rotamers

Bindings for core::chemical::rotamers namespace

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

Bases: pyrosetta.rosetta.core.chemical.rotamers.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.

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification) -> None
2. __init__(self: pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification, input: pyrosetta.rosetta.std.istream) -> None

__init_subclass__()

This method is called when a class is subclassed.

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

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

add_rotamer(self: pyrosetta.rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification, rotamer: pyrosetta.rosetta.std.map_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<class std::basic_string<char>, class numeric::xyzVector<double>, struct std::less<class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, 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<class std::basic_string<char>, class numeric::xyzVector<double>, struct std::less<class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class numeric::xyzVector<double> > > >, class std::allocator<class std::map<class std::basic_string<char>, class numeric::xyzVector<double>, struct std::less<class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, 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

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> > > > > > &

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

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