Technical Documentation
POTENTIAL ENERGY FUNCTION: The Potential Class

The Potential class manages a list of Energy objects. An instance of this class (the Energy list) should be created and each Energy object should be registered with this list. This list is in turn usually registered with an instance of the Model class.

Location

The Potential module is located in Yup.Taro.

Data Attributes

The following data attributes are writeable. For example: if P is a Potential object, P.numcalls is the value of the numcalls attribute of P and "P.numcalls = 0" sets the numcalls attribute to a new value (0).

Data Attribute

Description

numcalls

This is a counter. Each time the evaluate() method is applied to the Energy objects this is incremented by one (regardless of the value of numterms).

width

The width of a column of numbers. If set below 8, the output is as wide as needed and columns are separated by the tab character. If set to 8 or higher, numbers are formatted to fit in width-2 characters. The remaining space is filled with a trailing blank.

The following data attributes are read-only. These attributes should not be assigned new values. If you do assign to these attributes the old values will be "covered" by your definition and further use of the object will likely fail. To recover from this stupidity, delete the attribute.

Data Attribute

Description

banner

A text string that is the concatenation of the label attributes of all the objects that make up the Energy list. This is formatted according to the width setting. If a label is too wide, the excess characters are not included and the truncation is indicated by the character "&".

values

A text string containing the values of the energy of each of the objects that make up the Energy list. This is formatted according to the width setting.

MEMBERS

The Energy list

RESULTS

A list of numbers. These are the energy values of the objects in the Energy list. This is in contrast to values which is a single string containing all the values.

numterms

The number of items in the Energy list.

Methods

There are three methods.

The add_term() method adds the given object to the end of the Energy list. The specified object must be an Energy object.

Method Name
Number of Arguments
Return Value
add_term
1
None
Keyword
Argument Type
Preset Value
term
Energy object
-

The remove_term() method finds the first instance of the Energy object (starting from the top of the Energy list) that has the label specified in the argument and removes it from the list.

Method Name
Number of Arguments
Return Value
remove_term
1
None
Keyword
Argument Type
Preset Value
label
character string
-

The get_term() method finds the first instance of the Energy object (starting from the top of the Energy list) that has the label specified in the argument and returns the object. This is useful if you have lost all other references to the Energy object.

Method Name
Number of Arguments
Return Value
get_term
1
Energy object
Keyword
Argument Type
Preset Value
label
character string
-
OVERVIEW
Bonds
Angles
Torsions
SoftSphereI
ElectroI
VanderWaalsI
DistNOE
TorsionSeries
GenLJI
Potential
Hooke
Hand
Impropers
SoftSphereX
ElectroX
VanderWaalsX
SwissCheeseX
AngNOE
GenLJX

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