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- builtins.object
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- RotamerLibrarySpecification
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- BasicRotamerLibrarySpecification
- CenrotRotamerLibrarySpecification
- DunbrackRotamerLibrarySpecification
- NCAARotamerLibrarySpecification
- PDBRotamerLibrarySpecification
- PeptoidRotamerLibrarySpecification
- StoredRotamerLibrarySpecification
- RotamerLibrarySpecificationCreator
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- BasicRotamerLibrarySpecificationCreator
- CenrotRotamerLibrarySpecificationCreator
- DunbrackRotamerLibrarySpecificationCreator
- NCAARotamerLibrarySpecificationCreator
- PDBRotamerLibrarySpecificationCreator
- PeptoidRotamerLibrarySpecificationCreator
- StoredRotamerLibrarySpecificationCreator
- rosetta.utility.SingletonBase_core_chemical_rotamers_RotamerLibrarySpecificationFactory_t(builtins.object)
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- RotamerLibrarySpecificationFactory
class NCAARotamerLibrarySpecification(RotamerLibrarySpecification) |
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- Method resolution order:
- NCAARotamerLibrarySpecification
- RotamerLibrarySpecification
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, ncaa_rotlib_path : str) -> NoneType
3. __init__(self : handle, : std::istream) -> NoneType
4. __init__(handle, rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification, : rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification) -> rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification
- cache_tag(...) from builtins.PyCapsule
- cache_tag(self : rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification, : rosetta.core.chemical.ResidueType) -> str
- keyname(...) from builtins.PyCapsule
- keyname(rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification) -> str
- library_name(...) from builtins.PyCapsule
- library_name() -> str
- ncaa_rotlib_n_bin_per_rot(...) from builtins.PyCapsule
- ncaa_rotlib_n_bin_per_rot(*args, **kwargs)
Overloaded function.
1. ncaa_rotlib_n_bin_per_rot(self : rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification, n_bins_per_rot : rosetta.utility.vector1_unsigned_long) -> NoneType
Sets the number of rotamers for each rotatable bond described by the NCAA rotlib
2. ncaa_rotlib_n_bin_per_rot(rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification) -> rosetta.utility.vector1_unsigned_long
Returns the number of rotamers for each rotatable bond described by the NCAA rotlib for all bonds
- ncaa_rotlib_n_rotameric_bins(...) from builtins.PyCapsule
- ncaa_rotlib_n_rotameric_bins(rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification) -> int
Returns the number of rotatable bonds described by the NCAA rotlib (not nesesarily equal to nchi)
- ncaa_rotlib_path(...) from builtins.PyCapsule
- ncaa_rotlib_path(*args, **kwargs)
Overloaded function.
1. ncaa_rotlib_path(self : rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification, path : str) -> NoneType
Sets the path to the NCAA rotlib for the residue type
2. ncaa_rotlib_path(rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification) -> str
Returns the path to the NCAA rotlib for the residue type
- nrchi_start_angle(...) from builtins.PyCapsule
- nrchi_start_angle(*args, **kwargs)
Overloaded function.
1. nrchi_start_angle(self : rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification, setting : float) -> NoneType
2. nrchi_start_angle(rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification) -> float
- nrchi_symmetric(...) from builtins.PyCapsule
- nrchi_symmetric(*args, **kwargs)
Overloaded function.
1. nrchi_symmetric(self : rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification, setting : bool) -> NoneType
2. nrchi_symmetric(rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification) -> bool
- semirotameric_ncaa_rotlib(...) from builtins.PyCapsule
- semirotameric_ncaa_rotlib(*args, **kwargs)
Overloaded function.
1. semirotameric_ncaa_rotlib(self : rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification, setting : bool) -> NoneType
2. semirotameric_ncaa_rotlib(rosetta.core.chemical.rotamers.NCAARotamerLibrarySpecification) -> bool
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class PeptoidRotamerLibrarySpecification(RotamerLibrarySpecification) |
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- Method resolution order:
- PeptoidRotamerLibrarySpecification
- RotamerLibrarySpecification
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, peptoid_rotlib_path : str) -> NoneType
3. __init__(self : handle, input : std::istream) -> NoneType
4. __init__(handle, rosetta.core.chemical.rotamers.PeptoidRotamerLibrarySpecification) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.chemical.rotamers.PeptoidRotamerLibrarySpecification, : rosetta.core.chemical.rotamers.PeptoidRotamerLibrarySpecification) -> rosetta.core.chemical.rotamers.PeptoidRotamerLibrarySpecification
- cache_tag(...) from builtins.PyCapsule
- cache_tag(self : rosetta.core.chemical.rotamers.PeptoidRotamerLibrarySpecification, : rosetta.core.chemical.ResidueType) -> str
- keyname(...) from builtins.PyCapsule
- keyname(rosetta.core.chemical.rotamers.PeptoidRotamerLibrarySpecification) -> str
- library_name(...) from builtins.PyCapsule
- library_name() -> str
- peptoid_rotlib_n_bin_per_rot(...) from builtins.PyCapsule
- peptoid_rotlib_n_bin_per_rot(*args, **kwargs)
Overloaded function.
1. peptoid_rotlib_n_bin_per_rot(self : rosetta.core.chemical.rotamers.PeptoidRotamerLibrarySpecification, n_bins_per_rot : rosetta.utility.vector1_unsigned_long) -> NoneType
Sets the number of rotamers for each rotatable bond described by the Peptoid rotlib
2. peptoid_rotlib_n_bin_per_rot(rosetta.core.chemical.rotamers.PeptoidRotamerLibrarySpecification) -> rosetta.utility.vector1_unsigned_long
Returns the number of rotamers for each rotatable bond described by the Peptoid rotlib for all bonds
- peptoid_rotlib_n_rotameric_bins(...) from builtins.PyCapsule
- peptoid_rotlib_n_rotameric_bins(rosetta.core.chemical.rotamers.PeptoidRotamerLibrarySpecification) -> int
Returns the number of rotatable bonds described by the Peptoid rotlib (not nesesarily equal to nchi)
- peptoid_rotlib_path(...) from builtins.PyCapsule
- peptoid_rotlib_path(*args, **kwargs)
Overloaded function.
1. peptoid_rotlib_path(self : rosetta.core.chemical.rotamers.PeptoidRotamerLibrarySpecification, path : str) -> NoneType
Sets the path to the Peptoid rotlib for the residue type
2. peptoid_rotlib_path(rosetta.core.chemical.rotamers.PeptoidRotamerLibrarySpecification) -> str
Returns the path to the Peptoid rotlib for the residue type
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class RotamerLibrarySpecification(builtins.object) |
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.core.chemical.rotamers.RotamerLibrarySpecification) -> NoneType
2. __init__(rosetta.core.chemical.rotamers.RotamerLibrarySpecification, rosetta.core.chemical.rotamers.RotamerLibrarySpecification) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.chemical.rotamers.RotamerLibrarySpecification, : rosetta.core.chemical.rotamers.RotamerLibrarySpecification) -> rosetta.core.chemical.rotamers.RotamerLibrarySpecification
- cache_tag(...) from builtins.PyCapsule
- cache_tag(self : rosetta.core.chemical.rotamers.RotamerLibrarySpecification, : 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.
- keyname(...) from builtins.PyCapsule
- keyname(rosetta.core.chemical.rotamers.RotamerLibrarySpecification) -> str
Which type of SingleResidueRotamerLibrary does this specification sub-type correspond to?
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class StoredRotamerLibrarySpecification(RotamerLibrarySpecification) |
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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.
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- Method resolution order:
- StoredRotamerLibrarySpecification
- RotamerLibrarySpecification
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, input : std::istream) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_rotamer(...) from builtins.PyCapsule
- add_rotamer(self : rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification, rotamer : rosetta.std.map_std_string_numeric_xyzVector_double_t) -> NoneType
Add a particular rotamer to the list
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification, : rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification) -> rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification
- coordinates(...) from builtins.PyCapsule
- coordinates(rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification) -> 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
- keyname(...) from builtins.PyCapsule
- keyname(rosetta.core.chemical.rotamers.StoredRotamerLibrarySpecification) -> str
- library_name(...) from builtins.PyCapsule
- library_name() -> str
Methods inherited from RotamerLibrarySpecification:
- cache_tag(...) from builtins.PyCapsule
- cache_tag(self : rosetta.core.chemical.rotamers.RotamerLibrarySpecification, : 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.
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