csb.bio.io.wwpdb.AsyncStructureParser

Wraps StructureParser in an asynchronous call. Since a new process is started by Python internally (as opposed to only starting a new thread), this makes the parser slower, but provides a way to set a parse timeout limit.

If initialized with more than one worker, supports parallel parsing through the self.parse_async method.

init(self, workers=1)
(Constructor)

source code

x.__init__(...) initializes x; see help(type(x)) for signature

Parameters:

workers (int) - number of worker threads (1 by default)

Overrides: object.__init__

(inherited documentation)

parse_async(self, structure_files, timeout, model=None, parser=<class 'csb.bio.io.wwpdb.RegularStructureParser'>)

source code

Call self.parse_structure for a list of structure files simultaneously. The actual degree of parallelism will depend on the number of workers specified while constructing the parser object.

Parameters:

structure_files (tuple of str) - a list of structure files
timeout (int) - raise multiprocessing.TimeoutError if timeout seconds elapse before the parser completes its job
parser (type) - any implementing AbstractStructureParser class

Returns: list

a list of AsyncParseResult objects

Note: Don't be tempted to pass a large list of structures to this method. Every time a TimeoutError is encountered, the corresponding worker process in the pool will hang until the process terminates on its own. During that time, this worker is unusable. If a sufficiently high number of timeouts occur, the whole pool of workers will be unsable. At the end of the method however a pool cleanup is performed and any unusable workers are 'reactivated'. However, that only happens at the end of parse_async.

parse_structure(self, structure_file, timeout, model=None, parser=<class 'csb.bio.io.wwpdb.RegularStructureParser'>)

source code

Call StructureParser.parse_structure() in a separate process and return the output. Raise TimeoutError if the parser does not respond within timeout seconds.

Parameters:

structure_file (str) - structure file to parse
timeout (int) - raise multiprocessing.TimeoutError if timeout seconds elapse before the parser completes its job
parser (type) - any implementing AbstractStructureParser class

Returns: csb.structure.Structure

parsed structure

Properties
Inherited from `object`: `__class__`

Class AsyncStructureParser

__init__(self, workers=1) (Constructor)

parse_async(self, structure_files, timeout, model=None, parser=<class 'csb.bio.io.wwpdb.RegularStructureParser'>)

parse_structure(self, structure_file, timeout, model=None, parser=<class 'csb.bio.io.wwpdb.RegularStructureParser'>)

init(self, workers=1)
(Constructor)