schrodinger.application.mopac.results_main module

This module parses and stores the results of a MOPAC calculation. A MopacResultsMain class is populated with data from the output files from MOPAC_MAIN using a text parser.

exception schrodinger.application.mopac.results_main.MopacPropertyError

Bases: Exception

__cause__

exception cause

__class__

alias of builtins.type

__context__

exception context

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.mopac.results_main', '__weakref__': <attribute '__weakref__' of 'MopacPropertyError' 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.results_main'
__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.

exception schrodinger.application.mopac.results_main.MopacNumericalError

Bases: Exception

__cause__

exception cause

__class__

alias of builtins.type

__context__

exception context

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.mopac.results_main', '__weakref__': <attribute '__weakref__' of 'MopacNumericalError' 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.results_main'
__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.

exception schrodinger.application.mopac.results_main.MopacBasisError1

Bases: Exception

__cause__

exception cause

__class__

alias of builtins.type

__context__

exception context

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.mopac.results_main', '__weakref__': <attribute '__weakref__' of 'MopacBasisError1' 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.results_main'
__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.

exception schrodinger.application.mopac.results_main.MopacBasisError2

Bases: Exception

__cause__

exception cause

__class__

alias of builtins.type

__context__

exception context

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.mopac.results_main', '__weakref__': <attribute '__weakref__' of 'MopacBasisError2' 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.results_main'
__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.

exception schrodinger.application.mopac.results_main.MopacBasisError3

Bases: Exception

__cause__

exception cause

__class__

alias of builtins.type

__context__

exception context

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.mopac.results_main', '__weakref__': <attribute '__weakref__' of 'MopacBasisError3' 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.results_main'
__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.

exception schrodinger.application.mopac.results_main.MopacBasisError4

Bases: Exception

__cause__

exception cause

__class__

alias of builtins.type

__context__

exception context

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.mopac.results_main', '__weakref__': <attribute '__weakref__' of 'MopacBasisError4' 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.results_main'
__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.

exception schrodinger.application.mopac.results_main.MopacBasisError5

Bases: Exception

__cause__

exception cause

__class__

alias of builtins.type

__context__

exception context

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.mopac.results_main', '__weakref__': <attribute '__weakref__' of 'MopacBasisError5' 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.results_main'
__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.

exception schrodinger.application.mopac.results_main.MopacGradientParserError

Bases: Exception

__cause__

exception cause

__class__

alias of builtins.type

__context__

exception context

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.mopac.results_main', '__weakref__': <attribute '__weakref__' of 'MopacGradientParserError' 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.results_main'
__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.results_main.MopacMainTextParser(file_iter)

Bases: object

Parser for MOPAC_MAIN’s .out and .aux files. Using decorators, the callback() function below populates the “callbacks” dictionary in this class with key-value pairs of the form (regex,func) where “regex” is a regular expression to catch patterns in the output file, and “func” is the callback function which is triggered when the regex is matched.

In this way, each specific callback is triggered by a given pattern such as ‘HOMO LUMO ENERGIES (EV) =’, and the callback function processes the matched lines.

Note that multiple regex’s can be associated with a given callback function by associating it with two or more decorators. In this way, the same callback can be triggered multiple times. e.g. for both the .aux and .out files, perhaps for consistency checking etc.

Typically, however, only one regex is associated with each callback so that data for a given property is grepped from either the .out file OR the .aux file, but not both.

callbacks = OrderedDict([(re.compile('HEAT_OF_FORMATION:KCAL/MOL=(\\s*\\+?\\-?\\d+\\.\\d+D[\\+,\\-]\\d+)'), <function func>), (re.compile('FINAL HEAT OF FORMATION\\s+=(\\s*\\+?\\-?\\d+\\.\\d+)'), <function func>), (re.compile('TOTAL_ENERGY:EV=(\\s*\\+?\\-?\\d+\\.\\d+D[\\+,\\-]\\d+)'), <function func>), (re.compile('TOTAL ENERGY\\s+=(\\s*\\+?\\-?\\d+\\.\\d+)\\s+EV'), <function func>), (re.compile('FINAL POINT AND DERIVATIVES'), <function func>), (re.compile('\\s+(.*)\\s+CALCULATION RESULTS'), <function func>), (re.compile('IONIZATION_POTENTIAL:EV=(\\s*\\+?\\-?\\d+\\.\\d+D[\\+,\\-]\\d+)'), <function func>), (re.compile('HOMO LUMO ENERGIES \\(EV\\) =(\\s*\\+?\\-?\\d+\\.\\d+)\\s+(\\s*\\+?\\-?\\d+\\.\\d+)'), <function func>), (re.compile('ALPHA SOMO LUMO \\(EV\\)\\s+=(\\s*\\+?\\-?\\d+\\.\\d+)\\s+(\\s*\\+?\\-?\\d+\\.\\d+)'), <function func>), (re.compile('ALPHA HOMO LUMO \\(EV\\)\\s+=(\\s*\\+?\\-?\\d+\\.\\d+)\\s+(\\s*\\+?\\-?\\d+\\.\\d+)'), <function func>), (re.compile('BETA\\s+SOMO LUMO \\(EV\\)\\s+=(\\s*\\+?\\-?\\d+\\.\\d+)\\s+(\\s*\\+?\\-?\\d+\\.\\d+)'), <function func>), (re.compile('BETA\\s+HOMO LUMO \\(EV\\)\\s+=(\\s*\\+?\\-?\\d+\\.\\d+)\\s+(\\s*\\+?\\-?\\d+\\.\\d+)'), <function func>), (re.compile('Parr & Pople absolute hardness:(\\s*\\+?\\-?\\d+\\.\\d+)'), <function func>), (re.compile('Mulliken electronegativity:(\\s*\\+?\\-?\\d+\\.\\d+)'), <function func>), (re.compile('DIPOLE:DEBYE=(\\s*\\+?\\-?\\d+\\.\\d+D[\\+,\\-]\\d+)'), <function func>), (re.compile('DIP_VEC:DEBYE\\[3\\]=(\\s*\\+?\\-?\\d+\\.\\d+D[\\+,\\-]\\d+)\\s+(\\s*\\+?\\-?\\d+\\.\\d+D[\\+,\\-]\\d+)\\s+(\\s*\\+?\\-?\\d+\\.\\d+D[\\+,\\-]\\d+)'), <function func>), (re.compile('DIPOLE MOMENT EVALUATED FROM THE POINT CHARGES'), <function func>), (re.compile('ATOM_X:ANGSTROMS\\[(\\d+)\\]='), <function func>), (re.compile('ATOM_X_OPT:ANGSTROMS\\[(\\d+)\\]='), <function func>), (re.compile('^ ATOM_CHARGES\\[(\\d+)\\]='), <function func>), (re.compile('^ MULLIKEN_ATOM_CHARGES\\[(\\d+)\\]='), <function func>), (re.compile('^ ELECTOSTATIC_POTENTIAL_CHARGES\\[(\\d+)\\]='), <function func>), (re.compile('a\\s+n\\s+Dn\\(r\\)\\s+De\\(r\\)\\s+q\\(r\\) - Z\\(r\\)'), <function func>), (re.compile('a\\s+n\\s+piS\\(r\\)'), <function func>), (re.compile('^ ATOM_EL\\[(\\d+)\\]='), <function func>), (re.compile('^ NUM_ELECTRONS=(\\d+)'), <function func>), (re.compile('^ AO_ATOMINDEX\\[(\\d+)\\]='), <function func>), (re.compile('^ ATOM_SYMTYPE\\[(\\d+)\\]='), <function func>), (re.compile('^ AO_ZETA\\[(\\d+)\\]='), <function func>), (re.compile('^ ATOM_PQN\\[(\\d+)\\]='), <function func>), (re.compile('^ EIGENVALUES\\[(\\d+)\\]='), <function func>), (re.compile('^ MOLECULAR_ORBITAL_OCCUPANCIES\\[(\\d+)\\]='), <function func>), (re.compile('^ OVERLAP_MATRIX\\[(\\d+)\\]='), <function func>), (re.compile('^ EIGENVECTORS\\[(\\d+)\\]='), <function func>)])
__init__(file_iter)

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

parse()

Loop over self.file_iter and trigger the callbacks.

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.mopac.results_main', '__doc__': '\n Parser for MOPAC_MAIN\'s .out and .aux files.\n Using decorators, the callback() function below populates the "callbacks"\n dictionary in this class with key-value pairs of the form (regex,func)\n where "regex" is a regular expression to catch patterns in the output\n file, and "func" is the callback function which is triggered when the\n regex is matched.\n\n In this way, each specific callback is triggered by a given pattern\n such as \'HOMO LUMO ENERGIES (EV) =\', and the callback function\n processes the matched lines.\n\n Note that multiple regex\'s can be associated with a given callback\n function by associating it with two or more decorators. In this way,\n the same callback can be triggered multiple times. e.g. for both\n the .aux and .out files, perhaps for consistency checking etc.\n\n Typically, however, only one regex is associated with each callback\n so that data for a given property is grepped from either the .out\n file OR the .aux file, but not both.\n ', 'callbacks': OrderedDict([(re.compile('HEAT_OF_FORMATION:KCAL/MOL=(\\s*\\+?\\-?\\d+\\.\\d+D[\\+,\\-]\\d+)'), <function func>), (re.compile('FINAL HEAT OF FORMATION\\s+=(\\s*\\+?\\-?\\d+\\.\\d+)'), <function func>), (re.compile('TOTAL_ENERGY:EV=(\\s*\\+?\\-?\\d+\\.\\d+D[\\+,\\-]\\d+)'), <function func>), (re.compile('TOTAL ENERGY\\s+=(\\s*\\+?\\-?\\d+\\.\\d+)\\s+EV'), <function func>), (re.compile('FINAL POINT AND DERIVATIVES'), <function func>), (re.compile('\\s+(.*)\\s+CALCULATION RESULTS'), <function func>), (re.compile('IONIZATION_POTENTIAL:EV=(\\s*\\+?\\-?\\d+\\.\\d+D[\\+,\\-]\\d+)'), <function func>), (re.compile('HOMO LUMO ENERGIES \\(EV\\) =(\\s*\\+?\\-?\\d+\\.\\d+)\\s+(\\s*\\+?\\-?\\d+\\.\\d+)'), <function func>), (re.compile('ALPHA SOMO LUMO \\(EV\\)\\s+=(\\s*\\+?\\-?\\d+\\.\\d+)\\s+(\\s*\\+?\\-?\\d+\\.\\d+)'), <function func>), (re.compile('ALPHA HOMO LUMO \\(EV\\)\\s+=(\\s*\\+?\\-?\\d+\\.\\d+)\\s+(\\s*\\+?\\-?\\d+\\.\\d+)'), <function func>), (re.compile('BETA\\s+SOMO LUMO \\(EV\\)\\s+=(\\s*\\+?\\-?\\d+\\.\\d+)\\s+(\\s*\\+?\\-?\\d+\\.\\d+)'), <function func>), (re.compile('BETA\\s+HOMO LUMO \\(EV\\)\\s+=(\\s*\\+?\\-?\\d+\\.\\d+)\\s+(\\s*\\+?\\-?\\d+\\.\\d+)'), <function func>), (re.compile('Parr & Pople absolute hardness:(\\s*\\+?\\-?\\d+\\.\\d+)'), <function func>), (re.compile('Mulliken electronegativity:(\\s*\\+?\\-?\\d+\\.\\d+)'), <function func>), (re.compile('DIPOLE:DEBYE=(\\s*\\+?\\-?\\d+\\.\\d+D[\\+,\\-]\\d+)'), <function func>), (re.compile('DIP_VEC:DEBYE\\[3\\]=(\\s*\\+?\\-?\\d+\\.\\d+D[\\+,\\-]\\d+)\\s+(\\s*\\+?\\-?\\d+\\.\\d+D[\\+,\\-]\\d+)\\s+(\\s*\\+?\\-?\\d+\\.\\d+D[\\+,\\-]\\d+)'), <function func>), (re.compile('DIPOLE MOMENT EVALUATED FROM THE POINT CHARGES'), <function func>), (re.compile('ATOM_X:ANGSTROMS\\[(\\d+)\\]='), <function func>), (re.compile('ATOM_X_OPT:ANGSTROMS\\[(\\d+)\\]='), <function func>), (re.compile('^ ATOM_CHARGES\\[(\\d+)\\]='), <function func>), (re.compile('^ MULLIKEN_ATOM_CHARGES\\[(\\d+)\\]='), <function func>), (re.compile('^ ELECTOSTATIC_POTENTIAL_CHARGES\\[(\\d+)\\]='), <function func>), (re.compile('a\\s+n\\s+Dn\\(r\\)\\s+De\\(r\\)\\s+q\\(r\\) - Z\\(r\\)'), <function func>), (re.compile('a\\s+n\\s+piS\\(r\\)'), <function func>), (re.compile('^ ATOM_EL\\[(\\d+)\\]='), <function func>), (re.compile('^ NUM_ELECTRONS=(\\d+)'), <function func>), (re.compile('^ AO_ATOMINDEX\\[(\\d+)\\]='), <function func>), (re.compile('^ ATOM_SYMTYPE\\[(\\d+)\\]='), <function func>), (re.compile('^ AO_ZETA\\[(\\d+)\\]='), <function func>), (re.compile('^ ATOM_PQN\\[(\\d+)\\]='), <function func>), (re.compile('^ EIGENVALUES\\[(\\d+)\\]='), <function func>), (re.compile('^ MOLECULAR_ORBITAL_OCCUPANCIES\\[(\\d+)\\]='), <function func>), (re.compile('^ OVERLAP_MATRIX\\[(\\d+)\\]='), <function func>), (re.compile('^ EIGENVECTORS\\[(\\d+)\\]='), <function func>)]), '__init__': <function MopacMainTextParser.__init__>, 'parse': <function MopacMainTextParser.parse>, '__dict__': <attribute '__dict__' of 'MopacMainTextParser' objects>, '__weakref__': <attribute '__weakref__' of 'MopacMainTextParser' 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).

__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.results_main'
__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.results_main.fortfloat(val)

Convert a floating point number in Fortran notation to a regular float.

schrodinger.application.mopac.results_main.check_memory_use(nvals, name)

Check memory requirment for a long list of floats. Print message if size exceeds MEMORY_WARNING.

schrodinger.application.mopac.results_main.update_props(props, key, value, precision=5)

Update the props dictionary with the key-value pair, performing consistency checks if the key already exists.

schrodinger.application.mopac.results_main.callback(regex)

This decorator is just a convenient way to populate the callbacks dictionary in the MopacMainTextParser. The associated functions themselves are not actually decorated.

schrodinger.application.mopac.results_main.func(props, match, it)
class schrodinger.application.mopac.results_main.MopacResultsMain

Bases: schrodinger.application.mopac.mopac_results.MopacResults

A class to parse and store the results of a calculation from MOPAC_MAIN

__abstractmethods__ = frozenset()
__class__

alias of abc.ABCMeta

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.mopac.results_main', '__doc__': '\n A class to parse and store the results of a calculation from MOPAC_MAIN\n ', '__init__': <function MopacResultsMain.__init__>, 'structure': <property object>, 'method': <property object>, 'output_file': <property object>, 'set_method': <function MopacResultsMain.set_method>, 'set_status': <function MopacResultsMain.set_status>, 'set_output_file': <function MopacResultsMain.set_output_file>, 'statusOk': <function MopacResultsMain.statusOk>, 'get_error_text': <function MopacResultsMain.get_error_text>, 'populate_from_file': <function MopacResultsMain.populate_from_file>, 'set_final_structure': <function MopacResultsMain.set_final_structure>, '_get_basis_functions': <function MopacResultsMain._get_basis_functions>, 'write_vis_files': <function MopacResultsMain.write_vis_files>, '__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.results_main'
__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)

__init__()

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

structure

A Schrodinger Structure object which is populated with output data.

method
Type:str

name of semi-empirical method (i.e. a MOPAC keyword)

output_file
Type:str

name of output file generated by MOPAC.

set_method(value)
set_status(value)
set_output_file(value)
statusOk()

Needed to be consistent with legacy code

get_error_text()

Needed to be consistent with legacy code

populate_from_file(filename)

Parse “filename” containing MOPAC_MAIN’s versions’s output data.

set_final_structure(structure, filename)

Compile parsed results into the structure.properties dictionary.

write_vis_files(jobname, nplot, gridres, gridext)

This function will call the Fortran routines to generate the 3D data and .vis files for plotting surfaces.

Parameters:nplot (int) – number of MOs to plot around HOMO/LUMO gap.