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core::conformation::membrane::MembraneInfo Class Reference

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

#include <MembraneInfo.hh>

Inheritance diagram for core::conformation::membrane::MembraneInfo:
Inheritance graph
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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 (MembraneInfo const &src)
 Create a deep copy of all data in this object. More...
 
MembraneInfooperator= (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...
 
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...
 
SpanningTopologyOP spanning_topology () const
 Transmembrane spaning topology. More...
 
ImplicitLipidInfoOP implicit_lipids () const
 Get implicit lipid information. 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_
 
SpanningTopologyOP spanning_topology_
 
ImplicitLipidInfoOP implicit_lipids_
 

Detailed Description

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

Constructor & Destructor Documentation

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

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_.

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

Create a deep copy of all data in this object.

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

Destructor.

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

Create a default version of MembraneInfo (DONT USE)

Member Function Documentation

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

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

Get implicit lipid information.

References implicit_lipids_.

Referenced by in_membrane().

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

core membrane thickness

Elazar parameter - membrane core (currently defaults to 15)

References membrane_core_.

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

Indeitifier for the membrane jump.

References membrane_jump_.

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

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_.

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

Effective thickness of the membrane (default = 15)

References thickness_.

Referenced by in_membrane().

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

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

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

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

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.

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_.

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<<().

Member Data Documentation

ImplicitLipidInfoOP core::conformation::membrane::MembraneInfo::implicit_lipids_
private
core::Real core::conformation::membrane::MembraneInfo::membrane_core_
private

Referenced by membrane_core().

core::SSize core::conformation::membrane::MembraneInfo::membrane_jump_
private
core::Size core::conformation::membrane::MembraneInfo::membrane_rsd_num_
private
SpanningTopologyOP core::conformation::membrane::MembraneInfo::spanning_topology_
private

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

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

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

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

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


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