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

Class FFIOVdwTypesCombined

object --+    
         |    
 FFIOParam --+
             |
            FFIOVdwTypesCombined

The class that handles the FFIO combined VdW block

Instance Methods

[hide private]

__init__(self, cutoff, dielectric, charge_i, charge_j, *args)
Create an instance

schrodinger.application.desmond.ffiostructure._FFIOVdwtypescombined

getObject(self, fst)
Return the ffio VdwTypeCombined block

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

float

getAlphaParameter(self)
Return the alpha parameter.

float

getWidthParameter(self, cutoff, ewald_epsilon=1e-09)
Return the Ewald charge distribution width parameter.

dict

getScaledEwaldConstants(self)
Scale the given Ewald constant given the cutoff and exponent.

dict

getEwaldRealSpaceFFIOConstants(self)
Return the Ewald real space Coulomb potential FFIO constants.

list

getFFIOConstants(self)
Return the FFIO constants.

Inherited from FFIOParam: addConstantProperties, addNamedProperties, addParams, addToFFST

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

Class Variables

[hide private]

FUNCTION = 'polynomial_cij'

NAMED_PROPERTIES = ['name1', 'name2']

CONSTANT_PROPERTIES = {'t1': 1}

Inherited from FFIOParam: CSTART, PARAM_ORDER

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, cutoff, dielectric, charge_i, charge_j, args)
(Constructor)*

Create an instance

Parameters:

cutoff (float) - The force field cutoff parameter in Angstroms
dielectric (float) - The force field dielectric constant
charge_i (float) - the charge on the first site
charge_j (float) - the charge on the second site
See parent class for additional argument documentation

Overrides: object.__init__

getObject(self, fst)

Return the ffio VdwTypeCombined block

Parameters:

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

Returns: schrodinger.application.desmond.ffiostructure._FFIOVdwtypescombined

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 the cx parameters must be computed from the database data rather than using the data directly.

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

getAlphaParameter(self)

Return the alpha parameter.

Returns: float: the alpha parameter

getWidthParameter(self, cutoff, ewald_epsilon=1e-09)

Return the Ewald charge distribution width parameter.

Parameters:

cutoff (float) - The cutoff parameter in Angstroms
ewald_epsilon (float) - parameter in reciprocal Ang. used to determine the width

Returns: float

the width in reciprocal Ang.

getScaledEwaldConstants(self)

Scale the given Ewald constant given the cutoff and exponent.

Returns: dict: Keys are index and values are scaled Ewald constants to use for the parameter with that index

getEwaldRealSpaceFFIOConstants(self)

Return the Ewald real space Coulomb potential FFIO constants.

Returns: dict: The real space FFIO constants. Keys are 1-based parameter index as in r_ffio_c<idx>, and values are the constants

getFFIOConstants(self)

Return the FFIO constants.

Returns: list: the FFIO constants as a list in order from 0 to NTERMS. All constants, including those defined as zero, are included in the list.

Class FFIOVdwTypesCombined

__init__(self, cutoff, dielectric, charge_i, charge_j, *args) (Constructor)

getObject(self, fst)

extractData(self, data)

getAlphaParameter(self)

getWidthParameter(self, cutoff, ewald_epsilon=1e-09)

getScaledEwaldConstants(self)

getEwaldRealSpaceFFIOConstants(self)

getFFIOConstants(self)

init(self, cutoff, dielectric, charge_i, charge_j, args)
(Constructor)*