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

aa_ind(*args, **kwargs)

Overloaded function.

  1. 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

  1. 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.

  1. 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

  1. 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.

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

returns position in pose numbering

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

  1. 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.

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

returns probability

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

  1. 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.

  1. show(self: pyrosetta.rosetta.protocols.mean_field.AAProb) -> None
  2. 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

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) → pyrosetta.rosetta.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) → pyrosetta.rosetta.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.

  1. show(self: pyrosetta.rosetta.protocols.mean_field.DesignMeanField) -> None
  2. 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

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

  1. show(self: pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField) -> None
  2. 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

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

  1. show(self: pyrosetta.rosetta.protocols.mean_field.MeanField) -> None
  2. 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

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.

  1. show(self: pyrosetta.rosetta.protocols.mean_field.ResHashMap) -> None
  2. 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

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

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

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.

  1. 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> >
  2. 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.

  1. 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> >
  2. 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.

  1. capacity(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) -> int
  2. 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.

  1. clear(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) -> None
  2. 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.

  1. 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> > &

  1. 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.

  1. empty(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) -> bool
  2. 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.

  1. 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> >
  2. 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.

  1. 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> > &

  1. 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

  1. 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.

  1. max_size(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) -> int
  2. 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.

  1. pop_back(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) -> None
  2. 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.

  1. reserve(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t, __n: int) -> None
  2. 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.

  1. resize(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t, __new_size: int) -> None
  2. 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.

  1. show(self: pyrosetta.rosetta.protocols.mean_field.RotMatrix) -> None
  2. 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.

  1. size(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) -> int
  2. 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

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.

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

returns position

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

  1. 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.

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

returns probability

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

  1. 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.

  1. 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>

  1. 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.

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

returns rotamer index

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

  1. 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.

  1. show(self: pyrosetta.rosetta.protocols.mean_field.RotProb) -> None
  2. 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