schrodinger.application.qsite.input module¶
Module for reading and writing QSite input files.
See QSiteInput class for more documentation.
Copyright Schrodinger, LLC. All rights reserved.
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class
schrodinger.application.qsite.input.
Cut
(molid=None, chain=None, resnum=None, inscode=None, qmatom=None, mmatom=None, theory='qm')¶ Bases:
object
A class to handle representation and printing of general qm region cuts.
To avoid having to update individual attributes in the back end, attributes are read-only. To modify attributes, make a new Cut instance with the desired values. The clone method is provided as a convenience method to ease creation of a Cut with modified values.
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__init__
(molid=None, chain=None, resnum=None, inscode=None, qmatom=None, mmatom=None, theory='qm')¶ Initializer for a qmregion cut specification.
At least one of molid or qmatom to be defined.
Parameters: - molid (int) – A molecule id.
- chain (str) – A chain id.
- resnum (int) – A residue number.
- inscode (str) – An insertion code.
- qmatom (str) – The name of an atom to place on the quantum mechanical side of the cut.
- mmatom (str) – The name of an atom to place on the molecular mechanical side of the cut.
- theory (str) – The theoretical method to use for this cut (“nddo” or “qm” and case-insensitive)
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molid
¶ Read-only access to the molid attribute.
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chain
¶ Read-only access to the chain attribute.
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resnum
¶ Read-only access to the resnum attribute.
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inscode
¶ Read-only access to the resnum attribute.
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qmatom
¶ Read-only access to the qmatom attribute.
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mmatom
¶ Read-only access to the mmatom attribute.
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theory
¶ Read-only access to the theory attribute.
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clone
(**kwargs)¶ Create a copy of the current instance, modifying any attributes provided as keywords.
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header
()¶ Return the header definition for this cut that would be used in the QSite input file’s &qmregion section.
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__str__
()¶ Return str(self).
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__repr__
()¶ Return repr(self).
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__class__
¶ alias of
builtins.type
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__delattr__
¶ Implement delattr(self, name).
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__dict__
= mappingproxy({'__module__': 'schrodinger.application.qsite.input', '__doc__': '\n A class to handle representation and printing of general qm region cuts.\n\n To avoid having to update individual attributes in the back end,\n attributes are read-only. To modify attributes, make a new Cut instance\n with the desired values. The clone method is provided as a convenience\n method to ease creation of a Cut with modified values.\n\n ', '_attrs': [('molid', -9999), ('chain', ''), ('resnum', -9999), ('inscode', ''), ('qmatom', ''), ('mmatom', ''), ('theory', '')], '__init__': <function Cut.__init__>, 'molid': <property object>, 'chain': <property object>, 'resnum': <property object>, 'inscode': <property object>, 'qmatom': <property object>, 'mmatom': <property object>, 'theory': <property object>, 'clone': <function Cut.clone>, '_definedAttrs': <function Cut._definedAttrs>, 'header': <function Cut.header>, '__str__': <function Cut.__str__>, '__repr__': <function Cut.__repr__>, '__dict__': <attribute '__dict__' of 'Cut' objects>, '__weakref__': <attribute '__weakref__' of 'Cut' objects>})¶
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__dir__
() → list¶ default dir() implementation
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__eq__
¶ Return self==value.
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__format__
()¶ default object formatter
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__ge__
¶ Return self>=value.
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__getattribute__
¶ Return getattr(self, name).
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__gt__
¶ Return self>value.
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__hash__
¶ Return hash(self).
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__init_subclass__
()¶ This method is called when a class is subclassed.
The default implementation does nothing. It may be overridden to extend subclasses.
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__le__
¶ Return self<=value.
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__lt__
¶ Return self<value.
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__module__
= 'schrodinger.application.qsite.input'¶
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__ne__
¶ Return self!=value.
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__new__
()¶ Create and return a new object. See help(type) for accurate signature.
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__reduce__
()¶ helper for pickle
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__reduce_ex__
()¶ helper for pickle
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__setattr__
¶ Implement setattr(self, name, value).
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__sizeof__
() → int¶ size of object in memory, in bytes
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__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).
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__weakref__
¶ list of weak references to the object (if defined)
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class
schrodinger.application.qsite.input.
HydrogenCap
(qm=None, mm=None, distance=0.0, theory='qm')¶ Bases:
object
A class to handle representation and printing of hydrogen caps for the qm region.
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__init__
(qm=None, mm=None, distance=0.0, theory='qm')¶ Initialize the hydrogen cap. A quantum mechanical atom and molecular mechanical atom must always be specified.
Parameters: - qm (str) – The name of the quantum mechanical atom.
- mm (str) – The name of the molecular mechanical atom.
- distance (float) – The hydrogen cap distance.
- theory (str) – The theoretical model to use for the QM atom (Either “nddo” or “qm”, case-insensitive)
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qm
¶ Read-only access to the _qm attribute.
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mm
¶ Read-only access to the _mm attribute.
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theory
¶ Read-only access to the _theory attribute.
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distance
¶ Read-only access to the distance attribute.
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clone
(**kwargs)¶ Create a copy of the current instance, modifying any attributes provided as keywords.
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header
()¶ Return the header definition for this hydrogen cap that would be used in the QSite input file’s &qmregion section.
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__str__
()¶ Return str(self).
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__repr__
()¶ Return repr(self).
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__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
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__dict__
= mappingproxy({'__module__': 'schrodinger.application.qsite.input', '__doc__': '\n A class to handle representation and printing of hydrogen caps for the\n qm region.\n\n ', '__init__': <function HydrogenCap.__init__>, 'qm': <property object>, 'mm': <property object>, 'theory': <property object>, 'distance': <property object>, 'clone': <function HydrogenCap.clone>, 'header': <function HydrogenCap.header>, '__str__': <function HydrogenCap.__str__>, '__repr__': <function HydrogenCap.__repr__>, '__dict__': <attribute '__dict__' of 'HydrogenCap' objects>, '__weakref__': <attribute '__weakref__' of 'HydrogenCap' objects>})¶
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__dir__
() → list¶ default dir() implementation
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__eq__
¶ Return self==value.
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__format__
()¶ default object formatter
-
__ge__
¶ Return self>=value.
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__getattribute__
¶ Return getattr(self, name).
-
__gt__
¶ Return self>value.
-
__hash__
¶ Return hash(self).
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__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.qsite.input'¶
-
__ne__
¶ Return self!=value.
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__new__
()¶ Create and return a new object. See help(type) for accurate signature.
-
__reduce__
()¶ helper for pickle
-
__reduce_ex__
()¶ helper for pickle
-
__setattr__
¶ Implement setattr(self, name, value).
-
__sizeof__
() → int¶ size of object in memory, in bytes
-
__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).
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__weakref__
¶ list of weak references to the object (if defined)
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class
schrodinger.application.qsite.input.
QMRegion
(handle)¶ Bases:
object
A class to provide access to a &qmregion specification and the ability to create one on the fly.
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__init__
(handle)¶ Parameters: - handle – An MMIM handle.
- type – int
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__len__
()¶
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__getitem__
(index)¶
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__setitem__
(index, qmregion)¶
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modify
(index, **kwargs)¶ A method to modify attributes of a specific element in the qmregion list in-place.
This method is provided because Cut and HydrogenCap instances have read-only values.
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append
(qmregion)¶ Add a new QM region to the list.
Parameters: qmregion (Cut or HydrogenCap) – A specification of a QM region cut or hydrogen cap.
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__class__
¶ alias of
builtins.type
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__delattr__
¶ Implement delattr(self, name).
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__dict__
= mappingproxy({'__module__': 'schrodinger.application.qsite.input', '__doc__': '\n A class to provide access to a &qmregion specification and the ability\n to create one on the fly.\n\n ', '_list_defaults': {'molid': -9999, 'chain': '', 'resnum': -9999, 'inscode': '', 'qmatom': '', 'seatom': '', 'mmatom': '', 'hcap': 0, 'hcap_distance': 0.0, 'theory': 'qm'}, '__init__': <function QMRegion.__init__>, '__len__': <function QMRegion.__len__>, '__getitem__': <function QMRegion.__getitem__>, '__setitem__': <function QMRegion.__setitem__>, '_growLists': <function QMRegion._growLists>, 'modify': <function QMRegion.modify>, 'append': <function QMRegion.append>, '__dict__': <attribute '__dict__' of 'QMRegion' objects>, '__weakref__': <attribute '__weakref__' of 'QMRegion' objects>})¶
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__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.qsite.input'¶
-
__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).
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__weakref__
¶ list of weak references to the object (if defined)
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class
schrodinger.application.qsite.input.
QSiteInput
(name)¶ Bases:
object
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__init__
(name)¶ Create a QSite input object, either from a jobname or QSite input file path.
Parameters
- name (str)
- One of:
- jobname - Default parameters are used.
- or
- file path - Parameters are read from specified file.
- File must be in current working directory.
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__del__
()¶ Delete the mmjag handle and clean up the mmlibs.
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gen
¶ Provide dictionary-like access to &gen section
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mmkey
¶ Provide dictionary-like access to the &mmkey section.
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mopac
¶ Provide dictionary-like access to &mopac section
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qmregion
¶ Provide access to the &qmregion section.
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setStructureFile
(filename)¶ Set the mae structure file to be used. If the structure file name doesn’t match the current job/file name it will be copied to the current directory and renamed to <jobname>.<ext>.
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getStructureFile
()¶ Return the mae structure that is used.
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addQMMolecule
(index, theory='qm')¶ Add a QM molecule to the QM region specification.
This creates a Cut instance and adds it to the qmregion attribute.
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addQMCut
(**kwargs)¶ Add a QM cut to the QM region specification.
The keywords here are the same as the Cut class constructor. Calling this method is equivalent to creating a Cut instance and adding it to the QSiteInput instance by calling qmregion.append().
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addHydrogenCap
(qm=None, mm=None, distance=0.0, theory='qm')¶ Add a hydrogen cap to the QM region specification.
The keywords here are the same as the HydrogenCap class constructor. Calling this method is equivalent to creating a HydrogenCap instance and adding it to the QSiteInput instance by calling qmregion.append().
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__class__
¶ alias of
builtins.type
-
__delattr__
¶ Implement delattr(self, name).
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__dict__
= mappingproxy({'__module__': 'schrodinger.application.qsite.input', '__init__': <function QSiteInput.__init__>, '__del__': <function QSiteInput.__del__>, 'gen': <property object>, 'mmkey': <property object>, 'mopac': <property object>, 'qmregion': <property object>, 'setStructureFile': <function QSiteInput.setStructureFile>, 'getStructureFile': <function QSiteInput.getStructureFile>, 'addQMMolecule': <function QSiteInput.addQMMolecule>, 'addQMCut': <function QSiteInput.addQMCut>, 'addHydrogenCap': <function QSiteInput.addHydrogenCap>, '_setJobName': <function QSiteInput._setJobName>, '_getJobName': <function QSiteInput._getJobName>, 'jobname': <property object>, 'write': <function QSiteInput.write>, '__dict__': <attribute '__dict__' of 'QSiteInput' objects>, '__weakref__': <attribute '__weakref__' of 'QSiteInput' objects>, '__doc__': None})¶
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__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.qsite.input'¶
-
__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).
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__weakref__
¶ list of weak references to the object (if defined)
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jobname
¶ get/set the jobname; setting the jobname also sets the filename
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write
()¶ Write the input file to <jobname>.in. The structure file will also be written to <jobname>.<ext>, where <ext> is the extension of the specified structure file.
Structure file must be specified via setStructureFile() first.
Previous file with this name is overwritten.
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