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
structure (schrodinger.structure.Structure) – The structure to use in writing the file.
filename (str) – The name of the file to be written.
- 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.