core::conformation::membrane::membrane_geometry::DoubleVesicle Class Reference

#include <DoubleVesicle.hh>

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

Public Member Functions
	DoubleVesicle (core::Real steepness)
	DoubleVesicle (core::Real steepness, core::Real thickness)
	DoubleVesicle (core::Real steepness, core::Real thickness, core::Real inner_radius, core::Real distance)
	DoubleVesicle (core::Real steepness, core::Real thickness, core::Real inner_radius, core::Real distance, AqueousPoreParametersOP aqueous_pore)
	~DoubleVesicle () override
	Destructor. More...
MembraneGeometryOP	clone () const override
void	show () const override
	Generate a string representation of information represented by DoubleVesicle. More...
void	show (std::ostream &output) const override
	Generate a string representation of information represented by this MembraneGeometry. More...
void	set_distance (core::Real distance)
void	set_outer_radius (core::Real outer_r)
void	set_inner_radius (core::Real inner_r)
void	update_radii ()
core::Real	get_outer_radius () const
core::Real	get_inner_radius () const
core::Real	get_distance () 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	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

Protected Member Functions
core::Real	center (core::Vector xyz) const
core::Real	f_vesicle_membrane (Conformation const &conf, core::Vector xyz, core::Real radius) const
core::Real	f_double_vesicle (Conformation const &conf, core::Vector xyz) const
core::Real	f_deriv (Conformation const &conf, core::Vector xyz, core::Real radius) const
core::Real	f_vesicle_deriv (Conformation const &conf, core::Vector xyz) const
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

Private Attributes
core::Real	outer_radius_
core::Real	inner_radius_
core::Real	distance_

Constructor & Destructor Documentation

DoubleVesicle() [1/4]

core::conformation::membrane::membrane_geometry::DoubleVesicle::DoubleVesicle

(

core::Real

steepness

)

References update_radii().

Referenced by clone().

DoubleVesicle() [2/4]

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

References update_radii().

DoubleVesicle() [3/4]

core::conformation::membrane::membrane_geometry::DoubleVesicle::DoubleVesicle	(	core::Real	steepness,
		core::Real	thickness,
		core::Real	inner_radius,
		core::Real	distance
	)

References core::kinematics::distance(), set_distance(), and set_inner_radius().

DoubleVesicle() [4/4]

core::conformation::membrane::membrane_geometry::DoubleVesicle::DoubleVesicle	(	core::Real	steepness,
		core::Real	thickness,
		core::Real	inner_radius,
		core::Real	distance,
		AqueousPoreParametersOP	aqueous_pore
	)

References core::kinematics::distance(), set_distance(), and set_inner_radius().

~DoubleVesicle()

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

override

Destructor.

Member Function Documentation

center()

core::Real core::conformation::membrane::membrane_geometry::DoubleVesicle::center ( core::Vector  xyz ) const

protected

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

Referenced by f_deriv(), and f_vesicle_membrane().

clone()

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

overridevirtual

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

References DoubleVesicle().

f_deriv()

core::Real core::conformation::membrane::membrane_geometry::DoubleVesicle::f_deriv ( Conformation const &  conf, core::Vector  xyz, core::Real  radius  ) const

protected

References center(), core::conformation::membrane::MembraneGeometry::f_thickness_deriv(), and protocols::kinmatch::xyz().

Referenced by f_vesicle_deriv().

f_double_vesicle()

core::Real core::conformation::membrane::membrane_geometry::DoubleVesicle::f_double_vesicle ( Conformation const &  conf, core::Vector  xyz  ) const

protected

References f_vesicle_membrane(), inner_radius_, outer_radius_, and protocols::kinmatch::xyz().

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

f_transition()

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

f_transition_deriv()

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

References core::conformation::membrane::MembraneGeometry::corrected_xyz(), f_vesicle_deriv(), and protocols::kinmatch::xyz().

Referenced by f_transition_f1(), and f_transition_f2().

f_transition_f1()

core::Vector core::conformation::membrane::membrane_geometry::DoubleVesicle::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_double_vesicle(), f_transition_deriv(), core::conformation::membrane::MembraneGeometry::has_pore(), core::conformation::Conformation::membrane_info(), r_alpha(), and protocols::kinmatch::xyz().

f_transition_f2()

core::Vector core::conformation::membrane::membrane_geometry::DoubleVesicle::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_double_vesicle(), f_transition_deriv(), core::conformation::membrane::MembraneGeometry::has_pore(), core::conformation::Conformation::membrane_info(), r_alpha(), and protocols::kinmatch::xyz().

f_vesicle_deriv()

core::Real core::conformation::membrane::membrane_geometry::DoubleVesicle::f_vesicle_deriv ( Conformation const &  conf, core::Vector  xyz  ) const

protected

References f_deriv(), f_vesicle_membrane(), inner_radius_, outer_radius_, and protocols::kinmatch::xyz().

Referenced by f_transition_deriv().

f_vesicle_membrane()

core::Real core::conformation::membrane::membrane_geometry::DoubleVesicle::f_vesicle_membrane ( Conformation const &  conf, core::Vector  xyz, core::Real  radius  ) const

protected

References center(), core::conformation::membrane::MembraneGeometry::f_thickness(), and protocols::kinmatch::xyz().

Referenced by f_double_vesicle(), and f_vesicle_deriv().

fa_elec_lipid()

core::Real core::conformation::membrane::membrane_geometry::DoubleVesicle::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::DoubleVesicle::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::DoubleVesicle::geometry_enum ( ) const

overridevirtual

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

References core::conformation::membrane::DOUBLE_VESICLE.

geometry_string()

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

overridevirtual

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

get_distance()

core::Real core::conformation::membrane::membrane_geometry::DoubleVesicle::get_distance

(

)

const

References distance_.

get_inner_radius()

core::Real core::conformation::membrane::membrane_geometry::DoubleVesicle::get_inner_radius

(

)

const

References inner_radius_.

get_outer_radius()

core::Real core::conformation::membrane::membrane_geometry::DoubleVesicle::get_outer_radius

(

)

const

References outer_radius_.

r_alpha()

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

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

Referenced by f_transition_f1(), and f_transition_f2().

set_distance()

void core::conformation::membrane::membrane_geometry::DoubleVesicle::set_distance

(

core::Real

distance

)

References core::kinematics::distance(), distance_, inner_radius_, core::conformation::membrane::MembraneGeometry::membrane_thickness(), set_outer_radius(), and core::conformation::TR().

Referenced by DoubleVesicle(), and update_radii().

set_inner_radius()

void core::conformation::membrane::membrane_geometry::DoubleVesicle::set_inner_radius

(

core::Real

inner_r

)

References inner_radius_, and core::conformation::TR().

Referenced by DoubleVesicle(), and update_radii().

set_outer_radius()

void core::conformation::membrane::membrane_geometry::DoubleVesicle::set_outer_radius

(

core::Real

outer_r

)

References inner_radius_, outer_radius_, and core::conformation::TR().

Referenced by set_distance(), and update_radii().

show() [1/2]

void core::conformation::membrane::membrane_geometry::DoubleVesicle::show ( ) const

overridevirtual

Generate a string representation of information represented by DoubleVesicle.

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

show() [2/2]

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

overridevirtual

Generate a string representation of information represented by this MembraneGeometry.

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

References inner_radius_, and outer_radius_.

update_radii()

void core::conformation::membrane::membrane_geometry::DoubleVesicle::update_radii

(

)

References distance_, inner_radius_, core::conformation::membrane::MembraneGeometry::membrane_thickness(), outer_radius_, set_distance(), set_inner_radius(), set_outer_radius(), and core::conformation::TR().

Referenced by DoubleVesicle().

Member Data Documentation

distance_

core::Real core::conformation::membrane::membrane_geometry::DoubleVesicle::distance_

private

Referenced by get_distance(), set_distance(), and update_radii().

inner_radius_

core::Real core::conformation::membrane::membrane_geometry::DoubleVesicle::inner_radius_

private

Referenced by center(), f_double_vesicle(), f_vesicle_deriv(), get_inner_radius(), r_alpha(), set_distance(), set_inner_radius(), set_outer_radius(), show(), and update_radii().

outer_radius_

core::Real core::conformation::membrane::membrane_geometry::DoubleVesicle::outer_radius_

private

Referenced by f_double_vesicle(), f_vesicle_deriv(), get_outer_radius(), set_outer_radius(), show(), and update_radii().

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

• src/core/conformation/membrane/membrane_geometry/DoubleVesicle.hh
• src/core/conformation/membrane/membrane_geometry/DoubleVesicle.cc