rotamers¶

Bindings for core::chemical::rotamers namespace

class pyrosetta.rosetta.core.chemical.rotamers.BasicRotamerLibrarySpecification¶

Bases: RotamerLibrarySpecification

assign(self: pyrosetta.rosetta.core.chemical.rotamers.BasicRotamerLibrarySpecification, : pyrosetta.rosetta.core.chemical.rotamers.BasicRotamerLibrarySpecification) → pyrosetta.rosetta.core.chemical.rotamers.BasicRotamerLibrarySpecification¶: C++: core::chemical::rotamers::BasicRotamerLibrarySpecification::operator=(const class core::chemical::rotamers::BasicRotamerLibrarySpecification &) –> class core::chemical::rotamers::BasicRotamerLibrarySpecification &

cache_tag(self: pyrosetta.rosetta.core.chemical.rotamers.BasicRotamerLibrarySpecification, : pyrosetta.rosetta.core.chemical.ResidueType) → str¶: C++: core::chemical::rotamers::BasicRotamerLibrarySpecification::cache_tag(const class core::chemical::ResidueType &) const –> std::string

clone(self: pyrosetta.rosetta.core.chemical.rotamers.BasicRotamerLibrarySpecification) → pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecification¶: C++: core::chemical::rotamers::BasicRotamerLibrarySpecification::clone() const –> class std::shared_ptr<class core::chemical::rotamers::RotamerLibrarySpecification>

describe(self: pyrosetta.rosetta.core.chemical.rotamers.BasicRotamerLibrarySpecification, out: pyrosetta.rosetta.std.ostream) → None¶: C++: core::chemical::rotamers::BasicRotamerLibrarySpecification::describe(std::ostream &) const –> void

keyname(self: pyrosetta.rosetta.core.chemical.rotamers.BasicRotamerLibrarySpecification) → str¶

Which type of SingleResidueRotamerLibrary does this specification sub-type correspond to?

C++: core::chemical::rotamers::BasicRotamerLibrarySpecification::keyname() const –> std::string

static library_name() → str¶

Static function for access to type_name, to have a single string which is used for both: this class and for the SingleResidueRotamerLibraryCreator.

C++: core::chemical::rotamers::BasicRotamerLibrarySpecification::library_name() –> std::string

class pyrosetta.rosetta.core.chemical.rotamers.BasicRotamerLibrarySpecificationCreator¶

Bases: RotamerLibrarySpecificationCreator

assign(self: pyrosetta.rosetta.core.chemical.rotamers.BasicRotamerLibrarySpecificationCreator, : pyrosetta.rosetta.core.chemical.rotamers.BasicRotamerLibrarySpecificationCreator) → pyrosetta.rosetta.core.chemical.rotamers.BasicRotamerLibrarySpecificationCreator¶: C++: core::chemical::rotamers::BasicRotamerLibrarySpecificationCreator::operator=(const class core::chemical::rotamers::BasicRotamerLibrarySpecificationCreator &) –> class core::chemical::rotamers::BasicRotamerLibrarySpecificationCreator &

create(*args, **kwargs)¶

Overloaded function.

create(self: pyrosetta.rosetta.core.chemical.rotamers.BasicRotamerLibrarySpecificationCreator) -> pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecification

C++: core::chemical::rotamers::BasicRotamerLibrarySpecificationCreator::create() const –> class std::shared_ptr<class core::chemical::rotamers::RotamerLibrarySpecification>

create(self: pyrosetta.rosetta.core.chemical.rotamers.BasicRotamerLibrarySpecificationCreator, : pyrosetta.rosetta.std.istream) -> pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecification

C++: core::chemical::rotamers::BasicRotamerLibrarySpecificationCreator::create(std::istream &) const –> class std::shared_ptr<class core::chemical::rotamers::RotamerLibrarySpecification>

keyname(self: pyrosetta.rosetta.core.chemical.rotamers.BasicRotamerLibrarySpecificationCreator) → str¶: C++: core::chemical::rotamers::BasicRotamerLibrarySpecificationCreator::keyname() const –> std::string

class pyrosetta.rosetta.core.chemical.rotamers.CenrotRotamerLibrarySpecification¶

Bases: RotamerLibrarySpecification

aa(self: pyrosetta.rosetta.core.chemical.rotamers.CenrotRotamerLibrarySpecification, aa_setting: pyrosetta.rosetta.core.chemical.AA) → None¶: C++: core::chemical::rotamers::CenrotRotamerLibrarySpecification::aa(enum core::chemical::AA) –> void

assign(self: pyrosetta.rosetta.core.chemical.rotamers.CenrotRotamerLibrarySpecification, : pyrosetta.rosetta.core.chemical.rotamers.CenrotRotamerLibrarySpecification) → pyrosetta.rosetta.core.chemical.rotamers.CenrotRotamerLibrarySpecification¶: C++: core::chemical::rotamers::CenrotRotamerLibrarySpecification::operator=(const class core::chemical::rotamers::CenrotRotamerLibrarySpecification &) –> class core::chemical::rotamers::CenrotRotamerLibrarySpecification &

cache_tag(self: pyrosetta.rosetta.core.chemical.rotamers.CenrotRotamerLibrarySpecification, : pyrosetta.rosetta.core.chemical.ResidueType) → str¶

Return empty string, as Cenrot rotamer caching happens external to the Factory caching.

C++: core::chemical::rotamers::CenrotRotamerLibrarySpecification::cache_tag(const class core::chemical::ResidueType &) const –> std::string

clone(self: pyrosetta.rosetta.core.chemical.rotamers.CenrotRotamerLibrarySpecification) → pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecification¶: C++: core::chemical::rotamers::CenrotRotamerLibrarySpecification::clone() const –> class std::shared_ptr<class core::chemical::rotamers::RotamerLibrarySpecification>

describe(self: pyrosetta.rosetta.core.chemical.rotamers.CenrotRotamerLibrarySpecification, out: pyrosetta.rosetta.std.ostream) → None¶: C++: core::chemical::rotamers::CenrotRotamerLibrarySpecification::describe(std::ostream &) const –> void

get_aa(self: pyrosetta.rosetta.core.chemical.rotamers.CenrotRotamerLibrarySpecification) → pyrosetta.rosetta.core.chemical.AA¶

The AA for which we’re building the Rotamer library.

C++: core::chemical::rotamers::CenrotRotamerLibrarySpecification::get_aa() const –> enum core::chemical::AA

keyname(self: pyrosetta.rosetta.core.chemical.rotamers.CenrotRotamerLibrarySpecification) → str¶

Which type of SingleResidueRotamerLibrary does this specification sub-type correspond to?

C++: core::chemical::rotamers::CenrotRotamerLibrarySpecification::keyname() const –> std::string

static library_name() → str¶

Static function for access to type_name, to have a single string which is used for both: this class and for the SingleResidueRotamerLibraryCreator.

C++: core::chemical::rotamers::CenrotRotamerLibrarySpecification::library_name() –> std::string

class pyrosetta.rosetta.core.chemical.rotamers.CenrotRotamerLibrarySpecificationCreator¶

Bases: RotamerLibrarySpecificationCreator

assign(self: pyrosetta.rosetta.core.chemical.rotamers.CenrotRotamerLibrarySpecificationCreator, : pyrosetta.rosetta.core.chemical.rotamers.CenrotRotamerLibrarySpecificationCreator) → pyrosetta.rosetta.core.chemical.rotamers.CenrotRotamerLibrarySpecificationCreator¶: C++: core::chemical::rotamers::CenrotRotamerLibrarySpecificationCreator::operator=(const class core::chemical::rotamers::CenrotRotamerLibrarySpecificationCreator &) –> class core::chemical::rotamers::CenrotRotamerLibrarySpecificationCreator &

create(*args, **kwargs)¶

Overloaded function.

create(self: pyrosetta.rosetta.core.chemical.rotamers.CenrotRotamerLibrarySpecificationCreator) -> pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecification

C++: core::chemical::rotamers::CenrotRotamerLibrarySpecificationCreator::create() const –> class std::shared_ptr<class core::chemical::rotamers::RotamerLibrarySpecification>

create(self: pyrosetta.rosetta.core.chemical.rotamers.CenrotRotamerLibrarySpecificationCreator, : pyrosetta.rosetta.std.istream) -> pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecification

C++: core::chemical::rotamers::CenrotRotamerLibrarySpecificationCreator::create(std::istream &) const –> class std::shared_ptr<class core::chemical::rotamers::RotamerLibrarySpecification>

keyname(self: pyrosetta.rosetta.core.chemical.rotamers.CenrotRotamerLibrarySpecificationCreator) → str¶: C++: core::chemical::rotamers::CenrotRotamerLibrarySpecificationCreator::keyname() const –> std::string

class pyrosetta.rosetta.core.chemical.rotamers.DunbrackRotamerLibrarySpecification¶

Bases: RotamerLibrarySpecification

aa(self: pyrosetta.rosetta.core.chemical.rotamers.DunbrackRotamerLibrarySpecification, aa: pyrosetta.rosetta.core.chemical.AA) → None¶: C++: core::chemical::rotamers::DunbrackRotamerLibrarySpecification::aa(enum core::chemical::AA) –> void

assign(self: pyrosetta.rosetta.core.chemical.rotamers.DunbrackRotamerLibrarySpecification, : pyrosetta.rosetta.core.chemical.rotamers.DunbrackRotamerLibrarySpecification) → pyrosetta.rosetta.core.chemical.rotamers.DunbrackRotamerLibrarySpecification¶: C++: core::chemical::rotamers::DunbrackRotamerLibrarySpecification::operator=(const class core::chemical::rotamers::DunbrackRotamerLibrarySpecification &) –> class core::chemical::rotamers::DunbrackRotamerLibrarySpecification &

cache_tag(self: pyrosetta.rosetta.core.chemical.rotamers.DunbrackRotamerLibrarySpecification, : pyrosetta.rosetta.core.chemical.ResidueType) → str¶

Return empty string, as Dunbrack rotamer caching happens external to the Factory caching.

C++: core::chemical::rotamers::DunbrackRotamerLibrarySpecification::cache_tag(const class core::chemical::ResidueType &) const –> std::string

clone(self: pyrosetta.rosetta.core.chemical.rotamers.DunbrackRotamerLibrarySpecification) → pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecification¶: C++: core::chemical::rotamers::DunbrackRotamerLibrarySpecification::clone() const –> class std::shared_ptr<class core::chemical::rotamers::RotamerLibrarySpecification>

describe(self: pyrosetta.rosetta.core.chemical.rotamers.DunbrackRotamerLibrarySpecification, out: pyrosetta.rosetta.std.ostream) → None¶: C++: core::chemical::rotamers::DunbrackRotamerLibrarySpecification::describe(std::ostream &) const –> void

get_aa(self: pyrosetta.rosetta.core.chemical.rotamers.DunbrackRotamerLibrarySpecification) → pyrosetta.rosetta.core.chemical.AA¶

The AA for which we’re building the Rotamer library.

C++: core::chemical::rotamers::DunbrackRotamerLibrarySpecification::get_aa() const –> enum core::chemical::AA

keyname(self: pyrosetta.rosetta.core.chemical.rotamers.DunbrackRotamerLibrarySpecification) → str¶

Which type of SingleResidueRotamerLibrary does this specification sub-type correspond to?

C++: core::chemical::rotamers::DunbrackRotamerLibrarySpecification::keyname() const –> std::string

static library_name() → str¶

Static function for access to type_name, to have a single string which is used for both: this class and for the SingleResidueRotamerLibraryCreator.

C++: core::chemical::rotamers::DunbrackRotamerLibrarySpecification::library_name() –> std::string

class pyrosetta.rosetta.core.chemical.rotamers.DunbrackRotamerLibrarySpecificationCreator¶

Bases: RotamerLibrarySpecificationCreator

assign(self: pyrosetta.rosetta.core.chemical.rotamers.DunbrackRotamerLibrarySpecificationCreator, : pyrosetta.rosetta.core.chemical.rotamers.DunbrackRotamerLibrarySpecificationCreator) → pyrosetta.rosetta.core.chemical.rotamers.DunbrackRotamerLibrarySpecificationCreator¶: C++: core::chemical::rotamers::DunbrackRotamerLibrarySpecificationCreator::operator=(const class core::chemical::rotamers::DunbrackRotamerLibrarySpecificationCreator &) –> class core::chemical::rotamers::DunbrackRotamerLibrarySpecificationCreator &

create(*args, **kwargs)¶

Overloaded function.

create(self: pyrosetta.rosetta.core.chemical.rotamers.DunbrackRotamerLibrarySpecificationCreator) -> pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecification

C++: core::chemical::rotamers::DunbrackRotamerLibrarySpecificationCreator::create() const –> class std::shared_ptr<class core::chemical::rotamers::RotamerLibrarySpecification>

create(self: pyrosetta.rosetta.core.chemical.rotamers.DunbrackRotamerLibrarySpecificationCreator, : pyrosetta.rosetta.std.istream) -> pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecification

C++: core::chemical::rotamers::DunbrackRotamerLibrarySpecificationCreator::create(std::istream &) const –> class std::shared_ptr<class core::chemical::rotamers::RotamerLibrarySpecification>

keyname(self: pyrosetta.rosetta.core.chemical.rotamers.DunbrackRotamerLibrarySpecificationCreator) → str¶: C++: core::chemical::rotamers::DunbrackRotamerLibrarySpecificationCreator::keyname() const –> std::string

class pyrosetta.rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification¶

Bases: RotamerLibrarySpecification

add_rotamer_bb_torsion_index(self: pyrosetta.rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification, index: int) → None¶

Add a backbone torsion index that the rotamer library is dependent on.

Checks for zero or duplicated indices.

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::rotamers::NCAARotamerLibrarySpecification::add_rotamer_bb_torsion_index(const unsigned long) –> void

assign(self: pyrosetta.rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification, : pyrosetta.rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification) → pyrosetta.rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification¶: C++: core::chemical::rotamers::NCAARotamerLibrarySpecification::operator=(const class core::chemical::rotamers::NCAARotamerLibrarySpecification &) –> class core::chemical::rotamers::NCAARotamerLibrarySpecification &

cache_tag(self: pyrosetta.rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification, : pyrosetta.rosetta.core.chemical.ResidueType) → str¶: C++: core::chemical::rotamers::NCAARotamerLibrarySpecification::cache_tag(const class core::chemical::ResidueType &) const –> std::string

clear_rotamer_bb_torsion_indices(self: pyrosetta.rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification) → None¶

Empties the list of mainchain torsion indices that this rotamer library depends upon.

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::rotamers::NCAARotamerLibrarySpecification::clear_rotamer_bb_torsion_indices() –> void

clone(self: pyrosetta.rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification) → pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecification¶: C++: core::chemical::rotamers::NCAARotamerLibrarySpecification::clone() const –> class std::shared_ptr<class core::chemical::rotamers::RotamerLibrarySpecification>

describe(self: pyrosetta.rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification, out: pyrosetta.rosetta.std.ostream) → None¶: C++: core::chemical::rotamers::NCAARotamerLibrarySpecification::describe(std::ostream &) const –> void

keyname(self: pyrosetta.rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification) → str¶: C++: core::chemical::rotamers::NCAARotamerLibrarySpecification::keyname() const –> std::string

static library_name() → str¶: C++: core::chemical::rotamers::NCAARotamerLibrarySpecification::library_name() –> std::string

ncaa_rotlib_n_bin_per_rot(*args, **kwargs)¶

Overloaded function.

ncaa_rotlib_n_bin_per_rot(self: pyrosetta.rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification, n_bins_per_rot: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Sets the number of rotamers for each rotatable bond described by the NCAA rotlib

C++: core::chemical::rotamers::NCAARotamerLibrarySpecification::ncaa_rotlib_n_bin_per_rot(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

ncaa_rotlib_n_bin_per_rot(self: pyrosetta.rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification) -> pyrosetta.rosetta.utility.vector1_unsigned_long

Returns the number of rotamers for each rotatable bond described by the NCAA rotlib for all bonds

C++: core::chemical::rotamers::NCAARotamerLibrarySpecification::ncaa_rotlib_n_bin_per_rot() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

ncaa_rotlib_n_rotameric_bins(self: pyrosetta.rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification) → int¶

Returns the number of rotatable bonds described by the NCAA rotlib (not nesesarily equal to nchi)

C++: core::chemical::rotamers::NCAARotamerLibrarySpecification::ncaa_rotlib_n_rotameric_bins() const –> unsigned long

ncaa_rotlib_path(*args, **kwargs)¶

Overloaded function.

ncaa_rotlib_path(self: pyrosetta.rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification, path: str) -> None

Sets the path to the NCAA rotlib for the residue type

C++: core::chemical::rotamers::NCAARotamerLibrarySpecification::ncaa_rotlib_path(const std::string &) –> void

ncaa_rotlib_path(self: pyrosetta.rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification) -> str

Returns the path to the NCAA rotlib for the residue type

C++: core::chemical::rotamers::NCAARotamerLibrarySpecification::ncaa_rotlib_path() const –> const std::string &

nrchi_start_angle(*args, **kwargs)¶

Overloaded function.

nrchi_start_angle(self: pyrosetta.rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification, setting: float) -> None

C++: core::chemical::rotamers::NCAARotamerLibrarySpecification::nrchi_start_angle(double) –> void

nrchi_start_angle(self: pyrosetta.rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification) -> float

C++: core::chemical::rotamers::NCAARotamerLibrarySpecification::nrchi_start_angle() const –> double

nrchi_symmetric(*args, **kwargs)¶

Overloaded function.

nrchi_symmetric(self: pyrosetta.rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification, setting: bool) -> None

C++: core::chemical::rotamers::NCAARotamerLibrarySpecification::nrchi_symmetric(bool) –> void

nrchi_symmetric(self: pyrosetta.rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification) -> bool

C++: core::chemical::rotamers::NCAARotamerLibrarySpecification::nrchi_symmetric() const –> bool

rotamer_bb_torsion_indices(self: pyrosetta.rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification) → pyrosetta.rosetta.utility.vector1_unsigned_long¶

Get a const reference to the list of mainchain torsion indices that this rotamer library depends upon.

Vikram K. Mulligan (vmullig.edu).

C++: core::chemical::rotamers::NCAARotamerLibrarySpecification::rotamer_bb_torsion_indices() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

semirotameric_ncaa_rotlib(*args, **kwargs)¶

Overloaded function.

semirotameric_ncaa_rotlib(self: pyrosetta.rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification, setting: bool) -> None

C++: core::chemical::rotamers::NCAARotamerLibrarySpecification::semirotameric_ncaa_rotlib(bool) –> void

semirotameric_ncaa_rotlib(self: pyrosetta.rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification) -> bool

C++: core::chemical::rotamers::NCAARotamerLibrarySpecification::semirotameric_ncaa_rotlib() const –> bool

class pyrosetta.rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecificationCreator¶

Bases: RotamerLibrarySpecificationCreator

assign(self: pyrosetta.rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecificationCreator, : pyrosetta.rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecificationCreator) → pyrosetta.rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecificationCreator¶: C++: core::chemical::rotamers::NCAARotamerLibrarySpecificationCreator::operator=(const class core::chemical::rotamers::NCAARotamerLibrarySpecificationCreator &) –> class core::chemical::rotamers::NCAARotamerLibrarySpecificationCreator &

create(*args, **kwargs)¶

Overloaded function.

create(self: pyrosetta.rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecificationCreator) -> pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecification

C++: core::chemical::rotamers::NCAARotamerLibrarySpecificationCreator::create() const –> class std::shared_ptr<class core::chemical::rotamers::RotamerLibrarySpecification>

create(self: pyrosetta.rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecificationCreator, : pyrosetta.rosetta.std.istream) -> pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecification

C++: core::chemical::rotamers::NCAARotamerLibrarySpecificationCreator::create(std::istream &) const –> class std::shared_ptr<class core::chemical::rotamers::RotamerLibrarySpecification>

keyname(self: pyrosetta.rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecificationCreator) → str¶: C++: core::chemical::rotamers::NCAARotamerLibrarySpecificationCreator::keyname() const –> std::string

class pyrosetta.rosetta.core.chemical.rotamers.PDBRotamerLibrarySpecification¶

Bases: RotamerLibrarySpecification

assign(self: pyrosetta.rosetta.core.chemical.rotamers.PDBRotamerLibrarySpecification, : pyrosetta.rosetta.core.chemical.rotamers.PDBRotamerLibrarySpecification) → pyrosetta.rosetta.core.chemical.rotamers.PDBRotamerLibrarySpecification¶: C++: core::chemical::rotamers::PDBRotamerLibrarySpecification::operator=(const class core::chemical::rotamers::PDBRotamerLibrarySpecification &) –> class core::chemical::rotamers::PDBRotamerLibrarySpecification &

cache_tag(self: pyrosetta.rosetta.core.chemical.rotamers.PDBRotamerLibrarySpecification, : pyrosetta.rosetta.core.chemical.ResidueType) → str¶: C++: core::chemical::rotamers::PDBRotamerLibrarySpecification::cache_tag(const class core::chemical::ResidueType &) const –> std::string

clone(self: pyrosetta.rosetta.core.chemical.rotamers.PDBRotamerLibrarySpecification) → pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecification¶: C++: core::chemical::rotamers::PDBRotamerLibrarySpecification::clone() const –> class std::shared_ptr<class core::chemical::rotamers::RotamerLibrarySpecification>

describe(self: pyrosetta.rosetta.core.chemical.rotamers.PDBRotamerLibrarySpecification, out: pyrosetta.rosetta.std.ostream) → None¶: C++: core::chemical::rotamers::PDBRotamerLibrarySpecification::describe(std::ostream &) const –> void

keyname(self: pyrosetta.rosetta.core.chemical.rotamers.PDBRotamerLibrarySpecification) → str¶: C++: core::chemical::rotamers::PDBRotamerLibrarySpecification::keyname() const –> std::string

static library_name() → str¶: C++: core::chemical::rotamers::PDBRotamerLibrarySpecification::library_name() –> std::string

pdb_rotamers_file(*args, **kwargs)¶

Overloaded function.

pdb_rotamers_file(self: pyrosetta.rosetta.core.chemical.rotamers.PDBRotamerLibrarySpecification) -> str

C++: core::chemical::rotamers::PDBRotamerLibrarySpecification::pdb_rotamers_file() const –> const std::string &

pdb_rotamers_file(self: pyrosetta.rosetta.core.chemical.rotamers.PDBRotamerLibrarySpecification, filename: str) -> None

C++: core::chemical::rotamers::PDBRotamerLibrarySpecification::pdb_rotamers_file(const std::string &) –> void

class pyrosetta.rosetta.core.chemical.rotamers.PDBRotamerLibrarySpecificationCreator¶

Bases: RotamerLibrarySpecificationCreator

assign(self: pyrosetta.rosetta.core.chemical.rotamers.PDBRotamerLibrarySpecificationCreator, : pyrosetta.rosetta.core.chemical.rotamers.PDBRotamerLibrarySpecificationCreator) → pyrosetta.rosetta.core.chemical.rotamers.PDBRotamerLibrarySpecificationCreator¶: C++: core::chemical::rotamers::PDBRotamerLibrarySpecificationCreator::operator=(const class core::chemical::rotamers::PDBRotamerLibrarySpecificationCreator &) –> class core::chemical::rotamers::PDBRotamerLibrarySpecificationCreator &

create(*args, **kwargs)¶

Overloaded function.

create(self: pyrosetta.rosetta.core.chemical.rotamers.PDBRotamerLibrarySpecificationCreator) -> pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecification

C++: core::chemical::rotamers::PDBRotamerLibrarySpecificationCreator::create() const –> class std::shared_ptr<class core::chemical::rotamers::RotamerLibrarySpecification>

create(self: pyrosetta.rosetta.core.chemical.rotamers.PDBRotamerLibrarySpecificationCreator, : pyrosetta.rosetta.std.istream) -> pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecification

C++: core::chemical::rotamers::PDBRotamerLibrarySpecificationCreator::create(std::istream &) const –> class std::shared_ptr<class core::chemical::rotamers::RotamerLibrarySpecification>

keyname(self: pyrosetta.rosetta.core.chemical.rotamers.PDBRotamerLibrarySpecificationCreator) → str¶: C++: core::chemical::rotamers::PDBRotamerLibrarySpecificationCreator::keyname() const –> std::string

class pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecification¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecification, : pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecification) → pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecification¶: C++: core::chemical::rotamers::RotamerLibrarySpecification::operator=(const class core::chemical::rotamers::RotamerLibrarySpecification &) –> class core::chemical::rotamers::RotamerLibrarySpecification &

cache_tag(self: pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecification, : pyrosetta.rosetta.core.chemical.ResidueType) → str¶

How, if at all, should the corresponding SingleResidueRotamerLibrary be cached?

The default is to return an empty string, which turns off caching.

The SingleResidueRotamerLibraries are cached in the SingleResidueRotamerLibraryFactory based on keyname() and cache_tag() (as keys in a map< string, map< string, SRRL > > ). Two RotamerLibrarySpecifications with identical return values for keyname() and cache_tag() should correspond to (functionally) identical SingleResidueRotamerLibraries.

This has to be in the RotamerLibrarySpecification, as when reading we need to know the cache string before creating the library.

A note on writing RotamerLibrarySpecifications and SingleResidueRotamerLibrarys: The functions of a SingleResidueRotamerLibrary will normally have access to the actual RotamerLibrarySpecification from the passed Residue/ResidueType. Therefore, you don’t need to store all the information from a RLS in the SRRL. Not doing so allows you to have more general cache_tag(), as the cache_tag() function only needs to disambiguate RotamerLibrarySpecifications which result in different SingleResidueRotamerLibrarys. (That is, cache_tag() only needs to encapsulate data used by SingleResidueRotamerLibraryCreator to create the SingleResidueRotamerLibrary.)

The ResidueType is passed to cache_tag() so that if the SingleResidueRotamerLibraryCreator needs details from the ResidueType in order to correctly create the SingleResidueRotamerLibrary, that information can be extracted. In general, though, you want to avoid keying off of information in ResidueType as much as possible.

C++: core::chemical::rotamers::RotamerLibrarySpecification::cache_tag(const class core::chemical::ResidueType &) const –> std::string

clone(self: pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecification) → pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecification¶

Create a copy of the RotamerLibrarySpecification, respecting the subclassing

C++: core::chemical::rotamers::RotamerLibrarySpecification::clone() const –> class std::shared_ptr<class core::chemical::rotamers::RotamerLibrarySpecification>

describe(self: pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecification, out: pyrosetta.rosetta.std.ostream) → None¶

Write a params-file-like description of this RotamerLibrarySpecification to the given output stream.: Can be multi-line, will be ended with a newline.

C++: core::chemical::rotamers::RotamerLibrarySpecification::describe(std::ostream &) const –> void

keyname(self: pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecification) → str¶

Which type of SingleResidueRotamerLibrary does this specification sub-type correspond to?

C++: core::chemical::rotamers::RotamerLibrarySpecification::keyname() const –> std::string

class pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecificationCreator¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecificationCreator, : pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecificationCreator) → pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecificationCreator¶: C++: core::chemical::rotamers::RotamerLibrarySpecificationCreator::operator=(const class core::chemical::rotamers::RotamerLibrarySpecificationCreator &) –> class core::chemical::rotamers::RotamerLibrarySpecificationCreator &

create(*args, **kwargs)¶

Overloaded function.

create(self: pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecificationCreator) -> pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecification

C++: core::chemical::rotamers::RotamerLibrarySpecificationCreator::create() const –> class std::shared_ptr<class core::chemical::rotamers::RotamerLibrarySpecification>

create(self: pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecificationCreator, : pyrosetta.rosetta.std.istream) -> pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecification

C++: core::chemical::rotamers::RotamerLibrarySpecificationCreator::create(std::istream &) const –> class std::shared_ptr<class core::chemical::rotamers::RotamerLibrarySpecification>

keyname(self: pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecificationCreator) → str¶: C++: core::chemical::rotamers::RotamerLibrarySpecificationCreator::keyname() const –> std::string

class pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecificationFactory¶

Bases: SingletonBase_core_chemical_rotamers_RotamerLibrarySpecificationFactory_t

factory_register(self: pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecificationFactory, creator: pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecificationCreator) → None¶: C++: core::chemical::rotamers::RotamerLibrarySpecificationFactory::factory_register(class std::shared_ptr<class core::chemical::rotamers::RotamerLibrarySpecificationCreator>) –> void

get(*args, **kwargs)¶

Overloaded function.

get(self: pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecificationFactory, : str) -> pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecification

C++: core::chemical::rotamers::RotamerLibrarySpecificationFactory::get(const std::string &) const –> class std::shared_ptr<class core::chemical::rotamers::RotamerLibrarySpecification>

get(self: pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecificationFactory, : str, : pyrosetta.rosetta.std.istream) -> pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecification

C++: core::chemical::rotamers::RotamerLibrarySpecificationFactory::get(const std::string &, std::istream &) const –> class std::shared_ptr<class core::chemical::rotamers::RotamerLibrarySpecification>

static get_instance() → core::chemical::rotamers::RotamerLibrarySpecificationFactory¶: C++: utility::SingletonBase<core::chemical::rotamers::RotamerLibrarySpecificationFactory>::get_instance() –> class core::chemical::rotamers::RotamerLibrarySpecificationFactory *

has_type(self: pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecificationFactory, : str) → bool¶: C++: core::chemical::rotamers::RotamerLibrarySpecificationFactory::has_type(const std::string &) const –> bool

class pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification¶

Bases: RotamerLibrarySpecification

A class which stores atom coordinates for a rotamer library. Internally, this is stored as a list of name:coordinate maps.

This is intended as an analog to PDBRotamerLibrarySpecifications for those instances where the coordinates are generated internally or programmatically.

add_rotamer(self: pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification, rotamer: pyrosetta.rosetta.std.map_std_string_numeric_xyzVector_double_t_std_allocator_std_pair_const_std_string_numeric_xyzVector_double_t) → None¶

Add a particular rotamer to the list

C++: core::chemical::rotamers::StoredRotamerLibrarySpecification::add_rotamer(const class std::map<std::string, class numeric::xyzVector<double>, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class numeric::xyzVector<double> > > > &) –> void

add_rotamers(self: pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification, rotamers: pyrosetta.rosetta.utility.vector1_std_map_std_string_numeric_xyzVector_double_std_less_std_string_std_allocator_std_pair_const_std_string_numeric_xyzVector_double_t) → None¶

Add vector of rotamers to list

C++: core::chemical::rotamers::StoredRotamerLibrarySpecification::add_rotamers(const class utility::vector1<class std::map<std::string, class numeric::xyzVector<double>, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class numeric::xyzVector<double> > > >, class std::allocator<class std::map<std::string, class numeric::xyzVector<double>, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class numeric::xyzVector<double> > > > > > &) –> void

assign(self: pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification, : pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification) → pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification¶: C++: core::chemical::rotamers::StoredRotamerLibrarySpecification::operator=(const class core::chemical::rotamers::StoredRotamerLibrarySpecification &) –> class core::chemical::rotamers::StoredRotamerLibrarySpecification &

cache_tag(self: pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecification, : pyrosetta.rosetta.core.chemical.ResidueType) → str¶

How, if at all, should the corresponding SingleResidueRotamerLibrary be cached?

The default is to return an empty string, which turns off caching.

The SingleResidueRotamerLibraries are cached in the SingleResidueRotamerLibraryFactory based on keyname() and cache_tag() (as keys in a map< string, map< string, SRRL > > ). Two RotamerLibrarySpecifications with identical return values for keyname() and cache_tag() should correspond to (functionally) identical SingleResidueRotamerLibraries.

This has to be in the RotamerLibrarySpecification, as when reading we need to know the cache string before creating the library.

A note on writing RotamerLibrarySpecifications and SingleResidueRotamerLibrarys: The functions of a SingleResidueRotamerLibrary will normally have access to the actual RotamerLibrarySpecification from the passed Residue/ResidueType. Therefore, you don’t need to store all the information from a RLS in the SRRL. Not doing so allows you to have more general cache_tag(), as the cache_tag() function only needs to disambiguate RotamerLibrarySpecifications which result in different SingleResidueRotamerLibrarys. (That is, cache_tag() only needs to encapsulate data used by SingleResidueRotamerLibraryCreator to create the SingleResidueRotamerLibrary.)

The ResidueType is passed to cache_tag() so that if the SingleResidueRotamerLibraryCreator needs details from the ResidueType in order to correctly create the SingleResidueRotamerLibrary, that information can be extracted. In general, though, you want to avoid keying off of information in ResidueType as much as possible.

C++: core::chemical::rotamers::RotamerLibrarySpecification::cache_tag(const class core::chemical::ResidueType &) const –> std::string

clone(self: pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification) → pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecification¶: C++: core::chemical::rotamers::StoredRotamerLibrarySpecification::clone() const –> class std::shared_ptr<class core::chemical::rotamers::RotamerLibrarySpecification>

coordinates(self: pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification) → pyrosetta.rosetta.utility.vector1_std_map_std_string_numeric_xyzVector_double_std_less_std_string_std_allocator_std_pair_const_std_string_numeric_xyzVector_double_t¶: C++: core::chemical::rotamers::StoredRotamerLibrarySpecification::coordinates() const –> const class utility::vector1<class std::map<std::string, class numeric::xyzVector<double>, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class numeric::xyzVector<double> > > >, class std::allocator<class std::map<std::string, class numeric::xyzVector<double>, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class numeric::xyzVector<double> > > > > > &

describe(self: pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification, out: pyrosetta.rosetta.std.ostream) → None¶: C++: core::chemical::rotamers::StoredRotamerLibrarySpecification::describe(std::ostream &) const –> void

get_reference_energy(self: pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification) → float¶: C++: core::chemical::rotamers::StoredRotamerLibrarySpecification::get_reference_energy() const –> double

keyname(self: pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification) → str¶: C++: core::chemical::rotamers::StoredRotamerLibrarySpecification::keyname() const –> std::string

static library_name() → str¶: C++: core::chemical::rotamers::StoredRotamerLibrarySpecification::library_name() –> std::string

set_reference_energy(self: pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification, ref_E_in: float) → None¶: C++: core::chemical::rotamers::StoredRotamerLibrarySpecification::set_reference_energy(double) –> void

set_rotamers(self: pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification, confs: pyrosetta.rosetta.utility.vector1_std_map_std_string_numeric_xyzVector_double_std_less_std_string_std_allocator_std_pair_const_std_string_numeric_xyzVector_double_t) → None¶

Set the coordinates list in an all-at-once fashion

C++: core::chemical::rotamers::StoredRotamerLibrarySpecification::set_rotamers(const class utility::vector1<class std::map<std::string, class numeric::xyzVector<double>, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class numeric::xyzVector<double> > > >, class std::allocator<class std::map<std::string, class numeric::xyzVector<double>, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class numeric::xyzVector<double> > > > > > &) –> void

class pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecificationCreator¶

Bases: RotamerLibrarySpecificationCreator

assign(self: pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecificationCreator, : pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecificationCreator) → pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecificationCreator¶: C++: core::chemical::rotamers::StoredRotamerLibrarySpecificationCreator::operator=(const class core::chemical::rotamers::StoredRotamerLibrarySpecificationCreator &) –> class core::chemical::rotamers::StoredRotamerLibrarySpecificationCreator &

create(*args, **kwargs)¶

Overloaded function.

create(self: pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecificationCreator) -> pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecification

C++: core::chemical::rotamers::StoredRotamerLibrarySpecificationCreator::create() const –> class std::shared_ptr<class core::chemical::rotamers::RotamerLibrarySpecification>

create(self: pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecificationCreator, : pyrosetta.rosetta.std.istream) -> pyrosetta.rosetta.core.chemical.rotamers.RotamerLibrarySpecification

C++: core::chemical::rotamers::StoredRotamerLibrarySpecificationCreator::create(std::istream &) const –> class std::shared_ptr<class core::chemical::rotamers::RotamerLibrarySpecification>

keyname(self: pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecificationCreator) → str¶: C++: core::chemical::rotamers::StoredRotamerLibrarySpecificationCreator::keyname() const –> std::string

pyrosetta.rosetta.core.chemical.rotamers.deep_copy(source: core::chemical::rotamers::RotamerLibrarySpecification) → core::chemical::rotamers::RotamerLibrarySpecification¶: C++: core::chemical::rotamers::deep_copy(const class core::chemical::rotamers::RotamerLibrarySpecification &) –> class std::shared_ptr<class core::chemical::rotamers::RotamerLibrarySpecification>