Data structures

modpipe.serialize – Serialization of data structures

This module contains classes that represent some fundamental objects used in ModPipe (such as a Hit or Model). It also contains methods to serialize these objects, i.e. to write them out to or read them in from files (or any file-like object).

class modpipe.serialize.Hit(id, sequence, alignment, region, fold_assignment_method, highest_sequence_identity, templates)

Representation of a single hit found by ModPipe.

class modpipe.serialize.Model(id, sequence, alignment, region, fold_assignment_method, hetatms, waters, score, highest_sequence_identity, rating, templates)

Representation of a single model generated by ModPipe.

modpipe.serialize.write_hits_file(hits, stream, append=False)

Write a list of Hit objects to the given stream. If append is set to True, no version header is written to the stream (it is assumed that the header is already there).

modpipe.serialize.write_models_file(models, stream, append=False, separator=False)

Write a list of Model objects to the given stream. If append is set to True, no version header is written to the stream (it is assumed that the header is already there). If separator is set to True, then “—” will be written before the appended models.

modpipe.serialize.read_hits_file(stream)

Read and return a list of Hit objects from the given stream, as a generator. Some checking is done to make sure the file is valid YAML format (e.g. that the file starts with a version header, and that each object is really a Hit.)

modpipe.serialize.read_models_file(stream)

Read and return a list of Model objects from the given stream, as a generator. Some checking is done to make sure the file is valid YAML format (e.g. that the file starts with a version header, and that each object is really a Model.)

For an example of using this module, see Using ModPipe from your own programs.