Package schrodinger :: Package application :: Package qsite :: Module input :: Class Cut

Class Cut

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.

Instance Methods

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__init__(self, molid=None, chain=None, resnum=None, inscode=None, qmatom=None, mmatom=None, theory=QM)
Initializer for a qmregion cut specification.

molid(self)
Read-only access to the molid attribute.

chain(self)
Read-only access to the chain attribute.

resnum(self)
Read-only access to the resnum attribute.

inscode(self)
Read-only access to the resnum attribute.

qmatom(self)
Read-only access to the qmatom attribute.

mmatom(self)
Read-only access to the mmatom attribute.

theory(self)
Read-only access to the theory attribute.

clone(self, **kwargs)
Create a copy of the current instance, modifying any attributes provided as keywords.

_definedAttrs(self)
Return the defined attributes for this cut.

header(self)
Return the header definition for this cut that would be used in the QSite input file's &qmregion section.

__str__(self)

__repr__(self)

Class Variables

[hide private]

_attrs = [("molid", _qmregion_int_default), ("chain", _qmregio...

Method Details

[hide private]

init(self, molid=None, chain=None, resnum=None, inscode=None, qmatom=None, mmatom=None, theory=QM)
(Constructor)

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)

molid(self)

Read-only access to the molid attribute.

Decorators:

@property

chain(self)

Read-only access to the chain attribute.

Decorators:

@property

resnum(self)

Read-only access to the resnum attribute.

Decorators:

@property

inscode(self)

Read-only access to the resnum attribute.

Decorators:

@property

qmatom(self)

Read-only access to the qmatom attribute.

Decorators:

@property

mmatom(self)

Read-only access to the mmatom attribute.

Decorators:

@property

theory(self)

Read-only access to the theory attribute.

Decorators:

@property

Class Variable Details

[hide private]

_attrs

Value:

[("molid", _qmregion_int_default), ("chain", _qmregion_str_default), (
"resnum", _qmregion_int_default), ("inscode", _qmregion_str_default), 
("qmatom", _qmregion_str_default), ("mmatom", _qmregion_str_default), 
("theory", _qmregion_str_default),]

Class Cut

__init__(self, molid=None, chain=None, resnum=None, inscode=None, qmatom=None, mmatom=None, theory=QM) (Constructor)

molid(self)

chain(self)

resnum(self)

inscode(self)

qmatom(self)

mmatom(self)

theory(self)

_attrs

init(self, molid=None, chain=None, resnum=None, inscode=None, qmatom=None, mmatom=None, theory=QM)
(Constructor)