schrodinger.application.mopac.structure_launchers module

Currently, we assume this code is universal for all versions of MOPAC we support. i.e. on adding a support for a future MOPAC release, it should not be necessary to (substantially) modify this module.

Copyright Schrodinger, LLC. All rights reserved.

exception schrodinger.application.mopac.structure_launchers.StructureLauncherError

Bases: Exception

class schrodinger.application.mopac.structure_launchers.StructureLauncher(mopac_launcher, method, minimize=True, settings=None, keywords='')

Bases: object

A class for running MOPAC calculations on a Structure object. Typically, this should not be instantiated manually, but instead used via the MopacAPI class using the get_launcher() method etc.

CHARGE = 'CHARGE'
MMOK = 'MMOK'
NOMM = 'NOMM'
__init__(mopac_launcher, method, minimize=True, settings=None, keywords='')
Parameters

  • mopac_launcher (MopacLauncher object) – API to MOPAC backend.

  • method (module level constant) – The semi-empirical method to use for the calculation.

  • minimize (bool) – If True, minimize the molecule, otherwise calculate a single point energy.

  • settings (dict) – A settings dictionary for MOPAC input settings. If a MOPAC keyword does not take a value, set the dictionary value to True.

  • keywords (str) – A string of space-separated keywords to use directly in the MOPAC input file. Use of the settings argument is recommended over setting the keyword string directly.

setKeyword(key, value=True, raise_conflicts=False)

Set the MOPAC keyword to the provided value. If the keyword doesn’t take a value, use True. The keyword will be stored as uppercase regardless of the argument case.

Parameters

raise_conflicts – If True, raise an exception when conflicting keywords are detected. Otherwise, have the current keyword take precedence.

getValue(key)

Get the value for the provided keyword, whether it was provided a key/value pair or in a MOPAC keywords string. Note that if the keyword and value are specified as part of the keywords string, the value is always returned as a string.

If the keyword is specified but has no value, True is returned.

Raise a KeyError if the keyword isn’t defined.

delKeyword(key)

Delete the keyword from the keywords specification and the kwdict dictionary.

get_mopfile_text(structure)

Write a MOPAC input file to a StringIO buffer based on the current settings and the provided Structure object.

Parameters

structure (schrodinger.structure.Structure) – The structure to use in writing the file.

return StringIO buffer

write(structure, filename)

Write a MOPAC input file based on the current keyword argument settings and the provided Structure object.

Parameters
hasKeyword(keyword)

If the given keyword was set in the constructor keywords string or as a key in the kwdict dictionary, return True, otherwise return False.

run(structure, jobname=None, input_file=False, tmpdir='', scratch_cleanup='remove', save_output_file=False)

Run a MOPAC calculation on the provided structure given the object’s current settings.