Subsections

3.9 OEGenericFF

class OEMolPotential::OEGenericFF : public OEMolPotential::OEForceField

The OEGenericFF class is designed to be a generic force field collection object. Force fields can be implemented as a collection of interaction components (i.e. bond-stretch, Van der Waals). If components are implemented correctly, a force field itself need only be a simple collection object which ties together components and possibly a parameter (OEFFParams) class instance. The OEGenericFF class provides a general mechanism for defining force fields from interaction components.

3.9.1 Constructor

OEGenericFF()

Default constructor.

3.9.2 operator()

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

These methods perform an energy evaluation given a set of Cartesian coordinates for a molecule or conformer. In addition, the second of the two methods populates an array of gradients given a set of coordinates. The gradient array must be initialized before the call to the method, although this is normally performed by an optimizer (Section 3.18). The first three elements of the gradient array are the X, Y, and Z gradients for the first atom in the molecule, followed by the X, Y, and Z gradients of the second atom and so on up to the last atom.

3.9.3 Add

bool Add(OEMolPotential::OEMolFunc1 &f,bool own=false)

This method adds an externally declared function to an OEGenericFF instance. This method will never replace an existing molecule function. The second argument denotes whether the OEGenericFF instance is to take ownership of the memory occupied by the external function. If ownership is passed to the OEGenericFF instance then the C++ delete operator will be called for the function inside the destructor of the OEGenericFF instance. Any object derived from the OEMolFunc1 (Section 3.15) abstract class may be added using this method. The method returns true if the OEMolFunc1 is successfully added. Only one copy of a OEMolFunc1 may be added to an OEGenericFF instance. Subsequent attempts to add the OEMolFunc1 to an OEGenericFF instance that already contains the OEMolFunc1 will fail with a return value of false.

bool Add(const OEFFParams &ffp)

This method adds a copy of externally declared OEFFParams derived class to an internally stored list. The OEGenericFF::PrepMol method will call OEFFParams::PrepMol for each internally stored OEFFParams instance.

3.9.4 GetFComponents

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.

3.9.5 NumVar

unsigned int NumVar() const

This method returns the number of variables for which an OEGenericFF instance has been initialized using the OEGenericFF::Setup method. The value is normally equivalent to three times OEMolBase::GetMaxAtomIdx().

3.9.6 Remove

bool Remove(OEMolPotential::OEMolFunc1 &f)

The Remove method provides the ablity to remove a function previously added to an OEGenericFF instance. If the function is not contained in the OEGenericFF instance then the method will return false. If the OEMolFunc1 found and removed successfully, then the method will return true. If an OEMolFunc1 is owned by the OEGenericFF instance for which the method was called, then the OEMolFunc1's delete operator will be called.

3.9.7 Set

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

These methods assign interaction-control predicates to the components contained in the OEGenericFF 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.

3.9.8 Setup

bool Setup(const OEChem::OEMolBase &mol)

This method prepares an OEGenericFF instance for perfoming energy and gradient calculations for conformers of a molecule. The OEMolFunc1::Setup methods are called for all functions contained within the OEGenericFF instance. This method should only be called after the molecule has been prepared by the OEGenericFF::PrepMol method. If the method returns true then all interactions and parameters were perceived properly and the OEGenericFF instance is ready for energy calculations. If the method returns false then a failure was detected. Setup failures normally occur when at least one interaction requires parameters which are not defined for the force field. The return value for this method should always be verified prior to calling either OEGenericFF::operator() method.

3.9.9 PrepMol

bool PrepMol(OEChem::OEMolBase &mol,bool sweep = true) const

The PrepMol method calls the OEFFParams::PrepMol methods for all contained OEFFParams instances. The OEFFParams::PrepMol method applied changes to the molecule passed as the function argument that are necessary preparation for force field setup (OEMolFunc1::Setup). The PrepMol method may alter the contents of the passed molecule. The second argument to the method specifies whether a call to OEMolBase::Sweep is allowed during the preparation. By default, sweeping a molecule is allowed by the method. If all OEFFParams::PrepMol methods return true then OEGenericFF::PrepMol will return true. If any OEFFParams::PrepMol method returns false then OEGenericFF::PrepMol will return false.

				The CASE Toolkit Version 1.1.1

				The CASE Toolkit Version 1.1.1