Subsections

3.13 OEMolAdaptor

class OEMolAdaptor : public OEOpt::OEAdaptor,
                     public OEMolPotential::OEMolFunc1

This OEMolAdaptor abstract class defines the interface

3.13.1 operator()

virtual double operator()(const double *var)
virtual double operator()(const double *var, double *grad)

These pure virtual methods transform a set of variables, and call a function evaluation using the transformed set of coordinates. OEMolAdaptors contain an evaluation function used for energy evaluations. Typical transformations involve conversion of variables to a set of Cartesian coordinates for a molecule. In addition, the second of the two methods transforms computed gradients back into the coordinate type of the variables passed in the first argument. There is a one to one correspondence between the elements of the variable and gradient arrays (i.e. the first gradient element corresponds to the first variable element). Methods that override the gradient calculation operator must not initialize the gradient array, but rather assume the array has already been initialized. By convention, classes derived from OEOpt::OEOptimizer1 must initialize gradient arrays before calling a function evaluation.

3.13.2 AdaptVar

virtual bool AdaptVar(double *adaptedVar,const double *optVar) const

The AdaptVar method takes a set of variables as the second argument and copies a set of transformed variables into the first argument. This method is commonly used to transform optimized variables back into the coordinate system of the original reference variables.

3.13.3 GetFComponents

virtual OESystem::OEIterBase<OEOpt::OEFComponent>
                               *GetFComponents(const double *coord)

This method takes a pointer to a set of Cartesian coordinates, and returns an iterator over the names and component energies (Section 3.4) calculated for the coordinates.

3.13.4 GetMolFunc

virtual OEMolFunc1 &GetMolFunc() const
\end{end}

This method returns a reference to the molecule function stored in a
OEMolAdaptor derived instance.  \code{OEForceField} methods can be
accessed through this method as opposed to storing a reference or
pointer outside of the \code{OEMolAdaptor} derived class.

\subsection{GetVar}
\begin{verbatim}
virtual const double *GetVar(const double *refCoord)

The GetVar method takes reference variables as an argument, and transforms them into the variable type or coordinate system that will be used during an optimization. Reference variables normally use the same coordinate system as the function evaluations that will be performed in an optimization. Classes derived from OEMolAdaptor will typically take Cartesian reference coordinates as the argument to the GetVar method.

3.13.5 NumVar

virtual unsigned int NumVar() const

This pure virtual method defines the interface for returning the number of variables for which an OEMolAdaptor derived instance has been initialized using the OEMolAdaptor::Setup method.

3.13.6 Setup

virtual bool Setup(const OEChem::OEMolBase &mol)

This pure virtual method defines the interface for preparing a OEMolAdaptor derived class for energy and gradient calculations. Necessary information required to perform coordinate transformations will be stored in the OEMolAdaptor derived instance. The OEMolFunc::Setup method(s) of functions stored inside OEMolAdaptor derived instances will also be called.

				The CASE Toolkit Version 1.1.1

				The CASE Toolkit Version 1.1.1