Package schrodinger :: Package application :: Package qsite :: Module input :: Class QSiteInput
[hide private]
[frames] | no frames]

Class QSiteInput

Instance Methods [hide private]
 
__init__(self, name)
Create a QSite input object, either from a jobname or QSite input file path.
 
__del__(self)
Delete the mmjag handle and clean up the mmlibs.
 
gen(self)
Provide dictionary-like access to &gen section
 
mmkey(self)
Provide dictionary-like access to the &mmkey section.
 
mopac(self)
Provide dictionary-like access to &mopac section
 
qmregion(self)
Provide access to the &qmregion section.
 
setStructureFile(self, filename)
Set the mae structure file to be used.
 
getStructureFile(self)
Return the mae structure that is used.
 
addQMMolecule(self, index, theory=QM)
Add a QM molecule to the QM region specification.
 
addQMCut(self, **kwargs)
Add a QM cut to the QM region specification.
 
addHydrogenCap(self, qm=None, mm=None, distance=0.0, theory=QM)
Add a hydrogen cap to the QM region specification.
 
_setJobName(self, name)
Set the jobname and filename properties from an input filename or jobname.
 
_getJobName(self)
Return the name of the job.
 
write(self)
Write the input file to <jobname>.in.
Class Variables [hide private]
  jobname = property(_getJobName, _setJobName, doc= "get/set the...
Method Details [hide private]

__init__(self, name)
(Constructor)

 

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.

gen(self)

 

Provide dictionary-like access to &gen section

Decorators:
  • @property

mmkey(self)

 

Provide dictionary-like access to the &mmkey section.

Decorators:
  • @property

mopac(self)

 

Provide dictionary-like access to &mopac section

Decorators:
  • @property

qmregion(self)

 

Provide access to the &qmregion section.

Decorators:
  • @property

setStructureFile(self, 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>.

addQMMolecule(self, index, theory=QM)

 

Add a QM molecule to the QM region specification.

This creates a Cut instance and adds it to the qmregion attribute.

addQMCut(self, **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().

addHydrogenCap(self, 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().

_setJobName(self, name)

 

Set the jobname and filename properties from an input filename or jobname.

This method keeps the filename and jobname in sync.

write(self)

 

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.


Class Variable Details [hide private]

jobname

Value:
property(_getJobName, _setJobName, doc= "get/set the jobname; " "setti\
ng the jobname also sets the filename")