#include <Bicelle.hh>

Inheritance diagram for core::conformation::membrane::membrane_geometry::Bicelle:

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::Real	fa_elec_lipid (Conformation const &conf, core::Size resnum, core::Size atomnum) const override

core::Real	fa_elec_lipid_deriv (Conformation const &conf, core::Size resnum, core::Size atomnum) const override

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
	)

References protein_slice_diameter_at_mem_cen(), and set_protein_slice_diameter().

◆ Bicelle() [2/5]

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

References protein_slice_diameter_at_mem_cen(), and set_protein_slice_diameter().

◆ Bicelle() [3/5]

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

References bicelle_inner_radius(), set_inner_radius(), and update_outer_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
	)

References bicelle_inner_radius(), set_inner_radius(), and update_outer_radius().

◆ ~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

References bicelle_edge_steepness_.

◆ 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

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

References Bicelle().

◆ 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

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

Referenced by f_transition(), f_transition_f1(), and f_transition_f2().

◆ f_transition()

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

overridevirtual

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

References core::conformation::membrane::MembraneGeometry::corrected_xyz(), f_bicelle(), core::conformation::membrane::MembraneGeometry::f_hydration(), core::conformation::membrane::MembraneGeometry::f_thickness(), core::conformation::Conformation::membrane_info(), and protocols::kinmatch::xyz().

◆ f_transition_deriv()

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

References core::conformation::membrane::MembraneGeometry::corrected_xyz(), core::conformation::membrane::MembraneGeometry::f_hydration_deriv_dz(), core::conformation::membrane::MembraneGeometry::f_thickness(), h_bicelle_deriv_wrt_r(), core::conformation::membrane::MembraneGeometry::has_pore(), core::conformation::Conformation::membrane_info(), and protocols::kinmatch::xyz().

Referenced by f_transition_f1(), and f_transition_f2().

◆ 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

References core::conformation::membrane::MembraneGeometry::corrected_xyz(), core::conformation::membrane::MembraneGeometry::f_hydration_deriv_dz(), core::conformation::membrane::MembraneGeometry::f_thickness_deriv(), h_bicelle(), core::conformation::membrane::MembraneGeometry::has_pore(), core::conformation::Conformation::membrane_info(), and protocols::kinmatch::xyz().

Referenced by f_transition_f1(), and f_transition_f2().

◆ 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

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

References core::conformation::membrane::MembraneGeometry::corrected_xyz(), core::conformation::membrane::MembraneGeometry::f1(), core::conformation::membrane::MembraneGeometry::f1_pore(), f_bicelle(), core::conformation::membrane::MembraneGeometry::f_thickness(), f_transition_deriv(), f_transition_deriv_m(), core::conformation::membrane::MembraneGeometry::has_pore(), core::conformation::Conformation::membrane_info(), r_alpha(), r_alpha_m(), and protocols::kinmatch::xyz().

◆ 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

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

References core::conformation::membrane::MembraneGeometry::corrected_xyz(), core::conformation::membrane::MembraneGeometry::f2(), core::conformation::membrane::MembraneGeometry::f2_pore(), f_bicelle(), core::conformation::membrane::MembraneGeometry::f_thickness(), f_transition_deriv(), f_transition_deriv_m(), core::conformation::membrane::MembraneGeometry::has_pore(), core::conformation::Conformation::membrane_info(), r_alpha(), r_alpha_m(), and protocols::kinmatch::xyz().

◆ fa_elec_lipid()

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

overridevirtual

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

References core::conformation::membrane::MembraneGeometry::corrected_xyz(), core::conformation::Conformation::membrane_info(), core::conformation::TR(), and protocols::kinmatch::xyz().

◆ fa_elec_lipid_deriv()

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

overridevirtual

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

References core::conformation::membrane::MembraneGeometry::corrected_xyz(), core::conformation::Conformation::membrane_info(), core::conformation::TR(), and protocols::kinmatch::xyz().

◆ geometry_enum()

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

overridevirtual

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

References core::conformation::membrane::BICELLE.

◆ geometry_string()

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

overridevirtual

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

◆ h_bicelle()

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

private

References bicelle_edge_steepness_, bicelle_outer_radius_, and protocols::kinmatch::xyz().

Referenced by f_bicelle(), and f_transition_deriv_m().

◆ 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

References bicelle_edge_steepness_, bicelle_outer_radius_, and protocols::kinmatch::xyz().

Referenced by f_transition_deriv().

◆ protein_slice_diameter()

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

References protein_slice_diameter_.

◆ 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

References core::conformation::Residue::atom(), core::conformation::membrane::center, core::conformation::membrane::MembraneGeometry::corrected_coordinate(), core::conformation::membrane::normal, core::conformation::Conformation::residue(), core::conformation::Conformation::size(), core::conformation::membrane::thickness, and core::conformation::Atom::xyz().

Referenced by Bicelle().

◆ r_alpha()

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

References core::conformation::Conformation::membrane_info().

Referenced by f_transition_f1(), and f_transition_f2().

◆ r_alpha_m()

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