#include <Slab.hh>

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

Public Member Functions
	Slab (core::Real steepness)

	Slab (core::Real steepness, core::Real thickness)

	Slab (core::Real steepness, core::Real thickness, AqueousPoreParametersOP aqueous_pore)

	~Slab () override
	Destructor. More...

MembraneGeometryOP	clone () const override

void	show () const override
	Generate a string representation of information represented by Slab. More...

void	show (std::ostream &output) const override
	Generate a string representation of information represented by this MembraneGeometry. More...

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	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

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

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

◆ Slab() [1/3]

core::conformation::membrane::membrane_geometry::Slab::Slab ( core::Real steepness )

Referenced by clone().

◆ Slab() [2/3]

core::conformation::membrane::membrane_geometry::Slab::Slab	(	core::Real	steepness,
		core::Real	thickness
	)

◆ Slab() [3/3]

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

◆ ~Slab()

core::conformation::membrane::membrane_geometry::Slab::~Slab ( )

override

Destructor.

Member Function Documentation

◆ clone()

MembraneGeometryOP core::conformation::membrane::membrane_geometry::Slab::clone ( ) const

overridevirtual

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

References Slab().

◆ f_transition()

core::Real core::conformation::membrane::membrane_geometry::Slab::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(), core::conformation::membrane::MembraneGeometry::f_hydration(), core::conformation::membrane::MembraneGeometry::f_thickness(), and protocols::kinmatch::xyz().

◆ f_transition_deriv()

core::Real core::conformation::membrane::membrane_geometry::Slab::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_deriv(), core::conformation::membrane::MembraneGeometry::has_pore(), and protocols::kinmatch::xyz().

Referenced by f_transition_f1(), and f_transition_f2().

◆ f_transition_f1()

core::Vector core::conformation::membrane::membrane_geometry::Slab::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(), core::conformation::membrane::MembraneGeometry::f_thickness(), f_transition_deriv(), core::conformation::membrane::MembraneGeometry::has_pore(), r_alpha(), and protocols::kinmatch::xyz().

◆ f_transition_f2()

core::Vector core::conformation::membrane::membrane_geometry::Slab::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(), core::conformation::membrane::MembraneGeometry::f_thickness(), f_transition_deriv(), core::conformation::membrane::MembraneGeometry::has_pore(), r_alpha(), and protocols::kinmatch::xyz().

◆ fa_elec_lipid()

core::Real core::conformation::membrane::membrane_geometry::Slab::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(), and protocols::kinmatch::xyz().

◆ fa_elec_lipid_deriv()

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