membrane_geometry

Bindings for core::conformation::membrane::membrane_geometry namespace

class pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle

Bases: MembraneGeometry

assign(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle, : pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle) → pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle

C++: core::conformation::membrane::membrane_geometry::Bicelle::operator=(const class core::conformation::membrane::membrane_geometry::Bicelle &) –> class core::conformation::membrane::membrane_geometry::Bicelle &

bicelle_edge_steepness(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle) → float

C++: core::conformation::membrane::membrane_geometry::Bicelle::bicelle_edge_steepness() const –> double

bicelle_inner_radius(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle) → float

C++: core::conformation::membrane::membrane_geometry::Bicelle::bicelle_inner_radius() const –> double

bicelle_outer_radius(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle) → float

C++: core::conformation::membrane::membrane_geometry::Bicelle::bicelle_outer_radius() const –> double

clone(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle) → pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry

C++: core::conformation::membrane::membrane_geometry::Bicelle::clone() const –> class std::shared_ptr<class core::conformation::membrane::MembraneGeometry>

corrected_xyz(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, conf: pyrosetta.rosetta.core.conformation.Conformation, resnum: int, atomnum: int) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::conformation::membrane::MembraneGeometry::corrected_xyz(const class core::conformation::Conformation &, unsigned long, unsigned long) const –> class numeric::xyzVector<double>

f1(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, atom_xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, r_alpha: pyrosetta.rosetta.numeric.xyzVector_double_t, deriv: float) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::conformation::membrane::MembraneGeometry::f1(const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, double) const –> class numeric::xyzVector<double>

f1_pore(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, f_thk: float, xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, conf: pyrosetta.rosetta.core.conformation.Conformation, resnum: int, atomnum: int) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::conformation::membrane::MembraneGeometry::f1_pore(double, const class numeric::xyzVector<double> &, const class core::conformation::Conformation &, unsigned long, unsigned long) const –> class numeric::xyzVector<double>

f2(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, atom_xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, r_alpha: pyrosetta.rosetta.numeric.xyzVector_double_t, deriv: float) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::conformation::membrane::MembraneGeometry::f2(const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, double) const –> class numeric::xyzVector<double>

f2_pore(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, f_thk: float, xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, conf: pyrosetta.rosetta.core.conformation.Conformation, resnum: int, atomnum: int) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::conformation::membrane::MembraneGeometry::f2_pore(double, const class numeric::xyzVector<double> &, const class core::conformation::Conformation &, unsigned long, unsigned long) const –> class numeric::xyzVector<double>

f_cavity(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, p: pyrosetta.rosetta.numeric.xyzVector_double_t) → float

Calculate the hydration of an atom based on its location relative to

an aqueous pore or cavity

C++: core::conformation::membrane::MembraneGeometry::f_cavity(const class numeric::xyzVector<double> &) const –> double

f_cavity_dx(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, p: pyrosetta.rosetta.numeric.xyzVector_double_t, f_thk: float) → float

C++: core::conformation::membrane::MembraneGeometry::f_cavity_dx(const class numeric::xyzVector<double> &, double) const –> double

f_cavity_dy(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, p: pyrosetta.rosetta.numeric.xyzVector_double_t, f_thk: float) → float

C++: core::conformation::membrane::MembraneGeometry::f_cavity_dy(const class numeric::xyzVector<double> &, double) const –> double

f_cavity_dz(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, p: pyrosetta.rosetta.numeric.xyzVector_double_t, f_thk: float) → float

C++: core::conformation::membrane::MembraneGeometry::f_cavity_dz(const class numeric::xyzVector<double> &, double) const –> double

f_cavity_gradient(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, r: float) → float

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

C++: core::conformation::membrane::MembraneGeometry::f_cavity_gradient(const double) const –> double

f_franklin(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, z: float, tau: float, kappa: float) → float

C++: core::conformation::membrane::MembraneGeometry::f_franklin(const double, double, double) const –> double

f_franklin_gradient(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, z: float, tau: float, kappa: float) → float

C++: core::conformation::membrane::MembraneGeometry::f_franklin_gradient(const double, double, double) const –> double

f_hydration(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, f_thk: float, p: pyrosetta.rosetta.numeric.xyzVector_double_t) → float

C++: core::conformation::membrane::MembraneGeometry::f_hydration(double, const class numeric::xyzVector<double> &) const –> double

f_hydration_deriv_dz(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, p: pyrosetta.rosetta.numeric.xyzVector_double_t, f_thk_deriv_dz: float) → float

C++: core::conformation::membrane::MembraneGeometry::f_hydration_deriv_dz(const class numeric::xyzVector<double> &, double) const –> double

f_imm1(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, z_position: float) → float

C++: core::conformation::membrane::MembraneGeometry::f_imm1(double) const –> double

f_imm1_deriv(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, z_position: float) → float

C++: core::conformation::membrane::MembraneGeometry::f_imm1_deriv(double) const –> double

f_thickness(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, conf: pyrosetta.rosetta.core.conformation.Conformation, z: float) → float

C++: core::conformation::membrane::MembraneGeometry::f_thickness(const class core::conformation::Conformation &, const double) const –> double

f_thickness_deriv(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, conf: pyrosetta.rosetta.core.conformation.Conformation, z: float) → float

C++: core::conformation::membrane::MembraneGeometry::f_thickness_deriv(const class core::conformation::Conformation &, const double) const –> double

f_transition(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle, conf: pyrosetta.rosetta.core.conformation.Conformation, resnum: int, atomnum: int) → float

C++: core::conformation::membrane::membrane_geometry::Bicelle::f_transition(const class core::conformation::Conformation &, unsigned long, unsigned long) const –> double

f_transition_deriv(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle, conf: pyrosetta.rosetta.core.conformation.Conformation, resnum: int, atomnum: int) → float

C++: core::conformation::membrane::membrane_geometry::Bicelle::f_transition_deriv(const class core::conformation::Conformation &, unsigned long, unsigned long) const –> double

f_transition_deriv_m(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle, conf: pyrosetta.rosetta.core.conformation.Conformation, resnum: int, atomnum: int) → float

C++: core::conformation::membrane::membrane_geometry::Bicelle::f_transition_deriv_m(const class core::conformation::Conformation &, unsigned long, unsigned long) const –> double

f_transition_f1(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle, conf: pyrosetta.rosetta.core.conformation.Conformation, resnum: int, atomnum: int) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::conformation::membrane::membrane_geometry::Bicelle::f_transition_f1(const class core::conformation::Conformation &, unsigned long, unsigned long) const –> class numeric::xyzVector<double>

f_transition_f2(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle, conf: pyrosetta.rosetta.core.conformation.Conformation, resnum: int, atomnum: int) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::conformation::membrane::membrane_geometry::Bicelle::f_transition_f2(const class core::conformation::Conformation &, unsigned long, unsigned long) const –> class numeric::xyzVector<double>

g_radius(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, p: pyrosetta.rosetta.numeric.xyzVector_double_t) → float

Calculate the location of an atom relative to the pore structure

C++: core::conformation::membrane::MembraneGeometry::g_radius(const class numeric::xyzVector<double> &) const –> double

g_radius_gradient_dx(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, p: pyrosetta.rosetta.numeric.xyzVector_double_t) → float

C++: core::conformation::membrane::MembraneGeometry::g_radius_gradient_dx(const class numeric::xyzVector<double> &) const –> double

g_radius_gradient_dy(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, p: pyrosetta.rosetta.numeric.xyzVector_double_t) → float

C++: core::conformation::membrane::MembraneGeometry::g_radius_gradient_dy(const class numeric::xyzVector<double> &) const –> double

g_radius_gradient_dz(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, p: pyrosetta.rosetta.numeric.xyzVector_double_t) → float

C++: core::conformation::membrane::MembraneGeometry::g_radius_gradient_dz(const class numeric::xyzVector<double> &) const –> double

geometry_enum(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle) → pyrosetta.rosetta.core.conformation.membrane.MP_GEOMETRY_TRANSITION

C++: core::conformation::membrane::membrane_geometry::Bicelle::geometry_enum() const –> enum core::conformation::membrane::MP_GEOMETRY_TRANSITION

geometry_string(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle) → str

C++: core::conformation::membrane::membrane_geometry::Bicelle::geometry_string() const –> std::string

has_pore(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry) → bool

Does this protein have a water-filled pore?

C++: core::conformation::membrane::MembraneGeometry::has_pore() const –> bool

membrane_steepness(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry) → float

Steepness of hydrophobic -> hydrophillic transition (defualt = 10)

C++: core::conformation::membrane::MembraneGeometry::membrane_steepness() const –> double

membrane_thickness(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry) → float

Effective thickness of the membrane (default = 15)

C++: core::conformation::membrane::MembraneGeometry::membrane_thickness() const –> double

protein_slice_diameter(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle) → float

C++: core::conformation::membrane::membrane_geometry::Bicelle::protein_slice_diameter() const –> double

r_alpha(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle, conf: pyrosetta.rosetta.core.conformation.Conformation, resnum: int, atomnum: int) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::conformation::membrane::membrane_geometry::Bicelle::r_alpha(const class core::conformation::Conformation &, unsigned long, unsigned long) const –> class numeric::xyzVector<double>

r_alpha_m(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle, conf: pyrosetta.rosetta.core.conformation.Conformation, resnum: int, atomnum: int) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::conformation::membrane::membrane_geometry::Bicelle::r_alpha_m(const class core::conformation::Conformation &, unsigned long, unsigned long) const –> class numeric::xyzVector<double>

r_alpha_p_x(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, xyz: pyrosetta.rosetta.numeric.xyzVector_double_t) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::conformation::membrane::MembraneGeometry::r_alpha_p_x(const class numeric::xyzVector<double> &) const –> class numeric::xyzVector<double>

r_alpha_p_y(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, xyz: pyrosetta.rosetta.numeric.xyzVector_double_t) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::conformation::membrane::MembraneGeometry::r_alpha_p_y(const class numeric::xyzVector<double> &) const –> class numeric::xyzVector<double>

r_alpha_p_z(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, conf: pyrosetta.rosetta.core.conformation.Conformation, resnum: int, atomnum: int) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::conformation::membrane::MembraneGeometry::r_alpha_p_z(const class core::conformation::Conformation &, unsigned long, unsigned long) const –> class numeric::xyzVector<double>

set_aqueous_pore_parameters(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, aqueous_pore: pyrosetta.rosetta.core.conformation.membrane.AqueousPoreParameters) → None

Set membrane aqueous pore parameters

C++: core::conformation::membrane::MembraneGeometry::set_aqueous_pore_parameters(class std::shared_ptr<class core::conformation::membrane::AqueousPoreParameters>) –> void

set_bicelle_edge_steepness(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle, edge_steepness: float) → None

C++: core::conformation::membrane::membrane_geometry::Bicelle::set_bicelle_edge_steepness(double) –> void

set_inner_radius(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle, inner_r: float) → None

C++: core::conformation::membrane::membrane_geometry::Bicelle::set_inner_radius(double) –> void

set_outer_radius(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle, outer_r: float) → None

C++: core::conformation::membrane::membrane_geometry::Bicelle::set_outer_radius(double) –> void

set_protein_slice_diameter(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle, diameter: float) → None

C++: core::conformation::membrane::membrane_geometry::Bicelle::set_protein_slice_diameter(double) –> void

show(*args, **kwargs)

Overloaded function.

1. show(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle) -> None

C++: core::conformation::membrane::membrane_geometry::Bicelle::show() const –> void

2. show(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle, output: pyrosetta.rosetta.std.ostream) -> None

C++: core::conformation::membrane::membrane_geometry::Bicelle::show(std::ostream &) const –> void

update_radii(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Bicelle) → None

C++: core::conformation::membrane::membrane_geometry::Bicelle::update_radii() –> void

class pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle

Bases: MembraneGeometry

assign(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle, : pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle) → pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle

C++: core::conformation::membrane::membrane_geometry::DoubleVesicle::operator=(const class core::conformation::membrane::membrane_geometry::DoubleVesicle &) –> class core::conformation::membrane::membrane_geometry::DoubleVesicle &

clone(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle) → pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry

C++: core::conformation::membrane::membrane_geometry::DoubleVesicle::clone() const –> class std::shared_ptr<class core::conformation::membrane::MembraneGeometry>

corrected_xyz(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, conf: pyrosetta.rosetta.core.conformation.Conformation, resnum: int, atomnum: int) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::conformation::membrane::MembraneGeometry::corrected_xyz(const class core::conformation::Conformation &, unsigned long, unsigned long) const –> class numeric::xyzVector<double>

f1(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, atom_xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, r_alpha: pyrosetta.rosetta.numeric.xyzVector_double_t, deriv: float) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::conformation::membrane::MembraneGeometry::f1(const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, double) const –> class numeric::xyzVector<double>

f1_pore(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, f_thk: float, xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, conf: pyrosetta.rosetta.core.conformation.Conformation, resnum: int, atomnum: int) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::conformation::membrane::MembraneGeometry::f1_pore(double, const class numeric::xyzVector<double> &, const class core::conformation::Conformation &, unsigned long, unsigned long) const –> class numeric::xyzVector<double>

f2(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, atom_xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, r_alpha: pyrosetta.rosetta.numeric.xyzVector_double_t, deriv: float) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::conformation::membrane::MembraneGeometry::f2(const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, double) const –> class numeric::xyzVector<double>

f2_pore(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, f_thk: float, xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, conf: pyrosetta.rosetta.core.conformation.Conformation, resnum: int, atomnum: int) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::conformation::membrane::MembraneGeometry::f2_pore(double, const class numeric::xyzVector<double> &, const class core::conformation::Conformation &, unsigned long, unsigned long) const –> class numeric::xyzVector<double>

f_cavity(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, p: pyrosetta.rosetta.numeric.xyzVector_double_t) → float

Calculate the hydration of an atom based on its location relative to

an aqueous pore or cavity

C++: core::conformation::membrane::MembraneGeometry::f_cavity(const class numeric::xyzVector<double> &) const –> double

f_cavity_dx(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, p: pyrosetta.rosetta.numeric.xyzVector_double_t, f_thk: float) → float

C++: core::conformation::membrane::MembraneGeometry::f_cavity_dx(const class numeric::xyzVector<double> &, double) const –> double

f_cavity_dy(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, p: pyrosetta.rosetta.numeric.xyzVector_double_t, f_thk: float) → float

C++: core::conformation::membrane::MembraneGeometry::f_cavity_dy(const class numeric::xyzVector<double> &, double) const –> double

f_cavity_dz(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, p: pyrosetta.rosetta.numeric.xyzVector_double_t, f_thk: float) → float

C++: core::conformation::membrane::MembraneGeometry::f_cavity_dz(const class numeric::xyzVector<double> &, double) const –> double

f_cavity_gradient(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, r: float) → float

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

C++: core::conformation::membrane::MembraneGeometry::f_cavity_gradient(const double) const –> double

f_franklin(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, z: float, tau: float, kappa: float) → float

C++: core::conformation::membrane::MembraneGeometry::f_franklin(const double, double, double) const –> double

f_franklin_gradient(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, z: float, tau: float, kappa: float) → float

C++: core::conformation::membrane::MembraneGeometry::f_franklin_gradient(const double, double, double) const –> double

f_hydration(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, f_thk: float, p: pyrosetta.rosetta.numeric.xyzVector_double_t) → float

C++: core::conformation::membrane::MembraneGeometry::f_hydration(double, const class numeric::xyzVector<double> &) const –> double

f_hydration_deriv_dz(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, p: pyrosetta.rosetta.numeric.xyzVector_double_t, f_thk_deriv_dz: float) → float

C++: core::conformation::membrane::MembraneGeometry::f_hydration_deriv_dz(const class numeric::xyzVector<double> &, double) const –> double

f_imm1(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, z_position: float) → float

C++: core::conformation::membrane::MembraneGeometry::f_imm1(double) const –> double

f_imm1_deriv(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, z_position: float) → float

C++: core::conformation::membrane::MembraneGeometry::f_imm1_deriv(double) const –> double

f_thickness(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, conf: pyrosetta.rosetta.core.conformation.Conformation, z: float) → float

C++: core::conformation::membrane::MembraneGeometry::f_thickness(const class core::conformation::Conformation &, const double) const –> double

f_thickness_deriv(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, conf: pyrosetta.rosetta.core.conformation.Conformation, z: float) → float

C++: core::conformation::membrane::MembraneGeometry::f_thickness_deriv(const class core::conformation::Conformation &, const double) const –> double

f_transition(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle, conf: pyrosetta.rosetta.core.conformation.Conformation, resnum: int, atomnum: int) → float

C++: core::conformation::membrane::membrane_geometry::DoubleVesicle::f_transition(const class core::conformation::Conformation &, unsigned long, unsigned long) const –> double

f_transition_deriv(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle, conf: pyrosetta.rosetta.core.conformation.Conformation, resnum: int, atomnum: int) → float

C++: core::conformation::membrane::membrane_geometry::DoubleVesicle::f_transition_deriv(const class core::conformation::Conformation &, unsigned long, unsigned long) const –> double

f_transition_f1(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle, conf: pyrosetta.rosetta.core.conformation.Conformation, resnum: int, atomnum: int) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::conformation::membrane::membrane_geometry::DoubleVesicle::f_transition_f1(const class core::conformation::Conformation &, unsigned long, unsigned long) const –> class numeric::xyzVector<double>

f_transition_f2(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle, conf: pyrosetta.rosetta.core.conformation.Conformation, resnum: int, atomnum: int) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::conformation::membrane::membrane_geometry::DoubleVesicle::f_transition_f2(const class core::conformation::Conformation &, unsigned long, unsigned long) const –> class numeric::xyzVector<double>

g_radius(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, p: pyrosetta.rosetta.numeric.xyzVector_double_t) → float

Calculate the location of an atom relative to the pore structure

C++: core::conformation::membrane::MembraneGeometry::g_radius(const class numeric::xyzVector<double> &) const –> double

g_radius_gradient_dx(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, p: pyrosetta.rosetta.numeric.xyzVector_double_t) → float

C++: core::conformation::membrane::MembraneGeometry::g_radius_gradient_dx(const class numeric::xyzVector<double> &) const –> double

g_radius_gradient_dy(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, p: pyrosetta.rosetta.numeric.xyzVector_double_t) → float

C++: core::conformation::membrane::MembraneGeometry::g_radius_gradient_dy(const class numeric::xyzVector<double> &) const –> double

g_radius_gradient_dz(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, p: pyrosetta.rosetta.numeric.xyzVector_double_t) → float

C++: core::conformation::membrane::MembraneGeometry::g_radius_gradient_dz(const class numeric::xyzVector<double> &) const –> double

geometry_enum(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle) → pyrosetta.rosetta.core.conformation.membrane.MP_GEOMETRY_TRANSITION

C++: core::conformation::membrane::membrane_geometry::DoubleVesicle::geometry_enum() const –> enum core::conformation::membrane::MP_GEOMETRY_TRANSITION

geometry_string(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle) → str

C++: core::conformation::membrane::membrane_geometry::DoubleVesicle::geometry_string() const –> std::string

get_distance(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle) → float

C++: core::conformation::membrane::membrane_geometry::DoubleVesicle::get_distance() const –> double

get_inner_radius(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle) → float

C++: core::conformation::membrane::membrane_geometry::DoubleVesicle::get_inner_radius() const –> double

get_outer_radius(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle) → float

C++: core::conformation::membrane::membrane_geometry::DoubleVesicle::get_outer_radius() const –> double

has_pore(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry) → bool

Does this protein have a water-filled pore?

C++: core::conformation::membrane::MembraneGeometry::has_pore() const –> bool

membrane_steepness(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry) → float

Steepness of hydrophobic -> hydrophillic transition (defualt = 10)

C++: core::conformation::membrane::MembraneGeometry::membrane_steepness() const –> double

membrane_thickness(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry) → float

Effective thickness of the membrane (default = 15)

C++: core::conformation::membrane::MembraneGeometry::membrane_thickness() const –> double

r_alpha(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle, conf: pyrosetta.rosetta.core.conformation.Conformation, resnum: int, atomnum: int) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::conformation::membrane::membrane_geometry::DoubleVesicle::r_alpha(const class core::conformation::Conformation &, unsigned long, unsigned long) const –> class numeric::xyzVector<double>

r_alpha_p_x(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, xyz: pyrosetta.rosetta.numeric.xyzVector_double_t) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::conformation::membrane::MembraneGeometry::r_alpha_p_x(const class numeric::xyzVector<double> &) const –> class numeric::xyzVector<double>

r_alpha_p_y(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, xyz: pyrosetta.rosetta.numeric.xyzVector_double_t) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::conformation::membrane::MembraneGeometry::r_alpha_p_y(const class numeric::xyzVector<double> &) const –> class numeric::xyzVector<double>

r_alpha_p_z(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, conf: pyrosetta.rosetta.core.conformation.Conformation, resnum: int, atomnum: int) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::conformation::membrane::MembraneGeometry::r_alpha_p_z(const class core::conformation::Conformation &, unsigned long, unsigned long) const –> class numeric::xyzVector<double>

set_aqueous_pore_parameters(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, aqueous_pore: pyrosetta.rosetta.core.conformation.membrane.AqueousPoreParameters) → None

Set membrane aqueous pore parameters

C++: core::conformation::membrane::MembraneGeometry::set_aqueous_pore_parameters(class std::shared_ptr<class core::conformation::membrane::AqueousPoreParameters>) –> void

set_distance(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle, distance: float) → None

C++: core::conformation::membrane::membrane_geometry::DoubleVesicle::set_distance(double) –> void

set_inner_radius(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle, inner_r: float) → None

C++: core::conformation::membrane::membrane_geometry::DoubleVesicle::set_inner_radius(double) –> void

set_outer_radius(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle, outer_r: float) → None

C++: core::conformation::membrane::membrane_geometry::DoubleVesicle::set_outer_radius(double) –> void

show(*args, **kwargs)

Overloaded function.

1. show(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle) -> None

C++: core::conformation::membrane::membrane_geometry::DoubleVesicle::show() const –> void

2. show(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle, output: pyrosetta.rosetta.std.ostream) -> None

C++: core::conformation::membrane::membrane_geometry::DoubleVesicle::show(std::ostream &) const –> void

update_radii(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.DoubleVesicle) → None

C++: core::conformation::membrane::membrane_geometry::DoubleVesicle::update_radii() –> void

class pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Slab

Bases: MembraneGeometry

assign(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Slab, : pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Slab) → pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Slab

C++: core::conformation::membrane::membrane_geometry::Slab::operator=(const class core::conformation::membrane::membrane_geometry::Slab &) –> class core::conformation::membrane::membrane_geometry::Slab &

clone(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Slab) → pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry

C++: core::conformation::membrane::membrane_geometry::Slab::clone() const –> class std::shared_ptr<class core::conformation::membrane::MembraneGeometry>

corrected_xyz(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, conf: pyrosetta.rosetta.core.conformation.Conformation, resnum: int, atomnum: int) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::conformation::membrane::MembraneGeometry::corrected_xyz(const class core::conformation::Conformation &, unsigned long, unsigned long) const –> class numeric::xyzVector<double>

f1(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, atom_xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, r_alpha: pyrosetta.rosetta.numeric.xyzVector_double_t, deriv: float) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::conformation::membrane::MembraneGeometry::f1(const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, double) const –> class numeric::xyzVector<double>

f1_pore(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, f_thk: float, xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, conf: pyrosetta.rosetta.core.conformation.Conformation, resnum: int, atomnum: int) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::conformation::membrane::MembraneGeometry::f1_pore(double, const class numeric::xyzVector<double> &, const class core::conformation::Conformation &, unsigned long, unsigned long) const –> class numeric::xyzVector<double>

f2(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, atom_xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, r_alpha: pyrosetta.rosetta.numeric.xyzVector_double_t, deriv: float) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::conformation::membrane::MembraneGeometry::f2(const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, double) const –> class numeric::xyzVector<double>

f2_pore(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, f_thk: float, xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, conf: pyrosetta.rosetta.core.conformation.Conformation, resnum: int, atomnum: int) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::conformation::membrane::MembraneGeometry::f2_pore(double, const class numeric::xyzVector<double> &, const class core::conformation::Conformation &, unsigned long, unsigned long) const –> class numeric::xyzVector<double>

f_cavity(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, p: pyrosetta.rosetta.numeric.xyzVector_double_t) → float

Calculate the hydration of an atom based on its location relative to

an aqueous pore or cavity

C++: core::conformation::membrane::MembraneGeometry::f_cavity(const class numeric::xyzVector<double> &) const –> double

f_cavity_dx(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, p: pyrosetta.rosetta.numeric.xyzVector_double_t, f_thk: float) → float

C++: core::conformation::membrane::MembraneGeometry::f_cavity_dx(const class numeric::xyzVector<double> &, double) const –> double

f_cavity_dy(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, p: pyrosetta.rosetta.numeric.xyzVector_double_t, f_thk: float) → float

C++: core::conformation::membrane::MembraneGeometry::f_cavity_dy(const class numeric::xyzVector<double> &, double) const –> double

f_cavity_dz(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, p: pyrosetta.rosetta.numeric.xyzVector_double_t, f_thk: float) → float

C++: core::conformation::membrane::MembraneGeometry::f_cavity_dz(const class numeric::xyzVector<double> &, double) const –> double

f_cavity_gradient(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, r: float) → float

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

C++: core::conformation::membrane::MembraneGeometry::f_cavity_gradient(const double) const –> double

f_franklin(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, z: float, tau: float, kappa: float) → float

C++: core::conformation::membrane::MembraneGeometry::f_franklin(const double, double, double) const –> double

f_franklin_gradient(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, z: float, tau: float, kappa: float) → float

C++: core::conformation::membrane::MembraneGeometry::f_franklin_gradient(const double, double, double) const –> double

f_hydration(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, f_thk: float, p: pyrosetta.rosetta.numeric.xyzVector_double_t) → float

C++: core::conformation::membrane::MembraneGeometry::f_hydration(double, const class numeric::xyzVector<double> &) const –> double

f_hydration_deriv_dz(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, p: pyrosetta.rosetta.numeric.xyzVector_double_t, f_thk_deriv_dz: float) → float

C++: core::conformation::membrane::MembraneGeometry::f_hydration_deriv_dz(const class numeric::xyzVector<double> &, double) const –> double

f_imm1(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, z_position: float) → float

C++: core::conformation::membrane::MembraneGeometry::f_imm1(double) const –> double

f_imm1_deriv(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, z_position: float) → float

C++: core::conformation::membrane::MembraneGeometry::f_imm1_deriv(double) const –> double

f_thickness(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, conf: pyrosetta.rosetta.core.conformation.Conformation, z: float) → float

C++: core::conformation::membrane::MembraneGeometry::f_thickness(const class core::conformation::Conformation &, const double) const –> double

f_thickness_deriv(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, conf: pyrosetta.rosetta.core.conformation.Conformation, z: float) → float

C++: core::conformation::membrane::MembraneGeometry::f_thickness_deriv(const class core::conformation::Conformation &, const double) const –> double

f_transition(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Slab, conf: pyrosetta.rosetta.core.conformation.Conformation, resnum: int, atomnum: int) → float

C++: core::conformation::membrane::membrane_geometry::Slab::f_transition(const class core::conformation::Conformation &, unsigned long, unsigned long) const –> double

f_transition_deriv(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Slab, conf: pyrosetta.rosetta.core.conformation.Conformation, resnum: int, atomnum: int) → float

C++: core::conformation::membrane::membrane_geometry::Slab::f_transition_deriv(const class core::conformation::Conformation &, unsigned long, unsigned long) const –> double

f_transition_f1(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Slab, conf: pyrosetta.rosetta.core.conformation.Conformation, resnum: int, atomnum: int) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::conformation::membrane::membrane_geometry::Slab::f_transition_f1(const class core::conformation::Conformation &, unsigned long, unsigned long) const –> class numeric::xyzVector<double>

f_transition_f2(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Slab, conf: pyrosetta.rosetta.core.conformation.Conformation, resnum: int, atomnum: int) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::conformation::membrane::membrane_geometry::Slab::f_transition_f2(const class core::conformation::Conformation &, unsigned long, unsigned long) const –> class numeric::xyzVector<double>

g_radius(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, p: pyrosetta.rosetta.numeric.xyzVector_double_t) → float

Calculate the location of an atom relative to the pore structure

C++: core::conformation::membrane::MembraneGeometry::g_radius(const class numeric::xyzVector<double> &) const –> double

g_radius_gradient_dx(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, p: pyrosetta.rosetta.numeric.xyzVector_double_t) → float

C++: core::conformation::membrane::MembraneGeometry::g_radius_gradient_dx(const class numeric::xyzVector<double> &) const –> double

g_radius_gradient_dy(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, p: pyrosetta.rosetta.numeric.xyzVector_double_t) → float

C++: core::conformation::membrane::MembraneGeometry::g_radius_gradient_dy(const class numeric::xyzVector<double> &) const –> double

g_radius_gradient_dz(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, p: pyrosetta.rosetta.numeric.xyzVector_double_t) → float

C++: core::conformation::membrane::MembraneGeometry::g_radius_gradient_dz(const class numeric::xyzVector<double> &) const –> double

geometry_enum(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Slab) → pyrosetta.rosetta.core.conformation.membrane.MP_GEOMETRY_TRANSITION

C++: core::conformation::membrane::membrane_geometry::Slab::geometry_enum() const –> enum core::conformation::membrane::MP_GEOMETRY_TRANSITION

geometry_string(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Slab) → str

C++: core::conformation::membrane::membrane_geometry::Slab::geometry_string() const –> std::string

has_pore(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry) → bool

Does this protein have a water-filled pore?

C++: core::conformation::membrane::MembraneGeometry::has_pore() const –> bool

membrane_steepness(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry) → float

Steepness of hydrophobic -> hydrophillic transition (defualt = 10)

C++: core::conformation::membrane::MembraneGeometry::membrane_steepness() const –> double

membrane_thickness(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry) → float

Effective thickness of the membrane (default = 15)

C++: core::conformation::membrane::MembraneGeometry::membrane_thickness() const –> double

r_alpha(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Slab, conf: pyrosetta.rosetta.core.conformation.Conformation, resnum: int, atomnum: int) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::conformation::membrane::membrane_geometry::Slab::r_alpha(const class core::conformation::Conformation &, unsigned long, unsigned long) const –> class numeric::xyzVector<double>

r_alpha_p_x(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, xyz: pyrosetta.rosetta.numeric.xyzVector_double_t) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::conformation::membrane::MembraneGeometry::r_alpha_p_x(const class numeric::xyzVector<double> &) const –> class numeric::xyzVector<double>

r_alpha_p_y(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, xyz: pyrosetta.rosetta.numeric.xyzVector_double_t) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::conformation::membrane::MembraneGeometry::r_alpha_p_y(const class numeric::xyzVector<double> &) const –> class numeric::xyzVector<double>

r_alpha_p_z(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, conf: pyrosetta.rosetta.core.conformation.Conformation, resnum: int, atomnum: int) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::conformation::membrane::MembraneGeometry::r_alpha_p_z(const class core::conformation::Conformation &, unsigned long, unsigned long) const –> class numeric::xyzVector<double>

set_aqueous_pore_parameters(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, aqueous_pore: pyrosetta.rosetta.core.conformation.membrane.AqueousPoreParameters) → None

Set membrane aqueous pore parameters

C++: core::conformation::membrane::MembraneGeometry::set_aqueous_pore_parameters(class std::shared_ptr<class core::conformation::membrane::AqueousPoreParameters>) –> void

show(*args, **kwargs)

Overloaded function.

1. show(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Slab) -> None

C++: core::conformation::membrane::membrane_geometry::Slab::show() const –> void

2. show(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Slab, output: pyrosetta.rosetta.std.ostream) -> None

C++: core::conformation::membrane::membrane_geometry::Slab::show(std::ostream &) const –> void

class pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle

Bases: MembraneGeometry

assign(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle, : pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle) → pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle

C++: core::conformation::membrane::membrane_geometry::Vesicle::operator=(const class core::conformation::membrane::membrane_geometry::Vesicle &) –> class core::conformation::membrane::membrane_geometry::Vesicle &

clone(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle) → pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry

C++: core::conformation::membrane::membrane_geometry::Vesicle::clone() const –> class std::shared_ptr<class core::conformation::membrane::MembraneGeometry>

corrected_xyz(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, conf: pyrosetta.rosetta.core.conformation.Conformation, resnum: int, atomnum: int) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::conformation::membrane::MembraneGeometry::corrected_xyz(const class core::conformation::Conformation &, unsigned long, unsigned long) const –> class numeric::xyzVector<double>

f1(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, atom_xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, r_alpha: pyrosetta.rosetta.numeric.xyzVector_double_t, deriv: float) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::conformation::membrane::MembraneGeometry::f1(const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, double) const –> class numeric::xyzVector<double>

f1_pore(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, f_thk: float, xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, conf: pyrosetta.rosetta.core.conformation.Conformation, resnum: int, atomnum: int) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::conformation::membrane::MembraneGeometry::f1_pore(double, const class numeric::xyzVector<double> &, const class core::conformation::Conformation &, unsigned long, unsigned long) const –> class numeric::xyzVector<double>

f2(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, atom_xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, r_alpha: pyrosetta.rosetta.numeric.xyzVector_double_t, deriv: float) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::conformation::membrane::MembraneGeometry::f2(const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, double) const –> class numeric::xyzVector<double>

f2_pore(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, f_thk: float, xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, conf: pyrosetta.rosetta.core.conformation.Conformation, resnum: int, atomnum: int) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::conformation::membrane::MembraneGeometry::f2_pore(double, const class numeric::xyzVector<double> &, const class core::conformation::Conformation &, unsigned long, unsigned long) const –> class numeric::xyzVector<double>

f_cavity(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, p: pyrosetta.rosetta.numeric.xyzVector_double_t) → float

Calculate the hydration of an atom based on its location relative to

an aqueous pore or cavity

C++: core::conformation::membrane::MembraneGeometry::f_cavity(const class numeric::xyzVector<double> &) const –> double

f_cavity_dx(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, p: pyrosetta.rosetta.numeric.xyzVector_double_t, f_thk: float) → float

C++: core::conformation::membrane::MembraneGeometry::f_cavity_dx(const class numeric::xyzVector<double> &, double) const –> double

f_cavity_dy(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, p: pyrosetta.rosetta.numeric.xyzVector_double_t, f_thk: float) → float

C++: core::conformation::membrane::MembraneGeometry::f_cavity_dy(const class numeric::xyzVector<double> &, double) const –> double

f_cavity_dz(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, p: pyrosetta.rosetta.numeric.xyzVector_double_t, f_thk: float) → float

C++: core::conformation::membrane::MembraneGeometry::f_cavity_dz(const class numeric::xyzVector<double> &, double) const –> double

f_cavity_gradient(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, r: float) → float

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

C++: core::conformation::membrane::MembraneGeometry::f_cavity_gradient(const double) const –> double

f_franklin(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, z: float, tau: float, kappa: float) → float

C++: core::conformation::membrane::MembraneGeometry::f_franklin(const double, double, double) const –> double

f_franklin_gradient(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, z: float, tau: float, kappa: float) → float

C++: core::conformation::membrane::MembraneGeometry::f_franklin_gradient(const double, double, double) const –> double

f_hydration(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, f_thk: float, p: pyrosetta.rosetta.numeric.xyzVector_double_t) → float

C++: core::conformation::membrane::MembraneGeometry::f_hydration(double, const class numeric::xyzVector<double> &) const –> double

f_hydration_deriv_dz(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, p: pyrosetta.rosetta.numeric.xyzVector_double_t, f_thk_deriv_dz: float) → float

C++: core::conformation::membrane::MembraneGeometry::f_hydration_deriv_dz(const class numeric::xyzVector<double> &, double) const –> double

f_imm1(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, z_position: float) → float

C++: core::conformation::membrane::MembraneGeometry::f_imm1(double) const –> double

f_imm1_deriv(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, z_position: float) → float

C++: core::conformation::membrane::MembraneGeometry::f_imm1_deriv(double) const –> double

f_thickness(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, conf: pyrosetta.rosetta.core.conformation.Conformation, z: float) → float

C++: core::conformation::membrane::MembraneGeometry::f_thickness(const class core::conformation::Conformation &, const double) const –> double

f_thickness_deriv(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, conf: pyrosetta.rosetta.core.conformation.Conformation, z: float) → float

C++: core::conformation::membrane::MembraneGeometry::f_thickness_deriv(const class core::conformation::Conformation &, const double) const –> double

f_transition(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle, conf: pyrosetta.rosetta.core.conformation.Conformation, resnum: int, atomnum: int) → float

C++: core::conformation::membrane::membrane_geometry::Vesicle::f_transition(const class core::conformation::Conformation &, unsigned long, unsigned long) const –> double

f_transition_deriv(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle, conf: pyrosetta.rosetta.core.conformation.Conformation, resnum: int, atomnum: int) → float

C++: core::conformation::membrane::membrane_geometry::Vesicle::f_transition_deriv(const class core::conformation::Conformation &, unsigned long, unsigned long) const –> double

f_transition_f1(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle, conf: pyrosetta.rosetta.core.conformation.Conformation, resnum: int, atomnum: int) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::conformation::membrane::membrane_geometry::Vesicle::f_transition_f1(const class core::conformation::Conformation &, unsigned long, unsigned long) const –> class numeric::xyzVector<double>

f_transition_f2(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle, conf: pyrosetta.rosetta.core.conformation.Conformation, resnum: int, atomnum: int) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::conformation::membrane::membrane_geometry::Vesicle::f_transition_f2(const class core::conformation::Conformation &, unsigned long, unsigned long) const –> class numeric::xyzVector<double>

g_radius(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, p: pyrosetta.rosetta.numeric.xyzVector_double_t) → float

Calculate the location of an atom relative to the pore structure

C++: core::conformation::membrane::MembraneGeometry::g_radius(const class numeric::xyzVector<double> &) const –> double

g_radius_gradient_dx(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, p: pyrosetta.rosetta.numeric.xyzVector_double_t) → float

C++: core::conformation::membrane::MembraneGeometry::g_radius_gradient_dx(const class numeric::xyzVector<double> &) const –> double

g_radius_gradient_dy(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, p: pyrosetta.rosetta.numeric.xyzVector_double_t) → float

C++: core::conformation::membrane::MembraneGeometry::g_radius_gradient_dy(const class numeric::xyzVector<double> &) const –> double

g_radius_gradient_dz(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, p: pyrosetta.rosetta.numeric.xyzVector_double_t) → float

C++: core::conformation::membrane::MembraneGeometry::g_radius_gradient_dz(const class numeric::xyzVector<double> &) const –> double

geometry_enum(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle) → pyrosetta.rosetta.core.conformation.membrane.MP_GEOMETRY_TRANSITION

C++: core::conformation::membrane::membrane_geometry::Vesicle::geometry_enum() const –> enum core::conformation::membrane::MP_GEOMETRY_TRANSITION

geometry_string(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle) → str

C++: core::conformation::membrane::membrane_geometry::Vesicle::geometry_string() const –> std::string

get_radius(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle) → float

C++: core::conformation::membrane::membrane_geometry::Vesicle::get_radius() const –> double

has_pore(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry) → bool

Does this protein have a water-filled pore?

C++: core::conformation::membrane::MembraneGeometry::has_pore() const –> bool

membrane_steepness(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry) → float

Steepness of hydrophobic -> hydrophillic transition (defualt = 10)

C++: core::conformation::membrane::MembraneGeometry::membrane_steepness() const –> double

membrane_thickness(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry) → float

Effective thickness of the membrane (default = 15)

C++: core::conformation::membrane::MembraneGeometry::membrane_thickness() const –> double

r_alpha(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle, conf: pyrosetta.rosetta.core.conformation.Conformation, resnum: int, atomnum: int) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::conformation::membrane::membrane_geometry::Vesicle::r_alpha(const class core::conformation::Conformation &, unsigned long, unsigned long) const –> class numeric::xyzVector<double>

r_alpha_p_x(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, xyz: pyrosetta.rosetta.numeric.xyzVector_double_t) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::conformation::membrane::MembraneGeometry::r_alpha_p_x(const class numeric::xyzVector<double> &) const –> class numeric::xyzVector<double>

r_alpha_p_y(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, xyz: pyrosetta.rosetta.numeric.xyzVector_double_t) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::conformation::membrane::MembraneGeometry::r_alpha_p_y(const class numeric::xyzVector<double> &) const –> class numeric::xyzVector<double>

r_alpha_p_z(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, conf: pyrosetta.rosetta.core.conformation.Conformation, resnum: int, atomnum: int) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::conformation::membrane::MembraneGeometry::r_alpha_p_z(const class core::conformation::Conformation &, unsigned long, unsigned long) const –> class numeric::xyzVector<double>

set_aqueous_pore_parameters(self: pyrosetta.rosetta.core.conformation.membrane.MembraneGeometry, aqueous_pore: pyrosetta.rosetta.core.conformation.membrane.AqueousPoreParameters) → None

Set membrane aqueous pore parameters

C++: core::conformation::membrane::MembraneGeometry::set_aqueous_pore_parameters(class std::shared_ptr<class core::conformation::membrane::AqueousPoreParameters>) –> void

set_radius(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle, r: float) → None

C++: core::conformation::membrane::membrane_geometry::Vesicle::set_radius(double) –> void

show(*args, **kwargs)

Overloaded function.

1. show(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle) -> None

C++: core::conformation::membrane::membrane_geometry::Vesicle::show() const –> void

2. show(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle, output: pyrosetta.rosetta.std.ostream) -> None

C++: core::conformation::membrane::membrane_geometry::Vesicle::show(std::ostream &) const –> void

update_radius(self: pyrosetta.rosetta.core.conformation.membrane.membrane_geometry.Vesicle) → None

C++: core::conformation::membrane::membrane_geometry::Vesicle::update_radius() –> void