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.

exception schrodinger.application.mopac.structure_launchers.StructureLauncherError¶

Bases: Exception

__cause__¶: exception cause

__class__¶: alias of builtins.type

__context__¶: exception context

__delattr__¶: Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.mopac.structure_launchers', '__weakref__': <attribute '__weakref__' of 'StructureLauncherError' objects>, '__doc__': None})¶

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__¶: Initialize self. See help(type(self)) for accurate signature.

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__module__ = 'schrodinger.application.mopac.structure_launchers'¶

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__setstate__()¶

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__suppress_context__¶

__traceback__¶

__weakref__¶: list of weak references to the object (if defined)

args¶

with_traceback()¶: Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

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.

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.

__class__¶: alias of builtins.type

__delattr__¶: Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.mopac.structure_launchers', '__doc__': '\n A class for running MOPAC calculations on a Structure object.\n Typically, this should not be instantiated manually, but instead\n used via the MopacAPI class using the get_launcher() method etc.\n ', 'CHARGE': 'CHARGE', 'MMOK': 'MMOK', 'NOMM': 'NOMM', '__init__': <function StructureLauncher.__init__>, 'setKeyword': <function StructureLauncher.setKeyword>, 'getValue': <function StructureLauncher.getValue>, 'delKeyword': <function StructureLauncher.delKeyword>, 'write': <function StructureLauncher.write>, 'hasKeyword': <function StructureLauncher.hasKeyword>, 'run': <function StructureLauncher.run>, '__dict__': <attribute '__dict__' of 'StructureLauncher' objects>, '__weakref__': <attribute '__weakref__' of 'StructureLauncher' objects>})¶

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).