membrane

Bindings for core::conformation::membrane namespace

class pyrosetta.rosetta.core.conformation.membrane.AqueousPoreParameters

Bases: pybind11_builtins.pybind11_object

A class for defining an aqueous pore

assign(self: pyrosetta.rosetta.core.conformation.membrane.AqueousPoreParameters, : pyrosetta.rosetta.core.conformation.membrane.AqueousPoreParameters) pyrosetta.rosetta.core.conformation.membrane.AqueousPoreParameters

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

boundaries(self: pyrosetta.rosetta.core.conformation.membrane.AqueousPoreParameters, index: int) float

C++: core::conformation::membrane::AqueousPoreParameters::boundaries(unsigned long) const –> double

clone(self: pyrosetta.rosetta.core.conformation.membrane.AqueousPoreParameters) pyrosetta.rosetta.core.conformation.membrane.AqueousPoreParameters

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

pore_center_x(self: pyrosetta.rosetta.core.conformation.membrane.AqueousPoreParameters, zcoord: float) float

C++: core::conformation::membrane::AqueousPoreParameters::pore_center_x(const double) const –> double

pore_center_x_deriv(self: pyrosetta.rosetta.core.conformation.membrane.AqueousPoreParameters, zcoord: float) float

C++: core::conformation::membrane::AqueousPoreParameters::pore_center_x_deriv(const double) const –> double

pore_center_y(self: pyrosetta.rosetta.core.conformation.membrane.AqueousPoreParameters, zcoord: float) float

C++: core::conformation::membrane::AqueousPoreParameters::pore_center_y(const double) const –> double

pore_center_y_deriv(self: pyrosetta.rosetta.core.conformation.membrane.AqueousPoreParameters, zcoord: float) float

C++: core::conformation::membrane::AqueousPoreParameters::pore_center_y_deriv(const double) const –> double

pore_major_radius(self: pyrosetta.rosetta.core.conformation.membrane.AqueousPoreParameters, zcoord: float) float

C++: core::conformation::membrane::AqueousPoreParameters::pore_major_radius(const double) const –> double

pore_major_radius_deriv(self: pyrosetta.rosetta.core.conformation.membrane.AqueousPoreParameters, zcoord: float) float

C++: core::conformation::membrane::AqueousPoreParameters::pore_major_radius_deriv(const double) const –> double

pore_minor_radius(self: pyrosetta.rosetta.core.conformation.membrane.AqueousPoreParameters, zcoord: float) float

C++: core::conformation::membrane::AqueousPoreParameters::pore_minor_radius(const double) const –> double

pore_minor_radius_deriv(self: pyrosetta.rosetta.core.conformation.membrane.AqueousPoreParameters, zcoord: float) float

C++: core::conformation::membrane::AqueousPoreParameters::pore_minor_radius_deriv(const double) const –> double

pore_rotation(self: pyrosetta.rosetta.core.conformation.membrane.AqueousPoreParameters, zcoord: float) pyrosetta.rosetta.numeric.MathMatrix_double_t

C++: core::conformation::membrane::AqueousPoreParameters::pore_rotation(const double) const –> class numeric::MathMatrix<double>

pore_rotation_deriv(self: pyrosetta.rosetta.core.conformation.membrane.AqueousPoreParameters, zcood: float) float

C++: core::conformation::membrane::AqueousPoreParameters::pore_rotation_deriv(const double) const –> double

class pyrosetta.rosetta.core.conformation.membrane.EXCN_Illegal_Arguments

Bases: pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane

add_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None

C++: utility::excn::Exception::add_msg(const std::string &) –> void

assign(self: pyrosetta.rosetta.core.conformation.membrane.EXCN_Illegal_Arguments, : pyrosetta.rosetta.core.conformation.membrane.EXCN_Illegal_Arguments) pyrosetta.rosetta.core.conformation.membrane.EXCN_Illegal_Arguments

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

crash_log(self: pyrosetta.rosetta.utility.excn.Exception) None
Invoke a crash log for throwing this exception.

If your exception is one which is a “non-error” exception, override this function to do nothing.

C++: utility::excn::Exception::crash_log() const –> void

display(self: pyrosetta.rosetta.utility.excn.Exception) None
Present this exception to the user.

Will invoke crash log reporting, if applicable

C++: utility::excn::Exception::display() const –> void

file(self: pyrosetta.rosetta.utility.excn.Exception) str

C++: utility::excn::Exception::file() –> const std::string &

line(self: pyrosetta.rosetta.utility.excn.Exception) int

C++: utility::excn::Exception::line() –> int

msg(*args, **kwargs)

Overloaded function.

  1. msg(self: pyrosetta.rosetta.utility.excn.Exception) -> str

Will return a formatted message (with file/line information)

C++: utility::excn::Exception::msg() const –> std::string

  1. msg(self: pyrosetta.rosetta.utility.excn.Exception, m: str) -> None

Will set the raw message.

C++: utility::excn::Exception::msg(const std::string &) –> void

prepend_to_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None

C++: utility::excn::Exception::prepend_to_msg(const std::string &) –> void

raw_msg(self: pyrosetta.rosetta.utility.excn.Exception) str

Will return the raw message (without file/line information)

C++: utility::excn::Exception::raw_msg() const –> std::string

show(self: pyrosetta.rosetta.utility.excn.Exception, : pyrosetta.rosetta.std.ostream) None

C++: utility::excn::Exception::show(std::ostream &) const –> void

traceback(self: pyrosetta.rosetta.utility.excn.Exception) str

C++: utility::excn::Exception::traceback() –> const std::string &

what(self: pyrosetta.rosetta.std.exception) str

C++: std::exception::what() const –> const char *

class pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane

Bases: pyrosetta.rosetta.utility.excn.Exception

Parent Exception - Exception Membrane

add_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None

C++: utility::excn::Exception::add_msg(const std::string &) –> void

assign(self: pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane, : pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane) pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane

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

crash_log(self: pyrosetta.rosetta.utility.excn.Exception) None
Invoke a crash log for throwing this exception.

If your exception is one which is a “non-error” exception, override this function to do nothing.

C++: utility::excn::Exception::crash_log() const –> void

display(self: pyrosetta.rosetta.utility.excn.Exception) None
Present this exception to the user.

Will invoke crash log reporting, if applicable

C++: utility::excn::Exception::display() const –> void

file(self: pyrosetta.rosetta.utility.excn.Exception) str

C++: utility::excn::Exception::file() –> const std::string &

line(self: pyrosetta.rosetta.utility.excn.Exception) int

C++: utility::excn::Exception::line() –> int

msg(*args, **kwargs)

Overloaded function.

  1. msg(self: pyrosetta.rosetta.utility.excn.Exception) -> str

Will return a formatted message (with file/line information)

C++: utility::excn::Exception::msg() const –> std::string

  1. msg(self: pyrosetta.rosetta.utility.excn.Exception, m: str) -> None

Will set the raw message.

C++: utility::excn::Exception::msg(const std::string &) –> void

prepend_to_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None

C++: utility::excn::Exception::prepend_to_msg(const std::string &) –> void

raw_msg(self: pyrosetta.rosetta.utility.excn.Exception) str

Will return the raw message (without file/line information)

C++: utility::excn::Exception::raw_msg() const –> std::string

show(self: pyrosetta.rosetta.utility.excn.Exception, : pyrosetta.rosetta.std.ostream) None

C++: utility::excn::Exception::show(std::ostream &) const –> void

traceback(self: pyrosetta.rosetta.utility.excn.Exception) str

C++: utility::excn::Exception::traceback() –> const std::string &

what(self: pyrosetta.rosetta.std.exception) str

C++: std::exception::what() const –> const char *

class pyrosetta.rosetta.core.conformation.membrane.EXCN_MembraneFoldTree

Bases: pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane

Fold tree Exception for membrane proteins

add_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None

C++: utility::excn::Exception::add_msg(const std::string &) –> void

assign(self: pyrosetta.rosetta.core.conformation.membrane.EXCN_MembraneFoldTree, : pyrosetta.rosetta.core.conformation.membrane.EXCN_MembraneFoldTree) pyrosetta.rosetta.core.conformation.membrane.EXCN_MembraneFoldTree

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

crash_log(self: pyrosetta.rosetta.utility.excn.Exception) None
Invoke a crash log for throwing this exception.

If your exception is one which is a “non-error” exception, override this function to do nothing.

C++: utility::excn::Exception::crash_log() const –> void

display(self: pyrosetta.rosetta.utility.excn.Exception) None
Present this exception to the user.

Will invoke crash log reporting, if applicable

C++: utility::excn::Exception::display() const –> void

file(self: pyrosetta.rosetta.utility.excn.Exception) str

C++: utility::excn::Exception::file() –> const std::string &

line(self: pyrosetta.rosetta.utility.excn.Exception) int

C++: utility::excn::Exception::line() –> int

msg(*args, **kwargs)

Overloaded function.

  1. msg(self: pyrosetta.rosetta.utility.excn.Exception) -> str

Will return a formatted message (with file/line information)

C++: utility::excn::Exception::msg() const –> std::string

  1. msg(self: pyrosetta.rosetta.utility.excn.Exception, m: str) -> None

Will set the raw message.

C++: utility::excn::Exception::msg(const std::string &) –> void

prepend_to_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None

C++: utility::excn::Exception::prepend_to_msg(const std::string &) –> void

raw_msg(self: pyrosetta.rosetta.utility.excn.Exception) str

Will return the raw message (without file/line information)

C++: utility::excn::Exception::raw_msg() const –> std::string

show(self: pyrosetta.rosetta.utility.excn.Exception, : pyrosetta.rosetta.std.ostream) None

C++: utility::excn::Exception::show(std::ostream &) const –> void

traceback(self: pyrosetta.rosetta.utility.excn.Exception) str

C++: utility::excn::Exception::traceback() –> const std::string &

what(self: pyrosetta.rosetta.std.exception) str

C++: std::exception::what() const –> const char *

class pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane_Bounds

Bases: pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane

Membrane Out of Bounds Exception

add_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None

C++: utility::excn::Exception::add_msg(const std::string &) –> void

assign(self: pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane_Bounds, : pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane_Bounds) pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane_Bounds

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

crash_log(self: pyrosetta.rosetta.utility.excn.Exception) None
Invoke a crash log for throwing this exception.

If your exception is one which is a “non-error” exception, override this function to do nothing.

C++: utility::excn::Exception::crash_log() const –> void

display(self: pyrosetta.rosetta.utility.excn.Exception) None
Present this exception to the user.

Will invoke crash log reporting, if applicable

C++: utility::excn::Exception::display() const –> void

file(self: pyrosetta.rosetta.utility.excn.Exception) str

C++: utility::excn::Exception::file() –> const std::string &

line(self: pyrosetta.rosetta.utility.excn.Exception) int

C++: utility::excn::Exception::line() –> int

msg(*args, **kwargs)

Overloaded function.

  1. msg(self: pyrosetta.rosetta.utility.excn.Exception) -> str

Will return a formatted message (with file/line information)

C++: utility::excn::Exception::msg() const –> std::string

  1. msg(self: pyrosetta.rosetta.utility.excn.Exception, m: str) -> None

Will set the raw message.

C++: utility::excn::Exception::msg(const std::string &) –> void

prepend_to_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None

C++: utility::excn::Exception::prepend_to_msg(const std::string &) –> void

raw_msg(self: pyrosetta.rosetta.utility.excn.Exception) str

Will return the raw message (without file/line information)

C++: utility::excn::Exception::raw_msg() const –> std::string

show(self: pyrosetta.rosetta.utility.excn.Exception, : pyrosetta.rosetta.std.ostream) None

C++: utility::excn::Exception::show(std::ostream &) const –> void

traceback(self: pyrosetta.rosetta.utility.excn.Exception) str

C++: utility::excn::Exception::traceback() –> const std::string &

what(self: pyrosetta.rosetta.std.exception) str

C++: std::exception::what() const –> const char *

class pyrosetta.rosetta.core.conformation.membrane.EXCN_NonMembrane

Bases: pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane

Non Membrane Pose Exception

add_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None

C++: utility::excn::Exception::add_msg(const std::string &) –> void

assign(self: pyrosetta.rosetta.core.conformation.membrane.EXCN_NonMembrane, : pyrosetta.rosetta.core.conformation.membrane.EXCN_NonMembrane) pyrosetta.rosetta.core.conformation.membrane.EXCN_NonMembrane

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

crash_log(self: pyrosetta.rosetta.utility.excn.Exception) None
Invoke a crash log for throwing this exception.

If your exception is one which is a “non-error” exception, override this function to do nothing.

C++: utility::excn::Exception::crash_log() const –> void

display(self: pyrosetta.rosetta.utility.excn.Exception) None
Present this exception to the user.

Will invoke crash log reporting, if applicable

C++: utility::excn::Exception::display() const –> void

file(self: pyrosetta.rosetta.utility.excn.Exception) str

C++: utility::excn::Exception::file() –> const std::string &

line(self: pyrosetta.rosetta.utility.excn.Exception) int

C++: utility::excn::Exception::line() –> int

msg(*args, **kwargs)

Overloaded function.

  1. msg(self: pyrosetta.rosetta.utility.excn.Exception) -> str

Will return a formatted message (with file/line information)

C++: utility::excn::Exception::msg() const –> std::string

  1. msg(self: pyrosetta.rosetta.utility.excn.Exception, m: str) -> None

Will set the raw message.

C++: utility::excn::Exception::msg(const std::string &) –> void

prepend_to_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None

C++: utility::excn::Exception::prepend_to_msg(const std::string &) –> void

raw_msg(self: pyrosetta.rosetta.utility.excn.Exception) str

Will return the raw message (without file/line information)

C++: utility::excn::Exception::raw_msg() const –> std::string

show(self: pyrosetta.rosetta.utility.excn.Exception, : pyrosetta.rosetta.std.ostream) None

C++: utility::excn::Exception::show(std::ostream &) const –> void

traceback(self: pyrosetta.rosetta.utility.excn.Exception) str

C++: utility::excn::Exception::traceback() –> const std::string &

what(self: pyrosetta.rosetta.std.exception) str

C++: std::exception::what() const –> const char *

class pyrosetta.rosetta.core.conformation.membrane.EXCN_Resource_Definition

Bases: pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane

Resource Manager Exception

add_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None

C++: utility::excn::Exception::add_msg(const std::string &) –> void

assign(self: pyrosetta.rosetta.core.conformation.membrane.EXCN_Resource_Definition, : pyrosetta.rosetta.core.conformation.membrane.EXCN_Resource_Definition) pyrosetta.rosetta.core.conformation.membrane.EXCN_Resource_Definition

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

crash_log(self: pyrosetta.rosetta.utility.excn.Exception) None
Invoke a crash log for throwing this exception.

If your exception is one which is a “non-error” exception, override this function to do nothing.

C++: utility::excn::Exception::crash_log() const –> void

display(self: pyrosetta.rosetta.utility.excn.Exception) None
Present this exception to the user.

Will invoke crash log reporting, if applicable

C++: utility::excn::Exception::display() const –> void

file(self: pyrosetta.rosetta.utility.excn.Exception) str

C++: utility::excn::Exception::file() –> const std::string &

line(self: pyrosetta.rosetta.utility.excn.Exception) int

C++: utility::excn::Exception::line() –> int

msg(*args, **kwargs)

Overloaded function.

  1. msg(self: pyrosetta.rosetta.utility.excn.Exception) -> str

Will return a formatted message (with file/line information)

C++: utility::excn::Exception::msg() const –> std::string

  1. msg(self: pyrosetta.rosetta.utility.excn.Exception, m: str) -> None

Will set the raw message.

C++: utility::excn::Exception::msg(const std::string &) –> void

prepend_to_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None

C++: utility::excn::Exception::prepend_to_msg(const std::string &) –> void

raw_msg(self: pyrosetta.rosetta.utility.excn.Exception) str

Will return the raw message (without file/line information)

C++: utility::excn::Exception::raw_msg() const –> std::string

show(self: pyrosetta.rosetta.utility.excn.Exception, : pyrosetta.rosetta.std.ostream) None

C++: utility::excn::Exception::show(std::ostream &) const –> void

traceback(self: pyrosetta.rosetta.utility.excn.Exception) str

C++: utility::excn::Exception::traceback() –> const std::string &

what(self: pyrosetta.rosetta.std.exception) str

C++: std::exception::what() const –> const char *

class pyrosetta.rosetta.core.conformation.membrane.EXCN_VirtualRsd

Bases: pyrosetta.rosetta.core.conformation.membrane.EXCN_Membrane

Virtual Residue Definition Exception

add_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None

C++: utility::excn::Exception::add_msg(const std::string &) –> void

assign(self: pyrosetta.rosetta.core.conformation.membrane.EXCN_VirtualRsd, : pyrosetta.rosetta.core.conformation.membrane.EXCN_VirtualRsd) pyrosetta.rosetta.core.conformation.membrane.EXCN_VirtualRsd

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

crash_log(self: pyrosetta.rosetta.utility.excn.Exception) None
Invoke a crash log for throwing this exception.

If your exception is one which is a “non-error” exception, override this function to do nothing.

C++: utility::excn::Exception::crash_log() const –> void

display(self: pyrosetta.rosetta.utility.excn.Exception) None
Present this exception to the user.

Will invoke crash log reporting, if applicable

C++: utility::excn::Exception::display() const –> void

file(self: pyrosetta.rosetta.utility.excn.Exception) str

C++: utility::excn::Exception::file() –> const std::string &

line(self: pyrosetta.rosetta.utility.excn.Exception) int

C++: utility::excn::Exception::line() –> int

msg(*args, **kwargs)

Overloaded function.

  1. msg(self: pyrosetta.rosetta.utility.excn.Exception) -> str

Will return a formatted message (with file/line information)

C++: utility::excn::Exception::msg() const –> std::string

  1. msg(self: pyrosetta.rosetta.utility.excn.Exception, m: str) -> None

Will set the raw message.

C++: utility::excn::Exception::msg(const std::string &) –> void

prepend_to_msg(self: pyrosetta.rosetta.utility.excn.Exception, str: str) None

C++: utility::excn::Exception::prepend_to_msg(const std::string &) –> void

raw_msg(self: pyrosetta.rosetta.utility.excn.Exception) str

Will return the raw message (without file/line information)

C++: utility::excn::Exception::raw_msg() const –> std::string

show(self: pyrosetta.rosetta.utility.excn.Exception, : pyrosetta.rosetta.std.ostream) None

C++: utility::excn::Exception::show(std::ostream &) const –> void

traceback(self: pyrosetta.rosetta.utility.excn.Exception) str

C++: utility::excn::Exception::traceback() –> const std::string &

what(self: pyrosetta.rosetta.std.exception) str

C++: std::exception::what() const –> const char *

class pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo

Bases: pybind11_builtins.pybind11_object

Definition of an implicit membrane with parameters for different lipid compositions

assign(self: pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo, src: pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo) pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo

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

chain_type(self: pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo) str

Number of carbons and degrees of saturation in the chains

C++: core::conformation::membrane::ImplicitLipidInfo::chain_type() const –> std::string

clone(self: pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo) pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo

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

degrees_of_saturation(self: pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo) float

Number of degrees of saturation in the overall lipid

C++: core::conformation::membrane::ImplicitLipidInfo::degrees_of_saturation() const –> double

f_cavity(self: pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo, 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::ImplicitLipidInfo::f_cavity(const class numeric::xyzVector<double> &) const –> double

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

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

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

f_depth(self: pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo, z: float) float
Calcuclate the hydration of an atom based on its location in a

lipid-specific implicit bilayer

C++: core::conformation::membrane::ImplicitLipidInfo::f_depth(const double) const –> double

f_depth_gradient(self: pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo, z: float) float

Ccalcculate the gradient of f_depth

C++: core::conformation::membrane::ImplicitLipidInfo::f_depth_gradient(const double) const –> double

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

Overall hydration given the atomic depth and cavity structure

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

f_hydration_gradient(self: pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo, p: pyrosetta.rosetta.numeric.xyzVector_double_t) float

Gradient

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

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

Calculate the location of an atom relative to the pore structure

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

g_radius_gradient(self: pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo, p: pyrosetta.rosetta.numeric.xyzVector_double_t) float

Calcuclate the gradient of f_cavity

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

has_pore(*args, **kwargs)

Overloaded function.

  1. has_pore(self: pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo) -> bool

Does this protein have a water-filled pore?

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

  1. has_pore(self: pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo, is_there_a_pore: bool) -> None

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

headgroup_type(self: pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo) str

Chemical name of the headgroup

C++: core::conformation::membrane::ImplicitLipidInfo::headgroup_type() const –> std::string

initialize_implicit_lipid_parameters(self: pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo) None

Helper function to initialize the lipid composiiton data

C++: core::conformation::membrane::ImplicitLipidInfo::initialize_implicit_lipid_parameters() –> void

is_helical(*args, **kwargs)

Overloaded function.

  1. is_helical(self: pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo) -> bool

Is the protein alpha helical or beta barrel

C++: core::conformation::membrane::ImplicitLipidInfo::is_helical() const –> bool

  1. is_helical(self: pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo, is_helical: bool) -> None

C++: core::conformation::membrane::ImplicitLipidInfo::is_helical(const bool) –> void

lipid_composition_name(self: pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo) str

Abbreviated name of the lipid composition

C++: core::conformation::membrane::ImplicitLipidInfo::lipid_composition_name() const –> std::string

lipid_composition_name_long(self: pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo) str

Full name of the lipid composiiton

C++: core::conformation::membrane::ImplicitLipidInfo::lipid_composition_name_long() const –> std::string

make_no_pore_parameters(self: pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo) None

Make a set of parameters for the case with no pore

C++: core::conformation::membrane::ImplicitLipidInfo::make_no_pore_parameters() –> void

per_atom_lipid_accessibility(self: pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo, rsd: int, atom: int) float

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

C++: core::conformation::membrane::ImplicitLipidInfo::per_atom_lipid_accessibility(unsigned long, unsigned long) const –> double

pore_center_x(self: pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo, zcoord: float) float

Membrane Aqueous pore center - h parameter

C++: core::conformation::membrane::ImplicitLipidInfo::pore_center_x(const double) const –> double

pore_center_y(self: pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo, zcoord: float) float

Membrane aqueous pore center - k parameter

C++: core::conformation::membrane::ImplicitLipidInfo::pore_center_y(const double) const –> double

pore_major_radius(self: pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo, zcoord: float) float

Membrane aqueous pore - major radius

C++: core::conformation::membrane::ImplicitLipidInfo::pore_major_radius(const double) const –> double

pore_minor_radius(self: pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo, zcoord: float) float

Membrane aqueous pore - minor radius

C++: core::conformation::membrane::ImplicitLipidInfo::pore_minor_radius(const double) const –> double

pore_rotation(self: pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo, zcoord: float) pyrosetta.rosetta.numeric.MathMatrix_double_t

Membrane aqueous pore - rotation matrix

C++: core::conformation::membrane::ImplicitLipidInfo::pore_rotation(const double) const –> class numeric::MathMatrix<double>

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

Set membrane aqueous pore parameters

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

set_per_atom_lipid_accessibility(self: pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo, v: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t) None

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

C++: core::conformation::membrane::ImplicitLipidInfo::set_per_atom_lipid_accessibility(class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >) –> void

show(self: pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo, output: pyrosetta.rosetta.std.ostream) None

Generate a string representation of information represented by ths Lipid MembraneInfo

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

temperature(self: pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo) float

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

C++: core::conformation::membrane::ImplicitLipidInfo::temperature() const –> double

water_pseudo_thickness(*args, **kwargs)

Overloaded function.

  1. water_pseudo_thickness(self: pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo) -> float

Pseudo-thickness parameter

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

C++: core::conformation::membrane::ImplicitLipidInfo::water_pseudo_thickness() const –> double

  1. water_pseudo_thickness(self: pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo, p: float) -> None

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

A parameter in the logistic membrane definition

C++: core::conformation::membrane::ImplicitLipidInfo::water_pseudo_thickness(const double) –> void

water_steepness(*args, **kwargs)

Overloaded function.

  1. water_steepness(self: pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo) -> float

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)

C++: core::conformation::membrane::ImplicitLipidInfo::water_steepness() const –> double

  1. water_steepness(self: pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo, v: float) -> None

Access function to change the value of the transition steepness

Only change the steepness for the alpha v. beta case

C++: core::conformation::membrane::ImplicitLipidInfo::water_steepness(const double) –> void

water_thickness(self: pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo) float

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)

C++: core::conformation::membrane::ImplicitLipidInfo::water_thickness() const –> double

class pyrosetta.rosetta.core.conformation.membrane.MEM

Bases: pybind11_builtins.pybind11_object

Members:

thickness

center

normal

center = <MEM.center: 2>
property name
normal = <MEM.normal: 3>
thickness = <MEM.thickness: 1>
class pyrosetta.rosetta.core.conformation.membrane.MembraneInfo

Bases: pybind11_builtins.pybind11_object

Data describing the relationship between protein(s) and a membrane environment

assign(self: pyrosetta.rosetta.core.conformation.membrane.MembraneInfo, src: pyrosetta.rosetta.core.conformation.membrane.MembraneInfo) pyrosetta.rosetta.core.conformation.membrane.MembraneInfo

create a deep copy of all data in thsi object upon assignment

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

atom_z_position(self: pyrosetta.rosetta.core.conformation.membrane.MembraneInfo, conf: pyrosetta.rosetta.core.conformation.Conformation, resnum: int, atomnum: int) float

Compute atom position relative to membrane normal

C++: core::conformation::membrane::MembraneInfo::atom_z_position(const class core::conformation::Conformation &, unsigned long, unsigned long) const –> double

check_membrane_fold_tree(self: pyrosetta.rosetta.core.conformation.membrane.MembraneInfo, ft_in: pyrosetta.rosetta.core.kinematics.FoldTree) bool

Somewhat weak check that a membrane foldtree is valid

C++: core::conformation::membrane::MembraneInfo::check_membrane_fold_tree(const class core::kinematics::FoldTree &) const –> bool

implicit_lipids(self: pyrosetta.rosetta.core.conformation.membrane.MembraneInfo) pyrosetta.rosetta.core.conformation.membrane.ImplicitLipidInfo

Get implicit lipid information

C++: core::conformation::membrane::MembraneInfo::implicit_lipids() const –> class std::shared_ptr<class core::conformation::membrane::ImplicitLipidInfo>

in_membrane(self: pyrosetta.rosetta.core.conformation.membrane.MembraneInfo, conf: pyrosetta.rosetta.core.conformation.Conformation, resnum: int) bool

Is residue in the membrane?

C++: core::conformation::membrane::MembraneInfo::in_membrane(const class core::conformation::Conformation &, unsigned long) const –> bool

membrane_center(self: pyrosetta.rosetta.core.conformation.membrane.MembraneInfo, conf: pyrosetta.rosetta.core.conformation.Conformation) pyrosetta.rosetta.numeric.xyzVector_double_t

Membrane center

C++: core::conformation::membrane::MembraneInfo::membrane_center(const class core::conformation::Conformation &) const –> class numeric::xyzVector<double>

membrane_core(self: pyrosetta.rosetta.core.conformation.membrane.MembraneInfo) float

core membrane thickness

C++: core::conformation::membrane::MembraneInfo::membrane_core() const –> double

membrane_jump(self: pyrosetta.rosetta.core.conformation.membrane.MembraneInfo) int

Indeitifier for the membrane jump

C++: core::conformation::membrane::MembraneInfo::membrane_jump() const –> long

membrane_normal(self: pyrosetta.rosetta.core.conformation.membrane.MembraneInfo, conf: pyrosetta.rosetta.core.conformation.Conformation) pyrosetta.rosetta.numeric.xyzVector_double_t

Membrane normal

C++: core::conformation::membrane::MembraneInfo::membrane_normal(const class core::conformation::Conformation &) const –> class numeric::xyzVector<double>

membrane_rsd_num(self: pyrosetta.rosetta.core.conformation.membrane.MembraneInfo) int

Sequence position of the membrane residue

C++: core::conformation::membrane::MembraneInfo::membrane_rsd_num() const –> unsigned long

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

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

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

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

Effective thickness of the membrane (default = 15)

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

residue_z_position(self: pyrosetta.rosetta.core.conformation.membrane.MembraneInfo, conf: pyrosetta.rosetta.core.conformation.Conformation, resnum: int) float

Compute residue position relative to membrane normal

C++: core::conformation::membrane::MembraneInfo::residue_z_position(const class core::conformation::Conformation &, unsigned long) const –> double

set_membrane_jump(self: pyrosetta.rosetta.core.conformation.membrane.MembraneInfo, jumpnum: int) None

Allow a protocol to set a new jump number for the membrane jump

C++: core::conformation::membrane::MembraneInfo::set_membrane_jump(long) –> void

show(*args, **kwargs)

Overloaded function.

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

Generate a string representation of information represented by this MembraneInfo and send it to std::cout

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

  1. show(self: pyrosetta.rosetta.core.conformation.membrane.MembraneInfo, output: pyrosetta.rosetta.std.ostream) -> None

Generate a string representation of information represented by ths MembraneInfo

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

spanning_topology(self: pyrosetta.rosetta.core.conformation.membrane.MembraneInfo) core::conformation::membrane::SpanningTopology

Transmembrane spaning topology

C++: core::conformation::membrane::MembraneInfo::spanning_topology() const –> class std::shared_ptr<class core::conformation::membrane::SpanningTopology>

class pyrosetta.rosetta.core.conformation.membrane.Orientation

Bases: pybind11_builtins.pybind11_object

Define the orientation of a secondary structure span

relative to the membrane

Members:

in

out

in = <Orientation.in: 1>
property name
out = <Orientation.out: 2>
class pyrosetta.rosetta.core.conformation.membrane.Span

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.core.conformation.membrane.Span, src: pyrosetta.rosetta.core.conformation.membrane.Span) pyrosetta.rosetta.core.conformation.membrane.Span

Assignment Operator

Make a deep copy of this object

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

center(self: pyrosetta.rosetta.core.conformation.membrane.Span) int

Get residue closest to center

C++: core::conformation::membrane::Span::center() const –> unsigned long

end(self: pyrosetta.rosetta.core.conformation.membrane.Span) int

Get end position

Get the end position of a transmembrane span

C++: core::conformation::membrane::Span::end() const –> unsigned long

is_valid(self: pyrosetta.rosetta.core.conformation.membrane.Span) bool

Check that this Span is Valid

Check that this span describes a consecutive transmembrane span of nonzero length.

C++: core::conformation::membrane::Span::is_valid() const –> bool

not_valid(self: pyrosetta.rosetta.core.conformation.membrane.Span) None

C++: core::conformation::membrane::Span::not_valid() const –> void

orientation(*args, **kwargs)

Overloaded function.

  1. orientation(self: pyrosetta.rosetta.core.conformation.membrane.Span) -> pyrosetta.rosetta.core.conformation.membrane.Orientation

Get the orientation of the span

C++: core::conformation::membrane::Span::orientation() const –> enum core::conformation::membrane::Orientation

  1. orientation(self: pyrosetta.rosetta.core.conformation.membrane.Span, orient_in: pyrosetta.rosetta.core.conformation.membrane.Orientation) -> None

Set the orientation of the span

C++: core::conformation::membrane::Span::orientation(enum core::conformation::membrane::Orientation) –> void

shift(self: pyrosetta.rosetta.core.conformation.membrane.Span, offset: int) None

Shift by offset

Shift the transmembrane span by a user-provided offset

C++: core::conformation::membrane::Span::shift(unsigned long) –> void

show(self: pyrosetta.rosetta.core.conformation.membrane.Span) None

Show This Span

Show the information in this span. TODO: Should override base method

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

start(self: pyrosetta.rosetta.core.conformation.membrane.Span) int

Get start position

Get the Starting Position of a transmembrane span

C++: core::conformation::membrane::Span::start() const –> unsigned long

class pyrosetta.rosetta.core.conformation.membrane.SpanningTopology

Bases: pybind11_builtins.pybind11_object

add_span(*args, **kwargs)

Overloaded function.

  1. add_span(self: pyrosetta.rosetta.core.conformation.membrane.SpanningTopology, span: pyrosetta.rosetta.core.conformation.membrane.Span) -> None

  2. add_span(self: pyrosetta.rosetta.core.conformation.membrane.SpanningTopology, span: pyrosetta.rosetta.core.conformation.membrane.Span, offset: int) -> None

C++: core::conformation::membrane::SpanningTopology::add_span(const class core::conformation::membrane::Span &, unsigned long) –> void

  1. add_span(self: pyrosetta.rosetta.core.conformation.membrane.SpanningTopology, start: int, end: int) -> None

  2. add_span(self: pyrosetta.rosetta.core.conformation.membrane.SpanningTopology, start: int, end: int, offset: int) -> None

C++: core::conformation::membrane::SpanningTopology::add_span(unsigned long, unsigned long, unsigned long) –> void

assign(self: pyrosetta.rosetta.core.conformation.membrane.SpanningTopology, src: pyrosetta.rosetta.core.conformation.membrane.SpanningTopology) pyrosetta.rosetta.core.conformation.membrane.SpanningTopology

Assignment Operator

Overload assignemnt operator - required Rosetta method

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

concatenate_topology(self: pyrosetta.rosetta.core.conformation.membrane.SpanningTopology, topo: pyrosetta.rosetta.core.conformation.membrane.SpanningTopology) pyrosetta.rosetta.core.conformation.membrane.SpanningTopology

C++: core::conformation::membrane::SpanningTopology::concatenate_topology(const class core::conformation::membrane::SpanningTopology &) –> class core::conformation::membrane::SpanningTopology &

fill_from_spanfile(*args, **kwargs)

Overloaded function.

  1. fill_from_spanfile(self: pyrosetta.rosetta.core.conformation.membrane.SpanningTopology, spanfile: str, pdb2pose_map: pyrosetta.rosetta.std.map_std_string_unsigned_long) -> None

  2. fill_from_spanfile(self: pyrosetta.rosetta.core.conformation.membrane.SpanningTopology, spanfile: str, pdb2pose_map: pyrosetta.rosetta.std.map_std_string_unsigned_long, total_residues: int) -> None

C++: core::conformation::membrane::SpanningTopology::fill_from_spanfile(std::string, class std::map<std::string, unsigned long, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, unsigned long> > >, unsigned long) –> void

fill_from_structure(self: pyrosetta.rosetta.core.conformation.membrane.SpanningTopology, res_z_coord: pyrosetta.rosetta.utility.vector1_double, chainID: pyrosetta.rosetta.utility.vector1_unsigned_long, secstruct: pyrosetta.rosetta.utility.vector1_char, thickness: float) None

C++: core::conformation::membrane::SpanningTopology::fill_from_structure(class utility::vector1<double, class std::allocator<double> >, class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class utility::vector1<char, class std::allocator<char> >, double) –> void

get_spans(self: pyrosetta.rosetta.core.conformation.membrane.SpanningTopology) pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_membrane_Span_t

C++: core::conformation::membrane::SpanningTopology::get_spans() const –> class utility::vector1<class std::shared_ptr<class core::conformation::membrane::Span>, class std::allocator<class std::shared_ptr<class core::conformation::membrane::Span> > >

in_span(self: pyrosetta.rosetta.core.conformation.membrane.SpanningTopology, residue: int) bool

C++: core::conformation::membrane::SpanningTopology::in_span(unsigned long) const –> bool

is_valid(self: pyrosetta.rosetta.core.conformation.membrane.SpanningTopology) bool

Determine if this Spanning Topology Object is Valid

Check that spans still span the membrane

C++: core::conformation::membrane::SpanningTopology::is_valid() const –> bool

nres_topo(self: pyrosetta.rosetta.core.conformation.membrane.SpanningTopology) int

C++: core::conformation::membrane::SpanningTopology::nres_topo() const –> unsigned long

nspans(self: pyrosetta.rosetta.core.conformation.membrane.SpanningTopology) int

C++: core::conformation::membrane::SpanningTopology::nspans() const –> unsigned long

reorder_spans(self: pyrosetta.rosetta.core.conformation.membrane.SpanningTopology) None

C++: core::conformation::membrane::SpanningTopology::reorder_spans() –> void

show(*args, **kwargs)

Overloaded function.

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

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

Generate string representation of Spanning Topology Object for debugging purposes.

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

span(self: pyrosetta.rosetta.core.conformation.membrane.SpanningTopology, span_number: int) pyrosetta.rosetta.core.conformation.membrane.Span

C++: core::conformation::membrane::SpanningTopology::span(unsigned long) const –> class std::shared_ptr<class core::conformation::membrane::Span>

spanning(self: pyrosetta.rosetta.core.conformation.membrane.SpanningTopology, res_z_coord: pyrosetta.rosetta.utility.vector1_double, span: pyrosetta.rosetta.core.conformation.membrane.Span) bool

C++: core::conformation::membrane::SpanningTopology::spanning(class utility::vector1<double, class std::allocator<double> >, const class core::conformation::membrane::Span &) const –> bool

write_spanfile(self: pyrosetta.rosetta.core.conformation.membrane.SpanningTopology, output_filename: str) None

C++: core::conformation::membrane::SpanningTopology::write_spanfile(std::string) const –> void

pyrosetta.rosetta.core.conformation.membrane.spanfile_name() str

C++: core::conformation::membrane::spanfile_name() –> std::string

pyrosetta.rosetta.core.conformation.membrane.spanfile_names() pyrosetta.rosetta.utility.vector1_std_string

C++: core::conformation::membrane::spanfile_names() –> class utility::vector1<std::string, class std::allocator<std::string > >