schrodinger.application.mopac.mopac_launchers module

This module contains classes for launching different MOPAC versions.

exception schrodinger.application.mopac.mopac_launchers.MopacLicenseError

Bases: Exception

__cause__

exception cause

__class__

alias of builtins.type

__context__

exception context

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.mopac.mopac_launchers', '__weakref__': <attribute '__weakref__' of 'MopacLicenseError' 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.mopac_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.mopac_launchers.MopacLauncher

Bases: object

This abstract base class (ABC) is designed to guide developers writing code to support future MOPAC releases. It shouldn’t be instantiated.

The intention is that a new release will require a new MopacLauncher subclass and this ABC documents the required interface to be automatically compliant with the legacy code.

There are currently two subclasses:
  1. MopacLauncher71 - launches a customized open source Mopac 7.1
  2. MopacLauncherMain - launches the currently supported version of Mopac
default_method
valid_methods
method_synonyms
extra_keywords
results
run(inputfile, structure=None)

Run a MOPAC calculation in the local directory. The optional Structure object is updated with the output data.

Parameters:inputfile (str) – name of MOPAC .mop input file
Return type:MopacResults object
write_mop_file(ct, mopfile, method=None, geopt=True, keywords='', plotMO=None, gridres=None, gridext=None)

Write a new .mop MOPAC input file based on a Structure object and input keywords and settings.

Parameters:
  • ct (schrodinger.structure.Structure) – The structure to use in writing the file.
  • mopfile (str) – name of .mop file to write.
  • method (str) – The semi-empirical method to use for the calculation.
  • geopt (bool) – If True, find the minimum energy geometry.
  • keywords (str) – Space-separated keywords to use in MOPAC input file.
  • plotMO (int) – Plot <n> MOs around the HOMO/LUMO gap.
  • gridres (float) – Grid resolution for plots.
  • gridext (float) – Grid size beyond the nuclei.
__abstractmethods__ = frozenset({'valid_methods', 'run', 'results', 'default_method', 'extra_keywords', 'write_mop_file', 'method_synonyms'})
__class__

alias of abc.ABCMeta

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.mopac.mopac_launchers', '__doc__': "\n This abstract base class (ABC) is designed to guide developers writing\n code to support future MOPAC releases.\n It shouldn't be instantiated.\n\n The intention is that a new release will require a new MopacLauncher\n subclass and this ABC documents the required interface to be automatically\n compliant with the legacy code.\n\n There are currently two subclasses:\n (1) MopacLauncher71 - launches a customized open source Mopac 7.1\n (2) MopacLauncherMain - launches the currently supported version of Mopac\n ", 'default_method': <abc.abstractproperty object>, 'valid_methods': <abc.abstractproperty object>, 'method_synonyms': <abc.abstractproperty object>, 'extra_keywords': <abc.abstractproperty object>, 'results': <abc.abstractproperty object>, 'run': <function MopacLauncher.run>, 'write_mop_file': <function MopacLauncher.write_mop_file>, '__dict__': <attribute '__dict__' of 'MopacLauncher' objects>, '__weakref__': <attribute '__weakref__' of 'MopacLauncher' objects>, '__abstractmethods__': frozenset({'valid_methods', 'run', 'results', 'default_method', 'extra_keywords', 'write_mop_file', 'method_synonyms'}), '_abc_registry': <_weakrefset.WeakSet object>, '_abc_cache': <_weakrefset.WeakSet object>, '_abc_negative_cache': <_weakrefset.WeakSet object>, '_abc_negative_cache_version': 49})
__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.mopac_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).

__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).

__weakref__

list of weak references to the object (if defined)

class schrodinger.application.mopac.mopac_launchers.MopacLauncher71

Bases: schrodinger.application.mopac.mopac_launchers.MopacLauncher

This is the API for executing the MOPAC7.1 backend compiled from source, where we link to a shared library.

__init__()

Initialize self. See help(type(self)) for accurate signature.

default_method
valid_methods
method_synonyms
extra_keywords
results
write_mop_file(ct, mopfile, method='MNDO', geopt=True, keywords='', plotMO=None, gridres=None, gridext=None)

Write a new .mop MOPAC input file based on a Structure object and input keywords and settings.

Parameters:
  • ct (schrodinger.structure.Structure) – The structure to use in writing the file.
  • mopfile (str) – name of .mop file to write.
  • method (str) – The semi-empirical method to use for the calculation.
  • geopt (bool) – If True, find the minimum energy geometry.
  • keywords (str) – Space-separated keywords to use in MOPAC input file.
  • plotMO (int) – Plot <n> MOs around the HOMO/LUMO gap.
  • gridres (float) – Grid resolution for plots.
  • gridext (float) – Grid size beyond the nuclei.
run(inputfile, structure=None)

Run a MOPAC calculation in the local directory with a .mop input file. The optional Structure object is updated with the output data. Return a MopacResults object.

__abstractmethods__ = frozenset()
__class__

alias of abc.ABCMeta

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.mopac.mopac_launchers', '__doc__': '\n This is the API for executing the MOPAC7.1 backend compiled from source,\n where we link to a shared library.\n ', '_default_method': 'MNDO', '_valid_methods': ['AM1', 'MNDO', 'MNDOD', 'PM3', 'RM1'], '_method_synonyms': {'MNDO-D': 'MNDOD', 'MNDO/D': 'MNDOD'}, '__init__': <function MopacLauncher71.__init__>, 'default_method': <property object>, 'valid_methods': <property object>, 'method_synonyms': <property object>, 'extra_keywords': <property object>, 'results': <property object>, 'write_mop_file': <function MopacLauncher71.write_mop_file>, 'run': <function MopacLauncher71.run>, '__abstractmethods__': frozenset(), '_abc_registry': <_weakrefset.WeakSet object>, '_abc_cache': <_weakrefset.WeakSet object>, '_abc_negative_cache': <_weakrefset.WeakSet object>, '_abc_negative_cache_version': 49})
__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_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.mopac_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).

__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).

__weakref__

list of weak references to the object (if defined)

class schrodinger.application.mopac.mopac_launchers.MopacLauncherMain

Bases: schrodinger.application.mopac.mopac_launchers.MopacLauncher

This is the API for executing the backend of the currently supported version of MOPAC as an external binary.

MOPAC_EXEC = 'MOPAC2016.exe'
__init__()

Initialize self. See help(type(self)) for accurate signature.

default_method
valid_methods
method_synonyms
extra_keywords
results
write_mop_file(ct, mopfile, method='RM1', geopt=True, keywords='', plotMO=None, gridres=None, gridext=None)

Write a new .mop MOPAC input file based on a Structure object and input keywords and settings.

Parameters:
  • ct (schrodinger.structure.Structure) – The structure to use in writing the file.
  • mopfile (str) – name of .mop file to write.
  • method (str) – The semi-empirical method to use for the calculation.
  • geopt (bool) – If True, find the minimum energy geometry.
  • keywords (str) – Space-separated keywords to use in MOPAC input file.
  • plotMO (int) – Plot <n> MOs around the HOMO/LUMO gap.
  • gridres (float) – Grid resolution for plots.
  • gridext (float) – Grid size beyond the nuclei.
run(inputfile, structure=None)

Run a MOPAC calculation in the local directory with a .mop input file. The optional Structure object is updated with the output data. Return a MopacResults object.

Parameters:inputfile (str) – name of .mop input file (without suffix)
__abstractmethods__ = frozenset()
__class__

alias of abc.ABCMeta

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.mopac.mopac_launchers', '__doc__': '\n This is the API for executing the backend of the currently supported\n version of MOPAC as an external binary.\n ', 'MOPAC_EXEC': 'MOPAC2016.exe', '_default_method': 'RM1', '_valid_methods': ['AM1', 'MNDO', 'MNDOD', 'PM3', 'PM6', 'PM6-D3', 'PM6-DH+', 'PM6-DH2', 'PM6-DH2X', 'PM6-D3H4', 'PM6-D3H4X', 'PM7', 'PM7-TS', 'RM1'], '_method_synonyms': {'MNDO-D': 'MNDOD', 'MNDO/D': 'MNDOD'}, '__init__': <function MopacLauncherMain.__init__>, 'default_method': <property object>, 'valid_methods': <property object>, 'method_synonyms': <property object>, 'extra_keywords': <property object>, 'results': <property object>, 'write_mop_file': <function MopacLauncherMain.write_mop_file>, '_tail_output_file': <function MopacLauncherMain._tail_output_file>, '_execute_mopac_binary': <function MopacLauncherMain._execute_mopac_binary>, 'run': <function MopacLauncherMain.run>, '__abstractmethods__': frozenset(), '_abc_registry': <_weakrefset.WeakSet object>, '_abc_cache': <_weakrefset.WeakSet object>, '_abc_negative_cache': <_weakrefset.WeakSet object>, '_abc_negative_cache_version': 49})
__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_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.mopac_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).

__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).

__weakref__

list of weak references to the object (if defined)

schrodinger.application.mopac.mopac_launchers.get_mopac_launcher(version)

Return a MopacLauncher object for the requested MOPAC version.

schrodinger.application.mopac.mopac_launchers.get_mopac_results_instance(version)

Return a MopacResults object for the requested MOPAC version.