mean_field¶

Bindings for protocols::mean_field namespace

class pyrosetta.rosetta.protocols.mean_field.AAProb¶

Bases: pybind11_builtins.pybind11_object

encapsulates information about an amino acid at a position and its probability

used as the base unit in the specificity profile (AAMatrix) class

__add__(self: pyrosetta.rosetta.protocols.mean_field.AAProb, prob: float) → pyrosetta.rosetta.protocols.mean_field.AAProb¶

overloaded arithmetic operator for arithmetic with Real probability

adds prob to probability

C++: protocols::mean_field::AAProb::operator+(double) –> class protocols::mean_field::AAProb

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__div__(self: pyrosetta.rosetta.protocols.mean_field.AAProb, prob: float) → pyrosetta.rosetta.protocols.mean_field.AAProb¶

overloaded arithmetic operator for arithmetic with Real probability

divides probability by prob

C++: protocols::mean_field::AAProb::operator/(double) –> class protocols::mean_field::AAProb

__eq__(self: pyrosetta.rosetta.protocols.mean_field.AAProb, obj: pyrosetta.rosetta.protocols.mean_field.AAProb) → bool¶

overloaded equality operators to fix instantiation issues with PyRosetta

C++: protocols::mean_field::AAProb::operator==(const class protocols::mean_field::AAProb &) const –> bool

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__iadd__(*args, **kwargs)¶

Overloaded function.

__iadd__(self: pyrosetta.rosetta.protocols.mean_field.AAProb, obj: pyrosetta.rosetta.protocols.mean_field.AAProb) -> None

overloaded arithmetic operators to allow for easier matrix arithmetic

adds probability of obj to its own probability

only overloading operators that modify object so as to avoid confusion about identity of non-probability data members

C++: protocols::mean_field::AAProb::operator+=(const class protocols::mean_field::AAProb &) –> void

__iadd__(self: pyrosetta.rosetta.protocols.mean_field.AAProb, prob: float) -> None

overloaded arithmetic operator for arithmetic with Real probability

adds prob to its own probability

C++: protocols::mean_field::AAProb::operator+=(double) –> void

__idiv__(*args, **kwargs)¶

Overloaded function.

__idiv__(self: pyrosetta.rosetta.protocols.mean_field.AAProb, obj: pyrosetta.rosetta.protocols.mean_field.AAProb) -> None

overloaded arithmetic operators to allow for easier matrix arithmetic

divides its own probability by probability of obj

only overloading operators that modify object so as to avoid confusion about identity of non-probability data members

C++: protocols::mean_field::AAProb::operator/=(const class protocols::mean_field::AAProb &) –> void

__idiv__(self: pyrosetta.rosetta.protocols.mean_field.AAProb, prob: float) -> None

overloaded arithmetic operator for arithmetic with Real probability

divides its own probability by prob

C++: protocols::mean_field::AAProb::operator/=(double) –> void

__imul__(*args, **kwargs)¶

Overloaded function.

__imul__(self: pyrosetta.rosetta.protocols.mean_field.AAProb, obj: pyrosetta.rosetta.protocols.mean_field.AAProb) -> None

overloaded arithmetic operators to allow for easier matrix arithmetic

multiplies probability of obj by its own probability

only overloading operators that modify object so as to avoid confusion about identity of non-probability data members

C++: protocols::mean_field::AAProb::operator*=(const class protocols::mean_field::AAProb &) –> void

__imul__(self: pyrosetta.rosetta.protocols.mean_field.AAProb, prob: float) -> None

overloaded arithmetic operator for arithmetic with Real probability

multiplies its own probability by prob

C++: protocols::mean_field::AAProb::operator*=(double) –> void

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.mean_field.AAProb) -> None
__init__(self: pyrosetta.rosetta.protocols.mean_field.AAProb, prob: float, aa_ind: pyrosetta.rosetta.core.chemical.AA, pos: int, nrot: int) -> None
__init__(self: pyrosetta.rosetta.protocols.mean_field.AAProb, rp: protocols::mean_field::RotProb) -> None
__init__(self: pyrosetta.rosetta.protocols.mean_field.AAProb, arg0: pyrosetta.rosetta.protocols.mean_field.AAProb) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

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

__isub__(*args, **kwargs)¶

Overloaded function.

__isub__(self: pyrosetta.rosetta.protocols.mean_field.AAProb, obj: pyrosetta.rosetta.protocols.mean_field.AAProb) -> None

overloaded arithmetic operators to allow for easier matrix arithmetic

subtracts probability of obj from its own probability

only overloading operators that modify object so as to avoid confusion about identity of non-probability data members

C++: protocols::mean_field::AAProb::operator-=(const class protocols::mean_field::AAProb &) –> void

__isub__(self: pyrosetta.rosetta.protocols.mean_field.AAProb, prob: float) -> None

overloaded arithmetic operator for arithmetic with Real probability

subtracts prob from its own probability

C++: protocols::mean_field::AAProb::operator-=(double) –> void

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__mul__(self: pyrosetta.rosetta.protocols.mean_field.AAProb, prob: float) → pyrosetta.rosetta.protocols.mean_field.AAProb¶

overloaded arithmetic operator for arithmetic with Real probability

multiplies probability by prob

C++: protocols::mean_field::AAProb::operator*(double) –> class protocols::mean_field::AAProb

__ne__(self: pyrosetta.rosetta.protocols.mean_field.AAProb, obj: pyrosetta.rosetta.protocols.mean_field.AAProb) → bool¶

overloaded equality operators to fix instantiation issues with PyRosetta

C++: protocols::mean_field::AAProb::operator!=(const class protocols::mean_field::AAProb &) const –> bool

__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__(self: pyrosetta.rosetta.protocols.mean_field.AAProb) → str¶

__sub__(self: pyrosetta.rosetta.protocols.mean_field.AAProb, prob: float) → pyrosetta.rosetta.protocols.mean_field.AAProb¶

overloaded arithmetic operator for arithmetic with Real probability

subtracts prob from probability

C++: protocols::mean_field::AAProb::operator-(double) –> class protocols::mean_field::AAProb

__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).

aa_ind(*args, **kwargs)¶

Overloaded function.

aa_ind(self: pyrosetta.rosetta.protocols.mean_field.AAProb) -> pyrosetta.rosetta.core.chemical.AA

returns AA identity

C++: protocols::mean_field::AAProb::aa_ind() const –> enum core::chemical::AA

aa_ind(self: pyrosetta.rosetta.protocols.mean_field.AAProb, aa: pyrosetta.rosetta.core.chemical.AA) -> None

sets AA identity

C++: protocols::mean_field::AAProb::aa_ind(enum core::chemical::AA) –> void

assign(self: pyrosetta.rosetta.protocols.mean_field.AAProb, object_to_copy: pyrosetta.rosetta.protocols.mean_field.AAProb) → pyrosetta.rosetta.protocols.mean_field.AAProb¶

Assignment operator

C++: protocols::mean_field::AAProb::operator=(const class protocols::mean_field::AAProb &) –> class protocols::mean_field::AAProb &

nrot(*args, **kwargs)¶

Overloaded function.

nrot(self: pyrosetta.rosetta.protocols.mean_field.AAProb) -> int

returns number of rotamers corresponding to AA identity at this position

C++: protocols::mean_field::AAProb::nrot() const –> unsigned long

nrot(self: pyrosetta.rosetta.protocols.mean_field.AAProb, n: int) -> None

sets number of rotamers corresponding to AA identity at this position

C++: protocols::mean_field::AAProb::nrot(unsigned long) –> void

pos(*args, **kwargs)¶

Overloaded function.

pos(self: pyrosetta.rosetta.protocols.mean_field.AAProb) -> int

returns position in pose numbering

C++: protocols::mean_field::AAProb::pos() const –> unsigned long

pos(self: pyrosetta.rosetta.protocols.mean_field.AAProb, p: int) -> None

sets position in pose numbering

C++: protocols::mean_field::AAProb::pos(unsigned long) –> void

probability(*args, **kwargs)¶

Overloaded function.

probability(self: pyrosetta.rosetta.protocols.mean_field.AAProb) -> float

returns probability

C++: protocols::mean_field::AAProb::probability() const –> double

probability(self: pyrosetta.rosetta.protocols.mean_field.AAProb, prob: float) -> None

sets probability

C++: protocols::mean_field::AAProb::probability(double) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.mean_field.AAProb) -> None
show(self: pyrosetta.rosetta.protocols.mean_field.AAProb, output: pyrosetta.rosetta.std.ostream) -> None

Generate string representation of AAProb for debugging purposes.

C++: protocols::mean_field::AAProb::show(class std::basic_ostream<char> &) const –> void

class pyrosetta.rosetta.protocols.mean_field.DesignMeanField¶

Bases: pyrosetta.rosetta.protocols.mean_field.MeanField

calculator which conducts mean-field algorithm on one, designable pose to create a RotMatrix and AAMatrix

__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.

__init__(self: pyrosetta.rosetta.protocols.mean_field.DesignMeanField, option: int, poses: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, tasks: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_task_PackerTask_t, scfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None
__init__(self: pyrosetta.rosetta.protocols.mean_field.DesignMeanField, option: int, poses: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, tasks: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_task_PackerTask_t, scfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, lambda_mem: float, tolerance: float, temp: float, threshold: 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__(self: pyrosetta.rosetta.protocols.mean_field.DesignMeanField) → str¶

__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).

aa_matrix(self: pyrosetta.rosetta.protocols.mean_field.DesignMeanField) → pyrosetta.rosetta.protocols.mean_field.AAMatrix¶

returns const reference to AAMatrix

C++: protocols::mean_field::DesignMeanField::aa_matrix() const –> class std::shared_ptr<const class protocols::mean_field::AAMatrix>

alt_rot_matrix(self: pyrosetta.rosetta.protocols.mean_field.MeanField) → protocols::mean_field::RotMatrix¶

returns const pointer to alternate RotMatrix

C++: protocols::mean_field::MeanField::alt_rot_matrix() const –> class std::shared_ptr<const class protocols::mean_field::RotMatrix>

build_rot_matrix_for_pose(self: pyrosetta.rosetta.protocols.mean_field.MeanField, pose_ind: int) → None¶

build a RotMatrix for a specific pose in poses_

C++: protocols::mean_field::MeanField::build_rot_matrix_for_pose(unsigned long) –> void

converge(self: pyrosetta.rosetta.protocols.mean_field.MeanField) → None¶

tries to converge to a final RotMatrix

C++: protocols::mean_field::MeanField::converge() –> void

delete_pose(self: pyrosetta.rosetta.protocols.mean_field.MeanField, pose_ind: int) → None¶

delete a pose

C++: protocols::mean_field::MeanField::delete_pose(unsigned long) –> void

energies_matrix(self: pyrosetta.rosetta.protocols.mean_field.MeanField) → pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t¶

returns const reference to energies_matrix

C++: protocols::mean_field::MeanField::energies_matrix() const –> const class protocols::mean_field::jagged_array<double, class std::allocator<double> > &

init_option(self: pyrosetta.rosetta.protocols.mean_field.MeanField) → float¶

get init option (used to initialize RotMatrix)

C++: protocols::mean_field::MeanField::init_option() const –> double

lambda_memory(self: pyrosetta.rosetta.protocols.mean_field.MeanField) → float¶

get lambda memory, used in convergence process

C++: protocols::mean_field::MeanField::lambda_memory() const –> double

num_packed(self: pyrosetta.rosetta.protocols.mean_field.MeanField) → int¶

get number of residues that are packable

C++: protocols::mean_field::MeanField::num_packed() const –> unsigned long

num_poses(self: pyrosetta.rosetta.protocols.mean_field.MeanField) → int¶

get number of poses

while this is trivial for MeanField (poses_.size() == 1), useful for derived classes with FlexBB

C++: protocols::mean_field::MeanField::num_poses() const –> unsigned long

process(self: pyrosetta.rosetta.protocols.mean_field.DesignMeanField) → None¶

overrides process() method in MeanField to initialize AAMatrix from RotMatrix

C++: protocols::mean_field::DesignMeanField::process() –> void

rot_matrix(self: pyrosetta.rosetta.protocols.mean_field.MeanField) → protocols::mean_field::RotMatrix¶

returns const pointer to RotMatrix

C++: protocols::mean_field::MeanField::rot_matrix() const –> class std::shared_ptr<const class protocols::mean_field::RotMatrix>

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.mean_field.DesignMeanField) -> None
show(self: pyrosetta.rosetta.protocols.mean_field.DesignMeanField, output: pyrosetta.rosetta.std.ostream) -> None

Generate string representation of DesignMeanField for debugging purposes.

C++: protocols::mean_field::DesignMeanField::show(class std::basic_ostream<char> &) const –> void

temperature(self: pyrosetta.rosetta.protocols.mean_field.MeanField) → float¶

get temperature (kT)

C++: protocols::mean_field::MeanField::temperature() const –> double

threshold(self: pyrosetta.rosetta.protocols.mean_field.MeanField) → float¶

get threshold

C++: protocols::mean_field::MeanField::threshold() const –> double

tolerance(self: pyrosetta.rosetta.protocols.mean_field.MeanField) → float¶

get tolerance, used to determine if converged

C++: protocols::mean_field::MeanField::tolerance() const –> double

class pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField¶

Bases: pyrosetta.rosetta.protocols.mean_field.MeanField

calculator which conducts mean-field algorithm on several, non-designable poses to create a single, averaged RotMatrix

__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.

__init__(self: pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField, option: int, poses: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, tasks: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_task_PackerTask_t, scfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None
__init__(self: pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField, option: int, poses: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, tasks: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_task_PackerTask_t, scfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, lambda_mem: float, tolerance: float, temp: float, threshold: 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__(self: pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField) → str¶

__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).

alt_rot_matrix(self: pyrosetta.rosetta.protocols.mean_field.MeanField) → protocols::mean_field::RotMatrix¶

returns const pointer to alternate RotMatrix

C++: protocols::mean_field::MeanField::alt_rot_matrix() const –> class std::shared_ptr<const class protocols::mean_field::RotMatrix>

bb_boltz_probs(self: pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField) → pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t¶

used by derived classes for write-access to bb_boltz_probs_

would prefer for the method to be protected, but disallowed by Rosetta Coding Conventions

C++: protocols::mean_field::FlexBBMeanField::bb_boltz_probs() –> class protocols::mean_field::jagged_array<double, class std::allocator<double> > &

bb_boltz_probs_per_aa(self: pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField) → pyrosetta.rosetta.utility.vector1_protocols_mean_field_jagged_array_double_std_allocator_double_t¶: C++: protocols::mean_field::FlexBBMeanField::bb_boltz_probs_per_aa() –> const class utility::vector1<class protocols::mean_field::jagged_array<double, class std::allocator<double> >, class std::allocator<class protocols::mean_field::jagged_array<double, class std::allocator<double> > > > &

build_rot_matrix_for_pose(self: pyrosetta.rosetta.protocols.mean_field.MeanField, pose_ind: int) → None¶

build a RotMatrix for a specific pose in poses_

C++: protocols::mean_field::MeanField::build_rot_matrix_for_pose(unsigned long) –> void

calc_bb_boltz_probs(self: pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField) → None¶

calculate Boltzmann weights of each backbone

C++: protocols::mean_field::FlexBBMeanField::calc_bb_boltz_probs() –> void

calc_exp_value_rot_matrix(self: pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField) → None¶

calculate expected (averaged) RotMatrix

C++: protocols::mean_field::FlexBBMeanField::calc_exp_value_rot_matrix() –> void

converge(self: pyrosetta.rosetta.protocols.mean_field.MeanField) → None¶

tries to converge to a final RotMatrix

C++: protocols::mean_field::MeanField::converge() –> void

delete_pose(self: pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField, pose_ind: int) → None¶

deletes a pose from the list of poses

C++: protocols::mean_field::FlexBBMeanField::delete_pose(unsigned long) –> void

energies_matrix(self: pyrosetta.rosetta.protocols.mean_field.MeanField) → pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t¶

returns const reference to energies_matrix

C++: protocols::mean_field::MeanField::energies_matrix() const –> const class protocols::mean_field::jagged_array<double, class std::allocator<double> > &

energy_matrices(self: pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField) → pyrosetta.rosetta.utility.vector1_protocols_mean_field_jagged_array_double_std_allocator_double_t¶

returns const references to the utility vector of energy_matrices representing each pose in the backbone ensemble

C++: protocols::mean_field::FlexBBMeanField::energy_matrices() const –> const class utility::vector1<class protocols::mean_field::jagged_array<double, class std::allocator<double> >, class std::allocator<class protocols::mean_field::jagged_array<double, class std::allocator<double> > > > &

energy_matrix(self: pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField) → pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t¶

returns the expected (averaged) EnergyMatrix (exp_energy_matrix_)

C++: protocols::mean_field::FlexBBMeanField::energy_matrix() const –> class protocols::mean_field::jagged_array<double, class std::allocator<double> >

init_option(self: pyrosetta.rosetta.protocols.mean_field.MeanField) → float¶

get init option (used to initialize RotMatrix)

C++: protocols::mean_field::MeanField::init_option() const –> double

lambda_memory(self: pyrosetta.rosetta.protocols.mean_field.MeanField) → float¶

get lambda memory, used in convergence process

C++: protocols::mean_field::MeanField::lambda_memory() const –> double

num_packed(self: pyrosetta.rosetta.protocols.mean_field.MeanField) → int¶

get number of residues that are packable

C++: protocols::mean_field::MeanField::num_packed() const –> unsigned long

num_poses(self: pyrosetta.rosetta.protocols.mean_field.MeanField) → int¶

get number of poses

while this is trivial for MeanField (poses_.size() == 1), useful for derived classes with FlexBB

C++: protocols::mean_field::MeanField::num_poses() const –> unsigned long

process(self: pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField) → None¶

overrides process() method in MeanField to add convergence step for each pose and averaging step for all rot_matrices_

C++: protocols::mean_field::FlexBBMeanField::process() –> void

renumber_rotamers(self: pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField) → None¶

renumbers rotamers with a backbone-independent rotamer numbering scheme

C++: protocols::mean_field::FlexBBMeanField::renumber_rotamers() –> void

rot_matrices(self: pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField) → pyrosetta.rosetta.utility.vector1_protocols_mean_field_RotMatrix¶

returns const references to the utility vector of rot_matrices representing each pose in the backbone ensemble

C++: protocols::mean_field::FlexBBMeanField::rot_matrices() const –> const class utility::vector1<class protocols::mean_field::RotMatrix, class std::allocator<class protocols::mean_field::RotMatrix> > &

rot_matrix(self: pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField) → protocols::mean_field::RotMatrix¶

returns the expected (averaged) RotMatrix (exp_rot_matrix_)

C++: protocols::mean_field::FlexBBMeanField::rot_matrix() const –> class std::shared_ptr<const class protocols::mean_field::RotMatrix>

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField) -> None
show(self: pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField, output: pyrosetta.rosetta.std.ostream) -> None

Generate string representation of FlexBBMeanField for debugging purposes.

C++: protocols::mean_field::FlexBBMeanField::show(class std::basic_ostream<char> &) const –> void

temperature(self: pyrosetta.rosetta.protocols.mean_field.MeanField) → float¶

get temperature (kT)

C++: protocols::mean_field::MeanField::temperature() const –> double

threshold(self: pyrosetta.rosetta.protocols.mean_field.MeanField) → float¶

get threshold

C++: protocols::mean_field::MeanField::threshold() const –> double

tolerance(self: pyrosetta.rosetta.protocols.mean_field.MeanField) → float¶

get tolerance, used to determine if converged

C++: protocols::mean_field::MeanField::tolerance() const –> double

class pyrosetta.rosetta.protocols.mean_field.MeanField¶

Bases: pybind11_builtins.pybind11_object

calculator which conducts mean-field algorithm on either a single, non-designable pose or used as base class of other MeanFields

__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.

__init__(self: pyrosetta.rosetta.protocols.mean_field.MeanField, option: int, poses: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, tasks: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_task_PackerTask_t, scfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None
__init__(self: pyrosetta.rosetta.protocols.mean_field.MeanField, option: int, poses: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, tasks: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_task_PackerTask_t, scfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, lambda_mem: float, tolerance: float, temp: float, threshold: 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__(self: pyrosetta.rosetta.protocols.mean_field.MeanField) → str¶

__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).

alt_rot_matrix(self: pyrosetta.rosetta.protocols.mean_field.MeanField) → protocols::mean_field::RotMatrix¶

returns const pointer to alternate RotMatrix

C++: protocols::mean_field::MeanField::alt_rot_matrix() const –> class std::shared_ptr<const class protocols::mean_field::RotMatrix>

build_rot_matrix_for_pose(self: pyrosetta.rosetta.protocols.mean_field.MeanField, pose_ind: int) → None¶

build a RotMatrix for a specific pose in poses_

C++: protocols::mean_field::MeanField::build_rot_matrix_for_pose(unsigned long) –> void

converge(self: pyrosetta.rosetta.protocols.mean_field.MeanField) → None¶

tries to converge to a final RotMatrix

C++: protocols::mean_field::MeanField::converge() –> void

delete_pose(self: pyrosetta.rosetta.protocols.mean_field.MeanField, pose_ind: int) → None¶

delete a pose

C++: protocols::mean_field::MeanField::delete_pose(unsigned long) –> void

energies_matrix(self: pyrosetta.rosetta.protocols.mean_field.MeanField) → pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t¶

returns const reference to energies_matrix

C++: protocols::mean_field::MeanField::energies_matrix() const –> const class protocols::mean_field::jagged_array<double, class std::allocator<double> > &

init_option(self: pyrosetta.rosetta.protocols.mean_field.MeanField) → float¶

get init option (used to initialize RotMatrix)

C++: protocols::mean_field::MeanField::init_option() const –> double

lambda_memory(self: pyrosetta.rosetta.protocols.mean_field.MeanField) → float¶

get lambda memory, used in convergence process

C++: protocols::mean_field::MeanField::lambda_memory() const –> double

num_packed(self: pyrosetta.rosetta.protocols.mean_field.MeanField) → int¶

get number of residues that are packable

C++: protocols::mean_field::MeanField::num_packed() const –> unsigned long

num_poses(self: pyrosetta.rosetta.protocols.mean_field.MeanField) → int¶

get number of poses

while this is trivial for MeanField (poses_.size() == 1), useful for derived classes with FlexBB

C++: protocols::mean_field::MeanField::num_poses() const –> unsigned long

process(self: pyrosetta.rosetta.protocols.mean_field.MeanField) → None¶

simply calls the converge method to find a converged RotMatrix

C++: protocols::mean_field::MeanField::process() –> void

rot_matrix(self: pyrosetta.rosetta.protocols.mean_field.MeanField) → protocols::mean_field::RotMatrix¶

returns const pointer to RotMatrix

C++: protocols::mean_field::MeanField::rot_matrix() const –> class std::shared_ptr<const class protocols::mean_field::RotMatrix>

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.mean_field.MeanField) -> None
show(self: pyrosetta.rosetta.protocols.mean_field.MeanField, output: pyrosetta.rosetta.std.ostream) -> None

Generate string representation of MeanField for debugging purposes.

C++: protocols::mean_field::MeanField::show(class std::basic_ostream<char> &) const –> void

temperature(self: pyrosetta.rosetta.protocols.mean_field.MeanField) → float¶

get temperature (kT)

C++: protocols::mean_field::MeanField::temperature() const –> double

threshold(self: pyrosetta.rosetta.protocols.mean_field.MeanField) → float¶

get threshold

C++: protocols::mean_field::MeanField::threshold() const –> double

tolerance(self: pyrosetta.rosetta.protocols.mean_field.MeanField) → float¶

get tolerance, used to determine if converged

C++: protocols::mean_field::MeanField::tolerance() const –> double

class pyrosetta.rosetta.protocols.mean_field.ResHashMap¶

Bases: pybind11_builtins.pybind11_object

class ResHashMap holds a hashmap of rotamers

__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.mean_field.ResHashMap) → 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__(self: pyrosetta.rosetta.protocols.mean_field.ResHashMap) → str¶

__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).

attempt_insert(self: pyrosetta.rosetta.protocols.mean_field.ResHashMap, res: pyrosetta.rosetta.core.conformation.Residue) → int¶

Attempts to insert a residue res with a RotamerIndex ind into the hash map if it is not already there

C++: protocols::mean_field::ResHashMap::attempt_insert(class std::shared_ptr<const class core::conformation::Residue>) –> long

get_rot_ind(self: pyrosetta.rosetta.protocols.mean_field.ResHashMap, res: pyrosetta.rosetta.core.conformation.Residue) → int¶

Attempts to get the rotamer index of a residue res

C++: protocols::mean_field::ResHashMap::get_rot_ind(class std::shared_ptr<const class core::conformation::Residue>) const –> long

last_ind_assigned(self: pyrosetta.rosetta.protocols.mean_field.ResHashMap) → int¶

returns the last rotamer index that was assigned by the ResHashMap

C++: protocols::mean_field::ResHashMap::last_ind_assigned() const –> long

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.mean_field.ResHashMap) -> None
show(self: pyrosetta.rosetta.protocols.mean_field.ResHashMap, output: pyrosetta.rosetta.std.ostream) -> None

Generate string representation of ResHashMap for debugging purposes.

C++: protocols::mean_field::ResHashMap::show(class std::basic_ostream<char> &) const –> void

class pyrosetta.rosetta.protocols.mean_field.ResHasher¶

Bases: pyrosetta.rosetta.std.unary_function_std_shared_ptr_const_core_conformation_Residue_unsigned_long_t

uses default boost::hash combine to hash rotamers based on rounded chi angles

__call__(self: pyrosetta.rosetta.protocols.mean_field.ResHasher, res: pyrosetta.rosetta.core.conformation.Residue) → int¶

return hash value given ResidueCOP

C++: protocols::mean_field::ResHasher::operator()(class std::shared_ptr<const class core::conformation::Residue>) const –> unsigned long

__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.

__init__(self: pyrosetta.rosetta.protocols.mean_field.ResHasher) -> None
__init__(self: pyrosetta.rosetta.protocols.mean_field.ResHasher, arg0: pyrosetta.rosetta.protocols.mean_field.ResHasher) -> 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).

assign(self: pyrosetta.rosetta.protocols.mean_field.ResHasher, : pyrosetta.rosetta.protocols.mean_field.ResHasher) → pyrosetta.rosetta.protocols.mean_field.ResHasher¶: C++: protocols::mean_field::ResHasher::operator=(const struct protocols::mean_field::ResHasher &) –> struct protocols::mean_field::ResHasher &

class pyrosetta.rosetta.protocols.mean_field.ResPred¶

Bases: pyrosetta.rosetta.std.binary_function_std_shared_ptr_const_core_conformation_Residue_std_shared_ptr_const_core_conformation_Residue_bool_t

checks whether two rotamer hashes match - if the rounded values of their chi angles match

__call__(self: pyrosetta.rosetta.protocols.mean_field.ResPred, first_res: pyrosetta.rosetta.core.conformation.Residue, second_res: pyrosetta.rosetta.core.conformation.Residue) → bool¶

return bool depending on whether two Residues hashes match

C++: protocols::mean_field::ResPred::operator()(class std::shared_ptr<const class core::conformation::Residue>, class std::shared_ptr<const class core::conformation::Residue>) const –> bool

__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.

__init__(self: pyrosetta.rosetta.protocols.mean_field.ResPred) -> None
__init__(self: pyrosetta.rosetta.protocols.mean_field.ResPred, arg0: pyrosetta.rosetta.protocols.mean_field.ResPred) -> 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).

assign(self: pyrosetta.rosetta.protocols.mean_field.ResPred, : pyrosetta.rosetta.protocols.mean_field.ResPred) → pyrosetta.rosetta.protocols.mean_field.ResPred¶: C++: protocols::mean_field::ResPred::operator=(const struct protocols::mean_field::ResPred &) –> struct protocols::mean_field::ResPred &

class pyrosetta.rosetta.protocols.mean_field.RotMatrix¶

Bases: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t

derived from a jagged_array of RotProbs

used in MeanField family of classes

__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).

__getitem__(*args, **kwargs)¶

Overloaded function.

__getitem__(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t, i: int) -> utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >
__getitem__(self: utility::vector1<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >, std::allocator<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> > > >, i: int) -> utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.mean_field.RotMatrix) -> None
__init__(self: pyrosetta.rosetta.protocols.mean_field.RotMatrix, option: int, rs: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets) -> None
__init__(self: pyrosetta.rosetta.protocols.mean_field.RotMatrix, arg0: pyrosetta.rosetta.protocols.mean_field.RotMatrix) -> 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__(self: pyrosetta.rosetta.protocols.mean_field.RotMatrix) → str¶

__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).

assign(self: pyrosetta.rosetta.protocols.mean_field.RotMatrix, object_to_copy: pyrosetta.rosetta.protocols.mean_field.RotMatrix) → pyrosetta.rosetta.protocols.mean_field.RotMatrix¶

Assignment operator

C++: protocols::mean_field::RotMatrix::operator=(const class protocols::mean_field::RotMatrix &) –> class protocols::mean_field::RotMatrix &

at(*args, **kwargs)¶

Overloaded function.

at(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t, i: int) -> utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >
at(self: utility::vector1<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >, std::allocator<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> > > >, i: int) -> utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >

back(*args, **kwargs)¶

Overloaded function.

back(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) -> utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >
back(self: utility::vector1<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >, std::allocator<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> > > >) -> utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >

build_rot_matrix(self: pyrosetta.rosetta.protocols.mean_field.RotMatrix, option: int, rs: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets) → None¶

calls init so as to reinitialize the RotMatrix with the given params

C++: protocols::mean_field::RotMatrix::build_rot_matrix(const unsigned long, class std::shared_ptr<class core::pack::rotamer_set::RotamerSets>) –> void

capacity(*args, **kwargs)¶

Overloaded function.

capacity(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) -> int
capacity(self: utility::vector1<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >, std::allocator<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> > > >) -> int

clear(*args, **kwargs)¶

Overloaded function.

clear(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) -> None
clear(self: utility::vector1<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >, std::allocator<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> > > >) -> None

curr_rot(*args, **kwargs)¶

Overloaded function.

curr_rot(self: pyrosetta.rosetta.protocols.mean_field.RotMatrix) -> pyrosetta.rosetta.utility.vector1_unsigned_long

returns a vector of the current rotamers at each position

C++: protocols::mean_field::RotMatrix::curr_rot() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

curr_rot(self: pyrosetta.rosetta.protocols.mean_field.RotMatrix, cr: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

sets the curr_rot vector

C++: protocols::mean_field::RotMatrix::curr_rot(class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void

empty(*args, **kwargs)¶

Overloaded function.

empty(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) -> bool
empty(self: utility::vector1<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >, std::allocator<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> > > >) -> bool

equal_size(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t, other: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) → bool¶: C++: protocols::mean_field::jagged_array<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >::equal_size(const class protocols::mean_field::jagged_array<class protocols::mean_field::RotProb, class std::allocator<class protocols::mean_field::RotProb> > &) const –> bool

front(*args, **kwargs)¶

Overloaded function.

front(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) -> utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >
front(self: utility::vector1<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >, std::allocator<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> > > >) -> utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >

get_total(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) → protocols::mean_field::RotProb¶: C++: protocols::mean_field::jagged_array<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >::get_total() const –> class protocols::mean_field::RotProb

has_value(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t, t: protocols::mean_field::RotProb) → bool¶: C++: protocols::mean_field::jagged_array<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >::has_value(const class protocols::mean_field::RotProb &) const –> bool

index(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t, t: protocols::mean_field::RotProb) → int¶: C++: protocols::mean_field::jagged_array<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >::index(const class protocols::mean_field::RotProb &) const –> int

is_designed(*args, **kwargs)¶

Overloaded function.

is_designed(self: pyrosetta.rosetta.protocols.mean_field.RotMatrix) -> pyrosetta.rosetta.utility.vector1_bool

returns a vector of bools designating whether each position allows design or not

C++: protocols::mean_field::RotMatrix::is_designed() const –> const class utility::vector1<bool, class std::allocator<bool> > &

is_designed(self: pyrosetta.rosetta.protocols.mean_field.RotMatrix, id: pyrosetta.rosetta.utility.vector1_bool) -> None

sets a vector of bools designating whether each position allows design or not

C++: protocols::mean_field::RotMatrix::is_designed(class utility::vector1<bool, class std::allocator<bool> >) –> void

is_designed(self: pyrosetta.rosetta.protocols.mean_field.RotMatrix, pos: int) -> bool

returns a bool designating whether a specified position allows design

position to be examined within the RotMatrix

RotMatrix numbering may or may not match pose numbering

C++: protocols::mean_field::RotMatrix::is_designed(unsigned long) const –> bool

max_size(*args, **kwargs)¶

Overloaded function.

max_size(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) -> int
max_size(self: utility::vector1<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >, std::allocator<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> > > >) -> int

max_size_col(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) → int¶: C++: protocols::mean_field::jagged_array<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >::max_size_col() const –> unsigned long

n_designed(self: pyrosetta.rosetta.protocols.mean_field.RotMatrix) → int¶

returns the number of positions that allow design

C++: protocols::mean_field::RotMatrix::n_designed() const –> unsigned long

pop_back(*args, **kwargs)¶

Overloaded function.

pop_back(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) -> None
pop_back(self: utility::vector1<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >, std::allocator<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> > > >) -> None

reserve(*args, **kwargs)¶

Overloaded function.

reserve(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t, __n: int) -> None
reserve(self: utility::vector1<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >, std::allocator<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> > > >, __n: int) -> None

resize(*args, **kwargs)¶

Overloaded function.

resize(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t, __new_size: int) -> None
resize(self: utility::vector1<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >, std::allocator<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> > > >, __new_size: int) -> None

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.mean_field.RotMatrix) -> None
show(self: pyrosetta.rosetta.protocols.mean_field.RotMatrix, output: pyrosetta.rosetta.std.ostream) -> None

Generate string representation of RotMatrix for debugging purposes.

C++: protocols::mean_field::RotMatrix::show(class std::basic_ostream<char> &) const –> void

shrink_to_fit(self: utility::vector1<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >, std::allocator<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> > > >) → None¶

size(*args, **kwargs)¶

Overloaded function.

size(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) -> int
size(self: utility::vector1<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >, std::allocator<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> > > >) -> int

size_col(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t, col: int) → int¶: C++: protocols::mean_field::jagged_array<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >::size_col(unsigned long) const –> unsigned long

class pyrosetta.rosetta.protocols.mean_field.RotProb¶

Bases: pybind11_builtins.pybind11_object

encapsulates information about a rotamer at a position and its probability

used as the base unit in the conformational matrix (RotMatrix) class

__add__(self: pyrosetta.rosetta.protocols.mean_field.RotProb, prob: float) → pyrosetta.rosetta.protocols.mean_field.RotProb¶

overloaded arithmetic operator for arithmetic with Real probability

adds prob to probability

C++: protocols::mean_field::RotProb::operator+(double) –> class protocols::mean_field::RotProb

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__div__(self: pyrosetta.rosetta.protocols.mean_field.RotProb, prob: float) → pyrosetta.rosetta.protocols.mean_field.RotProb¶

overloaded arithmetic operator for arithmetic with Real probability

divides probability by prob

C++: protocols::mean_field::RotProb::operator/(double) –> class protocols::mean_field::RotProb

__eq__(self: pyrosetta.rosetta.protocols.mean_field.RotProb, obj: pyrosetta.rosetta.protocols.mean_field.RotProb) → bool¶

overloaded equality operators to fix instantiation issues with PyRosetta

C++: protocols::mean_field::RotProb::operator==(const class protocols::mean_field::RotProb &) const –> bool

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__iadd__(*args, **kwargs)¶

Overloaded function.

__iadd__(self: pyrosetta.rosetta.protocols.mean_field.RotProb, obj: pyrosetta.rosetta.protocols.mean_field.RotProb) -> None

overloaded arithmetic operators to allow for easier matrix arithmetic

adds probability of obj to its own probability

only overloading operators that modify object so as to avoid confusion about identity of non-probability data members

C++: protocols::mean_field::RotProb::operator+=(const class protocols::mean_field::RotProb &) –> void

__iadd__(self: pyrosetta.rosetta.protocols.mean_field.RotProb, prob: float) -> None

overloaded arithmetic operator for arithmetic with Real probability

adds prob to probability

C++: protocols::mean_field::RotProb::operator+=(double) –> void

__idiv__(*args, **kwargs)¶

Overloaded function.

__idiv__(self: pyrosetta.rosetta.protocols.mean_field.RotProb, obj: pyrosetta.rosetta.protocols.mean_field.RotProb) -> None

overloaded arithmetic operator not necessary but implemented due to its being expected

divides its probability by probability of obj

only overloading operators that modify object so as to avoid confusion about identity of non-probability data members

C++: protocols::mean_field::RotProb::operator/=(const class protocols::mean_field::RotProb &) –> void

__idiv__(self: pyrosetta.rosetta.protocols.mean_field.RotProb, prob: float) -> None

overloaded arithmetic operator for arithmetic with Real probability

divides probability by prob

C++: protocols::mean_field::RotProb::operator/=(double) –> void

__imul__(*args, **kwargs)¶

Overloaded function.

__imul__(self: pyrosetta.rosetta.protocols.mean_field.RotProb, obj: pyrosetta.rosetta.protocols.mean_field.RotProb) -> None

overloaded arithmetic operator not necessary but implemented due to its being expected

multiplies probability of obj by its own probability

only overloading operators that modify object so as to avoid confusion about identity of non-probability data members

C++: protocols::mean_field::RotProb::operator*=(const class protocols::mean_field::RotProb &) –> void

__imul__(self: pyrosetta.rosetta.protocols.mean_field.RotProb, prob: float) -> None

overloaded arithmetic operator for arithmetic with Real probability

multiplies probability by prob

C++: protocols::mean_field::RotProb::operator*=(double) –> void

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.mean_field.RotProb) -> None
__init__(self: pyrosetta.rosetta.protocols.mean_field.RotProb, prob: float, rot_ind: int, pos: int, res: pyrosetta.rosetta.core.conformation.Residue) -> None
__init__(self: pyrosetta.rosetta.protocols.mean_field.RotProb, arg0: pyrosetta.rosetta.protocols.mean_field.RotProb) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

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

__isub__(*args, **kwargs)¶

Overloaded function.

__isub__(self: pyrosetta.rosetta.protocols.mean_field.RotProb, obj: pyrosetta.rosetta.protocols.mean_field.RotProb) -> None

overloaded arithmetic operators to allow for easier matrix arithmetic

subtracts probability of obj from its own probability

only overloading operators that modify object so as to avoid confusion about identity of non-probability data members

C++: protocols::mean_field::RotProb::operator-=(const class protocols::mean_field::RotProb &) –> void

__isub__(self: pyrosetta.rosetta.protocols.mean_field.RotProb, prob: float) -> None

overloaded arithmetic operator for arithmetic with Real probability

subtracts prob from probability

C++: protocols::mean_field::RotProb::operator-=(double) –> void

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__mul__(self: pyrosetta.rosetta.protocols.mean_field.RotProb, prob: float) → pyrosetta.rosetta.protocols.mean_field.RotProb¶

overloaded arithmetic operator for arithmetic with Real probability

multiplies probability by prob

C++: protocols::mean_field::RotProb::operator*(double) –> class protocols::mean_field::RotProb

__ne__(self: pyrosetta.rosetta.protocols.mean_field.RotProb, obj: pyrosetta.rosetta.protocols.mean_field.RotProb) → bool¶

overloaded equality operators to fix instantiation issues with PyRosetta

C++: protocols::mean_field::RotProb::operator!=(const class protocols::mean_field::RotProb &) const –> bool

__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__(self: pyrosetta.rosetta.protocols.mean_field.RotProb) → str¶

__sub__(self: pyrosetta.rosetta.protocols.mean_field.RotProb, prob: float) → pyrosetta.rosetta.protocols.mean_field.RotProb¶

overloaded arithmetic operator for arithmetic with Real probability

subtracts prob from probability

C++: protocols::mean_field::RotProb::operator-(double) –> class protocols::mean_field::RotProb

__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).

aa_ind(self: pyrosetta.rosetta.protocols.mean_field.RotProb) → pyrosetta.rosetta.core.chemical.AA¶

returns AA type based on residue

C++: protocols::mean_field::RotProb::aa_ind() const –> enum core::chemical::AA

assign(self: pyrosetta.rosetta.protocols.mean_field.RotProb, object_to_copy: pyrosetta.rosetta.protocols.mean_field.RotProb) → pyrosetta.rosetta.protocols.mean_field.RotProb¶

Assignment operator

C++: protocols::mean_field::RotProb::operator=(const class protocols::mean_field::RotProb &) –> class protocols::mean_field::RotProb &

pos(*args, **kwargs)¶

Overloaded function.

pos(self: pyrosetta.rosetta.protocols.mean_field.RotProb) -> int

returns position

C++: protocols::mean_field::RotProb::pos() const –> unsigned long

pos(self: pyrosetta.rosetta.protocols.mean_field.RotProb, p: int) -> None

set position

C++: protocols::mean_field::RotProb::pos(unsigned long) –> void

probability(*args, **kwargs)¶

Overloaded function.

probability(self: pyrosetta.rosetta.protocols.mean_field.RotProb) -> float

returns probability

C++: protocols::mean_field::RotProb::probability() const –> double

probability(self: pyrosetta.rosetta.protocols.mean_field.RotProb, prob: float) -> None

set probability

C++: protocols::mean_field::RotProb::probability(double) –> void

res(*args, **kwargs)¶

Overloaded function.

res(self: pyrosetta.rosetta.protocols.mean_field.RotProb) -> pyrosetta.rosetta.core.conformation.Residue

returns COP to residue

C++: protocols::mean_field::RotProb::res() const –> class std::shared_ptr<const class core::conformation::Residue>

res(self: pyrosetta.rosetta.protocols.mean_field.RotProb, r: pyrosetta.rosetta.core.conformation.Residue) -> None

set ResidueCOP

C++: protocols::mean_field::RotProb::res(class std::shared_ptr<const class core::conformation::Residue>) –> void

rot_ind(*args, **kwargs)¶

Overloaded function.

rot_ind(self: pyrosetta.rosetta.protocols.mean_field.RotProb) -> int

returns rotamer index

C++: protocols::mean_field::RotProb::rot_ind() const –> unsigned long

rot_ind(self: pyrosetta.rosetta.protocols.mean_field.RotProb, aa: int) -> None

set rotamer index

C++: protocols::mean_field::RotProb::rot_ind(unsigned long) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.mean_field.RotProb) -> None
show(self: pyrosetta.rosetta.protocols.mean_field.RotProb, output: pyrosetta.rosetta.std.ostream) -> None

Generate string representation of RotProb for debugging and reporting purposes.

C++: protocols::mean_field::RotProb::show(class std::basic_ostream<char> &) const –> void