core::membrane::geometry Namespace Reference

Classes
class	Embedding
class	EmbeddingDef
	Embedding Setup Helper Class. More...

Typedefs
typedef utility::pointer::owning_ptr < Embedding >	EmbeddingOP
typedef utility::pointer::owning_ptr < Embedding const >	EmbeddingCOP
typedef utility::pointer::owning_ptr < EmbeddingDef >	EmbeddingDefOP
typedef utility::pointer::owning_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::PoseOP pose)
	Get z-coord and chainID. More...
void	membrane_normal_to_length_15 (pose::Pose &pose)
	Normalize normal vector to length 15 for visualization. More...

Typedef Documentation

typedef utility::pointer::owning_ptr< Embedding const > core::membrane::geometry::EmbeddingCOP

typedef utility::pointer::owning_ptr< EmbeddingDef const > core::membrane::geometry::EmbeddingDefCOP

typedef utility::pointer::owning_ptr< EmbeddingDef > core::membrane::geometry::EmbeddingDefOP

typedef utility::pointer::owning_ptr< Embedding > core::membrane::geometry::EmbeddingOP

Function Documentation

numeric::xyzVector< core::Real > core::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, center_of_mass(), core::conformation::Residue::is_protein(), core::conformation::Residue::nbr_atom_xyz(), core::pose::Pose::residue(), and core::conformation::Atom::xyz().

std::pair< utility::vector1< Real >, utility::vector1< Real > > core::membrane::geometry::get_chain_and_z

(

pose::PoseOP

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::TR.

void core::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::membrane::MembraneInfo::membrane_center(), core::conformation::Conformation::membrane_info(), core::conformation::membrane::MembraneInfo::membrane_normal(), core::conformation::membrane::normal, numeric::xyzVector< class >::normalize(), and core::conformation::Conformation::update_membrane_position().

core::SSize core::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 core::pose::return_nearest_residue().

core::SSize core::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::sequence::end, 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().