Rosetta
Public Member Functions | Private Member Functions | Private Attributes | List of all members
core::conformation::membrane::membrane_geometry::Bicelle Class Reference

#include <Bicelle.hh>

Inheritance diagram for core::conformation::membrane::membrane_geometry::Bicelle:
Inheritance graph
[legend]

Public Member Functions

 Bicelle (core::Real steepness, Conformation const &conf, core::Size membrane_pos)
 
 Bicelle (core::Real steepness, core::Real thickness, Conformation const &conf, core::Size membrane_pos)
 
 Bicelle (core::Real steepness, core::Real thickness, core::Real bicelle_inner_radius)
 
 Bicelle (core::Real steepness, core::Real thickness, core::Real bicelle_inner_radius, AqueousPoreParametersOP aqueous_pore)
 
 ~Bicelle () override
 Destructor. More...
 
MembraneGeometryOP clone () const override
 
void show () const override
 Generate a string representation of information represented by Bicelle. More...
 
void show (std::ostream &output) const override
 Generate a string representation of information represented by this MembraneGeometry. More...
 
void update_radii ()
 
void set_protein_slice_diameter (core::Real diameter)
 
void set_inner_radius (core::Real inner_r)
 
void set_outer_radius (core::Real outer_r)
 
void set_bicelle_edge_steepness (core::Real edge_steepness)
 
core::Real protein_slice_diameter () const
 
core::Real bicelle_edge_steepness () const
 
core::Real bicelle_inner_radius () const
 
core::Real bicelle_outer_radius () const
 
core::Real f_transition (Conformation const &conf, core::Size resnum, core::Size atomnum) const override
 
core::Real f_transition_deriv (Conformation const &conf, core::Size resnum, core::Size atomnum) const
 
core::Vector r_alpha (Conformation const &conf, core::Size resnum, core::Size atomnum) const
 
core::Vector r_alpha_m (Conformation const &conf, core::Size resnum, core::Size atomnum) const
 
core::Vector f_transition_f1 (Conformation const &conf, core::Size resnum, core::Size atomnum) const override
 
core::Vector f_transition_f2 (Conformation const &conf, core::Size resnum, core::Size atomnum) const override
 
core::Real f_transition_deriv_m (Conformation const &conf, core::Size resnum, core::Size atomnum) const
 
std::string geometry_string () const override
 
MP_GEOMETRY_TRANSITION geometry_enum () const override
 
- Public Member Functions inherited from core::conformation::membrane::MembraneGeometry
 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...
 
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 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
 

Private Member Functions

 Bicelle ()
 
void update_edge_steepness ()
 
core::Real protein_slice_diameter_at_mem_cen (Conformation const &conf, core::Size membrane_pos) const
 
void update_inner_radius ()
 
void update_outer_radius ()
 
core::Real h_bicelle (core::Vector xyz, const core::Vector mem_cen) const
 
core::Real f_bicelle (core::Real f_z, core::Vector xyz, const core::Vector mem_cen) const
 
core::Real h_bicelle_deriv_wrt_r (core::Vector xyz, const core::Vector mem_cen) const
 

Private Attributes

core::Real bicelle_inner_radius_ = 0.0
 
core::Real bicelle_outer_radius_ = 0.0
 
core::Real bicelle_edge_steepness_ = 0.0
 
core::Real protein_slice_diameter_ = 0.0
 

Additional Inherited Members

- Protected Member Functions inherited from core::conformation::membrane::MembraneGeometry
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
 

Constructor & Destructor Documentation

◆ Bicelle() [1/5]

core::conformation::membrane::membrane_geometry::Bicelle::Bicelle ( core::Real  steepness,
Conformation const &  conf,
core::Size  membrane_pos 
)

◆ Bicelle() [2/5]

core::conformation::membrane::membrane_geometry::Bicelle::Bicelle ( core::Real  steepness,
core::Real  thickness,
Conformation const &  conf,
core::Size  membrane_pos 
)

◆ Bicelle() [3/5]

core::conformation::membrane::membrane_geometry::Bicelle::Bicelle ( core::Real  steepness,
core::Real  thickness,
core::Real  bicelle_inner_radius 
)

◆ Bicelle() [4/5]

core::conformation::membrane::membrane_geometry::Bicelle::Bicelle ( core::Real  steepness,
core::Real  thickness,
core::Real  bicelle_inner_radius,
AqueousPoreParametersOP  aqueous_pore 
)

◆ ~Bicelle()

core::conformation::membrane::membrane_geometry::Bicelle::~Bicelle ( )
override

Destructor.

◆ Bicelle() [5/5]

core::conformation::membrane::membrane_geometry::Bicelle::Bicelle ( )
private

Referenced by clone().

Member Function Documentation

◆ bicelle_edge_steepness()

core::Real core::conformation::membrane::membrane_geometry::Bicelle::bicelle_edge_steepness ( ) const

◆ bicelle_inner_radius()

core::Real core::conformation::membrane::membrane_geometry::Bicelle::bicelle_inner_radius ( ) const

References bicelle_inner_radius_.

Referenced by Bicelle().

◆ bicelle_outer_radius()

core::Real core::conformation::membrane::membrane_geometry::Bicelle::bicelle_outer_radius ( ) const

References bicelle_outer_radius_.

◆ clone()

MembraneGeometryOP core::conformation::membrane::membrane_geometry::Bicelle::clone ( ) const
overridevirtual

◆ f_bicelle()

core::Real core::conformation::membrane::membrane_geometry::Bicelle::f_bicelle ( core::Real  f_z,
core::Vector  xyz,
const core::Vector  mem_cen 
) const
private

◆ f_transition()

core::Real core::conformation::membrane::membrane_geometry::Bicelle::f_transition ( Conformation const &  conf,
core::Size  resnum,
core::Size  atomnum 
) const
overridevirtual

◆ f_transition_deriv()

core::Real core::conformation::membrane::membrane_geometry::Bicelle::f_transition_deriv ( Conformation const &  conf,
core::Size  resnum,
core::Size  atomnum 
) const

◆ f_transition_deriv_m()

core::Real core::conformation::membrane::membrane_geometry::Bicelle::f_transition_deriv_m ( Conformation const &  conf,
core::Size  resnum,
core::Size  atomnum 
) const

◆ f_transition_f1()

core::Vector core::conformation::membrane::membrane_geometry::Bicelle::f_transition_f1 ( Conformation const &  conf,
core::Size  resnum,
core::Size  atomnum 
) const
overridevirtual

◆ f_transition_f2()

core::Vector core::conformation::membrane::membrane_geometry::Bicelle::f_transition_f2 ( Conformation const &  conf,
core::Size  resnum,
core::Size  atomnum 
) const
overridevirtual

◆ geometry_enum()

MP_GEOMETRY_TRANSITION core::conformation::membrane::membrane_geometry::Bicelle::geometry_enum ( ) const
overridevirtual

◆ geometry_string()

std::string core::conformation::membrane::membrane_geometry::Bicelle::geometry_string ( ) const
overridevirtual

◆ h_bicelle()

core::Real core::conformation::membrane::membrane_geometry::Bicelle::h_bicelle ( core::Vector  xyz,
const core::Vector  mem_cen 
) const
private

◆ h_bicelle_deriv_wrt_r()

core::Real core::conformation::membrane::membrane_geometry::Bicelle::h_bicelle_deriv_wrt_r ( core::Vector  xyz,
const core::Vector  mem_cen 
) const
private

◆ protein_slice_diameter()

core::Real core::conformation::membrane::membrane_geometry::Bicelle::protein_slice_diameter ( ) const

◆ protein_slice_diameter_at_mem_cen()

core::Real core::conformation::membrane::membrane_geometry::Bicelle::protein_slice_diameter_at_mem_cen ( Conformation const &  conf,
core::Size  membrane_pos 
) const
private

◆ r_alpha()

core::Vector core::conformation::membrane::membrane_geometry::Bicelle::r_alpha ( Conformation const &  conf,
core::Size  resnum,
core::Size  atomnum 
) const

◆ r_alpha_m()

core::Vector core::conformation::membrane::membrane_geometry::Bicelle::r_alpha_m ( Conformation const &  conf,
core::Size  resnum,
core::Size  atomnum 
) const

◆ set_bicelle_edge_steepness()

void core::conformation::membrane::membrane_geometry::Bicelle::set_bicelle_edge_steepness ( core::Real  edge_steepness)

◆ set_inner_radius()

void core::conformation::membrane::membrane_geometry::Bicelle::set_inner_radius ( core::Real  inner_r)

◆ set_outer_radius()

void core::conformation::membrane::membrane_geometry::Bicelle::set_outer_radius ( core::Real  outer_r)

◆ set_protein_slice_diameter()

void core::conformation::membrane::membrane_geometry::Bicelle::set_protein_slice_diameter ( core::Real  diameter)

◆ show() [1/2]

void core::conformation::membrane::membrane_geometry::Bicelle::show ( ) const
overridevirtual

Generate a string representation of information represented by Bicelle.

Implements core::conformation::membrane::MembraneGeometry.

◆ show() [2/2]

void core::conformation::membrane::membrane_geometry::Bicelle::show ( std::ostream &  output) const
overridevirtual

Generate a string representation of information represented by this MembraneGeometry.

Implements core::conformation::membrane::MembraneGeometry.

References bicelle_inner_radius_.

◆ update_edge_steepness()

void core::conformation::membrane::membrane_geometry::Bicelle::update_edge_steepness ( )
private

◆ update_inner_radius()

void core::conformation::membrane::membrane_geometry::Bicelle::update_inner_radius ( )
private

◆ update_outer_radius()

void core::conformation::membrane::membrane_geometry::Bicelle::update_outer_radius ( )
private

◆ update_radii()

void core::conformation::membrane::membrane_geometry::Bicelle::update_radii ( )

Member Data Documentation

◆ bicelle_edge_steepness_

core::Real core::conformation::membrane::membrane_geometry::Bicelle::bicelle_edge_steepness_ = 0.0
private

◆ bicelle_inner_radius_

core::Real core::conformation::membrane::membrane_geometry::Bicelle::bicelle_inner_radius_ = 0.0
private

◆ bicelle_outer_radius_

core::Real core::conformation::membrane::membrane_geometry::Bicelle::bicelle_outer_radius_ = 0.0
private

◆ protein_slice_diameter_

core::Real core::conformation::membrane::membrane_geometry::Bicelle::protein_slice_diameter_ = 0.0
private

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