membrane¶

Bindings for core::conformation::membrane namespace

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 class std::basic_string<char> &) –> 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 &

msg(*args, **kwargs)¶

Overloaded function.

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

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

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

C++: utility::excn::Exception::msg(const class std::basic_string<char> &) –> void

show(self: pyrosetta.rosetta.utility.excn.Exception, : pyrosetta.rosetta.std.ostream) → None¶: C++: utility::excn::Exception::show(class std::basic_ostream<char> &) const –> void

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 class std::basic_string<char> &) –> 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 &

msg(*args, **kwargs)¶

Overloaded function.

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

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

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

C++: utility::excn::Exception::msg(const class std::basic_string<char> &) –> void

show(self: pyrosetta.rosetta.utility.excn.Exception, : pyrosetta.rosetta.std.ostream) → None¶: C++: utility::excn::Exception::show(class std::basic_ostream<char> &) const –> void

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 class std::basic_string<char> &) –> 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 &

msg(*args, **kwargs)¶

Overloaded function.

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

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

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

C++: utility::excn::Exception::msg(const class std::basic_string<char> &) –> void

show(self: pyrosetta.rosetta.utility.excn.Exception, : pyrosetta.rosetta.std.ostream) → None¶: C++: utility::excn::Exception::show(class std::basic_ostream<char> &) const –> void

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 class std::basic_string<char> &) –> 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 &

msg(*args, **kwargs)¶

Overloaded function.

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

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

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

C++: utility::excn::Exception::msg(const class std::basic_string<char> &) –> void

show(self: pyrosetta.rosetta.utility.excn.Exception, : pyrosetta.rosetta.std.ostream) → None¶: C++: utility::excn::Exception::show(class std::basic_ostream<char> &) const –> void

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 class std::basic_string<char> &) –> 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 &

msg(*args, **kwargs)¶

Overloaded function.

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

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

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

C++: utility::excn::Exception::msg(const class std::basic_string<char> &) –> void

show(self: pyrosetta.rosetta.utility.excn.Exception, : pyrosetta.rosetta.std.ostream) → None¶: C++: utility::excn::Exception::show(class std::basic_ostream<char> &) const –> void

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 class std::basic_string<char> &) –> 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 &

msg(*args, **kwargs)¶

Overloaded function.

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

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

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

C++: utility::excn::Exception::msg(const class std::basic_string<char> &) –> void

show(self: pyrosetta.rosetta.utility.excn.Exception, : pyrosetta.rosetta.std.ostream) → None¶: C++: utility::excn::Exception::show(class std::basic_ostream<char> &) const –> void

what(self: pyrosetta.rosetta.std.exception) → str¶: C++: std::exception::what() const –> const char *

class pyrosetta.rosetta.core.conformation.membrane.LipidAccInfo¶

Bases: pybind11_builtins.pybind11_object

Membrane Lipid Accessibility Data

Stores lipid accessibility data derived from OCTOPUS spanning file: and psiblast search using run_lips.pl script

assign(self: pyrosetta.rosetta.core.conformation.membrane.LipidAccInfo, src: pyrosetta.rosetta.core.conformation.membrane.LipidAccInfo) → pyrosetta.rosetta.core.conformation.membrane.LipidAccInfo¶

Assignment Operator

Create a deep copy of this object, overloading the assignment operator

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

lipid_burial(self: pyrosetta.rosetta.core.conformation.membrane.LipidAccInfo) → pyrosetta.rosetta.utility.vector1_double¶

Access Lipid buried surface area per-residue

C++: core::conformation::membrane::LipidAccInfo::lipid_burial() –> class utility::vector1<double, class std::allocator<double> >

lipid_exposure(self: pyrosetta.rosetta.core.conformation.membrane.LipidAccInfo) → pyrosetta.rosetta.utility.vector1_double¶

Access Lipid exposed surface area per-residue

C++: core::conformation::membrane::LipidAccInfo::lipid_exposure() –> class utility::vector1<double, class std::allocator<double> >

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

Bases: pybind11_builtins.pybind11_object

Members:

thickness

center

normal

class pyrosetta.rosetta.core.conformation.membrane.MembraneInfo¶

Bases: pybind11_builtins.pybind11_object

MembraneInfo describes the membrane bilayer and its relationship with the protein

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

Calculate the z coordinate of the atom, projected onto the membrane normal axis. Objective is to maintain correct coordinates in relative coordinate frame.

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. Use checks in: protocols/membrane/util.hh instead!

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

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

Is residue in the membrane? Takes CA coordinate

Uses the thickness stored in MembraneInfon and the residue_z_position

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

include_lips(self: pyrosetta.rosetta.core.conformation.membrane.MembraneInfo) → bool¶

Does this MembraneInfo includes lipophilicity information?

C++: core::conformation::membrane::MembraneInfo::include_lips() const –> bool

lipid_acc_data(self: pyrosetta.rosetta.core.conformation.membrane.MembraneInfo) → pyrosetta.rosetta.core.conformation.membrane.LipidAccInfo¶

Per-residue lipophilicity (probability of exposure to lipid)

Returns a LipidAccInfo describing per residue probability of exposure to lipid. Data calcualted via the run_lips.pl script and provided by the user on the commandline if applicable

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

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

Membrane center

Returns the xyzVector describing the center of the membrane This is the same as the MPct atom of the membrane (MEM) residue.

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

Returns an integer (core::Size) denoting the jump number in the foldtree representing the jump relating the membrane residue to the rest of the molecule

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

Returns the membrane normal, which describes the membrane orientation. This is the same as the xyzVector in the MPnm atom in the membrane residue.

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

Return the residue number of MEM (rsd.seqpos()) in the pose

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

For IMM - default is 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

For IMM = default is 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

Calculate the z coordinate of the residue, projected onto the membrane normal axis. Objective is to maintain correct coordinates in relative coordinate frame.

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

Set the membrane jump number (core::SSize)

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

show(*args, **kwargs)¶

Overloaded function.

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

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(class std::basic_ostream<char> &) const –> void

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

Transmembrane spaning topology

Return a SpanningTopology object, which includes a list of Span objects, describing the start and end sequence positions of each transmembrane span

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

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 > >