	Residue Center of Mass. More...

core::SSize	return_nearest_residue (pose::Pose const &pose, core::SSize const begin, core::SSize const end, Vector center)
	Return nearest residue. More...

std::pair< utility::vector1 < Real >, utility::vector1 < Real > >	get_chain_and_z (pose::Pose const &pose)
	Get z-coord and chainID. More...

void	compute_structure_based_embedding (pose::Pose const &pose, SpanningTopology const &topology, Vector &center, Vector &normal)
	Compute Membrane Center/Normal from Membrane Spanning topology. More...

void	compute_structure_based_embedding (pose::Pose const &pose, Vector &center, Vector &normal)
	Compute Membrane Center/Normal from Membrane Spanning topology, uses topology from MembraneInfo. More...

EmbeddingDefOP	compute_structure_based_embedding (pose::Pose const &pose, SpanningTopology const &topo)
	Compute Membrane Center/Normal from Membrane Spanning topology. More...

EmbeddingDefOP	compute_structure_based_embedding (pose::Pose const &pose)
	Compute Membrane Center/Normal from Membrane Spanning topology, uses topology from MembraneInfo. More...

void	check_vector (core::Vector const vector)
	Check reasonable range of vector. More...

EmbeddingDefOP	average_embeddings (utility::vector1< EmbeddingDefOP > const parts)
	Average EmbeddingDefs as they are without vector inversion accounting for topology. More...

EmbeddingDefOP	average_antiparallel_embeddings (utility::vector1< EmbeddingDefOP > const parts)
	Average EmbeddingDefs after first inverting some vectors accounting for topology. More...

void	membrane_normal_to_length_15 (pose::Pose &pose)
	Normalize normal vector to length 15 for visualization. More...

void	reorder_membrane_foldtree (pose::Pose &pose)
	Set membrane residue to root of foldtree. More...

core::Vector const	membrane_axis (core::pose::Pose &pose, int jumpnum)
	Calculates translation axis lying in the membrane (= projection of COM axis into the membrane plane) More...

void	split_topology_by_jump (Pose const &pose, Size const jumpnum, SpanningTopology const &topo, Pose &pose_up, Pose &pose_down, SpanningTopology &topo_up, SpanningTopology &topo_down)
	Splits the SpanningTopology object into two objects, depending on given jump number. More...

Typedef Documentation

typedef utility::pointer::shared_ptr< Embedding const > protocols::membrane::geometry::EmbeddingCOP

typedef utility::pointer::shared_ptr< EmbeddingDef const > protocols::membrane::geometry::EmbeddingDefCOP

typedef utility::pointer::shared_ptr< EmbeddingDef > protocols::membrane::geometry::EmbeddingDefOP

typedef utility::pointer::shared_ptr< Embedding > protocols::membrane::geometry::EmbeddingOP

Function Documentation

EmbeddingDefOP protocols::membrane::geometry::average_antiparallel_embeddings ( utility::vector1< EmbeddingDefOP > const parts )

Average EmbeddingDefs after first inverting some vectors accounting for topology.

Get average center and normal from a vector of EmbeddingDefs

References numeric::angle_degrees(), core::conformation::membrane::center, core::conformation::membrane::mem_thickness, core::conformation::membrane::normal, numeric::xyzVector< class >::normalize(), and core::conformation::TR().

Referenced by protocols::membrane::geometry::Embedding::Embedding().

EmbeddingDefOP protocols::membrane::geometry::average_embeddings ( utility::vector1< EmbeddingDefOP > const parts )

Average EmbeddingDefs as they are without vector inversion accounting for topology.

Average EmbeddingDefs as they are (without vector inversion accounting for topology)

Get average center and normal from a vector of EmbeddingDefs

References core::conformation::membrane::center, core::conformation::membrane::mem_thickness, core::conformation::membrane::normal, and numeric::xyzVector< class >::normalize().

Referenced by protocols::membrane::geometry::Embedding::Embedding().

numeric::xyzVector< core::Real > protocols::membrane::geometry::center_of_mass	(	pose::Pose const &	pose,
		core::SSize const	start,
		core::SSize const	stop
	)

Center of Mass.

Calculates the center of mass of a pose - Stop and start positions (or residues) used ot find the starting and finishing locations the start and stop positions (or residues) within the pose are used to find the starting and finishing locations

Author: Monica Berrondo, Modified by Javier Castellanos and Rebecca Alford

References core::conformation::Residue::atom(), core::conformation::membrane::center, core::conformation::Residue::is_protein(), core::conformation::Residue::nbr_atom_xyz(), core::pose::Pose::residue(), protocols::loops::stop, and core::conformation::Atom::xyz().

Referenced by protocols::environment::com_calc(), protocols::sic_dock::get_rg(), protocols::match::NumNeighborsMPM::modified_match_positions(), protocols::features::SmotifFeatures::report_features(), and residue_center_of_mass().

void protocols::membrane::geometry::check_vector ( core::Vector const vector )

Check reasonable range of vector.

References numeric::xyzVector< class >::to_string(), core::conformation::TR(), numeric::xyzVector< class >::x(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

Referenced by protocols::membrane::geometry::EmbeddingDef::check_range().

void protocols::membrane::geometry::compute_structure_based_embedding	(	pose::Pose const &	pose,
		SpanningTopology const &	topology,
		Vector &	center,
		Vector &	normal
	)

Compute Membrane Center/Normal from Membrane Spanning topology.

References numeric::xyzVector< class >::center, and compute_structure_based_embedding().

Referenced by protocols::membrane::MembranePositionFromTopologyMover::apply(), protocols::membrane::FlipMover::apply(), and protocols::membrane::TransformIntoMembraneMover::apply().

void protocols::membrane::geometry::compute_structure_based_embedding	(	pose::Pose const &	pose,
		Vector &	center,
		Vector &	normal
	)

Compute Membrane Center/Normal from Membrane Spanning topology, uses topology from MembraneInfo.

References compute_structure_based_embedding(), core::pose::Pose::conformation(), and core::conformation::Conformation::membrane_info().

protocols::membrane::geometry::EmbeddingDefOP protocols::membrane::geometry::compute_structure_based_embedding	(	pose::Pose const &	pose,
		SpanningTopology const &	topo
	)

Compute Membrane Center/Normal from Membrane Spanning topology.

References core::conformation::membrane::SpanningTopology::nspans(), and utility_exit_with_message.

protocols::membrane::geometry::EmbeddingDefOP protocols::membrane::geometry::compute_structure_based_embedding ( pose::Pose const & pose )

Compute Membrane Center/Normal from Membrane Spanning topology, uses topology from MembraneInfo.

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

Referenced by compute_structure_based_embedding().

std::pair< utility::vector1< Real >, utility::vector1< Real > > protocols::membrane::geometry::get_chain_and_z ( pose::Pose const & pose )

Get z-coord and chainID.

Helper function that creates input for SpanningTopology which is not built at the time the Pose is built returns a pair of vectors: vector1 is z-coord of CA atoms of the pose vector2 is chainID of CA atoms of the pose

References core::conformation::Residue::atom(), core::pose::Pose::chain(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), core::conformation::TR(), core::conformation::Atom::xyz(), and numeric::xyzVector< class >::z().

Referenced by protocols::membrane::AddMembraneMover::apply().

core::Vector const protocols::membrane::geometry::membrane_axis	(	core::pose::Pose &	pose,
		int	jumpnum
	)

Calculates translation axis lying in the membrane (= projection of COM axis into the membrane plane)

References core::pose::Pose::conformation(), cross(), core::conformation::Conformation::membrane_info(), core::conformation::membrane::normal, and core::conformation::TR().

Referenced by protocols::docking::DockingPrepackProtocol::apply(), protocols::docking::DockingSlideIntoContact::apply(), protocols::docking::calc_interaction_energy(), and protocols::electron_density::dockPoseIntoMap().

void protocols::membrane::geometry::membrane_normal_to_length_15 ( pose::Pose & pose )

Normalize normal vector to length 15 for visualization.

References core::conformation::membrane::center, core::pose::Pose::conformation(), core::conformation::Conformation::membrane_info(), core::conformation::membrane::normal, numeric::xyzVector< class >::normalize(), and core::conformation::Conformation::update_membrane_position().

void protocols::membrane::geometry::reorder_membrane_foldtree ( pose::Pose & pose )

Set membrane residue to root of foldtree.

Requires MembraneInfo to be constructed beforehand; use AddMembraneMover to do that

References core::pose::Pose::conformation(), core::pose::Pose::fold_tree(), core::conformation::Conformation::membrane_info(), and core::kinematics::FoldTree::reorder().

Referenced by protocols::docking::membrane::MPDockingSetupMover::apply(), and protocols::docking::membrane::MPDockingSetupMover::transform_pose_into_membrane().

core::SSize protocols::membrane::geometry::residue_center_of_mass	(	pose::Pose const &	pose,
		core::SSize const	start,
		core::SSize const	stop
	)

Residue Center of Mass.

Calcualte the center of mass of a pose.

Author: Monica Berrondo, Modified by Javier Castellanos and Rebecca Alford

References core::conformation::membrane::center, center_of_mass(), and return_nearest_residue().

Referenced by protocols::protein_interface_design::movers::SetAtomTree::apply(), and protocols::relax::membrane::MPFastRelaxMover::setup_relax_foldtree().

core::SSize protocols::membrane::geometry::return_nearest_residue	(	pose::Pose const &	pose,
		core::SSize const	begin,
		core::SSize const	end,
		Vector	center
	)

Return nearest residue.

Find the residue nearest some position passed in (normally a center of mass)

Author: Monica Berrondo, Modified by Javier Castellanos and Rebecca Alford

References core::conformation::Residue::atom(), core::conformation::membrane::center, core::conformation::Residue::is_protein(), numeric::xyzVector< class >::length_squared(), core::conformation::Residue::nbr_atom_xyz(), core::pose::Pose::residue(), and core::conformation::Atom::xyz().

Referenced by residue_center_of_mass().

void protocols::membrane::geometry::split_topology_by_jump	(	Pose const &	pose,
		Size const	jumpnum,
		SpanningTopology const &	topo,
		Pose &	pose_up,
		Pose &	pose_down,
		SpanningTopology &	topo_up,
		SpanningTopology &	topo_down
	)

Splits the SpanningTopology object into two objects, depending on given jump number.

This is useful for calculating an embedding for parts of the structure: this can now easily be accomplished by creating two empty topology objects, call this function, and then use both topology objects and subposes to call compute_structure_based_membrane_embedding

References core::conformation::membrane::SpanningTopology::add_span(), end, nres_protein(), core::conformation::membrane::SpanningTopology::nspans(), partition_pose_by_jump(), core::conformation::membrane::SpanningTopology::show(), core::conformation::membrane::SpanningTopology::span(), protocols::loops::start, core::pose::Pose::total_residue(), and core::conformation::TR().

Referenced by protocols::membrane::FlipMover::apply().

Classes

Typedefs

Functions

Typedef Documentation

Function Documentation