Namespaces
	geometry

	io

	symmetry

	visualize

Classes
class	AddMembraneMover
	Add Membrane components to the pose, sets up MembraneInfo object includes: spanning topology, lips info, embeddings, and a membrane virtual residue describing the membrane position. More...

class	AddMembraneMoverCreator
	Mover Creator. More...

class	FlipMover
	Takes a pose and flips the downstream partner around the axis between the COMs of the partners, projected into the membrane plane. CAUTION: THIS MOVER ONLY WORKS FOR A FIXED MEMBRANE WHERE THE MEMBRANE VIRTUAL RESIDUE IS AT THE ROOT OF THE FOLDTREE!!! More...

class	FlipMoverCreator
	Mover Creator. More...

class	MembranePositionFromTopologyMover
	Compute the initial position of the membrane based upon sequence or structure. More...

class	MembranePositionFromTopologyMoverCreator
	Mover Creator. More...

class	RandomPositionRotationMover
	Random Position Rotation Move. More...

class	RandomPositionTranslationMover
	Random Position Translation Move. More...

class	RotationMover
	Rotates the pose such that a vector in the old orientation will be overlayed in the new orientation. Requires two vectors (old and new) and a point on the new vector around which the rotation takes place. The mover is a general mover but used mainly on membrane proteins. For membrane proteins, the two vectors will be the old and new normal and the point will be the new center. The default jump is going to be the membrane jump, but you can also specify your own. The rotation happens around the axis perpendicular to both vectors with an angle enclosed by both vectors. More...

class	RotationMoverCreator
	Mover Creator. More...

class	SetMembraneCenterMover
	Membrane Position Translation Move. More...

class	SetMembraneCenterMoverCreator
	Mover Creator for membrane translation mover. More...

class	SetMembraneNormalMover
	Membrane Position Rotation Move. More...

class	SetMembraneNormalMoverCreator
	Mover creator for membrane rotation mover. More...

class	SetMembranePositionMover
	Membrane Position Translation-Rotation Mover. More...

class	SetMembranePositionMoverCreator
	Mover Creator for composed RT mover. More...

class	TransformIntoMembraneMover
	Takes a pose, calculates the best possible center and normal from the topology object (through spanfile from OCTOPUS) and the coordinates of the pose CAUTION: THIS MOVER ONLY WORKS FOR A FIXED MEMBRANE WHERE THE MEMBRANE VIRTUAL RESIDUE IS AT THE ROOT OF THE FOLDTREE!!! More...

class	TransformIntoMembraneMoverCreator
	Mover Creator. More...

class	TranslationMover
	Translation vector can be defined in -mp:setup center flag to translate the new pose to. The mover is a general mover but used mainly on membrane proteins, that's why we use this flag here The default jump is going to be the membrane jump, but you can also specify your own. More...

class	TranslationMoverCreator
	Mover Creator. More...

class	TranslationRotationMover
	Translation and Rotation of a pose. The new position can be defined by the -mp:setup center and normal flags. The mover is a general mover, but used mainly on membrane proteins, that's why we use this flag here. The default jump is going to be the membrane jump, but you can also specify your own. See above for the TranslationMover and the RotationMover. More...

class	TranslationRotationMoverCreator
	Mover Creator. More...

Typedefs
typedef utility::pointer::shared_ptr < AddMembraneMover >	AddMembraneMoverOP

typedef utility::pointer::shared_ptr < AddMembraneMover const >	AddMembraneMoverCOP

typedef utility::pointer::shared_ptr < FlipMover >	FlipMoverOP

typedef utility::pointer::shared_ptr < FlipMover const >	FlipMoverCOP

typedef utility::pointer::shared_ptr < MembranePositionFromTopologyMover >	MembranePositionFromTopologyMoverOP

typedef utility::pointer::shared_ptr < MembranePositionFromTopologyMover const >	MembranePositionFromTopologyMoverCOP

typedef utility::pointer::shared_ptr < RandomPositionRotationMover >	RandomPositionRotationMoverOP

typedef utility::pointer::shared_ptr < RandomPositionRotationMover const >	RandomPositionRotationMoverCOP

typedef utility::pointer::shared_ptr < RandomPositionTranslationMover >	RandomPositionTranslationMoverOP

typedef utility::pointer::shared_ptr < RandomPositionTranslationMover const >	RandomPositionTranslationMoverCOP

typedef utility::pointer::shared_ptr < SetMembranePositionMover >	SetMembranePositionMoverOP

typedef utility::pointer::shared_ptr < SetMembranePositionMover const >	SetMembranePositionMoverCOP

typedef utility::pointer::shared_ptr < SetMembraneNormalMover >	SetMembraneNormalMoverOP

typedef utility::pointer::shared_ptr < SetMembraneNormalMover const >	SetMembraneNormalMoverCOP

typedef utility::pointer::shared_ptr < SetMembraneCenterMover >	SetMembraneCenterMoverOP

typedef utility::pointer::shared_ptr < SetMembraneCenterMover const >	SetMembraneCenterMoverCOP

typedef utility::pointer::shared_ptr < TransformIntoMembraneMover >	TransformIntoMembraneMoverOP

typedef utility::pointer::shared_ptr < TransformIntoMembraneMover const >	TransformIntoMembraneMoverCOP

typedef utility::pointer::shared_ptr < TranslationMover >	TranslationMoverOP

typedef utility::pointer::shared_ptr < TranslationMover const >	TranslationMoverCOP

typedef utility::pointer::shared_ptr < RotationMover >	RotationMoverOP

typedef utility::pointer::shared_ptr < RotationMover const >	RotationMoverCOP

typedef utility::pointer::shared_ptr < TranslationRotationMover >	TranslationRotationMoverOP

typedef utility::pointer::shared_ptr < TranslationRotationMover const >	TranslationRotationMoverCOP

Functions
core::Real	mem_bb_rmsd_no_super (Pose &native_pose, Pose &pose)
	Compute No Super Membrane RMSD. More...

core::Real	mem_all_atom_rmsd_no_super (Pose &native_pose, Pose &pose)
	Compute No Super Membrane RMSD - all atom without super. More...

core::Real	mem_bb_rmsd_with_super (Pose &native_pose, Pose &pose)
	Compute Membrane RMSD. More...

core::Real	mem_all_atom_rmsd_with_super (Pose &native_pose, Pose &pose)
	Compute Membrane RMSD - all atom with superposiiton. More...

Typedef Documentation

typedef utility::pointer::shared_ptr< AddMembraneMover const > protocols::membrane::AddMembraneMoverCOP

typedef utility::pointer::shared_ptr< AddMembraneMover > protocols::membrane::AddMembraneMoverOP

typedef utility::pointer::shared_ptr< FlipMover const > protocols::membrane::FlipMoverCOP

typedef utility::pointer::shared_ptr< FlipMover > protocols::membrane::FlipMoverOP

typedef utility::pointer::shared_ptr< MembranePositionFromTopologyMover const > protocols::membrane::MembranePositionFromTopologyMoverCOP

typedef utility::pointer::shared_ptr< MembranePositionFromTopologyMover > protocols::membrane::MembranePositionFromTopologyMoverOP

typedef utility::pointer::shared_ptr< RandomPositionRotationMover const > protocols::membrane::RandomPositionRotationMoverCOP

typedef utility::pointer::shared_ptr< RandomPositionRotationMover > protocols::membrane::RandomPositionRotationMoverOP

typedef utility::pointer::shared_ptr< RandomPositionTranslationMover const > protocols::membrane::RandomPositionTranslationMoverCOP

typedef utility::pointer::shared_ptr< RandomPositionTranslationMover > protocols::membrane::RandomPositionTranslationMoverOP

typedef utility::pointer::shared_ptr< RotationMover const > protocols::membrane::RotationMoverCOP

typedef utility::pointer::shared_ptr< RotationMover > protocols::membrane::RotationMoverOP

typedef utility::pointer::shared_ptr< SetMembraneCenterMover const > protocols::membrane::SetMembraneCenterMoverCOP

typedef utility::pointer::shared_ptr< SetMembraneCenterMover > protocols::membrane::SetMembraneCenterMoverOP

typedef utility::pointer::shared_ptr< SetMembraneNormalMover const > protocols::membrane::SetMembraneNormalMoverCOP

typedef utility::pointer::shared_ptr< SetMembraneNormalMover > protocols::membrane::SetMembraneNormalMoverOP

typedef utility::pointer::shared_ptr< SetMembranePositionMover const > protocols::membrane::SetMembranePositionMoverCOP

typedef utility::pointer::shared_ptr< SetMembranePositionMover > protocols::membrane::SetMembranePositionMoverOP

typedef utility::pointer::shared_ptr< TransformIntoMembraneMover const > protocols::membrane::TransformIntoMembraneMoverCOP

typedef utility::pointer::shared_ptr< TransformIntoMembraneMover > protocols::membrane::TransformIntoMembraneMoverOP

typedef utility::pointer::shared_ptr< TranslationMover const > protocols::membrane::TranslationMoverCOP

typedef utility::pointer::shared_ptr< TranslationMover > protocols::membrane::TranslationMoverOP

typedef utility::pointer::shared_ptr< TranslationRotationMover const > protocols::membrane::TranslationRotationMoverCOP

typedef utility::pointer::shared_ptr< TranslationRotationMover > protocols::membrane::TranslationRotationMoverOP

Function Documentation

core::Real protocols::membrane::mem_all_atom_rmsd_no_super	(	Pose &	native_pose,
		Pose &	pose
	)

Compute No Super Membrane RMSD - all atom without super.

Compute the root mean squared deviation of the backbone atoms between in the transmembrane spanning regions of a membrane protein

Exceptions

If	not a membrane protein

References core::pose::Pose::conformation(), is_heavyatom(), core::conformation::Conformation::is_membrane(), core::conformation::Conformation::membrane_info(), rmsd_no_super_subset(), core::pose::Pose::total_residue(), and utility_exit_with_message.

core::Real protocols::membrane::mem_all_atom_rmsd_with_super	(	Pose &	native_pose,
		Pose &	pose
	)

Compute Membrane RMSD - all atom with superposiiton.

Compute the root mean squared deviation of the backbone atoms between in the transmembrane spanning regions of a membrane protein

References core::pose::Pose::conformation(), is_heavyatom(), core::conformation::Conformation::is_membrane(), core::conformation::Conformation::membrane_info(), rmsd_with_super_subset(), core::pose::Pose::total_residue(), and utility_exit_with_message.

core::Real protocols::membrane::mem_bb_rmsd_no_super	(	Pose &	native_pose,
		Pose &	pose
	)

Compute No Super Membrane RMSD.

Compute the root mean squared deviation of the backbone atoms between in the transmembrane spanning regions of a membrane protein

Exceptions

If	not a membrane protein

References core::pose::Pose::conformation(), core::conformation::Conformation::is_membrane(), is_protein_backbone(), core::conformation::Conformation::membrane_info(), rmsd_no_super_subset(), core::pose::Pose::total_residue(), and utility_exit_with_message.

core::Real protocols::membrane::mem_bb_rmsd_with_super	(	Pose &	native_pose,
		Pose &	pose
	)

Compute Membrane RMSD.

Compute the root mean squared deviation of the backbone atoms between in the transmembrane spanning regions of a membrane protein

References core::pose::Pose::conformation(), core::conformation::Conformation::is_membrane(), is_protein_backbone(), core::conformation::Conformation::membrane_info(), rmsd_with_super_subset(), core::pose::Pose::total_residue(), and utility_exit_with_message.

Namespaces

Classes

Typedefs

Functions

Typedef Documentation

Function Documentation