Package schrodinger :: Package application :: Package matsci :: Module desmondutils :: Class BrownieMSJStringer

Class BrownieMSJStringer

 object --+    
          |    
MSJStringer --+
              |
             BrownieMSJStringer

An MSJStringer class for Brownie stages

Instance Methods

__init__(self, time=100.0, temp=10.0, timestep='[0.001 0.001 0.003]', last=False, **kwargs)
Create a BrownieMSJStringer object

str

formLine(self, key, value)
Create the line that should go in the .msj file for this key.

str

getTitle(self)
Return a title for the stage describing the main parameters.

Inherited from MSJStringer: createString

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Class Variables

Properties

Inherited from object: __class__

Method Details

Create a BrownieMSJStringer object

Desmond config does not have a specific set of defaults for Brownie stages, so the defaults are supplied here for all keywords.

Parameters:

time (float) - Time in picoseconds
temp (float) - Temperature in Kelvin
timestep (str or list) - The timestep in picoseconds, either as a list of three floats or a string. If a string, it is used directly so must be in the proper [ x y z ] format used in .msj and .cfg files.
last (bool) - Whether the msj lines typically associated with the last stage (dir, compress) should be included
All other keyword arguments are turned into lines in the .msj file. See parent class for additional information.

Overrides: object.__init__

Create the line that should go in the .msj file for this key.

Subclasses should use this function to create custom strings for specific key values

Parameters:

Returns: str

The line (or lines) to put in the .msj file for this key/value pair

(inherited documentation)

Return a title for the stage describing the main parameters.