core::conformation::membrane Namespace Reference

Namespaces
	membrane_geometry

Classes
class	AqueousPoreParameters
	A class for defining an aqueous pore. More...
class	EXCN_Membrane
	Parent Exception - Exception Membrane. More...
class	EXCN_Resource_Definition
	Resource Manager Exception. More...
class	EXCN_Illegal_Arguments
class	EXCN_Membrane_Bounds
	Membrane Out of Bounds Exception. More...
class	EXCN_VirtualRsd
	Virtual Residue Definition Exception. More...
class	EXCN_NonMembrane
	Non Membrane Pose Exception. More...
class	EXCN_MembraneFoldTree
	Fold tree Exception for membrane proteins. More...
class	ImplicitLipidInfo
	Definition of an implicit membrane with parameters for different lipid compositions. More...
class	MembraneGeometry
	Data describing the geometry of the membrane. More...
class	MembraneInfo
	Data describing the relationship between protein(s) and a membrane environment. More...
class	Span
class	SpanningTopology

Typedefs
typedef utility::vector1< numeric::CubicPolynomial >	piecewise_poly
typedef utility::pointer::shared_ptr< AqueousPoreParameters >	AqueousPoreParametersOP
typedef utility::pointer::shared_ptr< AqueousPoreParameters const >	AqueousPoreParametersCOP
typedef utility::pointer::shared_ptr< ImplicitLipidInfo >	ImplicitLipidInfoOP
typedef utility::pointer::shared_ptr< ImplicitLipidInfo const >	ImplicitLipidInfoCOP
typedef utility::pointer::shared_ptr< MembraneGeometry >	MembraneGeometryOP
typedef utility::pointer::shared_ptr< MembraneGeometry const >	MembraneGeometryCOP
typedef utility::pointer::shared_ptr< MembraneInfo >	MembraneInfoOP
typedef utility::pointer::shared_ptr< MembraneInfo const >	MembraneInfoCOP
typedef utility::pointer::shared_ptr< Span >	SpanOP
typedef utility::pointer::shared_ptr< Span const >	SpanCOP
typedef utility::pointer::shared_ptr< SpanningTopology >	SpanningTopologyOP
typedef utility::pointer::shared_ptr< SpanningTopology const >	SpanningTopologyCOP

Enumerations
enum class	MP_GEOMETRY_TRANSITION { SLAB = 1 , BICELLE = 2 , VESICLE = 3 , DOUBLE_VESICLE = 4 }
enum	MEM { thickness = 1 , center = 2 , normal = 3 }
enum	Orientation { in = 1 , out = 2 }
	Define the orientation of a secondary structure span relative to the membrane. More...

Functions
std::ostream &	operator<< (std::ostream &os, MembraneInfo const &mem_info)
	Show MembraneInfo method for pyrosetta. More...
std::ostream &	operator<< (std::ostream &os, SpanningTopology const &spans)
	Show Spanning topology. More...
utility::vector1< std::string >	spanfile_names ()
std::string	spanfile_name ()

Typedef Documentation

AqueousPoreParametersCOP

typedef utility::pointer::shared_ptr< AqueousPoreParameters const > core::conformation::membrane::AqueousPoreParametersCOP

AqueousPoreParametersOP

typedef utility::pointer::shared_ptr< AqueousPoreParameters > core::conformation::membrane::AqueousPoreParametersOP

ImplicitLipidInfoCOP

typedef utility::pointer::shared_ptr< ImplicitLipidInfo const > core::conformation::membrane::ImplicitLipidInfoCOP

ImplicitLipidInfoOP

typedef utility::pointer::shared_ptr< ImplicitLipidInfo > core::conformation::membrane::ImplicitLipidInfoOP

MembraneGeometryCOP

typedef utility::pointer::shared_ptr< MembraneGeometry const > core::conformation::membrane::MembraneGeometryCOP

MembraneGeometryOP

typedef utility::pointer::shared_ptr< MembraneGeometry > core::conformation::membrane::MembraneGeometryOP

MembraneInfoCOP

typedef utility::pointer::shared_ptr< MembraneInfo const > core::conformation::membrane::MembraneInfoCOP

MembraneInfoOP

typedef utility::pointer::shared_ptr< MembraneInfo > core::conformation::membrane::MembraneInfoOP

piecewise_poly

typedef utility::vector1< numeric::CubicPolynomial > core::conformation::membrane::piecewise_poly

SpanCOP

typedef utility::pointer::shared_ptr< Span const > core::conformation::membrane::SpanCOP

SpanningTopologyCOP

typedef utility::pointer::shared_ptr< SpanningTopology const > core::conformation::membrane::SpanningTopologyCOP

SpanningTopologyOP

typedef utility::pointer::shared_ptr< SpanningTopology > core::conformation::membrane::SpanningTopologyOP

SpanOP

typedef utility::pointer::shared_ptr< Span > core::conformation::membrane::SpanOP

Enumeration Type Documentation

MEM

enum core::conformation::membrane::MEM

Enumerator
thickness
center
normal

MP_GEOMETRY_TRANSITION

enum core::conformation::membrane::MP_GEOMETRY_TRANSITION

strong

Enumerator
SLAB
BICELLE
VESICLE
DOUBLE_VESICLE

Orientation

enum core::conformation::membrane::Orientation

Define the orientation of a secondary structure span relative to the membrane.

Enumerator
in
out

Function Documentation

operator<<() [1/2]

std::ostream & core::conformation::membrane::operator<<	(	std::ostream &	os,
		MembraneInfo const &	mem_info
	)

Show MembraneInfo method for pyrosetta.

References core::conformation::membrane::MembraneInfo::membrane_rsd_num(), and core::conformation::membrane::MembraneInfo::spanning_topology().

operator<<() [2/2]

std::ostream & core::conformation::membrane::operator<<	(	std::ostream &	os,
		SpanningTopology const &	spans
	)

Show Spanning topology.

For PyRosetta!

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

spanfile_name()

std::string core::conformation::membrane::spanfile_name

(

)

References spanfile_names().

spanfile_names()

utility::vector1< std::string > core::conformation::membrane::spanfile_names

(

)

Referenced by protocols::docking::membrane::MPDockingSetupMover::read_spanfiles(), and spanfile_name().