The distance NOE term is of the Inclusion type (i.e., indexed by the Atom Inclusion Type) and an individual term is: { KL[ dL - rij ]m , if rij < dL 0 , if dL <= rij <= dH KH[ rij - dH ]n , if rij > dH where rij is the distance between atoms i and j, KL and KH are force constants, dL and dH are contact distances and m and n are integer exponents and must be greater than 1. The constants are assigned to this particular interaction based on the Atom Inclusion Types of the two participating atoms. The Noens module is located in the Energy sub-directory of the Yup package, hence: Yup.Energy.Noens. The distance NOE term is introduced into a simulation by first creating an (empty) instance of the Noens object. Participating atom pairs are then added to this object. Previously added interactions may also be deleted or modified. All these actions affect only a list of candidate bonds. The compile process binds Coordinate and Gradient AtomVectors to the Noens module and then goes through the candidate interactions to form a compiled NOE list in which all the atoms that are involved and the NOE parameters that they are to use are positively identified. Only then can the NOE term be evaluated. (Prior attempts at evaluation will either yield an exception or null results.) The evaluate method would now be called many times as part of a molecular mechanics calculation. Each call would yield different results even though the compiled NOE list is fixed because the Coordinates are different at each call. However, it is possible to modify the NOE parameters (force constants and contacts distances) continuously during a calculation. The parameters are accessed through the subscript operator. More radical changes can be made by adding new interaction and modifying or deleting existing terms. These actions affect the candidate list and immediately clear the compiled list. Therefore the Noens module must be compiled again before evaluation can resume. The state of the Noens module can be judged by examining the data attributes. The compiled NOEs can also be examined in great detail by printing the object. This manual is divided into several pages: Name Content Noens Introduction: this page. Create Creating a new Noens object. The function Noens(). Data The data attributes of a Noens object; some of which may be assigned new values. Manage Managing NOEs: add new interactions, modifying existing terms and deleting existing NOEs. The methods: add(), modify() and delete(). Compile Preparing a Noens object for evaluation of the energy and gradients. The methods: update() and compile(). Evaluate Evaluate the NOE energy and gradients. The method: evaluate(). Subscript The subscript [] operator: used to access and to assign values to the NOE parameters Print Documents the print, repr, delete and compare operators. Write Writing the finalized bond record to the force field file. Noens Create Data Manage Compile Evaluate Subscript Print Write OVERVIEW Bonds Angles Torsions SoftSphereI ElectroI VanderWaalsI DistNOE TorsionSeries GenLJI Potential Hooke Hand Impropers SoftSphereX ElectroX VanderWaalsX SwissCheeseX AngNOE GenLJX