Data describing the relationship between protein(s) and a membrane environment. More...

#include <MembraneInfo.hh>

Inheritance diagram for core::conformation::membrane::MembraneInfo:

Public Member Functions
	MembraneInfo (core::Size membrane_pos, core::SSize membrane_jump, core::Size membrane_core, core::Real thickness, core::Real steepness, SpanningTopologyOP topology)
	Create MembraneInfo from initialized data. More...

	MembraneInfo (core::Size membrane_pos, core::SSize membrane_jump, core::Real steepness, SpanningTopologyOP topology, std::string lipid_composition_name, core::Real lipid_composition_temp)
	Create MembraneInfo from initialized data. More...

	MembraneInfo (core::Size membrane_pos, core::SSize membrane_jump, core::Real steepness, SpanningTopologyOP topology, std::string lipid_composition_name, core::Real lipid_composition_temp, MP_GEOMETRY_TRANSITION mp_geometry, Conformation const &conf)
	Create MembraneInfo from initialized data. More...

	MembraneInfo (core::Size membrane_pos, core::SSize membrane_jump, core::Size membrane_core, core::Real steepness, SpanningTopologyOP topology, std::string lipid_composition_name, core::Real lipid_composition_temp, MP_GEOMETRY_TRANSITION mp_geometry, Conformation const &conf)

	MembraneInfo (core::Size membrane_pos, core::SSize membrane_jump, core::Size membrane_core, core::Real thickness, core::Real steepness, SpanningTopologyOP topology, MP_GEOMETRY_TRANSITION mp_geometry, Conformation const &conf)
	Create MembraneInfo from initialized data. More...

	MembraneInfo (core::Size membrane_pos, core::SSize membrane_jump, core::Size membrane_core, core::Real thickness, core::Real steepness, SpanningTopologyOP topology, MembraneGeometryCOP membrane_geometry)

	MembraneInfo (MembraneInfo const &src)
	Create a deep copy of all data in this object. More...

MembraneInfo &	operator= (MembraneInfo const &src)
	create a deep copy of all data in thsi object upon assignment More...

	~MembraneInfo () override
	Destructor. More...

virtual void	show () const
	Generate a string representation of information represented by this MembraneInfo and send it to std::cout. More...

virtual void	show (std::ostream &output) const
	Generate a string representation of information represented by ths MembraneInfo. More...

virtual core::Real	membrane_thickness () const
	Effective thickness of the membrane (default = 15) More...

virtual core::Real	membrane_steepness () const
	Steepness of hydrophobic -> hydrophillic transition (defualt = 10) More...

core::Real	membrane_core () const
	core membrane thickness More...

Vector	membrane_center (Conformation const &conf) const
	Membrane center. More...

Vector	membrane_normal (Conformation const &conf) const
	Membrane normal. More...

bool	in_membrane (Conformation const &conf, core::Size resnum) const
	Is residue in the membrane? More...

bool	in_membrane_atom (Conformation const &conf, core::Size resnum, core::ShortSize atomnum) const
	Is atom in the membrane? More...

bool	use_franklin () const

Real	residue_z_position (Conformation const &conf, core::Size resnum) const
	Compute residue position relative to membrane normal. More...

Real	atom_z_position (Conformation const &conf, core::Size resnum, core::Size atomnum) const
	Compute atom position relative to membrane normal. More...

core::Size	membrane_rsd_num () const
	Sequence position of the membrane residue. More...

core::SSize	membrane_jump () const
	Indeitifier for the membrane jump. More...

void	set_membrane_jump (core::SSize jumpnum)
	Allow a protocol to set a new jump number for the membrane jump. More...

bool	check_membrane_fold_tree (core::kinematics::FoldTree const &ft_in) const
	Somewhat weak check that a membrane foldtree is valid. More...

bool	is_helical () const
	Is the protein alpha helical or beta barrel. More...

void	is_helical (bool const is_helical)

SpanningTopologyOP	spanning_topology () const
	Transmembrane spaning topology. More...

ImplicitLipidInfoOP	implicit_lipids () const
	Get implicit lipid information. More...

MembraneGeometryCOP	membrane_geometry () const
	Get membrane_geometry info. More...

void	set_membrane_geometry (MembraneGeometryCOP mem_geo)

core::Real	per_atom_lipid_accessibility (core::Size rsd, core::Size atom) const
	Per-atom accessibility to membrane lipids (0 = not exposed, 50 = exposed) More...

void	set_per_atom_lipid_accessibility (utility::vector1< utility::vector1< core::Real > > const &v)
	Per-atom accessibility to membrane lipids (0 = not exposed, 50 = exposed) More...

Private Member Functions
	MembraneInfo ()
	Create a default version of MembraneInfo (DONT USE) More...

Private Attributes
core::Real	thickness_

core::Real	steepness_

core::Real	membrane_core_

core::Size	membrane_rsd_num_

core::SSize	membrane_jump_

bool	is_helical_

SpanningTopologyOP	spanning_topology_

ImplicitLipidInfoOP	implicit_lipids_

utility::vector1< utility::vector1< core::Real > >	per_atom_lipid_accessibility_

MembraneGeometryCOP	membrane_geometry_

Detailed Description

Data describing the relationship between protein(s) and a membrane environment.

Constructor & Destructor Documentation

◆ MembraneInfo() [1/8]

core::conformation::membrane::MembraneInfo::MembraneInfo	(	core::Size	membrane_pos,
		core::SSize	membrane_jump,
		core::Size	membrane_core,
		core::Real	thickness,
		core::Real	steepness,
		SpanningTopologyOP	topology
	)

Create MembraneInfo from initialized data.

Creates a MembraneInfo object by linking the conformation to the pose, specify the membrane residue number, membrane jump number, spanning topology object and optional lipophilicity data. Thickness and steepness are currently constants

◆ MembraneInfo() [2/8]

core::conformation::membrane::MembraneInfo::MembraneInfo	(	core::Size	membrane_pos,
		core::SSize	membrane_jump,
		core::Real	steepness,
		SpanningTopologyOP	topology,
		std::string	lipid_composition_name,
		core::Real	lipid_composition_temp
	)

Create MembraneInfo from initialized data.

Creates a MembraneInfo object by linking the conformation to the pose, specify the membrane residue number, membrane jump number, spanning topology object and optional lipophilicity data. Thickness and steepness are currently constants

References implicit_lipids_, membrane_geometry_, core::conformation::membrane::thickness, and thickness_.

◆ MembraneInfo() [3/8]

core::conformation::membrane::MembraneInfo::MembraneInfo	(	core::Size	membrane_pos,
		core::SSize	membrane_jump,
		core::Real	steepness,
		SpanningTopologyOP	topology,
		std::string	lipid_composition_name,
		core::Real	lipid_composition_temp,
		MP_GEOMETRY_TRANSITION	mp_geometry,
		Conformation const &	conf
	)

Create MembraneInfo from initialized data.

References core::conformation::membrane::BICELLE, core::conformation::membrane::DOUBLE_VESICLE, implicit_lipids_, membrane_geometry_, core::conformation::membrane::SLAB, thickness_, core::conformation::TR(), and core::conformation::membrane::VESICLE.

◆ MembraneInfo() [4/8]

core::conformation::membrane::MembraneInfo::MembraneInfo	(	core::Size	membrane_pos,
		core::SSize	membrane_jump,
		core::Size	membrane_core,
		core::Real	steepness,
		SpanningTopologyOP	topology,
		std::string	lipid_composition_name,
		core::Real	lipid_composition_temp,
		MP_GEOMETRY_TRANSITION	mp_geometry,
		Conformation const &	conf
	)

References core::conformation::membrane::BICELLE, core::conformation::membrane::DOUBLE_VESICLE, implicit_lipids_, membrane_geometry_, core::conformation::membrane::SLAB, thickness_, core::conformation::TR(), and core::conformation::membrane::VESICLE.

◆ MembraneInfo() [5/8]

core::conformation::membrane::MembraneInfo::MembraneInfo	(	core::Size	membrane_pos,
		core::SSize	membrane_jump,
		core::Size	membrane_core,
		core::Real	thickness,
		core::Real	steepness,
		SpanningTopologyOP	topology,
		MP_GEOMETRY_TRANSITION	mp_geometry,
		Conformation const &	conf
	)

Create MembraneInfo from initialized data.

Creates a MembraneInfo object by linking the conformation to the pose, specify the membrane residue number, membrane jump number, spanning topology object and optional lipophilicity data. Thickness and steepness are currently constants

References core::conformation::membrane::BICELLE, core::conformation::membrane::DOUBLE_VESICLE, membrane_geometry_, core::conformation::membrane::SLAB, core::conformation::membrane::thickness, core::conformation::TR(), and core::conformation::membrane::VESICLE.

◆ MembraneInfo() [6/8]

core::conformation::membrane::MembraneInfo::MembraneInfo	(	core::Size	membrane_pos,
		core::SSize	membrane_jump,
		core::Size	membrane_core,
		core::Real	thickness,
		core::Real	steepness,
		SpanningTopologyOP	topology,
		MembraneGeometryCOP	membrane_geometry
	)

◆ MembraneInfo() [7/8]

core::conformation::membrane::MembraneInfo::MembraneInfo ( MembraneInfo const & src )

Create a deep copy of all data in this object.

◆ ~MembraneInfo()

core::conformation::membrane::MembraneInfo::~MembraneInfo ( )

override

Destructor.

◆ MembraneInfo() [8/8]

core::conformation::membrane::MembraneInfo::MembraneInfo ( )

private

Create a default version of MembraneInfo (DONT USE)

Member Function Documentation

◆ atom_z_position()

Real core::conformation::membrane::MembraneInfo::atom_z_position	(	Conformation const &	conf,
		core::Size	resnum,
		core::Size	atomnum
	)		const

Compute atom position relative to membrane normal.

References core::conformation::Residue::atom(), membrane_center(), membrane_normal(), core::conformation::Conformation::residue(), core::conformation::Atom::xyz(), and protocols::kinmatch::xyz().

◆ check_membrane_fold_tree()

bool core::conformation::membrane::MembraneInfo::check_membrane_fold_tree ( core::kinematics::FoldTree const & ft_in ) const

Somewhat weak check that a membrane foldtree is valid.

References core::kinematics::FoldTree::check_fold_tree(), core::kinematics::FoldTree::is_jump_point(), and membrane_rsd_num_.

◆ implicit_lipids()

ImplicitLipidInfoOP core::conformation::membrane::MembraneInfo::implicit_lipids ( ) const

Get implicit lipid information.

References implicit_lipids_.

◆ in_membrane()

bool core::conformation::membrane::MembraneInfo::in_membrane	(	Conformation const &	conf,
		core::Size	resnum
	)		const

Is residue in the membrane?

References membrane_geometry_, and protocols::kinmatch::xyz().

◆ in_membrane_atom()

bool core::conformation::membrane::MembraneInfo::in_membrane_atom	(	Conformation const &	conf,
		core::Size	resnum,
		core::ShortSize	atomnum
	)		const

Is atom in the membrane?

References membrane_geometry_, and protocols::kinmatch::xyz().

◆ is_helical() [1/2]

bool core::conformation::membrane::MembraneInfo::is_helical ( ) const

Is the protein alpha helical or beta barrel.

References is_helical_.

Referenced by is_helical().

◆ is_helical() [2/2]

void core::conformation::membrane::MembraneInfo::is_helical ( bool const is_helical )

References implicit_lipids_, is_helical(), and is_helical_.

◆ membrane_center()

Vector core::conformation::membrane::MembraneInfo::membrane_center ( Conformation const & conf ) const

Membrane center.

References core::conformation::membrane::center, membrane_rsd_num(), core::conformation::Conformation::residue(), and core::conformation::Residue::xyz().

Referenced by atom_z_position(), membrane_normal(), and residue_z_position().

◆ membrane_core()

core::Real core::conformation::membrane::MembraneInfo::membrane_core ( ) const

core membrane thickness

Elazar parameter - membrane core (currently defaults to 15)

References membrane_core_.

◆ membrane_geometry()

MembraneGeometryCOP core::conformation::membrane::MembraneInfo::membrane_geometry ( ) const

Get membrane_geometry info.

Get const membrane_geometry information.

References membrane_geometry_.

◆ membrane_jump()

core::SSize core::conformation::membrane::MembraneInfo::membrane_jump ( ) const

Indeitifier for the membrane jump.

References membrane_jump_.

◆ membrane_normal()

Vector core::conformation::membrane::MembraneInfo::membrane_normal ( Conformation const & conf ) const

Membrane normal.

References membrane_center(), membrane_rsd_num(), core::conformation::membrane::normal, core::conformation::Conformation::residue(), and core::conformation::Residue::xyz().

Referenced by atom_z_position(), and residue_z_position().

◆ membrane_rsd_num()

core::Size core::conformation::membrane::MembraneInfo::membrane_rsd_num ( ) const

Sequence position of the membrane residue.

References membrane_rsd_num_.

Referenced by membrane_center(), membrane_normal(), and core::conformation::membrane::operator<<().

◆ membrane_steepness()

core::Real core::conformation::membrane::MembraneInfo::membrane_steepness ( ) const

virtual

Steepness of hydrophobic -> hydrophillic transition (defualt = 10)

Steepness of hydrophobic -> hydrophillic transition (default = 15)

References steepness_.

◆ membrane_thickness()

core::Real core::conformation::membrane::MembraneInfo::membrane_thickness ( ) const

virtual

Effective thickness of the membrane (default = 15)

References thickness_.

◆ operator=()

MembraneInfo & core::conformation::membrane::MembraneInfo::operator= ( MembraneInfo const & src )

create a deep copy of all data in thsi object upon assignment

create a deep copy of all data in this object upon assignment

References implicit_lipids_, is_helical_, membrane_geometry_, membrane_jump_, membrane_rsd_num_, per_atom_lipid_accessibility_, spanning_topology_, steepness_, and thickness_.

◆ per_atom_lipid_accessibility()

core::Real core::conformation::membrane::MembraneInfo::per_atom_lipid_accessibility	(	core::Size	rsd,
		core::Size	atom
	)		const

Per-atom accessibility to membrane lipids (0 = not exposed, 50 = exposed)

Per-atom accessibility to membrane lipids (0 = not exposed, 15 = exposed)

References per_atom_lipid_accessibility_.

◆ residue_z_position()

Real core::conformation::membrane::MembraneInfo::residue_z_position	(	Conformation const &	conf,
		core::Size	resnum
	)		const

Compute residue position relative to membrane normal.

References core::conformation::Residue::atom(), membrane_center(), membrane_normal(), core::conformation::Conformation::residue(), core::conformation::Atom::xyz(), and protocols::kinmatch::xyz().

◆ set_membrane_geometry()

void core::conformation::membrane::MembraneInfo::set_membrane_geometry ( MembraneGeometryCOP mem_geo )

References membrane_geometry_.

◆ set_membrane_jump()

void core::conformation::membrane::MembraneInfo::set_membrane_jump ( core::SSize jumpnum )

Allow a protocol to set a new jump number for the membrane jump.

References membrane_jump_, and core::conformation::TR().

◆ set_per_atom_lipid_accessibility()

void core::conformation::membrane::MembraneInfo::set_per_atom_lipid_accessibility ( utility::vector1< utility::vector1< core::Real > > const & v )

Per-atom accessibility to membrane lipids (0 = not exposed, 50 = exposed)

Per-atom accessibility to membrane lipids.

References per_atom_lipid_accessibility_.

◆ show() [1/2]

void core::conformation::membrane::MembraneInfo::show ( ) const

virtual

Generate a string representation of information represented by this MembraneInfo and send it to std::cout.

Generate a string representation of information represented by ths MembraneInfo.

◆ show() [2/2]

void core::conformation::membrane::MembraneInfo::show ( std::ostream & output ) const

virtual

Generate a string representation of information represented by ths MembraneInfo.

References implicit_lipids_, membrane_jump_, membrane_rsd_num_, spanning_topology_, steepness_, and thickness_.

◆ spanning_topology()

SpanningTopologyOP core::conformation::membrane::MembraneInfo::spanning_topology ( ) const

Transmembrane spaning topology.

Return a SpanningTopology object, which includes a list of Span objects, describing the start and end sequence positions of each transmembrane span

References spanning_topology_.

Referenced by core::conformation::membrane::operator<<().

◆ use_franklin()

bool core::conformation::membrane::MembraneInfo::use_franklin ( ) const

References implicit_lipids_.

Member Data Documentation

◆ implicit_lipids_

ImplicitLipidInfoOP core::conformation::membrane::MembraneInfo::implicit_lipids_

private

Referenced by implicit_lipids(), is_helical(), MembraneInfo(), operator=(), show(), and use_franklin().

◆ is_helical_

bool core::conformation::membrane::MembraneInfo::is_helical_

private

Referenced by is_helical(), and operator=().

◆ membrane_core_

core::Real core::conformation::membrane::MembraneInfo::membrane_core_

private

Referenced by membrane_core().

◆ membrane_geometry_

MembraneGeometryCOP core::conformation::membrane::MembraneInfo::membrane_geometry_

private

Referenced by in_membrane(), in_membrane_atom(), membrane_geometry(), MembraneInfo(), operator=(), and set_membrane_geometry().

◆ membrane_jump_

core::SSize core::conformation::membrane::MembraneInfo::membrane_jump_

private

Referenced by membrane_jump(), operator=(), set_membrane_jump(), and show().

◆ membrane_rsd_num_

core::Size core::conformation::membrane::MembraneInfo::membrane_rsd_num_

private

Referenced by check_membrane_fold_tree(), membrane_rsd_num(), operator=(), and show().

◆ per_atom_lipid_accessibility_

utility::vector1< utility::vector1< core::Real > > core::conformation::membrane::MembraneInfo::per_atom_lipid_accessibility_

private

Referenced by operator=(), per_atom_lipid_accessibility(), and set_per_atom_lipid_accessibility().

◆ spanning_topology_

SpanningTopologyOP core::conformation::membrane::MembraneInfo::spanning_topology_

private

Referenced by operator=(), show(), and spanning_topology().

◆ steepness_

core::Real core::conformation::membrane::MembraneInfo::steepness_

private

Referenced by membrane_steepness(), operator=(), and show().

◆ thickness_

core::Real core::conformation::membrane::MembraneInfo::thickness_

private

Referenced by membrane_thickness(), MembraneInfo(), operator=(), and show().

The documentation for this class was generated from the following files:

src/core/conformation/membrane/MembraneInfo.hh
src/core/conformation/membrane/MembraneInfo.cc

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ MembraneInfo() [1/8]

◆ MembraneInfo() [2/8]

◆ MembraneInfo() [3/8]

◆ MembraneInfo() [4/8]

◆ MembraneInfo() [5/8]

◆ MembraneInfo() [6/8]

◆ MembraneInfo() [7/8]

◆ ~MembraneInfo()

◆ MembraneInfo() [8/8]

Member Function Documentation

◆ atom_z_position()

◆ check_membrane_fold_tree()

◆ implicit_lipids()

◆ in_membrane()

◆ in_membrane_atom()

◆ is_helical() [1/2]

◆ is_helical() [2/2]

◆ membrane_center()

◆ membrane_core()

◆ membrane_geometry()

◆ membrane_jump()

◆ membrane_normal()

◆ membrane_rsd_num()

◆ membrane_steepness()

◆ membrane_thickness()

◆ operator=()

◆ per_atom_lipid_accessibility()

◆ residue_z_position()

◆ set_membrane_geometry()

◆ set_membrane_jump()

◆ set_per_atom_lipid_accessibility()

◆ show() [1/2]

◆ show() [2/2]

◆ spanning_topology()

◆ use_franklin()

Member Data Documentation

◆ implicit_lipids_

◆ is_helical_

◆ membrane_core_

◆ membrane_geometry_

◆ membrane_jump_

◆ membrane_rsd_num_

◆ per_atom_lipid_accessibility_

◆ spanning_topology_

◆ steepness_

◆ thickness_