Subsections

3.15 OEMolFunc1

class OEMolFunc1 : public OEOpt::OEFunc1,
                   public OEMolPotential::OEMolSetup

The OEMolFunc1 base class defines the interface for stateful functions which operate on molecules and conformers. OEMolFunc1 extends the OEFunc1 interface by adding the Setup method defined in OEMolSetup. Classes derived from OEFunc1 are intended for use with optimizers which utilize gradients.

3.15.1 operator()

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

The operator() pure virtual methods define the interface for function evaluation given a set of molecule coordinates. In addition, the second method computes a set of gradients for the molecule coordinates. 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.

3.15.2 ClearPredicates

virtual void ClearPredicates()

The ClearPredicates method deletes all stored predicates set previously using one of the overloaded Set methods. Predicates control function initialization behavior of overridden OEMolFunc1::Setup methods.

3.15.3 GetFComponents

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

This pure virtual method defines the interface for retrieving function component name and value information given a set of molecular coordinates. Overrides of this method take a pointer to a set of molecular coordinates, and returns an iterator over the names and component energies (Section 3.4) calculated for the coordinates.

3.15.4 GetInteractions

virtual OESystem::OEIterBase<OEInteraction>
                            *GetInteractions(const OEChem::OEMolBase &mol,
                                             const double *coord,
                                             unsigned functype=0) const

The GetInteractions method defines the interface for retrieving interaction level information computed by the OEMolFunc1 instance, given a molecule and a set of coordinates. See the section describing the OEInteraction class (Section 3.11) for details regarding interaction interrogation and reporting. If the OEMolFunc1 is a composition of multiple components, the last argument may be used to request the interactions of only a single component by passing a value from the OEFuncType namespace. The GetInteractions method is beta in the CASE v1.0 release.

3.15.5 NumVar

virtual unsigned int NumVar() const

The NumVar pure virtual method defines the interface for returning the number of variables for which an OEMolFunc1 derived instance has been initialized using the OEMolFunc1::Setup method.

3.15.6 Set

virtual bool Set(const OESystem::OEUnaryPredicate<OEChem::OEAtomBase> &pred,
                 unsigned int flag)
virtual bool Set(const OESystem::OEUnaryPredicate<OEChem::OEBondBase> &pred,
                 unsigned int flag)
virtual bool Set(const OESystem::OEBinaryPredicate<OEChem::OEAtomBase,
                                                   OEChem::OEAtomBase> &pred,
                   unsigned int flag)
virtual bool Set(const OESystem::OEBinaryPredicate<OEChem::OEBondBase,
                                                   OEChem::OEBondBase> &pred,
                 unsigned int flag)

These methods assign interaction-control predicates to the OEMolFunc1 derived instance. The first argument is the predicate type to be passed to the interaction component. The second argument is a value or a set of binary OR'ed values taken from the OEFuncType namespace which specifies the intended target for the predicate assignment. Classes derived from OEMolFunc1 do not need to define all OEMolFunc1::Set methods. Default implementations are provided for cases where definition of the method(s) are not appropriate.

3.15.7 Setup

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

The Setup pure virtual method defines the interface for initializing a OEMolFunc1 derived instance. Functions typically require perception of the passed molecule for efficient function evaluation.

3.15.8 SetupConf

virtual bool SetupConf(const double *coord)

The SetupConf pure virtual method defines the interface for initializing a OEMolFunc0 derived instance with coordinates of a particular conformer. Functions and adaptors that require initial coordinates of a conformer for evaluation, but do not need a call to Setup for every conformer may instead acquire a new set of conformer coordinates by the SetupConf method. Constraint functions, for example, may only require a single call to Setup with a connection table, but subsequent conformer evaluations may be performed after calling SetupConf.

				The CASE Toolkit Version 1.1.1

				The CASE Toolkit Version 1.1.1