core::membrane::geometry Namespace Reference

Classes
class	EmbeddingFactory
	Create an embedding definition from opts. More...
class	MembraneResidueFactory
	Class: MembraneResidueFactory Build an implicit definition of a membrane as a set of virtual residues representing the normal and center of the membrane and membrane embedding within the pose framework. More...

Typedefs
typedef utility::pointer::owning_ptr < EmbeddingFactory >	EmbeddingFactoryOP
typedef utility::pointer::owning_ptr < EmbeddingFactory const >	EmbeddingFactoryCOP
typedef utility::pointer::owining_ptr < MembraneResidueFactory >	MembraneResidueFactoryOP
typedef utility::pointer::owning_ptr < MembraneResidueFactory const >	MembraneResidueFactoryCOP

Functions
bool	virtual_rsd_equal (core::conformation::ResidueOP rsd1, core::conformation::ResidueOP rsd2)
	Virtual residue Equals. More...
core::Real	get_mpDepth (core::Vector normal, core::Vector center, core::conformation::Residue rsd)
	Get Residue Depth in Membrane. More...
bool	check_spanning (core::pose::Pose const &pose, core::Vector const &normal, core::Vector const &center, SpanningTopologyOP topology)
	Check Membrane Spanning. More...
numeric::xyzVector< core::Real >	center_of_mass (pose::Pose const &pose, int const start, int const stop)
	Center of Mass. More...
int	residue_center_of_mass (pose::Pose const &pose, int const start, int const stop)
	Residue Center of Mass. More...
int	return_nearest_residue (pose::Pose const &pose, int const begin, int const end, Vector center)
	Return nearest residue. More...

Typedef Documentation

typedef utility::pointer::owning_ptr< EmbeddingFactory const > core::membrane::geometry::EmbeddingFactoryCOP

typedef utility::pointer::owning_ptr< EmbeddingFactory > core::membrane::geometry::EmbeddingFactoryOP

typedef utility::pointer::owning_ptr< MembraneResidueFactory const > core::membrane::geometry::MembraneResidueFactoryCOP

typedef utility::pointer::owning_ptr< MembraneResidueFactory > core::membrane::geometry::MembraneResidueFactoryOP

Function Documentation

numeric::xyzVector< core::Real > core::membrane::geometry::center_of_mass	(	pose::Pose const &	pose,
		int const	start,
		int 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(), center(), center_of_mass(), core::conformation::Residue::is_protein(), core::conformation::Residue::nbr_atom_xyz(), core::pose::Pose::residue(), and core::conformation::Atom::xyz().

bool core::membrane::geometry::check_spanning	(	core::pose::Pose const &	pose,
		core::Vector const &	normal,
		core::Vector const &	center,
		SpanningTopologyOP	topology
	)

Check Membrane Spanning.

Check that caucluated membrane spanning respects new normal and center definitions

Exceptions

<none>

Note

Needs refactoring!!!

Check that caucluated membrane spanning respects new normal and center definitions

Exceptions

<none>

References core::conformation::Residue::atom(), dot(), j, core::pose::Pose::residue(), and core::conformation::Atom::xyz().

core::Real core::membrane::geometry::get_mpDepth	(	core::Vector	normal,
		core::Vector	center,
		core::conformation::Residue	rsd
	)

Get Residue Depth in Membrane.

Calculate the depth of a residue with respect to membrane players

Parameters

normal	provided normal vector to membrane
center	provided center point for embedding for membrane

Calculate the depth of a residue with respect to membrane players

Parameters

normal
center

References core::conformation::Residue::atom(), depth, dot(), xyz, and core::conformation::Atom::xyz().

int core::membrane::geometry::residue_center_of_mass	(	pose::Pose const &	pose,
		int const	start,
		int 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 center(), center_of_mass(), and return_nearest_residue().

int core::membrane::geometry::return_nearest_residue	(	pose::Pose const &	pose,
		int const	begin,
		int 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::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().

Referenced by residue_center_of_mass().

bool core::membrane::geometry::virtual_rsd_equal	(	core::conformation::ResidueOP	rsd1,
		core::conformation::ResidueOP	rsd2
	)

Virtual residue Equals.

Virtual residue Equals Custom equality method - Checks two virtual atoms are equal in typesets and cartesian coordinates.

Custom equality method - Checks two virtual atoms are equal in typesets and cartesian coordinates

Precondition: (Checked) Both residues are virtual residues

Parameters

rsd1	first atom to investigate
rsd2	second residue to investigate
fullatom	specifies if the atom typesef of the pose is fullatom

Returns

bool

Parameters

rsd1	first atom to investigate
rsd2	second residue to investigate

Returns

bool

References core::chemical::aa_vrt.