dunbrack

Bindings for core::pack::dunbrack namespace

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackAAParameterSet

Bases: pybind11_builtins.pybind11_object

A small structure to hold overview parameters about the Dunbrack Libraries

get_dun02_aa_parameters() → pyrosetta.rosetta.core.pack.dunbrack.DunbrackAAParameterSet

C++: core::pack::dunbrack::DunbrackAAParameterSet::get_dun02_aa_parameters() –> struct core::pack::dunbrack::DunbrackAAParameterSet

get_dun10_aa_parameters() → pyrosetta.rosetta.core.pack.dunbrack.DunbrackAAParameterSet

C++: core::pack::dunbrack::DunbrackAAParameterSet::get_dun10_aa_parameters() –> struct core::pack::dunbrack::DunbrackAAParameterSet

class pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraintCreator

Bases: pyrosetta.rosetta.core.scoring.constraints.ConstraintCreator

Mover creator for the DunbrackConstraint constraint

assign(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraintCreator, : pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraintCreator) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraintCreator

C++: core::pack::dunbrack::DunbrackConstraintCreator::operator=(const class core::pack::dunbrack::DunbrackConstraintCreator &) –> class core::pack::dunbrack::DunbrackConstraintCreator &

create_constraint(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraintCreator) → pyrosetta.rosetta.core.scoring.constraints.Constraint

C++: core::pack::dunbrack::DunbrackConstraintCreator::create_constraint() const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

keyname(self: pyrosetta.rosetta.core.pack.dunbrack.DunbrackConstraintCreator) → str

C++: core::pack::dunbrack::DunbrackConstraintCreator::keyname() const –> std::string

class pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData

Bases: pybind11_builtins.pybind11_object

a simple class for passing data around in virtual function calls of the rotamer creating process. Derived classes will be simple containers for interpolated rotameric data that 1) has to be available to the derived class when building rotamers and 2) cannot be stored as member data in the derived class in a thread-safe manner. Derived classes of the RotamerBuildingData can be declared on the stack, passed into the RotamericSingleResidueDunbrackLibrary::build_chi_sets function, and then in the (virtual) chisamples_for_rotamer function, the derived classes may be downcast.

assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData, : pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData) → pyrosetta.rosetta.core.pack.dunbrack.RotamerBuildingData

C++: core::pack::dunbrack::RotamerBuildingData::operator=(const class core::pack::dunbrack::RotamerBuildingData &) –> class core::pack::dunbrack::RotamerBuildingData &

class pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint

Bases: pyrosetta.rosetta.core.scoring.constraints.Constraint

This class favors a particular rotamer at a particular position by reducing its Dunbrack energy.

Specifically, the given rotamer well(s) receive a bonus equal to the difference between their minimum energy (for the ideal rotamer in this well) and the minimum energy of any rotamer (at the current phi,psi). This class is used to implement the scoring component of the -unboundrot flag; actually adding those rotamers to the library occurs in core/pack/rotamer_set/UnboundRotamersOperation.

add_residue(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint, rsd: pyrosetta.rosetta.core.conformation.Residue) → None

C++: core::pack::dunbrack::RotamerConstraint::add_residue(const class core::conformation::Residue &) –> void

atom(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint, index: int) → pyrosetta.rosetta.core.id.AtomID

C++: core::pack::dunbrack::RotamerConstraint::atom(const unsigned long) const –> const class core::id::AtomID &

choose_effective_sequence_separation(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, sp: pyrosetta.rosetta.core.kinematics.ShortestPathInFoldTree, : pyrosetta.rosetta.numeric.random.RandomGenerator) → int

C++: core::scoring::constraints::Constraint::choose_effective_sequence_separation(const class core::kinematics::ShortestPathInFoldTree &, class numeric::random::RandomGenerator &) –> unsigned long

clone(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint) → pyrosetta.rosetta.core.scoring.constraints.Constraint

C++: core::pack::dunbrack::RotamerConstraint::clone() const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

dist(*args, **kwargs)

Overloaded function.

  1. dist(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint, : pyrosetta.rosetta.core.pose.Pose) -> float
  2. dist(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint, : core::scoring::func::XYZ_Func) -> float

Is ithere a “distance” that we can give for RotamerConstraints?

C++: core::pack::dunbrack::RotamerConstraint::dist(const class core::scoring::func::XYZ_Func &) const –> double

effective_sequence_separation(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.core.kinematics.ShortestPathInFoldTree) → int

C++: core::scoring::constraints::Constraint::effective_sequence_separation(const class core::kinematics::ShortestPathInFoldTree &) const –> unsigned long

fill_f1_f2(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint, atom: pyrosetta.rosetta.core.id.AtomID, xyz: core::scoring::func::XYZ_Func, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t, weights: pyrosetta.rosetta.core.scoring.EMapVector) → None

C++: core::pack::dunbrack::RotamerConstraint::fill_f1_f2(const class core::id::AtomID &, const class core::scoring::func::XYZ_Func &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &, const class core::scoring::EMapVector &) const –> void

get_func(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) → core::scoring::func::Func

Returns the func::Func object associated with this Constraint object.

C++: core::scoring::constraints::Constraint::get_func() const –> const class core::scoring::func::Func &

natoms(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint) → int

C++: core::pack::dunbrack::RotamerConstraint::natoms() const –> unsigned long

read_constraint(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.std.istream, : pyrosetta.rosetta.core.pose.Pose) → None
This method is totally redundant with read_def YAY
DON’T USE THIS ONE.. Most Constraint classes have not overloaded this one, but read_def ! OL

C++: core::scoring::constraints::Constraint::read_constraint(class std::basic_istream<char> &, const class core::pose::Pose &) –> void

read_data(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.std.istream) → None
initialize this Constraint from the given std::istream. It’s amazing
that there are three functions for doing this inside of Constraint.hh. SO WHAT IS THIS SUPPOSED TO DO ? not overloaded by e.g., AtomPairConstraint or CoordinateConstraint,

C++: core::scoring::constraints::Constraint::read_data(class std::basic_istream<char> &) –> void

read_def(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.std.istream, : pyrosetta.rosetta.core.pose.Pose, : core::scoring::func::FuncFactory) → None
Reads the definition of a Constraint from the given std::istream,
using the given Pose, and the given func::FuncFactory. This method is intended to be overridden by derived classes if they’d like to use the ConstraintIO machinery.

C++: core::scoring::constraints::Constraint::read_def(class std::basic_istream<char> &, const class core::pose::Pose &, const class core::scoring::func::FuncFactory &) –> void

remap_resid(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.core.id.SequenceMapping) → pyrosetta.rosetta.core.scoring.constraints.Constraint
apply a resid remapping to this constraint, returns the remapped
constraint Does this return an owning pointer to this constraint or a copy? Documentation would be nice.

C++: core::scoring::constraints::Constraint::remap_resid(const class core::id::SequenceMapping &) const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

remapped_clone(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pose.Pose, map: pyrosetta.rosetta.core.id.SequenceMapping) → pyrosetta.rosetta.core.scoring.constraints.Constraint
Copies the data from this Constraint into a new object and returns
an OP atoms are mapped to atoms with the same name in dest pose ( e.g. for switch from centroid to fullatom ) if a sequence_mapping is present it is used to map residue numbers .. NULL = identity mapping to the new object. Intended to be implemented by derived classes.

C++: core::scoring::constraints::Constraint::remapped_clone(const class core::pose::Pose &, const class core::pose::Pose &, class std::shared_ptr<const class core::id::SequenceMapping>) const –> class std::shared_ptr<class core::scoring::constraints::Constraint>

residues(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) → pyrosetta.rosetta.utility.vector1_unsigned_long

Returns the pose numbers of the residues involved in this constraint, in no particular order.

Used in determining one-body/two-body/multi-body status. For historical reasons, the default uses a simple protocol based on natoms()/atom() - feel free to reimplement more efficiently.

C++: core::scoring::constraints::Constraint::residues() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

same_type_as_me(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint, other: pyrosetta.rosetta.core.scoring.constraints.Constraint) → bool

C++: core::pack::dunbrack::RotamerConstraint::same_type_as_me(const class core::scoring::constraints::Constraint &) const –> bool

score(*args, **kwargs)

Overloaded function.

  1. score(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint, pose: pyrosetta.rosetta.core.pose.Pose, weights: pyrosetta.rosetta.core.scoring.EMapVector) -> float
  2. score(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint, pose: pyrosetta.rosetta.core.pose.Pose) -> float
  3. score(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint, xyz_func: core::scoring::func::XYZ_Func, weights: pyrosetta.rosetta.core.scoring.EMapVector, emap: pyrosetta.rosetta.core.scoring.EMapVector) -> None

C++: core::pack::dunbrack::RotamerConstraint::score(const class core::scoring::func::XYZ_Func &, const class core::scoring::EMapVector &, class core::scoring::EMapVector &) const –> void

score_type(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) → pyrosetta.rosetta.core.scoring.ScoreType

Returns the ScoreType that this Constraint object will use.

C++: core::scoring::constraints::Constraint::score_type() const –> const enum core::scoring::ScoreType &

setup_for_derivatives(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : core::scoring::func::XYZ_Func, : pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: core::scoring::constraints::Constraint::setup_for_derivatives(const class core::scoring::func::XYZ_Func &, const class core::scoring::ScoreFunction &) const –> void

setup_for_scoring(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : core::scoring::func::XYZ_Func, : pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: core::scoring::constraints::Constraint::setup_for_scoring(const class core::scoring::func::XYZ_Func &, const class core::scoring::ScoreFunction &) const –> void

show(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint, out: pyrosetta.rosetta.std.ostream) → None
This gets used to compare one constraint to another, so it should
uniquely reflect all the parameters.

C++: core::pack::dunbrack::RotamerConstraint::show(class std::basic_ostream<char> &) const –> void

show_def(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose) → None
Prints the definition of a Constraint to the given std::ostream,
using the given Pose, and the given func::FuncFactory. This method is intended to be overridden by derived classes if they’d like to use the ConstraintIO machinery. It’s also not clear why this method takes a Pose, other than to be symmetric with read_def.

C++: core::scoring::constraints::Constraint::show_def(class std::basic_ostream<char> &, const class core::pose::Pose &) const –> void

show_violations(*args, **kwargs)

Overloaded function.

  1. show_violations(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, out: pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose, : int) -> int
  2. show_violations(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, out: pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose, : int, threshold: float) -> int
Prints the violations of this constraint to the given
std::ostream. What are violations? It’s not defined, and it depends on the constraint and the function! also - wtf is threshold? it was defined as a Size in CoordinateConstraint, I don’t know which definition is the right one. Documentation would be nice …

C++: core::scoring::constraints::Constraint::show_violations(class std::basic_ostream<char> &, const class core::pose::Pose &, unsigned long, double) const –> unsigned long

steal_def(self: pyrosetta.rosetta.core.scoring.constraints.Constraint, : pyrosetta.rosetta.core.pose.Pose) → None

take coordinates, distances, angles, etc from given pose

C++: core::scoring::constraints::Constraint::steal_def(const class core::pose::Pose &) –> void

to_string(self: pyrosetta.rosetta.core.scoring.constraints.Constraint) → str
Convenience function, returns the results of show() as a string.
Not to be overriden by derived classes.

C++: core::scoring::constraints::Constraint::to_string() const –> std::string

type(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerConstraint) → str

C++: core::pack::dunbrack::RotamerConstraint::type() const –> std::string

class pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary

Bases: pyrosetta.rosetta.utility.SingletonBase_core_pack_dunbrack_RotamerLibrary_t

A class to manage the Dunbrack Rotamer Libraries

This class no longer manages arbitrary rotamer libraries. Use core::pack::rotamers::SingleResidueRotamerLibraryFactory::get_instance()->get( restype ); to get rotamer libraries for an arbitrary ResidueType.

best_rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, curr_rotamer_only: bool, scratch: core::pack::dunbrack::RotamerLibraryScratchSpace) → float

C++: core::pack::dunbrack::RotamerLibrary::best_rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, bool, class core::pack::dunbrack::RotamerLibraryScratchSpace &) const –> double

decide_read_from_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary) → bool

C++: core::pack::dunbrack::RotamerLibrary::decide_read_from_binary() const –> bool

get_binary_name(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary) → str

C++: core::pack::dunbrack::RotamerLibrary::get_binary_name() const –> std::string

get_instance() → core::pack::dunbrack::RotamerLibrary

C++: utility::SingletonBase<core::pack::dunbrack::RotamerLibrary>::get_instance() –> class core::pack::dunbrack::RotamerLibrary *

get_library_by_aa(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary, aa: pyrosetta.rosetta.core.chemical.AA) → core::pack::rotamers::SingleResidueRotamerLibrary

C++: core::pack::dunbrack::RotamerLibrary::get_library_by_aa(const enum core::chemical::AA &) const –> class std::shared_ptr<const class core::pack::rotamers::SingleResidueRotamerLibrary>

initialize_dun02_aa_parameters(nchi_for_aa: pyrosetta.rosetta.utility.vector1_unsigned_long, nbb_for_aa: pyrosetta.rosetta.utility.vector1_unsigned_long, n_rotameric_aas: int) → None

C++: core::pack::dunbrack::RotamerLibrary::initialize_dun02_aa_parameters(class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, unsigned long &) –> void

rotamer_energy(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, scratch: core::pack::dunbrack::RotamerLibraryScratchSpace) → float

C++: core::pack::dunbrack::RotamerLibrary::rotamer_energy(const class core::conformation::Residue &, const class core::pose::Pose &, class core::pack::dunbrack::RotamerLibraryScratchSpace &) const –> double

rotamer_energy_deriv(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, scratch: core::pack::dunbrack::RotamerLibraryScratchSpace) → float

to do:

C++: core::pack::dunbrack::RotamerLibrary::rotamer_energy_deriv(const class core::conformation::Residue &, const class core::pose::Pose &, class core::pack::dunbrack::RotamerLibraryScratchSpace &) const –> double

validate_dunbrack_binary(self: pyrosetta.rosetta.core.pack.dunbrack.RotamerLibrary) → bool
Reload the Dunbrack Rotamer libraries from ASCII, and make sure that they match the ones loaded from binary.
Return true if the binary file is valid, false if the binary is invalid. NOTE WELL: This is not a const function, as reloading from ASCII modifies internals. It’s also VERY thread unsafe. Never call this function from a multithreaded context.

C++: core::pack::dunbrack::RotamerLibrary::validate_dunbrack_binary() –> bool

class pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser

Bases: pybind11_builtins.pybind11_object

A helper class to assist in parsing rotamer libraries.

Vikram K. Mulligan (vmullig.edu).

assign(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, : pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser) → pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::operator=(const class core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser &) –> class core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser &

calc_product(*args, **kwargs)

Overloaded function.

  1. calc_product(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, factors: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::calc_product(class utility::fixedsizearray1<unsigned long, 1>) const –> unsigned long

  1. calc_product(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, factors: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::calc_product(class utility::fixedsizearray1<unsigned long, 2>) const –> unsigned long

  1. calc_product(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, factors: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::calc_product(class utility::fixedsizearray1<unsigned long, 3>) const –> unsigned long

  1. calc_product(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, factors: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::calc_product(class utility::fixedsizearray1<unsigned long, 4>) const –> unsigned long

  1. calc_product(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, factors: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::calc_product(class utility::fixedsizearray1<unsigned long, 5>) const –> unsigned long

clear_imporated_data(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser) → None

Clear all of the data read from a file.

Also resets read_file_was_called_ to false.

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::clear_imporated_data() –> void

clone(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser) → pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::clone() const –> class std::shared_ptr<class core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser>

configure_rotameric_single_residue_dunbrack_library(*args, **kwargs)

Overloaded function.

  1. configure_rotameric_single_residue_dunbrack_library(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, library: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1ul, 1ul>, n_bb_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(class core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<core::pack::dunbrack::ONE, core::pack::dunbrack::ONE> &, const class utility::fixedsizearray1<unsigned long, 1> &) const –> void

  1. configure_rotameric_single_residue_dunbrack_library(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, library: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1ul, 2ul>, n_bb_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(class core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<core::pack::dunbrack::ONE, core::pack::dunbrack::TWO> &, const class utility::fixedsizearray1<unsigned long, 2> &) const –> void

  1. configure_rotameric_single_residue_dunbrack_library(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, library: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1ul, 3ul>, n_bb_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(class core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<core::pack::dunbrack::ONE, core::pack::dunbrack::THREE> &, const class utility::fixedsizearray1<unsigned long, 3> &) const –> void

  1. configure_rotameric_single_residue_dunbrack_library(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, library: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1ul, 4ul>, n_bb_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(class core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<core::pack::dunbrack::ONE, core::pack::dunbrack::FOUR> &, const class utility::fixedsizearray1<unsigned long, 4> &) const –> void

  1. configure_rotameric_single_residue_dunbrack_library(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, library: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<1ul, 5ul>, n_bb_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(class core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<core::pack::dunbrack::ONE, core::pack::dunbrack::FIVE> &, const class utility::fixedsizearray1<unsigned long, 5> &) const –> void

  1. configure_rotameric_single_residue_dunbrack_library(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, library: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2ul, 1ul>, n_bb_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(class core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<core::pack::dunbrack::TWO, core::pack::dunbrack::ONE> &, const class utility::fixedsizearray1<unsigned long, 1> &) const –> void

  1. configure_rotameric_single_residue_dunbrack_library(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, library: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2ul, 2ul>, n_bb_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(class core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<core::pack::dunbrack::TWO, core::pack::dunbrack::TWO> &, const class utility::fixedsizearray1<unsigned long, 2> &) const –> void

  1. configure_rotameric_single_residue_dunbrack_library(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, library: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2ul, 3ul>, n_bb_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(class core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<core::pack::dunbrack::TWO, core::pack::dunbrack::THREE> &, const class utility::fixedsizearray1<unsigned long, 3> &) const –> void

  1. configure_rotameric_single_residue_dunbrack_library(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, library: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2ul, 4ul>, n_bb_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(class core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<core::pack::dunbrack::TWO, core::pack::dunbrack::FOUR> &, const class utility::fixedsizearray1<unsigned long, 4> &) const –> void

  1. configure_rotameric_single_residue_dunbrack_library(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, library: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<2ul, 5ul>, n_bb_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(class core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<core::pack::dunbrack::TWO, core::pack::dunbrack::FIVE> &, const class utility::fixedsizearray1<unsigned long, 5> &) const –> void

  1. configure_rotameric_single_residue_dunbrack_library(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, library: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3ul, 1ul>, n_bb_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(class core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<core::pack::dunbrack::THREE, core::pack::dunbrack::ONE> &, const class utility::fixedsizearray1<unsigned long, 1> &) const –> void

  1. configure_rotameric_single_residue_dunbrack_library(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, library: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3ul, 2ul>, n_bb_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(class core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<core::pack::dunbrack::THREE, core::pack::dunbrack::TWO> &, const class utility::fixedsizearray1<unsigned long, 2> &) const –> void

  1. configure_rotameric_single_residue_dunbrack_library(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, library: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3ul, 3ul>, n_bb_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(class core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<core::pack::dunbrack::THREE, core::pack::dunbrack::THREE> &, const class utility::fixedsizearray1<unsigned long, 3> &) const –> void

  1. configure_rotameric_single_residue_dunbrack_library(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, library: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3ul, 4ul>, n_bb_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(class core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<core::pack::dunbrack::THREE, core::pack::dunbrack::FOUR> &, const class utility::fixedsizearray1<unsigned long, 4> &) const –> void

  1. configure_rotameric_single_residue_dunbrack_library(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, library: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<3ul, 5ul>, n_bb_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(class core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<core::pack::dunbrack::THREE, core::pack::dunbrack::FIVE> &, const class utility::fixedsizearray1<unsigned long, 5> &) const –> void

  1. configure_rotameric_single_residue_dunbrack_library(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, library: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4ul, 1ul>, n_bb_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(class core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<core::pack::dunbrack::FOUR, core::pack::dunbrack::ONE> &, const class utility::fixedsizearray1<unsigned long, 1> &) const –> void

  1. configure_rotameric_single_residue_dunbrack_library(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, library: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4ul, 2ul>, n_bb_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(class core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<core::pack::dunbrack::FOUR, core::pack::dunbrack::TWO> &, const class utility::fixedsizearray1<unsigned long, 2> &) const –> void

  1. configure_rotameric_single_residue_dunbrack_library(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, library: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4ul, 3ul>, n_bb_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(class core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<core::pack::dunbrack::FOUR, core::pack::dunbrack::THREE> &, const class utility::fixedsizearray1<unsigned long, 3> &) const –> void

  1. configure_rotameric_single_residue_dunbrack_library(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, library: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4ul, 4ul>, n_bb_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(class core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<core::pack::dunbrack::FOUR, core::pack::dunbrack::FOUR> &, const class utility::fixedsizearray1<unsigned long, 4> &) const –> void

  1. configure_rotameric_single_residue_dunbrack_library(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, library: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<4ul, 5ul>, n_bb_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(class core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<core::pack::dunbrack::FOUR, core::pack::dunbrack::FIVE> &, const class utility::fixedsizearray1<unsigned long, 5> &) const –> void

  1. configure_rotameric_single_residue_dunbrack_library(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, library: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5ul, 1ul>, n_bb_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(class core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<core::pack::dunbrack::FIVE, core::pack::dunbrack::ONE> &, const class utility::fixedsizearray1<unsigned long, 1> &) const –> void

  1. configure_rotameric_single_residue_dunbrack_library(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, library: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5ul, 2ul>, n_bb_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(class core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<core::pack::dunbrack::FIVE, core::pack::dunbrack::TWO> &, const class utility::fixedsizearray1<unsigned long, 2> &) const –> void

  1. configure_rotameric_single_residue_dunbrack_library(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, library: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5ul, 3ul>, n_bb_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(class core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<core::pack::dunbrack::FIVE, core::pack::dunbrack::THREE> &, const class utility::fixedsizearray1<unsigned long, 3> &) const –> void

  1. configure_rotameric_single_residue_dunbrack_library(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, library: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5ul, 4ul>, n_bb_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(class core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<core::pack::dunbrack::FIVE, core::pack::dunbrack::FOUR> &, const class utility::fixedsizearray1<unsigned long, 4> &) const –> void

  1. configure_rotameric_single_residue_dunbrack_library(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, library: core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<5ul, 5ul>, n_bb_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::configure_rotameric_single_residue_dunbrack_library(class core::pack::dunbrack::RotamericSingleResidueDunbrackLibrary<core::pack::dunbrack::FIVE, core::pack::dunbrack::FIVE> &, const class utility::fixedsizearray1<unsigned long, 5> &) const –> void

read_file(self: pyrosetta.rosetta.core.pack.dunbrack.RotamericSingleResidueDunbrackLibraryParser, infile: pyrosetta.rosetta.utility.io.izstream, first_line_three_letter_code_already_read: bool, aa: pyrosetta.rosetta.core.chemical.AA) → str

Read an input stream to set up this object.

The RotamericSingleResidueDunbrackLibraryParser stores the information from the rotamer library in a very one-to-one format, and can subsequently be used to configure a RotamericSingleResidueDunbrackLibrary object (requiring some interpretation of the data).

We might be starting the read in the middle of the file, and the three-letter code from the first line might already have been read.

The name of the next amino acid specified in the input stream, or alternatively an empty string if EOF is reached.

C++: core::pack::dunbrack::RotamericSingleResidueDunbrackLibraryParser::read_file(class utility::io::izstream &, bool, const enum core::chemical::AA) –> std::string

pyrosetta.rosetta.core.pack.dunbrack.bit_is_set(num: int, num_len: int, pos: int) → bool

C++: core::pack::dunbrack::bit_is_set(unsigned long, unsigned long, unsigned long) –> bool

pyrosetta.rosetta.core.pack.dunbrack.interpolate_polylinear_by_value(*args, **kwargs)

Overloaded function.

  1. interpolate_polylinear_by_value(vals: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t, bbd: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t, binrange: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t, angles: bool, val: float, dval_dbb: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t) -> None

C++: core::pack::dunbrack::interpolate_polylinear_by_value(const class utility::fixedsizearray1<double, 2> &, const class utility::fixedsizearray1<double, 1> &, const class utility::fixedsizearray1<double, 1> &, bool, double &, class utility::fixedsizearray1<double, 1> &) –> void

  1. interpolate_polylinear_by_value(vals: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t, bbd: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t, binrange: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t, angles: bool, val: float, dval_dbb: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t) -> None

C++: core::pack::dunbrack::interpolate_polylinear_by_value(const class utility::fixedsizearray1<double, 4> &, const class utility::fixedsizearray1<double, 2> &, const class utility::fixedsizearray1<double, 2> &, bool, double &, class utility::fixedsizearray1<double, 2> &) –> void

  1. interpolate_polylinear_by_value(vals: pyrosetta.rosetta.utility.fixedsizearray1_double_8_t, bbd: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, binrange: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, angles: bool, val: float, dval_dbb: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t) -> None

C++: core::pack::dunbrack::interpolate_polylinear_by_value(const class utility::fixedsizearray1<double, 8> &, const class utility::fixedsizearray1<double, 3> &, const class utility::fixedsizearray1<double, 3> &, bool, double &, class utility::fixedsizearray1<double, 3> &) –> void

  1. interpolate_polylinear_by_value(vals: pyrosetta.rosetta.utility.fixedsizearray1_double_16_t, bbd: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t, binrange: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t, angles: bool, val: float, dval_dbb: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t) -> None

C++: core::pack::dunbrack::interpolate_polylinear_by_value(const class utility::fixedsizearray1<double, 16> &, const class utility::fixedsizearray1<double, 4> &, const class utility::fixedsizearray1<double, 4> &, bool, double &, class utility::fixedsizearray1<double, 4> &) –> void

  1. interpolate_polylinear_by_value(vals: pyrosetta.rosetta.utility.fixedsizearray1_double_32_t, bbd: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t, binrange: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t, angles: bool, val: float, dval_dbb: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> None

C++: core::pack::dunbrack::interpolate_polylinear_by_value(const class utility::fixedsizearray1<double, 32> &, const class utility::fixedsizearray1<double, 5> &, const class utility::fixedsizearray1<double, 5> &, bool, double &, class utility::fixedsizearray1<double, 5> &) –> void

pyrosetta.rosetta.core.pack.dunbrack.load_unboundrot(*args, **kwargs)

Overloaded function.

  1. load_unboundrot(pose: pyrosetta.rosetta.core.pose.Pose) -> None
Convenience function adds constraints to the supplied pose based on
the -unboundrot command line flag.

C++: core::pack::dunbrack::load_unboundrot(class core::pose::Pose &) –> void

  1. load_unboundrot(pose: pyrosetta.rosetta.core.pose.Pose, unboundrot_poses: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_pose_Pose_t) -> None
Convenience function adds constraints to the supplied pose based on
the list of provided poses.

C++: core::pack::dunbrack::load_unboundrot(class core::pose::Pose &, const class utility::vector1<class std::shared_ptr<const class core::pose::Pose>, class std::allocator<class std::shared_ptr<const class core::pose::Pose> > > &) –> void

pyrosetta.rosetta.core.pack.dunbrack.make_conditional_index(*args, **kwargs)

Overloaded function.

  1. make_conditional_index(num_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t, cond_i: int, bin_true: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t, bin_false: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t) -> int

C++: core::pack::dunbrack::make_conditional_index(class utility::fixedsizearray1<unsigned long, 1>, unsigned long, class utility::fixedsizearray1<unsigned long, 1>, class utility::fixedsizearray1<unsigned long, 1>) –> unsigned long

  1. make_conditional_index(num_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t, cond_i: int, bin_true: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t, bin_false: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t) -> int

C++: core::pack::dunbrack::make_conditional_index(class utility::fixedsizearray1<unsigned long, 2>, unsigned long, class utility::fixedsizearray1<unsigned long, 2>, class utility::fixedsizearray1<unsigned long, 2>) –> unsigned long

  1. make_conditional_index(num_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t, cond_i: int, bin_true: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t, bin_false: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t) -> int

C++: core::pack::dunbrack::make_conditional_index(class utility::fixedsizearray1<unsigned long, 3>, unsigned long, class utility::fixedsizearray1<unsigned long, 3>, class utility::fixedsizearray1<unsigned long, 3>) –> unsigned long

  1. make_conditional_index(num_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t, cond_i: int, bin_true: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t, bin_false: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t) -> int

C++: core::pack::dunbrack::make_conditional_index(class utility::fixedsizearray1<unsigned long, 4>, unsigned long, class utility::fixedsizearray1<unsigned long, 4>, class utility::fixedsizearray1<unsigned long, 4>) –> unsigned long

  1. make_conditional_index(num_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t, cond_i: int, bin_true: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t, bin_false: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

C++: core::pack::dunbrack::make_conditional_index(class utility::fixedsizearray1<unsigned long, 5>, unsigned long, class utility::fixedsizearray1<unsigned long, 5>, class utility::fixedsizearray1<unsigned long, 5>) –> unsigned long

pyrosetta.rosetta.core.pack.dunbrack.make_index(*args, **kwargs)

Overloaded function.

  1. make_index(num_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t) -> int

C++: core::pack::dunbrack::make_index(class utility::fixedsizearray1<unsigned long, 1>, class utility::fixedsizearray1<unsigned long, 1>) –> unsigned long

  1. make_index(num_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t) -> int

C++: core::pack::dunbrack::make_index(class utility::fixedsizearray1<unsigned long, 2>, class utility::fixedsizearray1<unsigned long, 2>) –> unsigned long

  1. make_index(num_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t) -> int

C++: core::pack::dunbrack::make_index(class utility::fixedsizearray1<unsigned long, 3>, class utility::fixedsizearray1<unsigned long, 3>) –> unsigned long

  1. make_index(num_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t) -> int

C++: core::pack::dunbrack::make_index(class utility::fixedsizearray1<unsigned long, 4>, class utility::fixedsizearray1<unsigned long, 4>) –> unsigned long

  1. make_index(num_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

C++: core::pack::dunbrack::make_index(class utility::fixedsizearray1<unsigned long, 5>, class utility::fixedsizearray1<unsigned long, 5>) –> unsigned long

  1. make_index(num_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t) -> int

C++: core::pack::dunbrack::make_index(class utility::fixedsizearray1<unsigned long, 1>, class utility::fixedsizearray1<unsigned long, 2>) –> unsigned long

  1. make_index(num_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t) -> int

C++: core::pack::dunbrack::make_index(class utility::fixedsizearray1<unsigned long, 2>, class utility::fixedsizearray1<unsigned long, 3>) –> unsigned long

  1. make_index(num_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t) -> int

C++: core::pack::dunbrack::make_index(class utility::fixedsizearray1<unsigned long, 3>, class utility::fixedsizearray1<unsigned long, 4>) –> unsigned long

  1. make_index(num_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

C++: core::pack::dunbrack::make_index(class utility::fixedsizearray1<unsigned long, 4>, class utility::fixedsizearray1<unsigned long, 5>) –> unsigned long

  1. make_index(num_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t, bb_bin: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_6_t) -> int

C++: core::pack::dunbrack::make_index(class utility::fixedsizearray1<unsigned long, 5>, class utility::fixedsizearray1<unsigned long, 6>) –> unsigned long

  1. make_index(num_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t, bb_bin: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

C++: core::pack::dunbrack::make_index(class utility::fixedsizearray1<unsigned long, 1>, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> unsigned long

  1. make_index(num_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t, bb_bin: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

C++: core::pack::dunbrack::make_index(class utility::fixedsizearray1<unsigned long, 2>, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> unsigned long

  1. make_index(num_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t, bb_bin: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

C++: core::pack::dunbrack::make_index(class utility::fixedsizearray1<unsigned long, 3>, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> unsigned long

  1. make_index(num_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t, bb_bin: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

C++: core::pack::dunbrack::make_index(class utility::fixedsizearray1<unsigned long, 4>, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> unsigned long

  1. make_index(num_bins: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t, bb_bin: pyrosetta.rosetta.utility.vector1_unsigned_long) -> int

C++: core::pack::dunbrack::make_index(class utility::fixedsizearray1<unsigned long, 5>, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> unsigned long

pyrosetta.rosetta.core.pack.dunbrack.polycubic_interpolation(*args, **kwargs)

Overloaded function.

  1. polycubic_interpolation(n_derivs: pyrosetta.rosetta.utility.fixedsizearray1_utility_fixedsizearray1_double_2_2_t, dbbp: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t, binwbb: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t, val: float, dvaldbb: pyrosetta.rosetta.utility.fixedsizearray1_double_1_t) -> None

C++: core::pack::dunbrack::polycubic_interpolation(class utility::fixedsizearray1<class utility::fixedsizearray1<double, 2>, 2>, class utility::fixedsizearray1<double, 1>, class utility::fixedsizearray1<double, 1>, double &, class utility::fixedsizearray1<double, 1> &) –> void

  1. polycubic_interpolation(n_derivs: pyrosetta.rosetta.utility.fixedsizearray1_utility_fixedsizearray1_double_4_4_t, dbbp: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t, binwbb: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t, val: float, dvaldbb: pyrosetta.rosetta.utility.fixedsizearray1_double_2_t) -> None

C++: core::pack::dunbrack::polycubic_interpolation(class utility::fixedsizearray1<class utility::fixedsizearray1<double, 4>, 4>, class utility::fixedsizearray1<double, 2>, class utility::fixedsizearray1<double, 2>, double &, class utility::fixedsizearray1<double, 2> &) –> void

  1. polycubic_interpolation(n_derivs: pyrosetta.rosetta.utility.fixedsizearray1_utility_fixedsizearray1_double_8_8_t, dbbp: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, binwbb: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t, val: float, dvaldbb: pyrosetta.rosetta.utility.fixedsizearray1_double_3_t) -> None

C++: core::pack::dunbrack::polycubic_interpolation(class utility::fixedsizearray1<class utility::fixedsizearray1<double, 8>, 8>, class utility::fixedsizearray1<double, 3>, class utility::fixedsizearray1<double, 3>, double &, class utility::fixedsizearray1<double, 3> &) –> void

  1. polycubic_interpolation(n_derivs: pyrosetta.rosetta.utility.fixedsizearray1_utility_fixedsizearray1_double_16_16_t, dbbp: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t, binwbb: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t, val: float, dvaldbb: pyrosetta.rosetta.utility.fixedsizearray1_double_4_t) -> None

C++: core::pack::dunbrack::polycubic_interpolation(class utility::fixedsizearray1<class utility::fixedsizearray1<double, 16>, 16>, class utility::fixedsizearray1<double, 4>, class utility::fixedsizearray1<double, 4>, double &, class utility::fixedsizearray1<double, 4> &) –> void

  1. polycubic_interpolation(n_derivs: pyrosetta.rosetta.utility.fixedsizearray1_utility_fixedsizearray1_double_32_32_t, dbbp: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t, binwbb: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t, val: float, dvaldbb: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t) -> None

C++: core::pack::dunbrack::polycubic_interpolation(class utility::fixedsizearray1<class utility::fixedsizearray1<double, 32>, 32>, class utility::fixedsizearray1<double, 5>, class utility::fixedsizearray1<double, 5>, double &, class utility::fixedsizearray1<double, 5> &) –> void

  1. polycubic_interpolation(n_derivs: pyrosetta.rosetta.utility.fixedsizearray1_utility_fixedsizearray1_double_64_64_t, dbbp: pyrosetta.rosetta.utility.fixedsizearray1_double_6_t, binwbb: pyrosetta.rosetta.utility.fixedsizearray1_double_6_t, val: float, dvaldbb: pyrosetta.rosetta.utility.fixedsizearray1_double_6_t) -> None

C++: core::pack::dunbrack::polycubic_interpolation(class utility::fixedsizearray1<class utility::fixedsizearray1<double, 64>, 64>, class utility::fixedsizearray1<double, 6>, class utility::fixedsizearray1<double, 6>, double &, class utility::fixedsizearray1<double, 6> &) –> void

pyrosetta.rosetta.core.pack.dunbrack.positive_pow(mantissa: int, exponent: int) → int

C++: core::pack::dunbrack::positive_pow(unsigned long, unsigned long) –> unsigned long

pyrosetta.rosetta.core.pack.dunbrack.product(*args, **kwargs)

Overloaded function.

  1. product(factors: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_1_t) -> int

C++: core::pack::dunbrack::product(class utility::fixedsizearray1<unsigned long, 1>) –> unsigned long

  1. product(factors: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_2_t) -> int

C++: core::pack::dunbrack::product(class utility::fixedsizearray1<unsigned long, 2>) –> unsigned long

  1. product(factors: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_3_t) -> int

C++: core::pack::dunbrack::product(class utility::fixedsizearray1<unsigned long, 3>) –> unsigned long

  1. product(factors: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_4_t) -> int

C++: core::pack::dunbrack::product(class utility::fixedsizearray1<unsigned long, 4>) –> unsigned long

  1. product(factors: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> int

C++: core::pack::dunbrack::product(class utility::fixedsizearray1<unsigned long, 5>) –> unsigned long

pyrosetta.rosetta.core.pack.dunbrack.psc_compare(left: pyrosetta.rosetta.core.pack.dunbrack.ProbSortClass, right: pyrosetta.rosetta.core.pack.dunbrack.ProbSortClass) → bool

C++: core::pack::dunbrack::psc_compare(class core::pack::dunbrack::ProbSortClass, class core::pack::dunbrack::ProbSortClass) –> bool

pyrosetta.rosetta.core.pack.dunbrack.rotamer_from_chi(*args, **kwargs)

Overloaded function.

  1. rotamer_from_chi(rsd: pyrosetta.rosetta.core.conformation.Residue, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::pack::dunbrack::rotamer_from_chi(const class core::conformation::Residue &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

  1. rotamer_from_chi(rsd_type: pyrosetta.rosetta.core.chemical.ResidueType, chi: pyrosetta.rosetta.utility.vector1_double, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: core::pack::dunbrack::rotamer_from_chi(const class core::chemical::ResidueType &, const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

pyrosetta.rosetta.core.pack.dunbrack.rotamer_from_chi_02(*args, **kwargs)

Overloaded function.

  1. rotamer_from_chi_02(chi: pyrosetta.rosetta.utility.vector1_double, res: pyrosetta.rosetta.core.chemical.AA, rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None
Do not bother calling this function if you’re interested in staying
up to date with changes in the rotamer library. Call rotamer_from_chi instead. It will eventually call this function iff dun10 is not set to true.

C++: core::pack::dunbrack::rotamer_from_chi_02(const class utility::vector1<double, class std::allocator<double> > &, const enum core::chemical::AA, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

  1. rotamer_from_chi_02(chi: pyrosetta.rosetta.utility.fixedsizearray1_double_5_t, res: pyrosetta.rosetta.core.chemical.AA, nchi: int, rot: pyrosetta.rosetta.utility.fixedsizearray1_unsigned_long_5_t) -> None

C++: core::pack::dunbrack::rotamer_from_chi_02(const class utility::fixedsizearray1<double, 5> &, const enum core::chemical::AA, unsigned long, class utility::fixedsizearray1<unsigned long, 5> &) –> void

pyrosetta.rosetta.core.pack.dunbrack.subtract_chi_angles(chi1: float, chi2: float, aa: pyrosetta.rosetta.core.chemical.AA, chino: int) → float
Find the difference in angles between two chi values using hard-coded
symmetry information for the symmetric amino acids. Disappears for 2010 library.

C++: core::pack::dunbrack::subtract_chi_angles(double, double, const enum core::chemical::AA &, int) –> double