Package schrodinger :: Package application :: Package matsci :: Module cgforcefield :: Class FFIOSite

Class FFIOSite

object --+    
         |    
 FFIOParam --+
             |
            FFIOSite

The class that handles the FFIO site block

Instance Methods

[hide private]

schrodinger.application.desmond.ffiostructure._FFIOSite

getObject(self, fst)
Return the ffio Site block

extractData(self, data)
Extract the data from the database parameters.

addNamedProperties(self, fobject, named_props)
Add the parameters passed to the addToFST method to the FFIO block.

Inherited from FFIOParam: __init__, addConstantProperties, addParams, addToFFST

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

Class Variables

[hide private]

NAMED_PROPERTIES = ['site', 'vdwtype', 'mass', 'charge']

CONSTANT_PROPERTIES = {'type': 'atom'}

Inherited from FFIOParam: CSTART, FUNCTION, PARAM_ORDER

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

getObject(self, fst)

Return the ffio Site block

Parameters:

fst (CGFFIOStructure) - The structure to get the block object from

Returns: schrodinger.application.desmond.ffiostructure._FFIOSite

The block object for this parameter

Overrides: FFIOParam.getObject

extractData(self, data)

Extract the data from the database parameters. Modified from the parent class because unlike other blocks, sites do not have cx parameters but do have named parameters that appear in the database dictionary.

Parameters:

data (dict) - The two-level dictionary of forcefield data for this parameter. The top-level dictionary has one key - the function parameter for this object. The value is another dictionary. The keys in the inner dictionary are force field parameter names and the values are the values for those parameters.

Overrides: FFIOParam.extractData

addNamedProperties(self, fobject, named_props)

Add the parameters passed to the addToFST method to the FFIO block. These parameters generally have custom names. Modified from the parent class to include the mass and charge parameters which have been extracted from the database dictionary.

@type fobject:schrodinger.application.desmond.ffiostructure._FFIOSite

Parameters:

fobject - The object to add the parameters to
named_props (list) - Two item list, first item is the name of the site and second is the vdw type of the site

Overrides: FFIOParam.addNamedProperties