A Linear layer with built-in nonstandard initializations. Called just like torch.nn.Linear. Implements the initializers in 1.11.4, plus

A 3D rotation. Depending on how the object is initialized, the rotation is represented by either a rotation matrix or a quate

A class representing a rigid transformation. Little more than a wrapper around two objects: a Rotation object and a [*, 3] translatio

Class representing a parsed MSA file

Returned by the parse function. Contains: mmcif_object: A MmcifObject, may be None if no chain could be successfully parsed.

An error indicating that the query can't be aligned to the template.

Class representing a template hit.

An error indicating that the hit align ratio to the query was too small.

An error indicating that a CA atom distance exceeds a threshold.

An error indicating that the hit date was after the max allowed date.

An error indicating that the hit was an exact subsequence of the query.

An error indicating that the hit was too short.

Representation of a parsed mmCIF file. Contains: file_id: A meaningful name, e.g. a pdb_id. Should be unique amongst all files bein

An error indicating that multiple chains were found for a given ID.

Python wrapper of the Jackhmmer binary.

An error indicating that template mmCIF didn't contain atom positions.

An error indicating that template mmCIF didn't have any chains.

An error indicating that template mmCIF didn't contain the sequence.

An error indicating that template mmCIF had all atom positions masked.

Base class for exceptions.

Base class for exceptions.

Python wrapper of the HHblits binary.

Python wrapper of the HHsearch binary.

Python wrapper of the hmmbuild binary.

Python wrapper of the hmmsearch binary.

Python wrapper of the Jackhmmer binary.

Python wrapper of the Kalign binary.

An error indicating that an mmCIF file could not be parsed.

A base class for template prefilter exceptions.

An abstract base class for turning template hits to features.