Definition of an implicit membrane with parameters for different lipid compositions. More...

#include <ImplicitLipidInfo.hh>

Inheritance diagram for core::conformation::membrane::ImplicitLipidInfo:

Public Member Functions
	ImplicitLipidInfo (std::string lipid_composition_name, core::Real temperature)
	Custom constructor for ImplicitLipidInfo. More...

	~ImplicitLipidInfo () override

ImplicitLipidInfoOP	clone () const

virtual void	show (std::ostream &output) const
	Generate a string representation of information represented by ths Lipid MembraneInfo. More...

std::string	chain_type () const
	Number of carbons and degrees of saturation in the chains. More...

std::string	headgroup_type () const
	Chemical name of the headgroup. More...

std::string	lipid_composition_name () const
	Abbreviated name of the lipid composition. More...

std::string	lipid_composition_name_long () const
	Full name of the lipid composiiton. More...

core::Real	degrees_of_saturation () const
	Number of degrees of saturation in the overall lipid. More...

core::Real	temperature () const
	Temperature at which the Db parameter was measured/calculated (in celcius) More...

bool	is_helical () const
	Is the protein alpha helical or beta barrel. More...

void	is_helical (bool const is_helical)

void	make_no_pore_parameters ()
	Make a set of parameters for the case with no pore. More...

core::Real	pore_center_x (core::Real const zcoord) const
	Membrane Aqueous pore center - h parameter. More...

core::Real	pore_center_y (core::Real const zcoord) const
	Membrane aqueous pore center - k parameter. More...

core::Real	pore_major_radius (core::Real const zcoord) const
	Membrane aqueous pore - major radius. More...

core::Real	pore_minor_radius (core::Real const zcoord) const
	Membrane aqueous pore - minor radius. More...

numeric::MathMatrix< core::Real >	pore_rotation (core::Real const zcoord) const
	Membrane aqueous pore - rotation matrix. More...

void	set_aqueous_pore_parameters (AqueousPoreParametersOP aqueous_pore)
	Set membrane aqueous pore parameters. More...

core::Real	water_thickness () const
	Water thickness of the membrane @detail Thickness of the membrane, defined by the pair of z coordinates with a water density of 50% (SAXS Db value) More...

core::Real	water_steepness () const
	Change in water density from membrane core to water bulk water @detail Steepness defined by the number of waters lost per increase in z from the membrane center (s = b) More...

void	water_steepness (core::Real const v)
	Access function to change the value of the transition steepness @detail Only change the steepness for the alpha v. beta case. More...

core::Real	water_pseudo_thickness () const
	Pseudo-thickness parameter. More...

void	water_pseudo_thickness (core::Real const p)
	Access function to change the value of the pseudo-thickness parameter. More...

core::Real	f_elec_field (core::Real z) const
	Calculates the electric field due to lipid layer, water and salt based on pre-calculated fitting parameters from md-runs. More...

core::Real	f_elec_field_gradient (core::Real z) const
	Calculates the gradient of electric field. More...

void	initialize_implicit_lipid_parameters ()
	Helper function to initialize the lipid composiiton data. More...

void	initialize_implicit_lipid_electricfield_parameters ()
	Helper function to initialize the electrostatic properties of lipid layer. More...

Private Types
typedef utility::vector1< numeric::CubicPolynomial >	piecewise_poly

Private Member Functions
	ImplicitLipidInfo ()

Private Attributes
core::Real	water_thickness_

core::Real	change_in_water_density_

core::Real	transformed_water_thickness_

core::Real	center_a_

core::Real	center_b_

core::Real	center_c_

core::Real	center_d_

core::Real	center_e_

core::Real	center_root_

core::Real	pp_a_

core::Real	pp_b_

core::Real	pp_c_

core::Real	pp_d_

std::string	chain_type_

std::string	headgroup_type_

std::string	lipid_composition_name_

std::string	lipid_composition_name_long_

core::Real	degrees_of_saturation_

core::Real	temperature_

bool	is_helical_

AqueousPoreParametersOP	pore_params_

Detailed Description

Definition of an implicit membrane with parameters for different lipid compositions.

Member Typedef Documentation

◆ piecewise_poly

typedef utility::vector1< numeric::CubicPolynomial > core::conformation::membrane::ImplicitLipidInfo::piecewise_poly

private

Constructor & Destructor Documentation

◆ ImplicitLipidInfo() [1/2]

core::conformation::membrane::ImplicitLipidInfo::ImplicitLipidInfo	(	std::string	lipid_composition_name,
		core::Real	temperature
	)

Custom constructor for ImplicitLipidInfo.

References initialize_implicit_lipid_electricfield_parameters(), and initialize_implicit_lipid_parameters().

◆ ~ImplicitLipidInfo()

core::conformation::membrane::ImplicitLipidInfo::~ImplicitLipidInfo ( )

override

◆ ImplicitLipidInfo() [2/2]

core::conformation::membrane::ImplicitLipidInfo::ImplicitLipidInfo ( )

private

Referenced by clone().

Member Function Documentation

◆ chain_type()

std::string core::conformation::membrane::ImplicitLipidInfo::chain_type ( ) const

Number of carbons and degrees of saturation in the chains.

References chain_type_.

Referenced by initialize_implicit_lipid_parameters().

◆ clone()

ImplicitLipidInfoOP core::conformation::membrane::ImplicitLipidInfo::clone ( ) const

References ImplicitLipidInfo().

◆ degrees_of_saturation()

core::Real core::conformation::membrane::ImplicitLipidInfo::degrees_of_saturation ( ) const

Number of degrees of saturation in the overall lipid.

References degrees_of_saturation_.

Referenced by initialize_implicit_lipid_parameters().

◆ f_elec_field()

core::Real core::conformation::membrane::ImplicitLipidInfo::f_elec_field ( core::Real z ) const

Calculates the electric field due to lipid layer, water and salt based on pre-calculated fitting parameters from md-runs.

Overall hydration given the atomic depth and cavity structure.

References center_a_, center_b_, center_c_, center_d_, center_e_, center_root_, pp_a_, pp_b_, pp_c_, and pp_d_.

◆ f_elec_field_gradient()

core::Real core::conformation::membrane::ImplicitLipidInfo::f_elec_field_gradient ( core::Real z ) const

Calculates the gradient of electric field.

Gradient.

References center_a_, center_b_, center_c_, center_d_, center_root_, pp_a_, pp_b_, pp_c_, and pp_d_.

◆ headgroup_type()

std::string core::conformation::membrane::ImplicitLipidInfo::headgroup_type ( ) const

Chemical name of the headgroup.

References headgroup_type_.

Referenced by initialize_implicit_lipid_parameters().

◆ initialize_implicit_lipid_electricfield_parameters()

void core::conformation::membrane::ImplicitLipidInfo::initialize_implicit_lipid_electricfield_parameters ( )

Helper function to initialize the electrostatic properties of lipid layer.

Helper function to initialize the lipid composiiton data.

References center_a_, center_b_, center_c_, center_d_, center_e_, center_root_, lipid_composition_name_, pp_a_, pp_b_, pp_c_, pp_d_, and core::conformation::TR().

Referenced by ImplicitLipidInfo().

◆ initialize_implicit_lipid_parameters()

void core::conformation::membrane::ImplicitLipidInfo::initialize_implicit_lipid_parameters ( )

Helper function to initialize the lipid composiiton data.

References chain_type(), chain_type_, change_in_water_density_, degrees_of_saturation(), degrees_of_saturation_, headgroup_type(), headgroup_type_, lipid_composition_name(), lipid_composition_name_, lipid_composition_name_long(), lipid_composition_name_long_, temperature(), temperature_, core::id::to_string(), transformed_water_thickness_, water_thickness(), and water_thickness_.

Referenced by ImplicitLipidInfo().

◆ is_helical() [1/2]

bool core::conformation::membrane::ImplicitLipidInfo::is_helical ( ) const

Is the protein alpha helical or beta barrel.

References is_helical_.

Referenced by is_helical().

◆ is_helical() [2/2]

void core::conformation::membrane::ImplicitLipidInfo::is_helical ( bool const is_helical )

References is_helical(), and is_helical_.

◆ lipid_composition_name()

std::string core::conformation::membrane::ImplicitLipidInfo::lipid_composition_name ( ) const

Abbreviated name of the lipid composition.

References lipid_composition_name_.

Referenced by initialize_implicit_lipid_parameters().

◆ lipid_composition_name_long()

std::string core::conformation::membrane::ImplicitLipidInfo::lipid_composition_name_long ( ) const

Full name of the lipid composiiton.

References lipid_composition_name_long_.

Referenced by initialize_implicit_lipid_parameters().

◆ make_no_pore_parameters()

void core::conformation::membrane::ImplicitLipidInfo::make_no_pore_parameters ( )

Make a set of parameters for the case with no pore.

Make empty pore parameters.

References pore_params_.

◆ pore_center_x()

core::Real core::conformation::membrane::ImplicitLipidInfo::pore_center_x ( core::Real const zcoord ) const

Membrane Aqueous pore center - h parameter.

References pore_params_.

◆ pore_center_y()

core::Real core::conformation::membrane::ImplicitLipidInfo::pore_center_y ( core::Real const zcoord ) const

Membrane aqueous pore center - k parameter.

References pore_params_.

◆ pore_major_radius()

core::Real core::conformation::membrane::ImplicitLipidInfo::pore_major_radius ( core::Real const zcoord ) const

Membrane aqueous pore - major radius.

References pore_params_.

◆ pore_minor_radius()

core::Real core::conformation::membrane::ImplicitLipidInfo::pore_minor_radius ( core::Real const zcoord ) const

Membrane aqueous pore - minor radius.

References pore_params_.

◆ pore_rotation()

numeric::MathMatrix< core::Real > core::conformation::membrane::ImplicitLipidInfo::pore_rotation ( core::Real const zcoord ) const

Membrane aqueous pore - rotation matrix.

References pore_params_.

◆ set_aqueous_pore_parameters()

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

Set membrane aqueous pore parameters.

References pore_params_.

◆ show()

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

virtual

Generate a string representation of information represented by ths Lipid MembraneInfo.

References chain_type_, change_in_water_density_, degrees_of_saturation_, headgroup_type_, is_helical_, lipid_composition_name_, lipid_composition_name_long_, temperature_, transformed_water_thickness_, and water_thickness_.

◆ temperature()

core::Real core::conformation::membrane::ImplicitLipidInfo::temperature ( ) const

Temperature at which the Db parameter was measured/calculated (in celcius)

References temperature_.

Referenced by initialize_implicit_lipid_parameters().

◆ water_pseudo_thickness() [1/2]

core::Real core::conformation::membrane::ImplicitLipidInfo::water_pseudo_thickness ( ) const

Pseudo-thickness parameter.

A parameter in the expotential membrane definition t = -(1/b) * ln(1/A)

References transformed_water_thickness_.

◆ water_pseudo_thickness() [2/2]

void core::conformation::membrane::ImplicitLipidInfo::water_pseudo_thickness ( core::Real const p )

inline

Access function to change the value of the pseudo-thickness parameter.

A parameter in the logistic membrane definition

References transformed_water_thickness_.

◆ water_steepness() [1/2]

core::Real core::conformation::membrane::ImplicitLipidInfo::water_steepness ( ) const

Change in water density from membrane core to water bulk water @detail Steepness defined by the number of waters lost per increase in z from the membrane center (s = b)

References change_in_water_density_.