mean_field

Bindings for protocols::mean_field namespace

class pyrosetta.rosetta.protocols.mean_field.AAMatrix

Bases: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t

append(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t, arg0: utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >) None

adds an element to the end

assign(self: pyrosetta.rosetta.protocols.mean_field.AAMatrix, object_to_copy: pyrosetta.rosetta.protocols.mean_field.AAMatrix) pyrosetta.rosetta.protocols.mean_field.AAMatrix

Assignment operator

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

at(*args, **kwargs)

Overloaded function.

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

  2. at(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t, i: int) -> utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >

ave_abs_diff(self: pyrosetta.rosetta.protocols.mean_field.AAMatrix, aa_matrix: pyrosetta.rosetta.protocols.mean_field.AAMatrix) pyrosetta.rosetta.utility.vector1_double

calculates vector of average absolute differences between vectors of this AAMatrix and a second AAMatrix

number of elements is the number of positions + 1. last element is the average abs diff between entire matrices

C++: protocols::mean_field::AAMatrix::ave_abs_diff(const class protocols::mean_field::AAMatrix &) const –> class utility::vector1<double, class std::allocator<double> >

back(*args, **kwargs)

Overloaded function.

  1. back(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t) -> utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >

  2. back(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t) -> utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >

begin(*args, **kwargs)

Overloaded function.

  1. begin(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t) -> __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >*, std::vector<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >, std::allocator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> > > > >

  2. begin(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t) -> __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >*, std::vector<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >, std::allocator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> > > > >

build_aa_matrix(*args, **kwargs)

Overloaded function.

  1. build_aa_matrix(self: pyrosetta.rosetta.protocols.mean_field.AAMatrix, rm: protocols::mean_field::RotMatrix, em: pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t, temp: float) -> None

builds AAMatrix from RotMatrix rm using private method init

C++: protocols::mean_field::AAMatrix::build_aa_matrix(const class protocols::mean_field::RotMatrix &, class protocols::mean_field::jagged_array<double, class std::allocator<double> >, double) –> void

  1. build_aa_matrix(self: pyrosetta.rosetta.protocols.mean_field.AAMatrix, aa_matrix_file: pyrosetta.rosetta.std.istream) -> None

builds AAMatrix from transfac file using private method init

C++: protocols::mean_field::AAMatrix::build_aa_matrix(std::istream &) –> void

capacity(*args, **kwargs)

Overloaded function.

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

  2. capacity(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t) -> int

cbegin(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t) __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> > const*, std::vector<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >, std::allocator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> > > > >
cend(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t) __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> > const*, std::vector<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >, std::allocator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> > > > >
clear(*args, **kwargs)

Overloaded function.

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

  2. clear(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t) -> None

cosine_distance(self: pyrosetta.rosetta.protocols.mean_field.AAMatrix, aa_matrix: pyrosetta.rosetta.protocols.mean_field.AAMatrix) pyrosetta.rosetta.utility.vector1_double

calculates vector of cosine distances between vectors of this AAMatrix and a second AAMatrix

number of elements is the number of positions + 1. last element is the cosine distance between entire matrices

C++: protocols::mean_field::AAMatrix::cosine_distance(const class protocols::mean_field::AAMatrix &) const –> class utility::vector1<double, class std::allocator<double> >

count(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t, arg0: utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >) int

counts the elements that are equal to value

curr_aa(self: pyrosetta.rosetta.protocols.mean_field.AAMatrix) pyrosetta.rosetta.utility.vector1_unsigned_long

returns vector of current amino acids at each position (if current rotamer is set for that position)

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

dump_transfac(self: pyrosetta.rosetta.protocols.mean_field.AAMatrix, filename: str) None

outputs AA Matrix in transfac format for dumping purposes

C++: protocols::mean_field::AAMatrix::dump_transfac(const std::string &) const –> void

empty(self: pyrosetta.rosetta.protocols.mean_field.AAMatrix) bool

returns true if all probabilities are 0

C++: protocols::mean_field::AAMatrix::empty() const –> bool

end(*args, **kwargs)

Overloaded function.

  1. end(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t) -> __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >*, std::vector<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >, std::allocator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> > > > >

  2. end(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t) -> __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >*, std::vector<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >, std::allocator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> > > > >

equal_size(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t, other: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t) bool

C++: protocols::mean_field::jagged_array<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >::equal_size(const class protocols::mean_field::jagged_array<class protocols::mean_field::AAProb, class std::allocator<class protocols::mean_field::AAProb> > &) const –> bool

erase(*args, **kwargs)

Overloaded function.

  1. erase(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t, __first: __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >*, std::vector<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >, std::allocator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> > > > >, __last: __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >*, std::vector<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >, std::allocator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> > > > >) -> __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >*, std::vector<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >, std::allocator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> > > > >

  2. erase(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t, __position: __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >*, std::vector<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >, std::allocator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> > > > >) -> __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >*, std::vector<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >, std::allocator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> > > > >

  3. erase(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t, __first: __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >*, std::vector<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >, std::allocator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> > > > >, __last: __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >*, std::vector<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >, std::allocator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> > > > >) -> __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >*, std::vector<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >, std::allocator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> > > > >

  4. erase(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t, __position: __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >*, std::vector<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >, std::allocator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> > > > >) -> __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >*, std::vector<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >, std::allocator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> > > > >

extend(othervec)
frob_distance(self: pyrosetta.rosetta.protocols.mean_field.AAMatrix, aa_matrix: pyrosetta.rosetta.protocols.mean_field.AAMatrix) pyrosetta.rosetta.utility.vector1_double

calculates vector of frob distances between vectors of this AAMatrix and a second AAMatrix

number of elements is the number of positions + 1. last element is the frob dist between entire matrices

C++: protocols::mean_field::AAMatrix::frob_distance(const class protocols::mean_field::AAMatrix &) const –> class utility::vector1<double, class std::allocator<double> >

front(*args, **kwargs)

Overloaded function.

  1. front(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t) -> utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >

  2. front(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t) -> utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >

get_total(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t) protocols::mean_field::AAProb

C++: protocols::mean_field::jagged_array<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >::get_total() const –> class protocols::mean_field::AAProb

has_value(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t, t: protocols::mean_field::AAProb) bool

C++: protocols::mean_field::jagged_array<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >::has_value(const class protocols::mean_field::AAProb &) const –> bool

index(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t, t: protocols::mean_field::AAProb) int

C++: protocols::mean_field::jagged_array<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >::index(const class protocols::mean_field::AAProb &) const –> int

l(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t) int

lower index

max_size(*args, **kwargs)

Overloaded function.

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

  2. max_size(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t) -> int

max_size_col(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t) int

C++: protocols::mean_field::jagged_array<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >::max_size_col() const –> unsigned long

pop(*args, **kwargs)

Overloaded function.

  1. pop(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t) -> utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >

remove and return last item

  1. pop(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t, arg0: int) -> utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >

remove and return item at index

pop_back(*args, **kwargs)

Overloaded function.

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

  2. pop_back(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t) -> None

remove(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t, arg0: utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >) None

Remove the first item from the list whose value is x. It is an error if there is no such item.

reserve(*args, **kwargs)

Overloaded function.

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

  2. reserve(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t, __n: int) -> None

resize(*args, **kwargs)

Overloaded function.

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

  2. resize(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t, __new_size: int) -> None

show(*args, **kwargs)

Overloaded function.

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

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

Generate string representation of AAMatrix for debugging purposes.

C++: protocols::mean_field::AAMatrix::show(std::ostream &) const –> void

shrink_to_fit(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t) None
size(*args, **kwargs)

Overloaded function.

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

  2. size(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t) -> int

size_col(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t, col: int) int

C++: protocols::mean_field::jagged_array<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >::size_col(unsigned long) const –> unsigned long

swap(*args, **kwargs)

Overloaded function.

  1. swap(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t, __x: pyrosetta.rosetta.std.vector_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t) -> None

  2. swap(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t, __x: pyrosetta.rosetta.std.vector_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t) -> None

u(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t) int

upper index

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(std::ostream &) 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) 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.

  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(std::ostream &) 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.EnergiesByTaskCalculator

Bases: pyrosetta.rosetta.core.pose.metrics.EnergyDependentCalculator

assign(self: pyrosetta.rosetta.protocols.mean_field.EnergiesByTaskCalculator, : pyrosetta.rosetta.protocols.mean_field.EnergiesByTaskCalculator) pyrosetta.rosetta.protocols.mean_field.EnergiesByTaskCalculator

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

clone(self: pyrosetta.rosetta.protocols.mean_field.EnergiesByTaskCalculator) pyrosetta.rosetta.core.pose.metrics.PoseMetricCalculator

C++: protocols::mean_field::EnergiesByTaskCalculator::clone() const –> class std::shared_ptr<class core::pose::metrics::PoseMetricCalculator>

get(*args, **kwargs)

Overloaded function.

  1. get(self: pyrosetta.rosetta.core.pose.metrics.EnergyDependentCalculator, key: str, val: pyrosetta.rosetta.basic.MetricValueBase, this_pose: pyrosetta.rosetta.core.pose.Pose) -> None

C++: core::pose::metrics::EnergyDependentCalculator::get(const std::string &, class basic::MetricValueBase &, const class core::pose::Pose &) –> void

  1. get(self: pyrosetta.rosetta.core.pose.metrics.EnergyDependentCalculator, key: str, this_pose: pyrosetta.rosetta.core.pose.Pose) -> str

C++: core::pose::metrics::EnergyDependentCalculator::get(const std::string &, const class core::pose::Pose &) –> std::string

notify_energy_change(self: pyrosetta.rosetta.core.pose.metrics.EnergyDependentCalculator) None

C++: core::pose::metrics::EnergyDependentCalculator::notify_energy_change() –> void

notify_structure_change(self: pyrosetta.rosetta.core.pose.metrics.PoseMetricCalculator) None

C++: core::pose::metrics::PoseMetricCalculator::notify_structure_change() –> void

show(self: pyrosetta.rosetta.protocols.mean_field.EnergiesByTaskCalculator, out: pyrosetta.rosetta.std.ostream) None

C++: protocols::mean_field::EnergiesByTaskCalculator::show(std::ostream &) const –> void

task(self: pyrosetta.rosetta.protocols.mean_field.EnergiesByTaskCalculator) pyrosetta.rosetta.core.pack.task.PackerTask

C++: protocols::mean_field::EnergiesByTaskCalculator::task() const –> class std::shared_ptr<const class core::pack::task::PackerTask>

total(self: pyrosetta.rosetta.protocols.mean_field.EnergiesByTaskCalculator) float

C++: protocols::mean_field::EnergiesByTaskCalculator::total() const –> double

class pyrosetta.rosetta.protocols.mean_field.FlexBBDesignMeanField

Bases: pyrosetta.rosetta.protocols.mean_field.FlexBBMeanField

aa_matrices(self: pyrosetta.rosetta.protocols.mean_field.FlexBBDesignMeanField) pyrosetta.rosetta.utility.vector1_protocols_mean_field_AAMatrix

returns a const vector of the AAMatrices constructed from each pose

C++: protocols::mean_field::FlexBBDesignMeanField::aa_matrices() const –> const class utility::vector1<class protocols::mean_field::AAMatrix, class std::allocator<class protocols::mean_field::AAMatrix> > &

aa_matrix(self: pyrosetta.rosetta.protocols.mean_field.FlexBBDesignMeanField) pyrosetta.rosetta.protocols.mean_field.AAMatrix

returns averaged AAMatrix

C++: protocols::mean_field::FlexBBDesignMeanField::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>

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.FlexBBDesignMeanField) None

overrides FlexBBMeanField::calc_bb_boltz_probs to filter out bb_boltz_probs that aren’t designable

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

calc_exp_value_aa_matrix(self: pyrosetta.rosetta.protocols.mean_field.FlexBBDesignMeanField) None

calculates expected value (averaged) AAMatrix

C++: protocols::mean_field::FlexBBDesignMeanField::calc_exp_value_aa_matrix() –> 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.FlexBBDesignMeanField, pose_ind: int) None

deletes a pose from the list of poses

C++: protocols::mean_field::FlexBBDesignMeanField::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.FlexBBDesignMeanField) None

overrides process() method in FlexBBMeanField to init AAMatrix for each rot_matrix and average them together

C++: protocols::mean_field::FlexBBDesignMeanField::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.FlexBBDesignMeanField) -> None

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

Generate string representation of FlexBBDesignMeanField for debugging purposes.

C++: protocols::mean_field::FlexBBDesignMeanField::show(std::ostream &) 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) 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(std::ostream &) 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.GenMeanFieldMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

apply(self: pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover, pose: pyrosetta.rosetta.core.pose.Pose) None

performs main work of Mover

C++: protocols::mean_field::GenMeanFieldMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover, : pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover) pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover

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

calc_mean_field(self: pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover) None

instantiates the appropriate MF class and calls processing methods

C++: protocols::mean_field::GenMeanFieldMover::calc_mean_field() –> void

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::mean_field::GenMeanFieldMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

static default_value_for_init_option() int

C++: protocols::mean_field::GenMeanFieldMover::default_value_for_init_option() –> unsigned long

static default_value_for_lambda_memory() float

C++: protocols::mean_field::GenMeanFieldMover::default_value_for_lambda_memory() –> double

static default_value_for_temperature() float

C++: protocols::mean_field::GenMeanFieldMover::default_value_for_temperature() –> double

static default_value_for_threshold() float

C++: protocols::mean_field::GenMeanFieldMover::default_value_for_threshold() –> double

static default_value_for_tolerance() float

C++: protocols::mean_field::GenMeanFieldMover::default_value_for_tolerance() –> double

static default_value_for_unbound() bool

C++: protocols::mean_field::GenMeanFieldMover::default_value_for_unbound() –> bool

fresh_instance(self: pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::mean_field::GenMeanFieldMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover) str

C++: protocols::mean_field::GenMeanFieldMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str

C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_std_allocator_std_string_t

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

init_option(*args, **kwargs)

Overloaded function.

  1. init_option(self: pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover) -> int

C++: protocols::mean_field::GenMeanFieldMover::init_option() const –> unsigned long

  1. init_option(self: pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover, iopt: int) -> None

C++: protocols::mean_field::GenMeanFieldMover::init_option(const unsigned long) –> void

lambda_memory(*args, **kwargs)

Overloaded function.

  1. lambda_memory(self: pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover) -> float

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

  1. lambda_memory(self: pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover, lm: float) -> None

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

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() str

C++: protocols::mean_field::GenMeanFieldMover::mover_name() –> std::string

static name() str

C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::mean_field::GenMeanFieldMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

prepare_task_poses(self: pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover, pose: pyrosetta.rosetta.core.pose.Pose) None

prepares the task and unbinds the poses if necessary

C++: protocols::mean_field::GenMeanFieldMover::prepare_task_poses(const class core::pose::Pose &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None
Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::mean_field::GenMeanFieldMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

read_aa_matrix(self: pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover) None

reads in a AAMatrix (generally the experimental gold standard with which to compare the predicted)

C++: protocols::mean_field::GenMeanFieldMover::read_aa_matrix() –> void

read_input_pdbs(self: pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover) None

reads in the input pdbs

C++: protocols::mean_field::GenMeanFieldMover::read_input_pdbs() –> void

static register_options() None

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on

each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

report_aa_matrix(self: pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover) None

reports the specificity profile (AAMatrix) and backbone boltzmann probs, as appropriate

C++: protocols::mean_field::GenMeanFieldMover::report_aa_matrix() const –> void

report_dist(self: pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover, am: pyrosetta.rosetta.protocols.mean_field.AAMatrix) None

reports distances between predicted AAMatrix and am

C++: protocols::mean_field::GenMeanFieldMover::report_dist(const class protocols::mean_field::AAMatrix &) const –> void

report_rot_prob(self: pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover) None

reports rotamer probabilities (RotMatrix)

C++: protocols::mean_field::GenMeanFieldMover::report_rot_prob() const –> void

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

scorefxn(*args, **kwargs)

Overloaded function.

  1. scorefxn(self: pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover) -> pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::mean_field::GenMeanFieldMover::scorefxn() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

  1. scorefxn(self: pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

C++: protocols::mean_field::GenMeanFieldMover::scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None

C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

  2. show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

task_factory(*args, **kwargs)

Overloaded function.

  1. task_factory(self: pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover) -> pyrosetta.rosetta.core.pack.task.TaskFactory

C++: protocols::mean_field::GenMeanFieldMover::task_factory() const –> class std::shared_ptr<class core::pack::task::TaskFactory>

  1. task_factory(self: pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover, task_factory: pyrosetta.rosetta.core.pack.task.TaskFactory) -> None

C++: protocols::mean_field::GenMeanFieldMover::task_factory(class std::shared_ptr<class core::pack::task::TaskFactory>) –> void

temperature(*args, **kwargs)

Overloaded function.

  1. temperature(self: pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover) -> float

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

  1. temperature(self: pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover, temp: float) -> None

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

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None
: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

threshold(*args, **kwargs)

Overloaded function.

  1. threshold(self: pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover) -> float

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

  1. threshold(self: pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover, threshold: float) -> None

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

tolerance(*args, **kwargs)

Overloaded function.

  1. tolerance(self: pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover) -> float

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

  1. tolerance(self: pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover, tol: float) -> None

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

type(*args, **kwargs)

Overloaded function.

  1. type(self: pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover) -> str

C++: protocols::mean_field::GenMeanFieldMover::type() const –> std::string

  1. type(self: pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover, s: str) -> None

C++: protocols::mean_field::GenMeanFieldMover::type(const std::string &) –> void

unbound(*args, **kwargs)

Overloaded function.

  1. unbound(self: pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover) -> bool

C++: protocols::mean_field::GenMeanFieldMover::unbound() const –> bool

  1. unbound(self: pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMover, ub: bool) -> None

C++: protocols::mean_field::GenMeanFieldMover::unbound(const bool) –> void

class pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMoverCreator, : pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMoverCreator) pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMoverCreator

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

create_mover(self: pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::mean_field::GenMeanFieldMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMoverCreator) str

C++: protocols::mean_field::GenMeanFieldMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.mean_field.GenMeanFieldMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::mean_field::GenMeanFieldMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

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) 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.

  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(std::ostream &) 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.MeanFieldFactory

Bases: pybind11_builtins.pybind11_object

static create_mean_field(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, conv_diff: float, temp: float, threshold: float) pyrosetta.rosetta.protocols.mean_field.MeanField

initializes MeanField class based on options

C++: protocols::mean_field::MeanFieldFactory::create_mean_field(unsigned long, class utility::vector1<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > > &, class utility::vector1<class std::shared_ptr<class core::pack::task::PackerTask>, class std::allocator<class std::shared_ptr<class core::pack::task::PackerTask> > >, class std::shared_ptr<class core::scoring::ScoreFunction>, double, double, double, double) –> class std::shared_ptr<class protocols::mean_field::MeanField>

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(std::ostream &) 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

append(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t, arg0: utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >) None

adds an element to the end

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: pyrosetta.rosetta.utility.vector1_utility_vector1_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> >

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: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) -> utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >

begin(*args, **kwargs)

Overloaded function.

  1. begin(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) -> __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >*, std::vector<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> > > > >

  2. begin(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) -> __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >*, std::vector<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> > > > >

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: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) -> int

cbegin(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> > const*, std::vector<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> > > > >
cend(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> > const*, std::vector<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> > > > >
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: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) -> None

count(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t, arg0: utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >) int

counts the elements that are equal to value

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: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) -> bool

end(*args, **kwargs)

Overloaded function.

  1. end(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) -> __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >*, std::vector<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> > > > >

  2. end(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) -> __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >*, std::vector<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> > > > >

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

erase(*args, **kwargs)

Overloaded function.

  1. erase(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t, __first: __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >*, std::vector<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> > > > >, __last: __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >*, std::vector<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> > > > >) -> __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >*, std::vector<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> > > > >

  2. erase(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t, __position: __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >*, std::vector<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> > > > >) -> __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >*, std::vector<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> > > > >

  3. erase(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t, __first: __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >*, std::vector<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> > > > >, __last: __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >*, std::vector<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> > > > >) -> __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >*, std::vector<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> > > > >

  4. erase(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t, __position: __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >*, std::vector<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> > > > >) -> __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >*, std::vector<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> > > > >

extend(othervec)
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: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) -> 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

l(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) int

lower index

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: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) -> 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(*args, **kwargs)

Overloaded function.

  1. pop(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) -> utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >

remove and return last item

  1. pop(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t, arg0: int) -> utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >

remove and return item at index

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: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) -> None

remove(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t, arg0: utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >) None

Remove the first item from the list whose value is x. It is an error if there is no such item.

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: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t, __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: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t, __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(std::ostream &) const –> void

shrink_to_fit(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) 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: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) -> 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

swap(*args, **kwargs)

Overloaded function.

  1. swap(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t, __x: pyrosetta.rosetta.std.vector_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) -> None

  2. swap(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t, __x: pyrosetta.rosetta.std.vector_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) -> None

u(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) int

upper index

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(std::ostream &) const –> void

class pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t

Bases: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t

append(self: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, arg0: pyrosetta.rosetta.utility.vector1_double) None

adds an element to the end

assign(*args, **kwargs)

Overloaded function.

  1. assign(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t, __n: int, __val: pyrosetta.rosetta.utility.vector1_double) -> None

  2. assign(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t, v: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t) -> pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t

  3. assign(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t, v: pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t) -> pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t

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

  1. assign(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t, dims: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: protocols::mean_field::jagged_array<double, std::allocator<double> >::assign(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

  1. assign(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t, dims: pyrosetta.rosetta.utility.vector1_unsigned_long, vals: pyrosetta.rosetta.utility.vector1_double) -> None

C++: protocols::mean_field::jagged_array<double, std::allocator<double> >::assign(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<double, class std::allocator<double> > &) –> void

  1. assign(self: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, __n: int, __val: pyrosetta.rosetta.utility.vector1_double) -> None

  2. assign(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t, v: pyrosetta.rosetta.std.vector_utility_vector1_double_std_allocator_double_t) -> pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t

C++: utility::vector1<utility::vector1<double, std::allocator<double> >, std::allocator<utility::vector1<double, std::allocator<double> > > >::operator=(const class std::vector<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &) –> class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &

  1. assign(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t, v: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t) -> pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t

C++: utility::vector1<utility::vector1<double, std::allocator<double> >, std::allocator<utility::vector1<double, std::allocator<double> > > >::operator=(const class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &) –> class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > > &

at(*args, **kwargs)

Overloaded function.

  1. at(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t, i: int) -> pyrosetta.rosetta.utility.vector1_double

  2. at(self: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, i: int) -> pyrosetta.rosetta.utility.vector1_double

back(*args, **kwargs)

Overloaded function.

  1. back(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t) -> pyrosetta.rosetta.utility.vector1_double

  2. back(self: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t) -> pyrosetta.rosetta.utility.vector1_double

begin(*args, **kwargs)

Overloaded function.

  1. begin(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t) -> __gnu_cxx::__normal_iterator<utility::vector1<double, std::allocator<double> >*, std::vector<utility::vector1<double, std::allocator<double> >, std::allocator<utility::vector1<double, std::allocator<double> > > > >

  2. begin(self: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t) -> __gnu_cxx::__normal_iterator<utility::vector1<double, std::allocator<double> >*, std::vector<utility::vector1<double, std::allocator<double> >, std::allocator<utility::vector1<double, std::allocator<double> > > > >

capacity(*args, **kwargs)

Overloaded function.

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

  2. capacity(self: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t) -> int

cbegin(self: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t) __gnu_cxx::__normal_iterator<utility::vector1<double, std::allocator<double> > const*, std::vector<utility::vector1<double, std::allocator<double> >, std::allocator<utility::vector1<double, std::allocator<double> > > > >
cend(self: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t) __gnu_cxx::__normal_iterator<utility::vector1<double, std::allocator<double> > const*, std::vector<utility::vector1<double, std::allocator<double> >, std::allocator<utility::vector1<double, std::allocator<double> > > > >
clear(*args, **kwargs)

Overloaded function.

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

  2. clear(self: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t) -> None

count(self: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, arg0: pyrosetta.rosetta.utility.vector1_double) int

counts the elements that are equal to value

empty(*args, **kwargs)

Overloaded function.

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

  2. empty(self: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t) -> bool

end(*args, **kwargs)

Overloaded function.

  1. end(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t) -> __gnu_cxx::__normal_iterator<utility::vector1<double, std::allocator<double> >*, std::vector<utility::vector1<double, std::allocator<double> >, std::allocator<utility::vector1<double, std::allocator<double> > > > >

  2. end(self: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t) -> __gnu_cxx::__normal_iterator<utility::vector1<double, std::allocator<double> >*, std::vector<utility::vector1<double, std::allocator<double> >, std::allocator<utility::vector1<double, std::allocator<double> > > > >

equal_size(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t, other: pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t) bool

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

erase(*args, **kwargs)

Overloaded function.

  1. erase(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t, __first: __gnu_cxx::__normal_iterator<utility::vector1<double, std::allocator<double> >*, std::vector<utility::vector1<double, std::allocator<double> >, std::allocator<utility::vector1<double, std::allocator<double> > > > >, __last: __gnu_cxx::__normal_iterator<utility::vector1<double, std::allocator<double> >*, std::vector<utility::vector1<double, std::allocator<double> >, std::allocator<utility::vector1<double, std::allocator<double> > > > >) -> __gnu_cxx::__normal_iterator<utility::vector1<double, std::allocator<double> >*, std::vector<utility::vector1<double, std::allocator<double> >, std::allocator<utility::vector1<double, std::allocator<double> > > > >

  2. erase(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t, __position: __gnu_cxx::__normal_iterator<utility::vector1<double, std::allocator<double> >*, std::vector<utility::vector1<double, std::allocator<double> >, std::allocator<utility::vector1<double, std::allocator<double> > > > >) -> __gnu_cxx::__normal_iterator<utility::vector1<double, std::allocator<double> >*, std::vector<utility::vector1<double, std::allocator<double> >, std::allocator<utility::vector1<double, std::allocator<double> > > > >

  3. erase(self: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, __first: __gnu_cxx::__normal_iterator<utility::vector1<double, std::allocator<double> >*, std::vector<utility::vector1<double, std::allocator<double> >, std::allocator<utility::vector1<double, std::allocator<double> > > > >, __last: __gnu_cxx::__normal_iterator<utility::vector1<double, std::allocator<double> >*, std::vector<utility::vector1<double, std::allocator<double> >, std::allocator<utility::vector1<double, std::allocator<double> > > > >) -> __gnu_cxx::__normal_iterator<utility::vector1<double, std::allocator<double> >*, std::vector<utility::vector1<double, std::allocator<double> >, std::allocator<utility::vector1<double, std::allocator<double> > > > >

  4. erase(self: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, __position: __gnu_cxx::__normal_iterator<utility::vector1<double, std::allocator<double> >*, std::vector<utility::vector1<double, std::allocator<double> >, std::allocator<utility::vector1<double, std::allocator<double> > > > >) -> __gnu_cxx::__normal_iterator<utility::vector1<double, std::allocator<double> >*, std::vector<utility::vector1<double, std::allocator<double> >, std::allocator<utility::vector1<double, std::allocator<double> > > > >

extend(othervec)
front(*args, **kwargs)

Overloaded function.

  1. front(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t) -> pyrosetta.rosetta.utility.vector1_double

  2. front(self: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t) -> pyrosetta.rosetta.utility.vector1_double

get_total(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t) float

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

get_totals_columns(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t) pyrosetta.rosetta.utility.vector1_double

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

has_value(*args, **kwargs)

Overloaded function.

  1. has_value(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t, t: float) -> bool

C++: protocols::mean_field::jagged_array<double, std::allocator<double> >::has_value(const double &) const –> bool

  1. has_value(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t, t: pyrosetta.rosetta.utility.vector1_double) -> bool

C++: utility::vector1<utility::vector1<double, std::allocator<double> >, std::allocator<utility::vector1<double, std::allocator<double> > > >::has_value(const class utility::vector1<double, class std::allocator<double> >) const –> bool

index(*args, **kwargs)

Overloaded function.

  1. index(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t, t: float) -> int

C++: protocols::mean_field::jagged_array<double, std::allocator<double> >::index(const double &) const –> int

  1. index(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t, t: pyrosetta.rosetta.utility.vector1_double) -> int

C++: utility::vector1<utility::vector1<double, std::allocator<double> >, std::allocator<utility::vector1<double, std::allocator<double> > > >::index(const class utility::vector1<double, class std::allocator<double> >) const –> int

insert(*args, **kwargs)

Overloaded function.

  1. insert(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t, __position: __gnu_cxx::__normal_iterator<utility::vector1<double, std::allocator<double> >*, std::vector<utility::vector1<double, std::allocator<double> >, std::allocator<utility::vector1<double, std::allocator<double> > > > >, __n: int, __x: pyrosetta.rosetta.utility.vector1_double) -> None

  2. insert(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t, __position: __gnu_cxx::__normal_iterator<utility::vector1<double, std::allocator<double> >*, std::vector<utility::vector1<double, std::allocator<double> >, std::allocator<utility::vector1<double, std::allocator<double> > > > >, __x: pyrosetta.rosetta.utility.vector1_double) -> __gnu_cxx::__normal_iterator<utility::vector1<double, std::allocator<double> >*, std::vector<utility::vector1<double, std::allocator<double> >, std::allocator<utility::vector1<double, std::allocator<double> > > > >

  3. insert(self: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, __position: __gnu_cxx::__normal_iterator<utility::vector1<double, std::allocator<double> >*, std::vector<utility::vector1<double, std::allocator<double> >, std::allocator<utility::vector1<double, std::allocator<double> > > > >, __n: int, __x: pyrosetta.rosetta.utility.vector1_double) -> None

  4. insert(self: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, __position: __gnu_cxx::__normal_iterator<utility::vector1<double, std::allocator<double> >*, std::vector<utility::vector1<double, std::allocator<double> >, std::allocator<utility::vector1<double, std::allocator<double> > > > >, __x: pyrosetta.rosetta.utility.vector1_double) -> __gnu_cxx::__normal_iterator<utility::vector1<double, std::allocator<double> >*, std::vector<utility::vector1<double, std::allocator<double> >, std::allocator<utility::vector1<double, std::allocator<double> > > > >

l(self: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t) int

lower index

max_size(*args, **kwargs)

Overloaded function.

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

  2. max_size(self: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t) -> int

max_size_col(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t) int

C++: protocols::mean_field::jagged_array<double, std::allocator<double> >::max_size_col() const –> unsigned long

pop(*args, **kwargs)

Overloaded function.

  1. pop(self: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t) -> pyrosetta.rosetta.utility.vector1_double

remove and return last item

  1. pop(self: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, arg0: int) -> pyrosetta.rosetta.utility.vector1_double

remove and return item at index

pop_back(*args, **kwargs)

Overloaded function.

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

  2. pop_back(self: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t) -> None

push_back(*args, **kwargs)

Overloaded function.

  1. push_back(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t, __x: pyrosetta.rosetta.utility.vector1_double) -> None

  2. push_back(self: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, __x: pyrosetta.rosetta.utility.vector1_double) -> None

remove(self: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, arg0: pyrosetta.rosetta.utility.vector1_double) None

Remove the first item from the list whose value is x. It is an error if there is no such item.

reserve(*args, **kwargs)

Overloaded function.

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

  2. reserve(self: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, __n: int) -> None

resize(*args, **kwargs)

Overloaded function.

  1. resize(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t, __new_size: int, __x: pyrosetta.rosetta.utility.vector1_double) -> None

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

  3. resize(self: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, __new_size: int, __x: pyrosetta.rosetta.utility.vector1_double) -> None

  4. resize(self: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, __new_size: int) -> None

show(*args, **kwargs)

Overloaded function.

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

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

C++: protocols::mean_field::jagged_array<double, std::allocator<double> >::show(std::ostream &) const –> void

shrink_to_fit(self: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t) None
size(*args, **kwargs)

Overloaded function.

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

  2. size(self: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t) -> int

size_col(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t, col: int) int

C++: protocols::mean_field::jagged_array<double, std::allocator<double> >::size_col(unsigned long) const –> unsigned long

swap(*args, **kwargs)

Overloaded function.

  1. swap(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_double_std_allocator_double_t, __x: pyrosetta.rosetta.std.vector_utility_vector1_double_std_allocator_double_t) -> None

  2. swap(self: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, __x: pyrosetta.rosetta.std.vector_utility_vector1_double_std_allocator_double_t) -> None

u(self: pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t) int

upper index

class pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t

Bases: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t

append(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t, arg0: utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >) None

adds an element to the end

assign(*args, **kwargs)

Overloaded function.

  1. assign(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t, v: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t) -> pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t

  2. assign(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t, v: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t) -> pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t

C++: protocols::mean_field::jagged_array<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >::operator=(const class protocols::mean_field::jagged_array<class protocols::mean_field::AAProb, class std::allocator<class protocols::mean_field::AAProb> > &) –> class protocols::mean_field::jagged_array<class protocols::mean_field::AAProb, class std::allocator<class protocols::mean_field::AAProb> > &

  1. assign(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t, dims: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: protocols::mean_field::jagged_array<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >::assign(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

  1. assign(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t, v: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t) -> pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t

C++: utility::vector1<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >, std::allocator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> > > >::operator=(const class utility::vector1<class utility::vector1<class protocols::mean_field::AAProb, class std::allocator<class protocols::mean_field::AAProb> >, class std::allocator<class utility::vector1<class protocols::mean_field::AAProb, class std::allocator<class protocols::mean_field::AAProb> > > > &) –> class utility::vector1<class utility::vector1<class protocols::mean_field::AAProb, class std::allocator<class protocols::mean_field::AAProb> >, class std::allocator<class utility::vector1<class protocols::mean_field::AAProb, class std::allocator<class protocols::mean_field::AAProb> > > > &

at(*args, **kwargs)

Overloaded function.

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

  2. at(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t, i: int) -> utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >

back(*args, **kwargs)

Overloaded function.

  1. back(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t) -> utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >

  2. back(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t) -> utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >

begin(*args, **kwargs)

Overloaded function.

  1. begin(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t) -> __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >*, std::vector<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >, std::allocator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> > > > >

  2. begin(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t) -> __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >*, std::vector<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >, std::allocator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> > > > >

capacity(*args, **kwargs)

Overloaded function.

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

  2. capacity(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t) -> int

cbegin(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t) __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> > const*, std::vector<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >, std::allocator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> > > > >
cend(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t) __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> > const*, std::vector<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >, std::allocator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> > > > >
clear(*args, **kwargs)

Overloaded function.

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

  2. clear(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t) -> None

count(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t, arg0: utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >) int

counts the elements that are equal to value

empty(*args, **kwargs)

Overloaded function.

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

  2. empty(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t) -> bool

end(*args, **kwargs)

Overloaded function.

  1. end(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t) -> __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >*, std::vector<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >, std::allocator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> > > > >

  2. end(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t) -> __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >*, std::vector<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >, std::allocator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> > > > >

equal_size(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t, other: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t) bool

C++: protocols::mean_field::jagged_array<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >::equal_size(const class protocols::mean_field::jagged_array<class protocols::mean_field::AAProb, class std::allocator<class protocols::mean_field::AAProb> > &) const –> bool

erase(*args, **kwargs)

Overloaded function.

  1. erase(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t, __first: __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >*, std::vector<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >, std::allocator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> > > > >, __last: __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >*, std::vector<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >, std::allocator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> > > > >) -> __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >*, std::vector<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >, std::allocator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> > > > >

  2. erase(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t, __position: __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >*, std::vector<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >, std::allocator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> > > > >) -> __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >*, std::vector<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >, std::allocator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> > > > >

  3. erase(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t, __first: __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >*, std::vector<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >, std::allocator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> > > > >, __last: __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >*, std::vector<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >, std::allocator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> > > > >) -> __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >*, std::vector<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >, std::allocator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> > > > >

  4. erase(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t, __position: __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >*, std::vector<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >, std::allocator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> > > > >) -> __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >*, std::vector<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >, std::allocator<utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> > > > >

extend(othervec)
front(*args, **kwargs)

Overloaded function.

  1. front(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t) -> utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >

  2. front(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t) -> utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >

get_total(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t) protocols::mean_field::AAProb

C++: protocols::mean_field::jagged_array<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >::get_total() const –> class protocols::mean_field::AAProb

has_value(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t, t: protocols::mean_field::AAProb) bool

C++: protocols::mean_field::jagged_array<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >::has_value(const class protocols::mean_field::AAProb &) const –> bool

index(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t, t: protocols::mean_field::AAProb) int

C++: protocols::mean_field::jagged_array<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >::index(const class protocols::mean_field::AAProb &) const –> int

l(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t) int

lower index

max_size(*args, **kwargs)

Overloaded function.

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

  2. max_size(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t) -> int

max_size_col(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t) int

C++: protocols::mean_field::jagged_array<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >::max_size_col() const –> unsigned long

pop(*args, **kwargs)

Overloaded function.

  1. pop(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t) -> utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >

remove and return last item

  1. pop(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t, arg0: int) -> utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >

remove and return item at index

pop_back(*args, **kwargs)

Overloaded function.

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

  2. pop_back(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t) -> None

remove(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t, arg0: utility::vector1<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >) None

Remove the first item from the list whose value is x. It is an error if there is no such item.

reserve(*args, **kwargs)

Overloaded function.

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

  2. reserve(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t, __n: int) -> None

resize(*args, **kwargs)

Overloaded function.

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

  2. resize(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t, __new_size: int) -> None

show(*args, **kwargs)

Overloaded function.

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

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

C++: protocols::mean_field::jagged_array<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >::show(std::ostream &) const –> void

shrink_to_fit(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t) None
size(*args, **kwargs)

Overloaded function.

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

  2. size(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t) -> int

size_col(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t, col: int) int

C++: protocols::mean_field::jagged_array<protocols::mean_field::AAProb, std::allocator<protocols::mean_field::AAProb> >::size_col(unsigned long) const –> unsigned long

swap(*args, **kwargs)

Overloaded function.

  1. swap(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t, __x: pyrosetta.rosetta.std.vector_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t) -> None

  2. swap(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t, __x: pyrosetta.rosetta.std.vector_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t) -> None

u(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_AAProb_std_allocator_protocols_mean_field_AAProb_t) int

upper index

class pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t

Bases: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t

append(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t, arg0: utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >) None

adds an element to the end

assign(*args, **kwargs)

Overloaded function.

  1. assign(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t, v: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) -> pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t

  2. assign(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t, v: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) -> pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t

C++: protocols::mean_field::jagged_array<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >::operator=(const class protocols::mean_field::jagged_array<class protocols::mean_field::RotProb, class std::allocator<class protocols::mean_field::RotProb> > &) –> class protocols::mean_field::jagged_array<class protocols::mean_field::RotProb, class std::allocator<class protocols::mean_field::RotProb> > &

  1. assign(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t, dims: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: protocols::mean_field::jagged_array<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >::assign(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

  1. assign(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t, v: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) -> pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t

C++: 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> > > >::operator=(const class utility::vector1<class utility::vector1<class protocols::mean_field::RotProb, class std::allocator<class protocols::mean_field::RotProb> >, class std::allocator<class utility::vector1<class protocols::mean_field::RotProb, class std::allocator<class protocols::mean_field::RotProb> > > > &) –> class utility::vector1<class utility::vector1<class protocols::mean_field::RotProb, class std::allocator<class protocols::mean_field::RotProb> >, class std::allocator<class utility::vector1<class protocols::mean_field::RotProb, class std::allocator<class protocols::mean_field::RotProb> > > > &

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: pyrosetta.rosetta.utility.vector1_utility_vector1_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> >

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: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) -> utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >

begin(*args, **kwargs)

Overloaded function.

  1. begin(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) -> __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >*, std::vector<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> > > > >

  2. begin(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) -> __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >*, std::vector<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> > > > >

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: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) -> int

cbegin(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> > const*, std::vector<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> > > > >
cend(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> > const*, std::vector<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> > > > >
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: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) -> None

count(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t, arg0: utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >) int

counts the elements that are equal to value

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: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) -> bool

end(*args, **kwargs)

Overloaded function.

  1. end(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) -> __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >*, std::vector<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> > > > >

  2. end(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) -> __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >*, std::vector<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> > > > >

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

erase(*args, **kwargs)

Overloaded function.

  1. erase(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t, __first: __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >*, std::vector<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> > > > >, __last: __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >*, std::vector<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> > > > >) -> __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >*, std::vector<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> > > > >

  2. erase(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t, __position: __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >*, std::vector<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> > > > >) -> __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >*, std::vector<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> > > > >

  3. erase(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t, __first: __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >*, std::vector<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> > > > >, __last: __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >*, std::vector<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> > > > >) -> __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >*, std::vector<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> > > > >

  4. erase(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t, __position: __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >*, std::vector<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> > > > >) -> __gnu_cxx::__normal_iterator<utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >*, std::vector<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> > > > >

extend(othervec)
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: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) -> 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

l(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) int

lower index

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: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) -> 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

pop(*args, **kwargs)

Overloaded function.

  1. pop(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) -> utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >

remove and return last item

  1. pop(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t, arg0: int) -> utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >

remove and return item at index

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: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) -> None

remove(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t, arg0: utility::vector1<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >) None

Remove the first item from the list whose value is x. It is an error if there is no such item.

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: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t, __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: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t, __new_size: int) -> None

show(*args, **kwargs)

Overloaded function.

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

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

C++: protocols::mean_field::jagged_array<protocols::mean_field::RotProb, std::allocator<protocols::mean_field::RotProb> >::show(std::ostream &) const –> void

shrink_to_fit(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) 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: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) -> 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

swap(*args, **kwargs)

Overloaded function.

  1. swap(self: pyrosetta.rosetta.protocols.mean_field.jagged_array_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t, __x: pyrosetta.rosetta.std.vector_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) -> None

  2. swap(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t, __x: pyrosetta.rosetta.std.vector_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) -> None

u(self: pyrosetta.rosetta.utility.vector1_utility_vector1_protocols_mean_field_RotProb_std_allocator_protocols_mean_field_RotProb_t) int

upper index