branch_angle

Bindings for protocols::branch_angle namespace

class pyrosetta.rosetta.protocols.branch_angle.BranchCoef1

Bases: pybind11_builtins.pybind11_object

a class to store coefficients for branching angle optimization around a single atom atom with three bonded neighbors

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.branch_angle.BranchCoef1, overall_Ktheta: float, overall_theta0: float, overall_energy0: float, b1_torsion_offset_A: float, b1_torsion_offset_B: float, b1_torsion_offset_C: float, b1_bond_angle_A: float, b1_bond_angle_B: float, b1_bond_angle_C: float) -> None
2. __init__(self: pyrosetta.rosetta.protocols.branch_angle.BranchCoef1, arg0: pyrosetta.rosetta.protocols.branch_angle.BranchCoef1) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

b1_bond_angle_A(self: pyrosetta.rosetta.protocols.branch_angle.BranchCoef1) → float

get branching atom 1 bond angle A coefficient (angle^0)

C++: protocols::branch_angle::BranchCoef1::b1_bond_angle_A() const –> double

b1_bond_angle_B(self: pyrosetta.rosetta.protocols.branch_angle.BranchCoef1) → float

get branching atom 1 bond angle B coefficient (angle^1)

C++: protocols::branch_angle::BranchCoef1::b1_bond_angle_B() const –> double

b1_bond_angle_C(self: pyrosetta.rosetta.protocols.branch_angle.BranchCoef1) → float

get branching atom 1 bond angle C coefficient (angle^2)

C++: protocols::branch_angle::BranchCoef1::b1_bond_angle_C() const –> double

b1_torsion_offset_A(self: pyrosetta.rosetta.protocols.branch_angle.BranchCoef1) → float

get branching atom 1 torsion offset A coefficient (angle^0)

C++: protocols::branch_angle::BranchCoef1::b1_torsion_offset_A() const –> double

b1_torsion_offset_B(self: pyrosetta.rosetta.protocols.branch_angle.BranchCoef1) → float

get branching atom 1 torsion offset B coefficient (angle^1)

C++: protocols::branch_angle::BranchCoef1::b1_torsion_offset_B() const –> double

b1_torsion_offset_C(self: pyrosetta.rosetta.protocols.branch_angle.BranchCoef1) → float

get branching atom 1 torsion offset C coefficient (angle^2)

C++: protocols::branch_angle::BranchCoef1::b1_torsion_offset_C() const –> double

evaluate(self: pyrosetta.rosetta.protocols.branch_angle.BranchCoef1, m2_bond_angle: float, b1_torsion_offset: float, b1_bond_angle: float) → None

calculate single branching angles for a main chain bond angle

C++: protocols::branch_angle::BranchCoef1::evaluate(const double, double &, double &) const –> void

overall_Ktheta(self: pyrosetta.rosetta.protocols.branch_angle.BranchCoef1) → float

get overall Ktheta parameter

C++: protocols::branch_angle::BranchCoef1::overall_Ktheta() const –> double

overall_energy0(self: pyrosetta.rosetta.protocols.branch_angle.BranchCoef1) → float

get overall energy0 parameter

C++: protocols::branch_angle::BranchCoef1::overall_energy0() const –> double

overall_theta0(self: pyrosetta.rosetta.protocols.branch_angle.BranchCoef1) → float

get overall theta0 parameter

C++: protocols::branch_angle::BranchCoef1::overall_theta0() const –> double

class pyrosetta.rosetta.protocols.branch_angle.BranchCoef2

Bases: pyrosetta.rosetta.protocols.branch_angle.BranchCoef1

a class to store coefficients for branching angle optimization around a single atom atom with three bonded neighbors

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(self: pyrosetta.rosetta.protocols.branch_angle.BranchCoef2, overall_Ktheta: float, overall_theta0: float, overall_energy0: float, b1_torsion_offset_A: float, b1_torsion_offset_B: float, b1_torsion_offset_C: float, b1_bond_angle_A: float, b1_bond_angle_B: float, b1_bond_angle_C: float, b2_torsion_offset_A: float, b2_torsion_offset_B: float, b2_torsion_offset_C: float, b2_bond_angle_A: float, b2_bond_angle_B: float, b2_bond_angle_C: float) → None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

b1_bond_angle_A(self: pyrosetta.rosetta.protocols.branch_angle.BranchCoef1) → float

get branching atom 1 bond angle A coefficient (angle^0)

C++: protocols::branch_angle::BranchCoef1::b1_bond_angle_A() const –> double

b1_bond_angle_B(self: pyrosetta.rosetta.protocols.branch_angle.BranchCoef1) → float

get branching atom 1 bond angle B coefficient (angle^1)

C++: protocols::branch_angle::BranchCoef1::b1_bond_angle_B() const –> double

b1_bond_angle_C(self: pyrosetta.rosetta.protocols.branch_angle.BranchCoef1) → float

get branching atom 1 bond angle C coefficient (angle^2)

C++: protocols::branch_angle::BranchCoef1::b1_bond_angle_C() const –> double

b1_torsion_offset_A(self: pyrosetta.rosetta.protocols.branch_angle.BranchCoef1) → float

get branching atom 1 torsion offset A coefficient (angle^0)

C++: protocols::branch_angle::BranchCoef1::b1_torsion_offset_A() const –> double

b1_torsion_offset_B(self: pyrosetta.rosetta.protocols.branch_angle.BranchCoef1) → float

get branching atom 1 torsion offset B coefficient (angle^1)

C++: protocols::branch_angle::BranchCoef1::b1_torsion_offset_B() const –> double

b1_torsion_offset_C(self: pyrosetta.rosetta.protocols.branch_angle.BranchCoef1) → float

get branching atom 1 torsion offset C coefficient (angle^2)

C++: protocols::branch_angle::BranchCoef1::b1_torsion_offset_C() const –> double

b2_bond_angle_A(self: pyrosetta.rosetta.protocols.branch_angle.BranchCoef2) → float

get branching atom 2 bond angle A coefficient (angle^0)

C++: protocols::branch_angle::BranchCoef2::b2_bond_angle_A() const –> double

b2_bond_angle_B(self: pyrosetta.rosetta.protocols.branch_angle.BranchCoef2) → float

get branching atom 2 bond angle B coefficient (angle^1)

C++: protocols::branch_angle::BranchCoef2::b2_bond_angle_B() const –> double

b2_bond_angle_C(self: pyrosetta.rosetta.protocols.branch_angle.BranchCoef2) → float

get branching atom 2 bond angle C coefficient (angle^2)

C++: protocols::branch_angle::BranchCoef2::b2_bond_angle_C() const –> double

b2_torsion_offset_A(self: pyrosetta.rosetta.protocols.branch_angle.BranchCoef2) → float

get branching atom 2 torsion offset A coefficient (angle^0)

C++: protocols::branch_angle::BranchCoef2::b2_torsion_offset_A() const –> double

b2_torsion_offset_B(self: pyrosetta.rosetta.protocols.branch_angle.BranchCoef2) → float

get branching atom 2 torsion offset B coefficient (angle^1)

C++: protocols::branch_angle::BranchCoef2::b2_torsion_offset_B() const –> double

b2_torsion_offset_C(self: pyrosetta.rosetta.protocols.branch_angle.BranchCoef2) → float

get branching atom 2 torsion offset C coefficient (angle^2)

C++: protocols::branch_angle::BranchCoef2::b2_torsion_offset_C() const –> double

evaluate(self: pyrosetta.rosetta.protocols.branch_angle.BranchCoef2, m2_bond_angle: float, b1_torsion_offset: float, b1_bond_angle: float, b2_torsion_offset: float, b2_bond_angle: float) → None

calculate single branching angles for a main chain bond angle

C++: protocols::branch_angle::BranchCoef2::evaluate(const double, double &, double &, double &, double &) const –> void

overall_Ktheta(self: pyrosetta.rosetta.protocols.branch_angle.BranchCoef1) → float

get overall Ktheta parameter

C++: protocols::branch_angle::BranchCoef1::overall_Ktheta() const –> double

overall_energy0(self: pyrosetta.rosetta.protocols.branch_angle.BranchCoef1) → float

get overall energy0 parameter

C++: protocols::branch_angle::BranchCoef1::overall_energy0() const –> double

overall_theta0(self: pyrosetta.rosetta.protocols.branch_angle.BranchCoef1) → float

get overall theta0 parameter

C++: protocols::branch_angle::BranchCoef1::overall_theta0() const –> double

class pyrosetta.rosetta.protocols.branch_angle.BranchParam1

Bases: pybind11_builtins.pybind11_object

a class to store bond angle energy parameters around a single atom atom with three bonded neighbors

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.branch_angle.BranchParam1, arg0: float, arg1: float, arg2: float, arg3: float, arg4: float, arg5: float) -> None

doc

2. __init__(self: pyrosetta.rosetta.protocols.branch_angle.BranchParam1, m1_m2_Ktheta: float, m1_m2_theta0: float, m1_b1_Ktheta: float, m1_b1_theta0: float, m2_b1_Ktheta: float, m2_b1_theta0: float, tolerance: float) -> None
3. __init__(self: pyrosetta.rosetta.protocols.branch_angle.BranchParam1, arg0: pyrosetta.rosetta.protocols.branch_angle.BranchParam1) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

m1_b1_Ktheta(self: pyrosetta.rosetta.protocols.branch_angle.BranchParam1) → float

get Ktheta for mainchain atom 1 - branching atom 1 angle

C++: protocols::branch_angle::BranchParam1::m1_b1_Ktheta() const –> double

m1_b1_theta0(self: pyrosetta.rosetta.protocols.branch_angle.BranchParam1) → float

get theta0 for mainchain atom 1 - branching atom 1 angle

C++: protocols::branch_angle::BranchParam1::m1_b1_theta0() const –> double

m1_m2_Ktheta(self: pyrosetta.rosetta.protocols.branch_angle.BranchParam1) → float

get Ktheta for mainchain atom 1 - mainchain atom 1 angle

C++: protocols::branch_angle::BranchParam1::m1_m2_Ktheta() const –> double

m1_m2_theta0(self: pyrosetta.rosetta.protocols.branch_angle.BranchParam1) → float

get theta0 for mainchain atom 1 - mainchain atom 1 angle

C++: protocols::branch_angle::BranchParam1::m1_m2_theta0() const –> double

m2_b1_Ktheta(self: pyrosetta.rosetta.protocols.branch_angle.BranchParam1) → float

get Ktheta for mainchain atom 2 - branching atom 1 angle

C++: protocols::branch_angle::BranchParam1::m2_b1_Ktheta() const –> double

m2_b1_theta0(self: pyrosetta.rosetta.protocols.branch_angle.BranchParam1) → float

get theta0 for mainchain atom 2 - branching atom 1 angle

C++: protocols::branch_angle::BranchParam1::m2_b1_theta0() const –> double

class pyrosetta.rosetta.protocols.branch_angle.BranchParam2

Bases: pyrosetta.rosetta.protocols.branch_angle.BranchParam1

a class to store bond angle energy parameters around a single atom atom with four bonded neighbors

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.branch_angle.BranchParam2, arg0: float, arg1: float, arg2: float, arg3: float, arg4: float, arg5: float, arg6: float, arg7: float, arg8: float, arg9: float, arg10: float, arg11: float) -> None

doc

2. __init__(self: pyrosetta.rosetta.protocols.branch_angle.BranchParam2, m1_m2_Ktheta: float, m1_m2_theta0: float, m1_b1_Ktheta: float, m1_b1_theta0: float, m2_b1_Ktheta: float, m2_b1_theta0: float, m1_b2_Ktheta: float, m1_b2_theta0: float, m2_b2_Ktheta: float, m2_b2_theta0: float, b1_b2_Ktheta: float, b1_b2_theta0: float, tolerance: float) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

b1_b2_Ktheta(self: pyrosetta.rosetta.protocols.branch_angle.BranchParam2) → float

get Ktheta for branching atom 1 - branching atom 2 angle

C++: protocols::branch_angle::BranchParam2::b1_b2_Ktheta() const –> double

b1_b2_theta0(self: pyrosetta.rosetta.protocols.branch_angle.BranchParam2) → float

get theta0 for branching atom 1 - branching atom 2 angle

C++: protocols::branch_angle::BranchParam2::b1_b2_theta0() const –> double

m1_b1_Ktheta(self: pyrosetta.rosetta.protocols.branch_angle.BranchParam1) → float

get Ktheta for mainchain atom 1 - branching atom 1 angle

C++: protocols::branch_angle::BranchParam1::m1_b1_Ktheta() const –> double

m1_b1_theta0(self: pyrosetta.rosetta.protocols.branch_angle.BranchParam1) → float

get theta0 for mainchain atom 1 - branching atom 1 angle

C++: protocols::branch_angle::BranchParam1::m1_b1_theta0() const –> double

m1_b2_Ktheta(self: pyrosetta.rosetta.protocols.branch_angle.BranchParam2) → float

get Ktheta for mainchain atom 1 - branching atom 2 angle

C++: protocols::branch_angle::BranchParam2::m1_b2_Ktheta() const –> double

m1_b2_theta0(self: pyrosetta.rosetta.protocols.branch_angle.BranchParam2) → float

get theta0 for mainchain atom 1 - branching atom 2 angle

C++: protocols::branch_angle::BranchParam2::m1_b2_theta0() const –> double

m1_m2_Ktheta(self: pyrosetta.rosetta.protocols.branch_angle.BranchParam1) → float

get Ktheta for mainchain atom 1 - mainchain atom 1 angle

C++: protocols::branch_angle::BranchParam1::m1_m2_Ktheta() const –> double

m1_m2_theta0(self: pyrosetta.rosetta.protocols.branch_angle.BranchParam1) → float

get theta0 for mainchain atom 1 - mainchain atom 1 angle

C++: protocols::branch_angle::BranchParam1::m1_m2_theta0() const –> double

m2_b1_Ktheta(self: pyrosetta.rosetta.protocols.branch_angle.BranchParam1) → float

get Ktheta for mainchain atom 2 - branching atom 1 angle

C++: protocols::branch_angle::BranchParam1::m2_b1_Ktheta() const –> double

m2_b1_theta0(self: pyrosetta.rosetta.protocols.branch_angle.BranchParam1) → float

get theta0 for mainchain atom 2 - branching atom 1 angle

C++: protocols::branch_angle::BranchParam1::m2_b1_theta0() const –> double

m2_b2_Ktheta(self: pyrosetta.rosetta.protocols.branch_angle.BranchParam2) → float

get Ktheta for mainchain atom 2 - branching atom 2 angle

C++: protocols::branch_angle::BranchParam2::m2_b2_Ktheta() const –> double

m2_b2_theta0(self: pyrosetta.rosetta.protocols.branch_angle.BranchParam2) → float

get theta0 for mainchain atom 2 - branching atom 2 angle

C++: protocols::branch_angle::BranchParam2::m2_b2_theta0() const –> double

pyrosetta.rosetta.protocols.branch_angle.branching_atomid1(pose: pyrosetta.rosetta.core.pose.Pose, main_atomid1: pyrosetta.rosetta.core.id.AtomID, center_atomid: pyrosetta.rosetta.core.id.AtomID, main_atomid2: pyrosetta.rosetta.core.id.AtomID, branch_atomid1: pyrosetta.rosetta.core.id.AtomID) → None

get 1 branching atom

C++: protocols::branch_angle::branching_atomid1(const class core::pose::Pose &, class core::id::AtomID, class core::id::AtomID, class core::id::AtomID, class core::id::AtomID &) –> void

pyrosetta.rosetta.protocols.branch_angle.branching_atomids2(pose: pyrosetta.rosetta.core.pose.Pose, main_atomid1: pyrosetta.rosetta.core.id.AtomID, center_atomid: pyrosetta.rosetta.core.id.AtomID, main_atomid2: pyrosetta.rosetta.core.id.AtomID, branch_atomid1: pyrosetta.rosetta.core.id.AtomID, branch_atomid2: pyrosetta.rosetta.core.id.AtomID) → None

get 2 branching atoms ordered according their torsion offsets

C++: protocols::branch_angle::branching_atomids2(const class core::pose::Pose &, class core::id::AtomID, class core::id::AtomID, class core::id::AtomID, class core::id::AtomID &, class core::id::AtomID &) –> void

pyrosetta.rosetta.protocols.branch_angle.get_branching_atoms2(main_atom2: pyrosetta.rosetta.core.kinematics.tree.Atom, branch_atom1: pyrosetta.rosetta.core.kinematics.tree.Atom, branch_atom2: pyrosetta.rosetta.core.kinematics.tree.Atom) → None

get 2 siblings of an atom ordered according their torsion offsets

C++: protocols::branch_angle::get_branching_atoms2(const class std::shared_ptr<const class core::kinematics::tree::Atom>, class std::shared_ptr<const class core::kinematics::tree::Atom> &, class std::shared_ptr<const class core::kinematics::tree::Atom> &) –> void