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 (ImplicitLipidInfo const &src)

ImplicitLipidInfo &	operator= (ImplicitLipidInfo const &src)

	~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	has_pore () const
	Does this protein have a water-filled pore? More...

void	has_pore (bool const is_there_a_pore)

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	per_atom_lipid_accessibility (core::Size rsd, core::Size atom) const
	Per-atom accessibility to membrane lipids (0 = not exposed, 50 = exposed) More...

void	set_per_atom_lipid_accessibility (utility::vector1< utility::vector1< core::Real > > v)
	Per-atom accessibility to membrane lipids (0 = not exposed, 50 = exposed) More...

core::Real	water_thickness () const
	Water thickness of the membrane 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 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 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_depth (core::Real const z) const
	UNDER CONSTRUCTION - Derivative functions ///. More...

core::Real	f_depth_gradient (core::Real const z) const
	Ccalcculate the gradient of f_depth. More...

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	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 (numeric::xyzVector< core::Real > const &p) const
	Calcuclate the gradient of f_cavity More...

core::Real	f_hydration (numeric::xyzVector< core::Real > const &p) const
	Overall hydration given the atomic depth and cavity structure. More...

core::Real	f_hydration_gradient (numeric::xyzVector< core::Real > const &p) const
	Gradient. More...

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

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	has_pore_

bool	is_helical_

AqueousPoreParametersOP	pore_params_

core::Real	pore_transition_steepness_

utility::vector1 < utility::vector1< core::Real > >	per_atom_lipid_accessibility_

Detailed Description

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

Member Typedef Documentation

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

private

Constructor & Destructor Documentation

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

Custom constructor for ImplicitLipidInfo.

References initialize_implicit_lipid_parameters().

core::conformation::membrane::ImplicitLipidInfo::ImplicitLipidInfo ( ImplicitLipidInfo const & src )

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

override

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

private

Referenced by clone().

Member Function Documentation

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().

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

References ImplicitLipidInfo().

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().

core::Real core::conformation::membrane::ImplicitLipidInfo::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.

References g_radius(), and pore_transition_steepness_.

Referenced by f_hydration(), and f_hydration_gradient().

core::Real core::conformation::membrane::ImplicitLipidInfo::f_cavity_gradient ( core::Real const r ) const

Calculate the derivative of f_cavity (without any r(x,y,z) dependence)

References pore_transition_steepness_.

Referenced by g_radius_gradient().

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

UNDER CONSTRUCTION - Derivative functions ///.

Calcuclate the hydration of an atom based on its location in a lipid-specific implicit bilayer.

Calcuclate the hydration of an atom based on its location in a lipid-specific implicit bilayer

References core::pose::motif::a(), protocols::match::upstream::b, change_in_water_density_, and transformed_water_thickness_.

Referenced by f_hydration(), and f_hydration_gradient().

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

Ccalcculate the gradient of f_depth.

References core::pose::motif::a(), protocols::match::upstream::b, change_in_water_density_, and transformed_water_thickness_.

Referenced by f_hydration_gradient().

core::Real core::conformation::membrane::ImplicitLipidInfo::f_hydration ( numeric::xyzVector< core::Real > const & p ) const

Overall hydration given the atomic depth and cavity structure.

References f_cavity(), f_depth(), has_pore_, and protocols::analysis::total.

core::Real core::conformation::membrane::ImplicitLipidInfo::f_hydration_gradient ( numeric::xyzVector< core::Real > const & p ) const

Gradient.

References f_cavity(), f_depth(), f_depth_gradient(), g_radius_gradient(), and has_pore_.

core::Real core::conformation::membrane::ImplicitLipidInfo::g_radius ( numeric::xyzVector< core::Real > const & p ) const

Calculate the location of an atom relative to the pore structure.

References pore_center_x(), pore_center_y(), pore_major_radius(), pore_minor_radius(), and pore_params_.

Referenced by f_cavity(), and g_radius_gradient().

core::Real core::conformation::membrane::ImplicitLipidInfo::g_radius_gradient ( numeric::xyzVector< core::Real > const & p ) const

Calcuclate the gradient of f_cavity

References f_cavity_gradient(), g_radius(), pore_params_, and protocols::hybridization::t.

Referenced by f_hydration_gradient().

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

Does this protein have a water-filled pore?

Are we accommodating the aqueous pore?

References has_pore_.

void core::conformation::membrane::ImplicitLipidInfo::has_pore ( bool const is_there_a_pore )

References has_pore_.

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

Chemical name of the headgroup.

References headgroup_type_.

Referenced by 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().

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

Is the protein alpha helical or beta barrel.

References is_helical_.

Referenced by is_helical().

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

References is_helical(), and is_helical_.

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().

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().

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_.

ImplicitLipidInfo & core::conformation::membrane::ImplicitLipidInfo::operator= ( ImplicitLipidInfo const & src )

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

core::Real core::conformation::membrane::ImplicitLipidInfo::per_atom_lipid_accessibility	(	core::Size	rsd,
		core::Size	atom
	)		const

Per-atom accessibility to membrane lipids (0 = not exposed, 50 = exposed)

Per-atom accessibility to membrane lipids (0 = not exposed, 15 = exposed)

References per_atom_lipid_accessibility_.

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

Membrane Aqueous pore center - h parameter.

References pore_params_.

Referenced by g_radius().

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

Membrane aqueous pore center - k parameter.

References pore_params_.

Referenced by g_radius().

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

Membrane aqueous pore - major radius.

References pore_params_.

Referenced by g_radius().

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

Membrane aqueous pore - minor radius.

References pore_params_.

Referenced by g_radius().

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

Membrane aqueous pore - rotation matrix.

References pore_params_.

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

Set membrane aqueous pore parameters.

References pore_params_.

void core::conformation::membrane::ImplicitLipidInfo::set_per_atom_lipid_accessibility ( utility::vector1< utility::vector1< core::Real > > v )

Per-atom accessibility to membrane lipids (0 = not exposed, 50 = exposed)

Per-atom accessibility to membrane lipids.

References per_atom_lipid_accessibility_.

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_, has_pore_, headgroup_type_, is_helical_, lipid_composition_name_, lipid_composition_name_long_, temperature_, transformed_water_thickness_, and water_thickness_.

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().

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_.

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_.

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

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

References change_in_water_density_.

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

inline

Access function to change the value of the transition steepness Only change the steepness for the alpha v. beta case.

References change_in_water_density_.

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

Water thickness of the membrane Thickness of the membrane, defined by the pair of z coordinates with a water density of 50% (SAXS Db value)

References water_thickness_.

Referenced by initialize_implicit_lipid_parameters().

Member Data Documentation

std::string core::conformation::membrane::ImplicitLipidInfo::chain_type_

private

Referenced by chain_type(), initialize_implicit_lipid_parameters(), operator=(), and show().

core::Real core::conformation::membrane::ImplicitLipidInfo::change_in_water_density_

private

Referenced by f_depth(), f_depth_gradient(), initialize_implicit_lipid_parameters(), operator=(), show(), and water_steepness().

core::Real core::conformation::membrane::ImplicitLipidInfo::degrees_of_saturation_

private

Referenced by degrees_of_saturation(), initialize_implicit_lipid_parameters(), operator=(), and show().

bool core::conformation::membrane::ImplicitLipidInfo::has_pore_

private

Referenced by f_hydration(), f_hydration_gradient(), has_pore(), operator=(), and show().

std::string core::conformation::membrane::ImplicitLipidInfo::headgroup_type_

private

Referenced by headgroup_type(), initialize_implicit_lipid_parameters(), operator=(), and show().

bool core::conformation::membrane::ImplicitLipidInfo::is_helical_

private

Referenced by is_helical(), operator=(), and show().

std::string core::conformation::membrane::ImplicitLipidInfo::lipid_composition_name_

private

Referenced by initialize_implicit_lipid_parameters(), lipid_composition_name(), operator=(), and show().

std::string core::conformation::membrane::ImplicitLipidInfo::lipid_composition_name_long_

private

Referenced by initialize_implicit_lipid_parameters(), lipid_composition_name_long(), operator=(), and show().

utility::vector1< utility::vector1< core::Real > > core::conformation::membrane::ImplicitLipidInfo::per_atom_lipid_accessibility_

private

Referenced by operator=(), per_atom_lipid_accessibility(), and set_per_atom_lipid_accessibility().

AqueousPoreParametersOP core::conformation::membrane::ImplicitLipidInfo::pore_params_

private

Referenced by g_radius(), g_radius_gradient(), make_no_pore_parameters(), pore_center_x(), pore_center_y(), pore_major_radius(), pore_minor_radius(), pore_rotation(), and set_aqueous_pore_parameters().

core::Real core::conformation::membrane::ImplicitLipidInfo::pore_transition_steepness_

private

Referenced by f_cavity(), f_cavity_gradient(), and operator=().

core::Real core::conformation::membrane::ImplicitLipidInfo::temperature_

private

Referenced by initialize_implicit_lipid_parameters(), operator=(), show(), and temperature().

core::Real core::conformation::membrane::ImplicitLipidInfo::transformed_water_thickness_

private

Referenced by f_depth(), f_depth_gradient(), initialize_implicit_lipid_parameters(), operator=(), show(), and water_pseudo_thickness().

core::Real core::conformation::membrane::ImplicitLipidInfo::water_thickness_

private

Referenced by initialize_implicit_lipid_parameters(), operator=(), show(), and water_thickness().

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

src/core/conformation/membrane/ImplicitLipidInfo.hh
src/core/conformation/membrane/ImplicitLipidInfo.cc

Public Member Functions

Private Types

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation