Rosetta
Public Member Functions | Protected Member Functions | Private Attributes | List of all members
core::conformation::membrane::MembraneGeometry Class Referenceabstract

Data describing the geometry of the membrane. More...

#include <MembraneGeometry.hh>

Inheritance diagram for core::conformation::membrane::MembraneGeometry:
Inheritance graph
[legend]

Public Member Functions

 MembraneGeometry ()=delete
 Create a default version of MembraneGeometry (DONT USE) More...
 
 MembraneGeometry (core::Real steepness)
 Create MembraneInfo from initialized data. More...
 
 MembraneGeometry (core::Real steepness, core::Real thickness)
 Create MembraneInfo from initialized data. More...
 
 MembraneGeometry (core::Real steepness, core::Real thickness, AqueousPoreParametersOP aqueous_pore)
 Create MembraneGeometry from initialized data. More...
 
 ~MembraneGeometry () override
 Destructor. More...
 
virtual MembraneGeometryOP clone () const =0
 
virtual void show () const =0
 Generate a string representation of information represented by this MembraneGeometry and send it to std::cout. More...
 
virtual void show (std::ostream &output) const =0
 Generate a string representation of information represented by this MembraneGeometry. More...
 
bool has_pore () const
 Does this protein have a water-filled pore? More...
 
core::Vector corrected_xyz (Conformation const &conf, core::Size resnum, core::Size atomnum) const
 
core::Real f_imm1 (core::Real z_position) const
 
core::Real f_imm1_deriv (core::Real z_position) const
 
core::Real f_franklin (core::Real const z, core::Real tau, core::Real kappa) const
 
core::Real f_franklin_gradient (core::Real const z, core::Real tau, core::Real kappa) const
 
core::Real f_thickness (Conformation const &conf, core::Real const z) const
 
core::Real f_thickness_deriv (Conformation const &conf, core::Real const z) const
 
core::Real f_hydration (core::Real f_thk, numeric::xyzVector< core::Real > const &p) const
 
core::Real f_hydration_deriv_dz (numeric::xyzVector< core::Real > const &p, core::Real f_thk_deriv_dz) const
 
core::Real f_cavity (numeric::xyzVector< core::Real > const &p) const
 Calculate the hydration of an atom based on its location relative to an aqueous pore or cavity. More...
 
core::Real f_cavity_gradient (core::Real const r) const
 Calculate the derivative of f_cavity (without any r(x,y,z) dependence) More...
 
core::Real f_cavity_dx (numeric::xyzVector< core::Real > const &p, core::Real f_thk) const
 
core::Real f_cavity_dy (numeric::xyzVector< core::Real > const &p, core::Real f_thk) const
 
core::Real f_cavity_dz (numeric::xyzVector< core::Real > const &p, core::Real f_thk) const
 
core::Real g_radius (numeric::xyzVector< core::Real > const &p) const
 Calculate the location of an atom relative to the pore structure. More...
 
core::Real g_radius_gradient_dz (numeric::xyzVector< core::Real > const &p) const
 
core::Real g_radius_gradient_dx (numeric::xyzVector< core::Real > const &p) const
 
core::Real g_radius_gradient_dy (numeric::xyzVector< core::Real > const &p) const
 
core::Vector r_alpha_p_x (numeric::xyzVector< core::Real > const &xyz) const
 
core::Vector r_alpha_p_y (numeric::xyzVector< core::Real > const &xyz) const
 
core::Vector r_alpha_p_z (Conformation const &conf, core::Size resnum, core::Size atomnum) const
 
core::Vector f1_pore (core::Real f_thk, numeric::xyzVector< core::Real > const &xyz, Conformation const &conf, core::Size resnum, core::Size atomnum) const
 
core::Vector f2_pore (core::Real f_thk, numeric::xyzVector< core::Real > const &xyz, Conformation const &conf, core::Size resnum, core::Size atomnum) const
 
void set_aqueous_pore_parameters (AqueousPoreParametersOP aqueous_pore)
 Set membrane aqueous pore parameters. More...
 
virtual std::string geometry_string () const =0
 
virtual MP_GEOMETRY_TRANSITION geometry_enum () const =0
 
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::Vector f1 (core::Vector const &atom_xyz, core::Vector const &r_alpha, core::Real deriv) const
 
core::Vector f2 (core::Vector const &atom_xyz, core::Vector const &r_alpha, core::Real deriv) const
 
virtual core::Real f_transition (Conformation const &conf, core::Size resnum, core::Size atomnum) const =0
 
virtual core::Vector f_transition_f1 (Conformation const &conf, core::Size resnum, core::Size atomnum) const =0
 
virtual core::Vector f_transition_f2 (Conformation const &conf, core::Size resnum, core::Size atomnum) const =0
 

Protected Member Functions

core::Vector thickness_vector (Conformation const &conf) const
 
core::Vector normal_vector (Conformation const &conf) const
 
core::Vector binormal_vector (Conformation const &conf) const
 
core::Real corrected_coordinate (core::Vector const &xyz, core::Vector const &x_axis) const
 

Private Attributes

core::Real thickness_
 
core::Real steepness_
 
core::Real pore_transition_steepness_
 
core::conformation::membrane::AqueousPoreParametersOP pore_params_
 

Detailed Description

Data describing the geometry of the membrane.

Constructor & Destructor Documentation

◆ MembraneGeometry() [1/4]

core::conformation::membrane::MembraneGeometry::MembraneGeometry ( )
delete

Create a default version of MembraneGeometry (DONT USE)

◆ MembraneGeometry() [2/4]

core::conformation::membrane::MembraneGeometry::MembraneGeometry ( core::Real  steepness)

Create MembraneInfo from initialized data.

◆ MembraneGeometry() [3/4]

core::conformation::membrane::MembraneGeometry::MembraneGeometry ( core::Real  steepness,
core::Real  thickness 
)

Create MembraneInfo from initialized data.

◆ MembraneGeometry() [4/4]

core::conformation::membrane::MembraneGeometry::MembraneGeometry ( core::Real  steepness,
core::Real  thickness,
AqueousPoreParametersOP  aqueous_pore 
)

Create MembraneGeometry from initialized data.

References set_aqueous_pore_parameters().

◆ ~MembraneGeometry()

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

Destructor.

Member Function Documentation

◆ binormal_vector()

core::Vector core::conformation::membrane::MembraneGeometry::binormal_vector ( Conformation const &  conf) const
protected

References normal_vector(), and thickness_vector().

Referenced by corrected_xyz().

◆ clone()

virtual MembraneGeometryOP core::conformation::membrane::MembraneGeometry::clone ( ) const
pure virtual

◆ corrected_coordinate()

core::Real core::conformation::membrane::MembraneGeometry::corrected_coordinate ( core::Vector const &  xyz,
core::Vector const &  x_axis 
) const
protected

◆ corrected_xyz()

core::Vector core::conformation::membrane::MembraneGeometry::corrected_xyz ( Conformation const &  conf,
core::Size  resnum,
core::Size  atomnum 
) const

References core::conformation::Residue::atom(), binormal_vector(), corrected_coordinate(), core::conformation::Conformation::membrane_info(), normal_vector(), core::conformation::Conformation::residue(), thickness_vector(), core::conformation::Atom::xyz(), and protocols::kinmatch::xyz().

Referenced by core::conformation::membrane::membrane_geometry::Bicelle::f_transition(), core::conformation::membrane::membrane_geometry::DoubleVesicle::f_transition(), core::conformation::membrane::membrane_geometry::Slab::f_transition(), core::conformation::membrane::membrane_geometry::Vesicle::f_transition(), core::conformation::membrane::membrane_geometry::Bicelle::f_transition_deriv(), core::conformation::membrane::membrane_geometry::DoubleVesicle::f_transition_deriv(), core::conformation::membrane::membrane_geometry::Slab::f_transition_deriv(), core::conformation::membrane::membrane_geometry::Vesicle::f_transition_deriv(), core::conformation::membrane::membrane_geometry::Bicelle::f_transition_deriv_m(), core::conformation::membrane::membrane_geometry::Bicelle::f_transition_f1(), core::conformation::membrane::membrane_geometry::DoubleVesicle::f_transition_f1(), core::conformation::membrane::membrane_geometry::Slab::f_transition_f1(), core::conformation::membrane::membrane_geometry::Vesicle::f_transition_f1(), core::conformation::membrane::membrane_geometry::Bicelle::f_transition_f2(), core::conformation::membrane::membrane_geometry::DoubleVesicle::f_transition_f2(), core::conformation::membrane::membrane_geometry::Slab::f_transition_f2(), core::conformation::membrane::membrane_geometry::Vesicle::f_transition_f2(), core::conformation::membrane::membrane_geometry::DoubleVesicle::r_alpha(), core::conformation::membrane::membrane_geometry::Vesicle::r_alpha(), and core::conformation::membrane::membrane_geometry::Bicelle::r_alpha_m().

◆ f1()

core::Vector core::conformation::membrane::MembraneGeometry::f1 ( core::Vector const &  atom_xyz,
core::Vector const &  r_alpha,
core::Real  deriv 
) const

◆ f1_pore()

core::Vector core::conformation::membrane::MembraneGeometry::f1_pore ( core::Real  f_thk,
numeric::xyzVector< core::Real > const &  xyz,
Conformation const &  conf,
core::Size  resnum,
core::Size  atomnum 
) const

◆ f2()

core::Vector core::conformation::membrane::MembraneGeometry::f2 ( core::Vector const &  atom_xyz,
core::Vector const &  r_alpha,
core::Real  deriv 
) const

◆ f2_pore()

core::Vector core::conformation::membrane::MembraneGeometry::f2_pore ( core::Real  f_thk,
numeric::xyzVector< core::Real > const &  xyz,
Conformation const &  conf,
core::Size  resnum,
core::Size  atomnum 
) const

◆ f_cavity()

core::Real core::conformation::membrane::MembraneGeometry::f_cavity ( numeric::xyzVector< core::Real > const &  p) const

Calculate the hydration of an atom based on its location relative to an aqueous pore or cavity.

References g_radius(), and pore_transition_steepness_.

Referenced by f_hydration(), and f_hydration_deriv_dz().

◆ f_cavity_dx()

core::Real core::conformation::membrane::MembraneGeometry::f_cavity_dx ( numeric::xyzVector< core::Real > const &  p,
core::Real  f_thk 
) const

◆ f_cavity_dy()

core::Real core::conformation::membrane::MembraneGeometry::f_cavity_dy ( numeric::xyzVector< core::Real > const &  p,
core::Real  f_thk 
) const

◆ f_cavity_dz()

core::Real core::conformation::membrane::MembraneGeometry::f_cavity_dz ( numeric::xyzVector< core::Real > const &  p,
core::Real  f_thk 
) const

◆ f_cavity_gradient()

core::Real core::conformation::membrane::MembraneGeometry::f_cavity_gradient ( core::Real const  r) const

Calculate the derivative of f_cavity (without any r(x,y,z) dependence)

References pore_transition_steepness_.

Referenced by f_cavity_dx(), f_cavity_dy(), and f_cavity_dz().

◆ f_franklin()

core::Real core::conformation::membrane::MembraneGeometry::f_franklin ( core::Real const  z,
core::Real  tau,
core::Real  kappa 
) const

References protocols::antibody::kappa.

Referenced by f_thickness().

◆ f_franklin_gradient()

core::Real core::conformation::membrane::MembraneGeometry::f_franklin_gradient ( core::Real const  z,
core::Real  tau,
core::Real  kappa 
) const

◆ f_hydration()

core::Real core::conformation::membrane::MembraneGeometry::f_hydration ( core::Real  f_thk,
numeric::xyzVector< core::Real > const &  p 
) const

◆ f_hydration_deriv_dz()

core::Real core::conformation::membrane::MembraneGeometry::f_hydration_deriv_dz ( numeric::xyzVector< core::Real > const &  p,
core::Real  f_thk_deriv_dz 
) const

◆ f_imm1()

core::Real core::conformation::membrane::MembraneGeometry::f_imm1 ( core::Real  z_position) const

◆ f_imm1_deriv()

core::Real core::conformation::membrane::MembraneGeometry::f_imm1_deriv ( core::Real  z_position) const

◆ f_thickness()

core::Real core::conformation::membrane::MembraneGeometry::f_thickness ( Conformation const &  conf,
core::Real const  z 
) const

◆ f_thickness_deriv()

core::Real core::conformation::membrane::MembraneGeometry::f_thickness_deriv ( Conformation const &  conf,
core::Real const  z 
) const

◆ f_transition()

virtual core::Real core::conformation::membrane::MembraneGeometry::f_transition ( Conformation const &  conf,
core::Size  resnum,
core::Size  atomnum 
) const
pure virtual

◆ f_transition_f1()

virtual core::Vector core::conformation::membrane::MembraneGeometry::f_transition_f1 ( Conformation const &  conf,
core::Size  resnum,
core::Size  atomnum 
) const
pure virtual

◆ f_transition_f2()

virtual core::Vector core::conformation::membrane::MembraneGeometry::f_transition_f2 ( Conformation const &  conf,
core::Size  resnum,
core::Size  atomnum 
) const
pure virtual

◆ g_radius()

core::Real core::conformation::membrane::MembraneGeometry::g_radius ( numeric::xyzVector< core::Real > const &  p) const

Calculate the location of an atom relative to the pore structure.

References pore_params_.

Referenced by f_cavity(), f_cavity_dx(), f_cavity_dy(), and f_cavity_dz().

◆ g_radius_gradient_dx()

core::Real core::conformation::membrane::MembraneGeometry::g_radius_gradient_dx ( numeric::xyzVector< core::Real > const &  p) const

◆ g_radius_gradient_dy()

core::Real core::conformation::membrane::MembraneGeometry::g_radius_gradient_dy ( numeric::xyzVector< core::Real > const &  p) const

◆ g_radius_gradient_dz()

core::Real core::conformation::membrane::MembraneGeometry::g_radius_gradient_dz ( numeric::xyzVector< core::Real > const &  p) const

◆ geometry_enum()

virtual MP_GEOMETRY_TRANSITION core::conformation::membrane::MembraneGeometry::geometry_enum ( ) const
pure virtual

◆ geometry_string()

virtual std::string core::conformation::membrane::MembraneGeometry::geometry_string ( ) const
pure virtual

◆ has_pore()

bool core::conformation::membrane::MembraneGeometry::has_pore ( ) const

◆ membrane_steepness()

core::Real core::conformation::membrane::MembraneGeometry::membrane_steepness ( ) const
virtual

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

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

References steepness_.

Referenced by f_imm1(), f_imm1_deriv(), and core::conformation::membrane::membrane_geometry::Bicelle::update_edge_steepness().

◆ membrane_thickness()

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

◆ normal_vector()

core::Vector core::conformation::membrane::MembraneGeometry::normal_vector ( Conformation const &  conf) const
protected

◆ r_alpha_p_x()

core::Vector core::conformation::membrane::MembraneGeometry::r_alpha_p_x ( numeric::xyzVector< core::Real > const &  xyz) const

◆ r_alpha_p_y()

core::Vector core::conformation::membrane::MembraneGeometry::r_alpha_p_y ( numeric::xyzVector< core::Real > const &  xyz) const

◆ r_alpha_p_z()

core::Vector core::conformation::membrane::MembraneGeometry::r_alpha_p_z ( Conformation const &  conf,
core::Size  resnum,
core::Size  atomnum 
) const

◆ set_aqueous_pore_parameters()

void core::conformation::membrane::MembraneGeometry::set_aqueous_pore_parameters ( AqueousPoreParametersOP  aqueous_pore)

Set membrane aqueous pore parameters.

References pore_params_.

Referenced by MembraneGeometry().

◆ show() [1/2]

virtual void core::conformation::membrane::MembraneGeometry::show ( ) const
pure virtual

◆ show() [2/2]

virtual void core::conformation::membrane::MembraneGeometry::show ( std::ostream &  output) const
pure virtual

◆ thickness_vector()

core::Vector core::conformation::membrane::MembraneGeometry::thickness_vector ( Conformation const &  conf) const
protected

Member Data Documentation

◆ pore_params_

core::conformation::membrane::AqueousPoreParametersOP core::conformation::membrane::MembraneGeometry::pore_params_
private

◆ pore_transition_steepness_

core::Real core::conformation::membrane::MembraneGeometry::pore_transition_steepness_
private

Referenced by f_cavity(), and f_cavity_gradient().

◆ steepness_

core::Real core::conformation::membrane::MembraneGeometry::steepness_
private

Referenced by membrane_steepness().

◆ thickness_

core::Real core::conformation::membrane::MembraneGeometry::thickness_
private

Referenced by membrane_thickness().


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