Namespaces
	benchmark

	geometry

	scoring

	symmetry

	visualize

Classes
struct	SpanInfo
	A utility class to store deferred parse span information. More...

class	AddMembraneMover
	Initialize the RosettaMP framework by adding representations of the membrane. More...

class	AddMembraneMoverCreator
	Mover Creator. More...

class	AddMembraneSpanConstraint

class	AddMembraneSpanConstraintCreator
	Mover Creator. More...

class	AddMembraneSpanTermZConstraint

class	AddMembraneSpanTermZConstraintCreator
	Mover Creator. More...

class	AddMPLigandMover
	Add Membrane protein ligand mover. More...

class	AddMPLigandMoverCreator
	Mover Creator. More...

class	AqueousPoreFinder
	Compute the center, major axis and minor axis of an ellipsoidal aqueous pore. More...

class	AqueousPoreFinderCreator

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	MPLipidAccessibility
	Mover that computes which residues are lipid accessible and puts that information into the B-factors: 50 is lipid accessible, 0 is lipid INaccessible. More...

class	MPLipidAccessibilityCreator

class	MPQuickRelaxMover

class	MPQuickRelaxMoverCreator
	Mover Creator. More...

class	OptimizeMembranePositionMover

class	OptimizeMembranePositionMoverCreator
	Mover Creator. More...

class	OptimizeProteinEmbeddingMover

class	OptimizeProteinEmbeddingMoverCreator
	Mover Creator. More...

class	RandomPositionRotationMover
	Random Position Rotation Move. More...

class	RandomPositionTranslationMover
	Random Position Translation Move. More...

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

class	SetMembraneNormalMover
	Membrane Position Rotation Move. More...

class	SetMembraneCenterMover
	Membrane Position Translation Move. More...

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

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

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

class	SpinAroundPartnerMover

class	SpinAroundPartnerMoverCreator
	Mover Creator. More...

class	TiltMover
	Tilts the downstream partner along the axis between the COMs of the partners. More...

class	TiltMoverCreator
	Mover Creator. More...

class	TransformIntoMembraneMover
	Transform a pose into membrane coordinates based on the current embedding of the protein. 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	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	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	TranslationMoverCreator
	Mover Creator. More...

class	RotationMoverCreator
	Mover Creator. More...

class	TranslationRotationMoverCreator
	Mover Creator. More...

class	HelixFromSequence
	Generates a (transmembrane) helix from a fasta file containing the sequence. More...

class	HelixFromSequenceCreator

class	MPMutateRelaxMover

class	MPMutateRelaxMoverCreator
	Mover Creator. More...

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

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

typedef utility::pointer::shared_ptr< AddMembraneSpanConstraint >	AddMembraneSpanConstraintOP

typedef utility::pointer::shared_ptr< AddMembraneSpanConstraint const >	AddMembraneSpanConstraintCOP

typedef utility::pointer::shared_ptr< AddMembraneSpanTermZConstraint >	AddMembraneSpanTermZConstraintOP

typedef utility::pointer::shared_ptr< AddMembraneSpanTermZConstraint const >	AddMembraneSpanTermZConstraintCOP

typedef utility::pointer::shared_ptr< AddMPLigandMover >	AddMPLigandMoverOP

typedef utility::pointer::shared_ptr< AddMPLigandMover const >	AddMPLigandMoverCOP

typedef utility::pointer::shared_ptr< AqueousPoreFinder >	AqueousPoreFinderOP

typedef utility::pointer::shared_ptr< AqueousPoreFinder const >	AqueousPoreFinderCOP

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< MPLipidAccessibility >	MPLipidAccessibilityOP

typedef utility::pointer::shared_ptr< MPLipidAccessibility const >	MPLipidAccessibilityCOP

typedef utility::pointer::shared_ptr< MPQuickRelaxMover >	MPQuickRelaxMoverOP

typedef utility::pointer::shared_ptr< MPQuickRelaxMover const >	MPQuickRelaxMoverCOP

typedef utility::pointer::shared_ptr< OptimizeMembranePositionMover >	OptimizeMembranePositionMoverOP

typedef utility::pointer::shared_ptr< OptimizeMembranePositionMover const >	OptimizeMembranePositionMoverCOP

typedef utility::pointer::shared_ptr< OptimizeProteinEmbeddingMover >	OptimizeProteinEmbeddingMoverOP

typedef utility::pointer::shared_ptr< OptimizeProteinEmbeddingMover const >	OptimizeProteinEmbeddingMoverCOP

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< SpinAroundPartnerMover >	SpinAroundPartnerMoverOP

typedef utility::pointer::shared_ptr< SpinAroundPartnerMover const >	SpinAroundPartnerMoverCOP

typedef utility::pointer::shared_ptr< TiltMover >	TiltMoverOP

typedef utility::pointer::shared_ptr< TiltMover const >	TiltMoverCOP

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

typedef utility::pointer::shared_ptr< HelixFromSequence >	HelixFromSequenceOP

typedef utility::pointer::shared_ptr< HelixFromSequence const >	HelixFromSequenceCOP

typedef utility::pointer::shared_ptr< MPMutateRelaxMover >	MPMutateRelaxMoverOP

typedef utility::pointer::shared_ptr< MPMutateRelaxMover const >	MPMutateRelaxMoverCOP

Functions
std::ostream &	operator<< (std::ostream &os, AqueousPoreFinder const &mover)

bool	check_orientation (core::pose::Pose &pose, core::Size span_no)
	Check if the orientation of the TM span matches the orientation of the span in the pose. More...

core::Real	mem_bb_rmsd_no_super (core::pose::Pose &native_pose, core::pose::Pose &pose)
	Compute backbone RMSD between TM regions - don't superimpose. More...

core::Real	mem_all_atom_rmsd_no_super (core::pose::Pose &native_pose, core::pose::Pose &pose)
	Compute all-atom RMSD between TM regions - don't superimpose. More...

core::Real	mem_bb_rmsd_with_super (core::pose::Pose &native_pose, core::pose::Pose &pose)
	Compute backbone RMSD between TM regions - do superimpose. More...

core::Real	mem_all_atom_rmsd_with_super (core::pose::Pose &native_pose, core::pose::Pose &pose)
	Compute all-atom RMSD between TM regions - do superimpose. More...

core::Real	calc_helix_tilt_angle (core::pose::Pose &pose, core::Size span_no)
	Calculate tilt of a TM span relative to the membrane normal. More...

core::Vector	calc_helix_axis (core::pose::Pose &pose, core::Size span_no)
	Determine the axis used to define a single TM Helix. More...

core::Vector	com (core::Vector a, core::Vector b, core::Vector c)
	Calculate center of mass between 3 xyz coords. More...

core::Real	calc_angle_rmsd (core::Real measured_angle, core::Real ref_angle)
	Calculate the RMSD between a helix tilt angle & reference. More...

utility::vector1< core::Real >	pose_tilt_angle_and_center_distance (core::pose::Pose &pose)
	Calculate tilt angle and distance from membrane center. More...

bool	is_membrane_fixed (core::pose::Pose &pose)
	Determine whether the membrane is modeled as fixed. More...

bool	is_membrane_moveable_by_itself (core::pose::Pose &pose)
	Determine whether membrane can move on its own. More...

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

core::Size	create_membrane_docking_foldtree_from_partners (core::pose::Pose &pose, std::string const &partners)
	Create a membrane foldtree with an interface. More...

core::Size	create_membrane_foldtree_anchor_com (core::pose::Pose &pose)
	Create membrane foldtree from scratch. More...

core::Size	create_membrane_foldtree_anchor_tmcom (core::pose::Pose &pose)
	Create membrane foldtree from scratch. More...

core::Size	create_membrane_foldtree_anchor_pose_tmcom (core::pose::Pose &pose)
	Create membrane foldtree from scratch. More...

utility::vector1< core::Size >	create_membrane_multi_partner_foldtree_anchor_tmcom (core::pose::Pose &pose, std::string partner)
	Create foldtree for multiple docking partners. More...

void	create_membrane_foldtree_from_anchors (core::pose::Pose &pose, utility::vector1< core::Size > anchors)
	Helper function to create membrane foldtrees. More...

core::Size	create_specific_membrane_foldtree (core::pose::Pose &pose, utility::vector1< core::Vector > anchors)
	Helper function to create a specific membrane foldtree. More...

utility::vector1< core::Size >	get_anchor_points_for_tmcom (core::pose::Pose &pose)
	Helper function to create membrane foldtrees. More...

core::Size	setup_foldtree_pose_com (core::pose::Pose &pose)
	Setup foldtree from scratch. More...

void	setup_foldtree_from_anchors (core::pose::Pose &pose, utility::vector1< core::Size > anchors)
	Helper function to setup foldtrees. More...

std::pair< utility::vector1< core::Real >, utility::vector1< core::Real > >	get_chain_and_z (core::pose::Pose const &pose)
	Grab the z-coordinates and chainIDs from the entire pose. More...

utility::vector1< char >	get_secstruct (core::pose::Pose &pose)
	Get dssp defined secondary structure from the pose. More...

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

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

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

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

protocols::membrane::geometry::EmbeddingOP	compute_embeddings_by_chain (core::pose::Pose const &pose)
	Compute embedding by chain. More...

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

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

void	update_partner_embeddings (core::pose::Pose const &pose, core::Size const jumpnum, protocols::membrane::geometry::EmbeddingDef &emb_up, protocols::membrane::geometry::EmbeddingDef &emb_down)
	Update embedding of the partners after a move. More...

core::Vector	pose_tm_com (core::pose::Pose const &pose)
	Pose transmembrane center-of-mass. More...

core::Vector	chain_com (core::pose::Pose const &pose, core::Size chainid)
	Chain center-of-mass. More...

core::Vector	chain_tm_com (core::pose::Pose const &pose, core::Size chain)
	Chain center-of-mass of TM regions. More...

core::Size	rsd_closest_to_pose_tm_com (core::pose::Pose const &pose)
	Residue closest to pose transmembrane center-of-mass. More...

core::Size	rsd_closest_to_chain_com (core::pose::Pose const &pose, core::Size chainid)
	Residue closest to chain center-of-mass. More...

core::Size	rsd_closest_to_chain_tm_com (core::pose::Pose const &pose, core::Size chainid)
	Residue closest to chain TM center-of-mass. More...

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

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

core::Vector const	membrane_axis (core::pose::Pose &pose, int jumpnum)
	Calculates translation axis lying in the membrane (= projection axis between embedding centers) More...

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

void	split_topology_by_jump_noshift (core::pose::Pose const &pose, core::Size const jumpnum, core::conformation::membrane::SpanningTopologyOP topo, core::conformation::membrane::SpanningTopologyOP topo_up, core::conformation::membrane::SpanningTopologyOP topo_down)
	Splits the SpanningTopology object into two objects, depending on given jump number. More...

utility::vector1< core::conformation::membrane::SpanningTopologyOP >	split_topology_by_chain_noshift (core::pose::Pose const &pose, core::conformation::membrane::SpanningTopologyOP const topo)
	Split topology by chain. More...

void	read_center_normal_from_tag (core::Vector &center, core::Vector &normal, utility::tag::TagCOP tag)
	Read in a user provided center/normal pair from RosettaScripts. More...

void	read_center_normal_from_cmd (core::Vector &center, core::Vector &normal)
	Read in a user provided center/normal pair from the commandline, safetly. More...

std::ostream &	operator<< (std::ostream &os, HelixFromSequence const &mover)

Typedef Documentation

◆ AddMembraneMoverCOP

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

◆ AddMembraneMoverOP

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

◆ AddMembraneSpanConstraintCOP

typedef utility::pointer::shared_ptr< AddMembraneSpanConstraint const > protocols::membrane::AddMembraneSpanConstraintCOP

◆ AddMembraneSpanConstraintOP

typedef utility::pointer::shared_ptr< AddMembraneSpanConstraint > protocols::membrane::AddMembraneSpanConstraintOP

◆ AddMembraneSpanTermZConstraintCOP

typedef utility::pointer::shared_ptr< AddMembraneSpanTermZConstraint const > protocols::membrane::AddMembraneSpanTermZConstraintCOP

◆ AddMembraneSpanTermZConstraintOP

typedef utility::pointer::shared_ptr< AddMembraneSpanTermZConstraint > protocols::membrane::AddMembraneSpanTermZConstraintOP

◆ AddMPLigandMoverCOP

typedef utility::pointer::shared_ptr< AddMPLigandMover const > protocols::membrane::AddMPLigandMoverCOP

◆ AddMPLigandMoverOP

typedef utility::pointer::shared_ptr< AddMPLigandMover > protocols::membrane::AddMPLigandMoverOP

◆ AqueousPoreFinderCOP

typedef utility::pointer::shared_ptr< AqueousPoreFinder const > protocols::membrane::AqueousPoreFinderCOP

◆ AqueousPoreFinderOP

typedef utility::pointer::shared_ptr< AqueousPoreFinder > protocols::membrane::AqueousPoreFinderOP

◆ FlipMoverCOP

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

◆ FlipMoverOP

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

◆ HelixFromSequenceCOP

typedef utility::pointer::shared_ptr< HelixFromSequence const > protocols::membrane::HelixFromSequenceCOP

◆ HelixFromSequenceOP

typedef utility::pointer::shared_ptr< HelixFromSequence > protocols::membrane::HelixFromSequenceOP

◆ MembranePositionFromTopologyMoverCOP

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

◆ MembranePositionFromTopologyMoverOP

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

◆ MPLipidAccessibilityCOP

typedef utility::pointer::shared_ptr< MPLipidAccessibility const > protocols::membrane::MPLipidAccessibilityCOP

◆ MPLipidAccessibilityOP

typedef utility::pointer::shared_ptr< MPLipidAccessibility > protocols::membrane::MPLipidAccessibilityOP

◆ MPMutateRelaxMoverCOP

typedef utility::pointer::shared_ptr< MPMutateRelaxMover const > protocols::membrane::MPMutateRelaxMoverCOP

◆ MPMutateRelaxMoverOP

typedef utility::pointer::shared_ptr< MPMutateRelaxMover > protocols::membrane::MPMutateRelaxMoverOP

◆ MPQuickRelaxMoverCOP

typedef utility::pointer::shared_ptr< MPQuickRelaxMover const > protocols::membrane::MPQuickRelaxMoverCOP

◆ MPQuickRelaxMoverOP

typedef utility::pointer::shared_ptr< MPQuickRelaxMover > protocols::membrane::MPQuickRelaxMoverOP

◆ OptimizeMembranePositionMoverCOP

typedef utility::pointer::shared_ptr< OptimizeMembranePositionMover const > protocols::membrane::OptimizeMembranePositionMoverCOP

◆ OptimizeMembranePositionMoverOP

typedef utility::pointer::shared_ptr< OptimizeMembranePositionMover > protocols::membrane::OptimizeMembranePositionMoverOP

◆ OptimizeProteinEmbeddingMoverCOP

typedef utility::pointer::shared_ptr< OptimizeProteinEmbeddingMover const > protocols::membrane::OptimizeProteinEmbeddingMoverCOP

◆ OptimizeProteinEmbeddingMoverOP

typedef utility::pointer::shared_ptr< OptimizeProteinEmbeddingMover > protocols::membrane::OptimizeProteinEmbeddingMoverOP

◆ RandomPositionRotationMoverCOP

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

◆ RandomPositionRotationMoverOP

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

◆ RandomPositionTranslationMoverCOP

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

◆ RandomPositionTranslationMoverOP

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

◆ RotationMoverCOP

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

◆ RotationMoverOP

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

◆ SetMembraneCenterMoverCOP

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

◆ SetMembraneCenterMoverOP

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

◆ SetMembraneNormalMoverCOP

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

◆ SetMembraneNormalMoverOP

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

◆ SetMembranePositionMoverCOP

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

◆ SetMembranePositionMoverOP

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

◆ SpinAroundPartnerMoverCOP

typedef utility::pointer::shared_ptr< SpinAroundPartnerMover const > protocols::membrane::SpinAroundPartnerMoverCOP

◆ SpinAroundPartnerMoverOP

typedef utility::pointer::shared_ptr< SpinAroundPartnerMover > protocols::membrane::SpinAroundPartnerMoverOP

◆ TiltMoverCOP

typedef utility::pointer::shared_ptr< TiltMover const > protocols::membrane::TiltMoverCOP

◆ TiltMoverOP

typedef utility::pointer::shared_ptr< TiltMover > protocols::membrane::TiltMoverOP

◆ TransformIntoMembraneMoverCOP

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

◆ TransformIntoMembraneMoverOP

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

◆ TranslationMoverCOP

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

◆ TranslationMoverOP

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

◆ TranslationRotationMoverCOP

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

◆ TranslationRotationMoverOP

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

Function Documentation

◆ average_antiparallel_embeddings()

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

Average EmbeddingDefs after first inverting some vectors accounting for topology.

Get average center and normal from a vector of EmbeddingDefs

References core::conformation::membrane::center, core::conformation::membrane::normal, and protocols::TR().

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

◆ average_embeddings()

protocols::membrane::geometry::EmbeddingDefOP protocols::membrane::average_embeddings ( utility::vector1< protocols::membrane::geometry::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, and core::conformation::membrane::normal.

Referenced by protocols::membrane::geometry::Embedding::add_span_embedding(), and protocols::membrane::geometry::Embedding::Embedding().

◆ calc_angle_rmsd()

core::Real protocols::membrane::calc_angle_rmsd	(	core::Real	measured_angle,
		core::Real	ref_angle
	)

Calculate the RMSD between a helix tilt angle & reference.

Given a reference angle and measured angle, calculate the root mean square deviation between the two single values. Takes the measured tilt angle and reference angle (typically from experiment)

References core::scoring::rms.

◆ calc_helix_axis()

core::Vector protocols::membrane::calc_helix_axis	(	core::pose::Pose &	pose,
		core::Size	span_no
	)

Determine the axis used to define a single TM Helix.

Using the COM of the helix start & end position, calculate a helix describing its geometry relative to the memrbane normal. Takes a pose & span number. Not a good approx for helices with kinks. TODO: CODE INSIDE SHOULD BE REPLACED WITH SPAN EMBEDDING CALCULATIONS! THAT'S WHAT THEY ARE THERE FOR! (JKLeman)

References core::conformation::Residue::atom(), com(), core::pose::Pose::membrane_info(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Atom::xyz().

Referenced by protocols::membrane::benchmark::SampleTiltAngles::apply(), calc_helix_tilt_angle(), and check_orientation().

◆ calc_helix_tilt_angle()

core::Real protocols::membrane::calc_helix_tilt_angle	(	core::pose::Pose &	pose,
		core::Size	span_no
	)

Calculate tilt of a TM span relative to the membrane normal.

Given a transmembrane span #, calculate the angle between the axis through the helix and the membrane normal. Works for relatively straight helices but less accurate for kinks. Takes a pose & span number

Given a transmembrane span #, calculate the angle between the axis through the helix and the membrane normal. Works for relatively straight helices but less accurate for kinks. Takes a pose & span number.

References calc_helix_axis(), core::pose::Pose::conformation(), core::pose::Pose::membrane_info(), and core::conformation::membrane::normal.

Referenced by protocols::membrane::benchmark::SampleTiltAngles::apply().

◆ chain_com()

core::Vector protocols::membrane::chain_com	(	core::pose::Pose const &	pose,
		core::Size	chainid
	)

Chain center-of-mass.

Gets the coordinates of the chain center-of-mass

References com(), core::pose::get_center_of_mass(), and core::pose::Pose::split_by_chain().

◆ chain_tm_com()

core::Vector protocols::membrane::chain_tm_com	(	core::pose::Pose const &	pose,
		core::Size	chain
	)

Chain center-of-mass of TM regions.

Gets the coordinates of the chain center-of-mass but only the TM regions BE AWARE THAT THE LAST CHAIN FOR MEMBRANE PROTEINS IS THE MEMBRANE RESIDUE!!!

Gets the coordinates of the chain center-of-mass but only the TM regions

References core::pose::Pose::chain(), com(), core::sequence::end, core::pose::get_center_of_mass(), core::pose::Pose::membrane_info(), protocols::magnesium::pdbslice(), core::pose::Pose::split_by_chain(), and split_topology_by_chain_noshift().

Referenced by rsd_closest_to_chain_tm_com().

◆ check_orientation()

bool protocols::membrane::check_orientation	(	core::pose::Pose &	pose,
		core::Size	span_no
	)

Check if the orientation of the TM span matches the orientation of the span in the pose.

References calc_helix_axis(), core::pose::Pose::conformation(), core::conformation::membrane::in, core::conformation::Conformation::membrane_info(), core::conformation::membrane::normal, and core::conformation::membrane::out.

◆ check_vector()

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

Check reasonable range of vector.

References protocols::TR().

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

◆ com()

core::Vector protocols::membrane::com	(	core::Vector	a,
		core::Vector	b,
		core::Vector	c
	)

Calculate center of mass between 3 xyz coords.

Given three xyz vectors, calculate the center of mass and return a vector. Helper method to calc_helix axis.

References core::pose::motif::a(), and protocols::match::upstream::b.

Referenced by protocols::hbnet::HBNet::apply(), protocols::rigid::RollMover::apply(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::apply(), protocols::electron_density::DockFragmentsIntoDensityMover::apply_multi(), protocols::simple_filters::ResidueDepthCalculator::bring_to_origin(), calc_helix_axis(), chain_com(), chain_tm_com(), protocols::constel::cnl_com(), protocols::forge::remodel::compute_center_of_mass(), protocols::membrane::MPLipidAccessibility::compute_slice_com(), protocols::cryst::MakeLayerMover::detect_connecting_subunits(), core::energy_methods::MPSpanAngleEnergy::find_helix_vector(), protocols::simple_filters::HelixHelixAngleFilter::find_helix_vector(), protocols::ligand_docking::ga_ligand_dock::get_atomic_contacting_sidechains(), protocols::ligand_docking::ga_ligand_dock::EntropyEstimator::get_contacting_reslist(), protocols::motif_grafting::movers::MotifMatch::get_homogeneous_transform_com_from_orig(), protocols::electron_density::get_radius(), protocols::electron_density::get_spectrum(), protocols::constraints_additional::BindingSiteConstraint::init(), protocols::constel::FilterByProxTerm::is_satisfied(), protocols::match::NumNeighborsMPM::passes_com_vector_criterion(), protocols::simple_moves::PeriodicBoxMover::perturb_molecule_move(), protocols::cryst::MakeLatticeMover::place_near_origin(), protocols::cryst::MakeLayerMover::place_near_origin(), pose_tm_com(), protocols::constraints_additional::BindingSiteConstraint::pre_align(), protocols::simple_moves::PeriodicBoxMover::recenter_pose(), rsd_closest_to_chain_tm_com(), rsd_closest_to_pose_tm_com(), protocols::electron_density::DockPDBIntoDensityMover::set_nRsteps_from_pose(), protocols::simple_moves::PeriodicBoxMover::setup_pose(), protocols::legacy_sewing::LegacyRepeatAssemblyMover::transform_segment_coords(), protocols::environment::CoMTrackerCM::update_com(), protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_conf(), and protocols::ligand_docking::ga_ligand_dock::LigandConformer::update_ligand_conf().

◆ compute_embeddings_by_chain()

protocols::membrane::geometry::EmbeddingOP protocols::membrane::compute_embeddings_by_chain ( core::pose::Pose const & pose )

Compute embedding by chain.

Compute embeddings by chain.

The embeddings can be computed either from pose and topology or they can be optimized differently; the function correlates each EmbeddingDef object in embeddings with a span object in the pose's topology

The embeddings can be computed either from pose and topology or they can be optimized differently; the function correlates each EmbeddingDef object in embeddings with a span object in the pose's topology; The bool means whether embeddings in Embedding object are antiparallel or not

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

◆ compute_structure_based_embedding() [1/4]

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

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

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

◆ compute_structure_based_embedding() [2/4]

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

Compute Membrane Center/Normal from Membrane Spanning topology.

References core::conformation::membrane::SpanningTopology::nspans(), and protocols::membrane::geometry::Embedding::total_embed().

◆ compute_structure_based_embedding() [3/4]

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

Compute Membrane Center/Normal from Membrane Spanning topology.

References core::conformation::membrane::center, and core::conformation::membrane::normal.

Referenced by protocols::membrane::benchmark::SampleTiltAngles::apply(), protocols::membrane::FlipMover::apply(), protocols::membrane::SpinAroundPartnerMover::apply(), protocols::membrane::TiltMover::apply(), protocols::membrane::TransformIntoMembraneMover::apply(), protocols::docking::membrane::QuickRelaxPartnersSeparately::apply(), protocols::membrane::MembranePositionFromTopologyMover::apply(), compute_embeddings_by_chain(), compute_structure_based_embedding(), pose_tilt_angle_and_center_distance(), protocols::qsar::scoring_grid::LipidMemGrid::refresh(), and update_partner_embeddings().

◆ compute_structure_based_embedding() [4/4]

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

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

References core::conformation::membrane::center, compute_structure_based_embedding(), core::pose::Pose::membrane_info(), and core::conformation::membrane::normal.

◆ create_membrane_docking_foldtree_from_partners()

core::Size protocols::membrane::create_membrane_docking_foldtree_from_partners	(	core::pose::Pose &	pose,
		std::string const &	partners
	)

Create a membrane foldtree with an interface.

Currently only works for two-body-docking. Both partners can have multiple chains in any order, the anchoring happens at the TM COM of each chain

__________________________________________

|________________ _________________ | |________ iJ ||________ | | | | || | | | ----— ----— ----— ----— ----— M=root chain1 chain2 chain3 chain4 ...

iJ = interface jump, will be returned from the function

Currently only works for two-body-docking. Both partners can have multiple chains in any order, the anchoring happens at the TM COM of each chain

__________________________________________

|________________ _________________ | |________ iJ ||________ | | | | || | | | ----— ----— ----— ----— ----— M=root chain1 chain2 chain3 chain4 ...

^-----------—^ ^--------------------—^ partner 1 partner 2

iJ = interface jump, will be returned from the function

References core::pose::chain_end_res(), core::pose::Pose::fold_tree(), core::pose::get_chain_id_from_chain(), core::pose::Pose::membrane_info(), core::kinematics::FoldTree::new_jump(), core::kinematics::FoldTree::reorder(), rsd_closest_to_chain_tm_com(), core::kinematics::FoldTree::show(), core::kinematics::FoldTree::simple_tree(), core::pose::Pose::size(), and protocols::TR().

Referenced by protocols::docking::DockingEnsemblePrepackProtocol::finalize_setup(), protocols::docking::DockingPrepackProtocol::finalize_setup(), and protocols::docking::membrane::MPFindInterfaceMover::finalize_setup().

◆ create_membrane_foldtree_anchor_com()

core::Size protocols::membrane::create_membrane_foldtree_anchor_com ( core::pose::Pose & pose )

Create membrane foldtree from scratch.

The foldtree is setup such that the membrane is at the root and anchored at the first chain COM residue with jumps from the first chain COM to each chain COM; requires the membrane to be present Returns the root anchoring point, i.e. rsd nearest chain COM of chain 1

|__________________________ | |_________________ | | |________ | | | | | | | | ----— ----— ----— ----— M=root chain1 chain2 chain3 chain4 ...

References core::pose::Pose::conformation(), create_membrane_foldtree_from_anchors(), core::pose::get_chains(), core::conformation::Conformation::is_membrane(), and rsd_closest_to_chain_com().

◆ create_membrane_foldtree_anchor_pose_tmcom()

core::Size protocols::membrane::create_membrane_foldtree_anchor_pose_tmcom ( core::pose::Pose & pose )

Create membrane foldtree from scratch.

The foldtree is setup such that the membrane is at the root and anchored at the residue closest to the pose TM COM with jumps from there to each chain TRANSMEMBRANE COM; requires the membrane to be present Returns the root anchoring point, i.e. rsd nearest pose TM COM that can be in any chain

         _______________________
        |_________________      |
        |________         |     |
________|        |        |     |

| | | | | ----— ----— ----— ----— M=root chain1 chain2 chain3 chain4 ...

The foldtree is setup such that the membrane is at the root and anchored at the residue closest to the pose TM COM with jumps from there to each chain TRANSMEMBRANE COM; requires the membrane to be present; Returns the root anchoring point, i.e. rsd nearest pose TM COM that can be in any chain

         _______________________
        |_________________      |
        |________         |     |
________|        |        |     |

| | | | | ----— ----— ----— ----— M=root chain1 chain2 chain3 chain4 ...

References core::pose::Pose::chain(), core::pose::Pose::conformation(), create_membrane_foldtree_from_anchors(), core::pose::get_chains(), core::conformation::Conformation::is_membrane(), rsd_closest_to_chain_tm_com(), and rsd_closest_to_pose_tm_com().

Referenced by protocols::membrane::OptimizeMembranePositionMover::apply(), protocols::membrane::OptimizeProteinEmbeddingMover::apply(), protocols::membrane::MembranePositionFromTopologyMover::apply(), and protocols::relax::membrane::MPRangeRelaxMover::apply().

◆ create_membrane_foldtree_anchor_tmcom()

core::Size protocols::membrane::create_membrane_foldtree_anchor_tmcom ( core::pose::Pose & pose )

Create membrane foldtree from scratch.

The foldtree is setup such that the membrane is at the root and anchored at the first chain TRANSMEMBRANE COM residue with jumps from the first chain COM to each chain TRANSMEMBRANE COM; requires the membrane to be present Returns the root anchoring point, i.e. rsd nearest chain TM COM of chain 1

________________________________

|__________________________ | |_________________ | | |________ | | | | | | | | ----— ----— ----— ----— M=root chain1 chain2 chain3 chain4 ...

References core::pose::Pose::conformation(), create_membrane_foldtree_from_anchors(), get_anchor_points_for_tmcom(), and core::conformation::Conformation::is_membrane().

◆ create_membrane_foldtree_from_anchors()

void protocols::membrane::create_membrane_foldtree_from_anchors	(	core::pose::Pose &	pose,
		utility::vector1< core::Size >	anchors
	)

Helper function to create membrane foldtrees.

The anchors vector is a vector of anchor residues in all chains, one per chain. This function assumes that the first entry in the vector is the root anchor point to which all other chains are connected;

|__________________________ | |_________________ | | |________ | | | | | | | | ----— ----— ----— ----— M=root chain1 chain2 chain3 chain4 ...

References core::pose::Pose::conformation(), core::pose::Pose::fold_tree(), core::conformation::Conformation::is_membrane(), core::pose::Pose::membrane_info(), core::kinematics::FoldTree::new_jump(), core::kinematics::FoldTree::reorder(), core::kinematics::FoldTree::show(), core::kinematics::FoldTree::simple_tree(), core::pose::Pose::size(), core::pose::Pose::split_by_chain(), and protocols::TR().

Referenced by protocols::membrane::AddMembraneMover::apply(), create_membrane_foldtree_anchor_com(), create_membrane_foldtree_anchor_pose_tmcom(), and create_membrane_foldtree_anchor_tmcom().

◆ create_membrane_multi_partner_foldtree_anchor_tmcom()

utility::vector1< core::Size > protocols::membrane::create_membrane_multi_partner_foldtree_anchor_tmcom	(	core::pose::Pose &	pose,
		std::string	partner
	)

Create foldtree for multiple docking partners.

The foldtree is setup such that the membrane is at the root and anchored at the residue closest to the TM COM of the first chain. The partner setup defines how the foldtree will look like: partners are anchored at the first chain, and multiple chains in a partner are anchored to the first chain of that partner, example below. Returns all interface jump numbers. Example: A_BCD_E

|________________________________ | | _______________ | | |_______ |_______ | | | | | | | | | | ----— ----— ----— ----— ----— M=root chain1 chain2 chain3 chain4 chain5...

^--—^ ^--------------------—^ ^--—^ partner1 partner2 partner3

References core::pose::chain_end_res(), create_specific_membrane_foldtree(), get_anchor_points_for_tmcom(), core::pose::get_chain_id_from_chain(), core::pose::get_chains(), core::pose::Pose::membrane_info(), and protocols::TR().

◆ create_specific_membrane_foldtree()

core::Size protocols::membrane::create_specific_membrane_foldtree	(	core::pose::Pose &	pose,
		utility::vector1< core::Vector >	anchors
	)

Helper function to create a specific membrane foldtree.

I am hijacking xyzVectors to hold the jumps that need to be created in the foldtree: xyz = ( rsd1, rsd2, cutpoint ) THE JUMP NUMBERS WILL BE CONSECUTIVE, ACCORDING TO THE VECTOR1

References core::pose::Pose::conformation(), core::pose::Pose::fold_tree(), core::conformation::Conformation::is_membrane(), core::pose::Pose::membrane_info(), core::kinematics::FoldTree::new_jump(), core::kinematics::FoldTree::reorder(), core::kinematics::FoldTree::show(), core::kinematics::FoldTree::simple_tree(), core::pose::Pose::size(), and protocols::TR().

Referenced by protocols::membrane::AddMPLigandMover::apply(), and create_membrane_multi_partner_foldtree_anchor_tmcom().

◆ get_anchor_points_for_tmcom()

utility::vector1< core::Size > protocols::membrane::get_anchor_points_for_tmcom ( core::pose::Pose & pose )

Helper function to create membrane foldtrees.

Returns the residues closest to the COMs for each chain

References core::pose::get_chains(), rsd_closest_to_chain_tm_com(), and protocols::TR().

Referenced by protocols::membrane::AddMembraneMover::apply(), protocols::membrane::AddMPLigandMover::apply(), create_membrane_foldtree_anchor_tmcom(), and create_membrane_multi_partner_foldtree_anchor_tmcom().

◆ get_chain_and_z()

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

Grab the z-coordinates and chainIDs from the entire pose.

From the pose, grab all of the z_coords of CA atoms and chain IDs, currently used for spanning topology construction. Returns a std::pair of two vectors: the first a vector1 of z coordinates and the second a vector1 of chainIDs for CA atoms

References core::conformation::Residue::atom(), core::pose::Pose::chain(), core::pose::Pose::residue(), core::pose::Pose::size(), protocols::TR(), and core::conformation::Atom::xyz().

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

◆ get_secstruct()

utility::vector1< char > protocols::membrane::get_secstruct ( core::pose::Pose & pose )

Get dssp defined secondary structure from the pose.

Given a pose, grab a vector of characters describing the secondary structure at each residue position in the pose, defined by DSSP

References core::pose::Pose::conformation(), protocols::simple_filters::dssp(), core::conformation::Conformation::secstruct(), core::pose::Pose::size(), and protocols::TR().

Referenced by protocols::membrane::AddMembraneMover::apply(), and protocols::membrane::MPLipidAccessibility::finalize_setup().

◆ is_membrane_fixed()

bool protocols::membrane::is_membrane_fixed ( core::pose::Pose & pose )

Determine whether the membrane is modeled as fixed.

Based on the setup of the foldtree, determined whether the membrane is currently fixed, meaning it is setup as the root in the FoldTree and has no upstream children. Takes a pose.

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

◆ is_membrane_moveable_by_itself()

bool protocols::membrane::is_membrane_moveable_by_itself ( core::pose::Pose & pose )

Determine whether membrane can move on its own.

Based on the setup of the FoldTree, determine whether the membrane is moveable, but when moved, won't cause anything in the protein to move (i.e. independently moveable). Takes a pose.

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

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

◆ mem_all_atom_rmsd_no_super()

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

Compute all-atom RMSD between TM regions - don't superimpose.

Calculate the rmsd between all atoms in the pose in the transmembrane regions, as defined by the spanning topology object. Do not superimpose the poses. Takes a native pose & current pose

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

◆ mem_all_atom_rmsd_with_super()

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

Compute all-atom RMSD between TM regions - do superimpose.

Calculate the rmsd between all atoms in the pose in the transmembrane regions, as defined by the spanning topology object. Superimpose the poses. Takes a native pose & current pose

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

◆ mem_bb_rmsd_no_super()

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

Compute backbone RMSD between TM regions - don't superimpose.

Calculate the rmsd between backbone atoms (N, CB, CA, O) in the transmembrane regions, as defined by the spanning topology object Do not superimpose the poses. Takes a native pose and current pose

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

◆ mem_bb_rmsd_with_super()

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

Compute backbone RMSD between TM regions - do superimpose.

Calculate the rmsd between backbone atoms (N, CB, CA, O) in the transmembrane regions, as defined by the spanning topology object Superimpose the poses. Takes a native pose and current pose

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

◆ membrane_axis()

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

Calculates translation axis lying in the membrane (= projection axis between embedding centers)

References protocols::membrane::geometry::EmbeddingDef::center(), core::pose::Pose::conformation(), core::pose::Pose::membrane_info(), and update_partner_embeddings().

Referenced by protocols::docking::DockingPrepackProtocol::apply(), protocols::docking::DockingSlideIntoContact::apply(), protocols::docking::membrane::MPFindInterfaceMover::apply(), protocols::docking::membrane::QuickRelaxPartnersSeparately::apply(), protocols::docking::calc_interaction_energy(), protocols::docking::calc_intf_score(), protocols::docking::DockingEnsemblePrepackProtocol::move_away(), and protocols::docking::DockingEnsemblePrepackProtocol::move_back().

◆ membrane_normal_to_length_15()

void protocols::membrane::membrane_normal_to_length_15 ( core::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, and core::conformation::Conformation::update_membrane_position().

◆ operator<<() [1/2]

std::ostream & protocols::membrane::operator<<	(	std::ostream &	os,
		AqueousPoreFinder const &	mover
	)

References protocols::membrane::AqueousPoreFinder::show().

◆ operator<<() [2/2]

std::ostream & protocols::membrane::operator<<	(	std::ostream &	os,
		HelixFromSequence const &	mover
	)

References protocols::membrane::HelixFromSequence::show().

◆ pose_tilt_angle_and_center_distance()

utility::vector1< core::Real > protocols::membrane::pose_tilt_angle_and_center_distance ( core::pose::Pose & pose )

Calculate tilt angle and distance from membrane center.

Computes the tilt angle and distance from membrane center for the protein embedding center and normal

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

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

◆ pose_tm_com()

core::Vector protocols::membrane::pose_tm_com ( core::pose::Pose const & pose )

Pose transmembrane center-of-mass.

Gets the coordinates of the TM span center-of-mass This only looks at the span start and end residues for calculation of the TM span COM, this should be faster than the real thing though

References com(), core::pose::Pose::membrane_info(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by protocols::membrane_benchmark::MembraneEnergyLandscapeSampler::apply(), protocols::membrane_benchmark::PeptideOrientationMover::apply(), protocols::relax::membrane::MPRangeRelaxMover::apply(), protocols::membrane_benchmark::MembraneEnergyLandscapeSampler::getaxis(), and rsd_closest_to_pose_tm_com().

◆ read_center_normal_from_cmd()

void protocols::membrane::read_center_normal_from_cmd	(	core::Vector &	center,
		core::Vector &	normal
	)

Read in a user provided center/normal pair from the commandline, safetly.

Read the membrane setup center & normal options form the command line from mp:setup:center and mp:setup:normal. Intended to reduce IO code duplication in membrane framework movers.

References core::conformation::membrane::center, and core::conformation::membrane::normal.

Referenced by protocols::membrane::AddMembraneMover::init_from_cmd(), protocols::membrane::TransformIntoMembraneMover::init_from_cmd(), and protocols::membrane::RotationMover::init_from_cmd().

◆ read_center_normal_from_tag()

void protocols::membrane::read_center_normal_from_tag	(	core::Vector &	center,
		core::Vector &	normal,
		utility::tag::TagCOP	tag
	)

Read in a user provided center/normal pair from RosettaScripts.

Given an XML tag from a RosettaScript read in a center & normal option into two xyzVector objects. This method is intended to reduce duplication accross membrane framework movers that use the same tricks for vectors. Takes two Vector references and a Tag&

References core::conformation::membrane::center, and core::conformation::membrane::normal.

Referenced by protocols::membrane::SetMembranePositionMover::parse_my_tag(), protocols::membrane::SetMembraneNormalMover::parse_my_tag(), protocols::membrane::SetMembraneCenterMover::parse_my_tag(), protocols::membrane::TransformIntoMembraneMover::parse_my_tag(), protocols::membrane::RotationMover::parse_my_tag(), protocols::membrane::TranslationRotationMover::parse_my_tag(), and protocols::membrane::AddMembraneMover::parse_my_tag().

◆ reorder_membrane_foldtree()

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

Set membrane residue to root of foldtree.

Naively sets the root of the foldtree to be the membrane residue. Should perform checks before doing this!

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

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

◆ rsd_closest_to_chain_com()

core::Size protocols::membrane::rsd_closest_to_chain_com	(	core::pose::Pose const &	pose,
		core::Size	chainid
	)

Residue closest to chain center-of-mass.

Gets the residue number closest to the chain center-of-mass

References core::pose::Pose::chain(), core::pose::Pose::conformation(), core::sequence::end, core::conformation::Conformation::is_membrane(), core::pose::Pose::membrane_info(), core::pose::nres_protein(), core::pose::residue_center_of_mass(), protocols::loops::start, and protocols::TR().

Referenced by create_membrane_foldtree_anchor_com(), and setup_foldtree_pose_com().

◆ rsd_closest_to_chain_tm_com()

core::Size protocols::membrane::rsd_closest_to_chain_tm_com	(	core::pose::Pose const &	pose,
		core::Size	chainid
	)

Residue closest to chain TM center-of-mass.

Gets the residue number closest to the chain TM center-of-mass

References core::conformation::Residue::atom(), core::conformation::Residue::chain(), core::pose::chain_end_res(), chain_tm_com(), com(), protocols::mpi_refinement::distance(), core::pose::get_chain_from_chain_id(), core::conformation::Residue::is_protein(), core::pose::Pose::membrane_info(), core::pose::nres_protein(), core::pose::Pose::residue(), protocols::TR(), and core::conformation::Atom::xyz().

Referenced by create_membrane_docking_foldtree_from_partners(), create_membrane_foldtree_anchor_pose_tmcom(), and get_anchor_points_for_tmcom().

◆ rsd_closest_to_pose_tm_com()

core::Size protocols::membrane::rsd_closest_to_pose_tm_com ( core::pose::Pose const & pose )

Residue closest to pose transmembrane center-of-mass.

Gets the coordinates of the residue closest to TM span center-of-mass This only looks at the span start and end residues for calculation of the TM span COM, this should be faster than the real thing though

References com(), core::pose::nres_protein(), pose_tm_com(), and core::pose::return_nearest_residue().

Referenced by create_membrane_foldtree_anchor_pose_tmcom(), and protocols::relax::RangeRelaxMover::finalize_setup().

◆ setup_foldtree_from_anchors()

void protocols::membrane::setup_foldtree_from_anchors	(	core::pose::Pose &	pose,
		utility::vector1< core::Size >	anchors
	)

Helper function to setup foldtrees.

The anchors vector is a vector of anchor residues in all chains, one per chain. This function assumes that the first entry in the vector is the root anchor point to which all other chains are connected;

|_________________ | |________ | | | | | |

chain1 chain2 chain3 chain4 ... ^ root anchor point

References core::pose::Pose::conformation(), core::pose::Pose::fold_tree(), core::conformation::Conformation::is_membrane(), core::kinematics::FoldTree::new_jump(), core::kinematics::FoldTree::reorder(), core::kinematics::FoldTree::show(), core::kinematics::FoldTree::simple_tree(), core::pose::Pose::size(), core::pose::Pose::split_by_chain(), and protocols::TR().

Referenced by setup_foldtree_pose_com().

◆ setup_foldtree_pose_com()

core::Size protocols::membrane::setup_foldtree_pose_com ( core::pose::Pose & pose )

Setup foldtree from scratch.

The foldtree is setup such that the residue closest to the COM is at the root, with jumps from there to each chain COM; requires the membrane to be present; Returns the root anchoring point, i.e. rsd nearest pose COM that can be in any chain

|________ | ________| | | | | | |

chain1 chain2 chain3 chain4 ... ^ root anchor point

References core::pose::Pose::chain(), core::pose::Pose::conformation(), core::pose::get_chains(), core::conformation::Conformation::is_membrane(), core::pose::residue_center_of_mass(), rsd_closest_to_chain_com(), setup_foldtree_from_anchors(), and core::pose::Pose::size().

Referenced by protocols::relax::RangeRelaxMover::finalize_setup().

◆ split_topology_by_chain_noshift()

utility::vector1< core::conformation::membrane::SpanningTopologyOP > protocols::membrane::split_topology_by_chain_noshift	(	core::pose::Pose const &	pose,
		core::conformation::membrane::SpanningTopologyOP const	topo
	)

Split topology by chain.

Split topology by chain and give vector of topology objects

References core::pose::Pose::chain(), core::sequence::end, core::pose::nres_protein(), and protocols::loops::start.

Referenced by chain_tm_com(), and compute_embeddings_by_chain().

◆ split_topology_by_jump()

void protocols::membrane::split_topology_by_jump	(	core::pose::Pose const &	pose,
		core::Size const	jumpnum,
		core::conformation::membrane::SpanningTopology const &	topo,
		core::pose::Pose &	pose_up,
		core::pose::Pose &	pose_down,
		core::conformation::membrane::SpanningTopology &	topo_up,
		core::conformation::membrane::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 BEWARE: this does not work for splitting topology by spans! It only works chainwise

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

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

◆ split_topology_by_jump_noshift()

void protocols::membrane::split_topology_by_jump_noshift	(	core::pose::Pose const &	pose,
		core::Size const	jumpnum,
		core::conformation::membrane::SpanningTopologyOP	topo,
		core::conformation::membrane::SpanningTopologyOP	topo_up,
		core::conformation::membrane::SpanningTopologyOP	topo_down
	)

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

This doesn't shift the topology to start at 1 for each partner, it remains exactly the same as it would be for the complete pose, just split BEWARE: this does not work for splitting topology by spans! It only works chainwise

References core::pose::Pose::chain(), core::kinematics::FoldTree::downstream_jump_residue(), core::sequence::end, core::pose::Pose::fold_tree(), core::pose::Pose::membrane_info(), and protocols::loops::start.

Referenced by protocols::membrane::SpinAroundPartnerMover::apply(), protocols::membrane::TiltMover::apply(), protocols::docking::membrane::MPFindInterfaceMover::finalize_setup(), protocols::docking::membrane::QuickRelaxPartnersSeparately::finalize_setup(), and update_partner_embeddings().

◆ update_partner_embeddings()

void protocols::membrane::update_partner_embeddings	(	core::pose::Pose const &	pose,
		core::Size const	jumpnum,
		protocols::membrane::geometry::EmbeddingDef &	emb_up,
		protocols::membrane::geometry::EmbeddingDef &	emb_down
	)

Update embedding of the partners after a move.

Requires the jump number between the partners, the topology will be taken from MembraneInfo and will be split accordingly; up and down means upstream and downstream

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

Referenced by protocols::docking::DockingSlideIntoContact::apply(), protocols::docking::membrane::MPFindInterfaceMover::apply(), membrane_axis(), protocols::docking::move_apart(), and protocols::docking::move_together().

Namespaces

Classes

Typedefs

Functions

Typedef Documentation

◆ AddMembraneMoverCOP

◆ AddMembraneMoverOP

◆ AddMembraneSpanConstraintCOP

◆ AddMembraneSpanConstraintOP

◆ AddMembraneSpanTermZConstraintCOP

◆ AddMembraneSpanTermZConstraintOP

◆ AddMPLigandMoverCOP

◆ AddMPLigandMoverOP

◆ AqueousPoreFinderCOP

◆ AqueousPoreFinderOP

◆ FlipMoverCOP

◆ FlipMoverOP

◆ HelixFromSequenceCOP

◆ HelixFromSequenceOP

◆ MembranePositionFromTopologyMoverCOP

◆ MembranePositionFromTopologyMoverOP

◆ MPLipidAccessibilityCOP

◆ MPLipidAccessibilityOP

◆ MPMutateRelaxMoverCOP

◆ MPMutateRelaxMoverOP

◆ MPQuickRelaxMoverCOP

◆ MPQuickRelaxMoverOP

◆ OptimizeMembranePositionMoverCOP

◆ OptimizeMembranePositionMoverOP

◆ OptimizeProteinEmbeddingMoverCOP

◆ OptimizeProteinEmbeddingMoverOP

◆ RandomPositionRotationMoverCOP

◆ RandomPositionRotationMoverOP

◆ RandomPositionTranslationMoverCOP

◆ RandomPositionTranslationMoverOP

◆ RotationMoverCOP

◆ RotationMoverOP

◆ SetMembraneCenterMoverCOP

◆ SetMembraneCenterMoverOP

◆ SetMembraneNormalMoverCOP

◆ SetMembraneNormalMoverOP

◆ SetMembranePositionMoverCOP

◆ SetMembranePositionMoverOP

◆ SpinAroundPartnerMoverCOP

◆ SpinAroundPartnerMoverOP

◆ TiltMoverCOP

◆ TiltMoverOP

◆ TransformIntoMembraneMoverCOP

◆ TransformIntoMembraneMoverOP

◆ TranslationMoverCOP

◆ TranslationMoverOP

◆ TranslationRotationMoverCOP

◆ TranslationRotationMoverOP

Function Documentation

◆ average_antiparallel_embeddings()

◆ average_embeddings()

◆ calc_angle_rmsd()

◆ calc_helix_axis()

◆ calc_helix_tilt_angle()

◆ chain_com()

◆ chain_tm_com()

◆ check_orientation()

◆ check_vector()

◆ com()

◆ compute_embeddings_by_chain()

◆ compute_structure_based_embedding() [1/4]

◆ compute_structure_based_embedding() [2/4]

◆ compute_structure_based_embedding() [3/4]

◆ compute_structure_based_embedding() [4/4]

◆ create_membrane_docking_foldtree_from_partners()

◆ create_membrane_foldtree_anchor_com()

◆ create_membrane_foldtree_anchor_pose_tmcom()

◆ create_membrane_foldtree_anchor_tmcom()

◆ create_membrane_foldtree_from_anchors()

◆ create_membrane_multi_partner_foldtree_anchor_tmcom()

◆ create_specific_membrane_foldtree()

◆ get_anchor_points_for_tmcom()

◆ get_chain_and_z()

◆ get_secstruct()

◆ is_membrane_fixed()