Helpers (chemistry_files.helpers)

Based on possible_file_extensions() and attempt_identification() of WithIdentificationMixin , the helpers submodule helps to open any chemistry files.

exception qcip_tools.chemistry_files.helpers.ProbablyNotAChemistryFile

Raised when the type of the file is not recognized

qcip_tools.chemistry_files.helpers.create_open_chemistry_file_action(must_be=None)

Create a custom argparse action.

from qcip_tools.chemistry_files import helpers, gaussian

parser = argparse.ArgumentParser()
parser.add_argument('-a', action=helpers.create_open_chemistry_file_action())
parser.add_argument('-b', action=helpers.create_open_chemistry_file_action(must_be=[gaussian.Input]))

String (or list) is parsed, and identifier can be added with IDENTIFIER:/path/to/file. Valid identifier are the values of file_type in the different ChemistryFile objects (a list can be found in the table on the beginning of this section).

Parameters:

must_be (list) – restrict the list of possibilities

Return type:

argparse.Action

qcip_tools.chemistry_files.helpers.identifiable_chemistry_file_objects(identifier_must_be=None)

Yield all objects with the WithIdentificationMixin.

Parameters:

identifier_must_be (list of str) – check if file_type is of the same type as the obj

qcip_tools.chemistry_files.helpers.open_chemistry_file(f, must_be=None, trust_extension=False)

Try to recognise a file in the different possibility, and return the (normally) correct class.

Note

Despite the fact that it uses the file extension to pre-sort the possibilities, the performances are bad.

Note

Use the trick from https://stackoverflow.com/a/31123030 to serve a binary file if needed.

Parameters:

• f (file) – file

• must_be (list) – restrict the list of possibilities

• trust_extension (bool) – do not run a second pass on every other possibility if the content does not match extension

Return type:

qcip_tools.chemistry_files.ChemistryFile