OETorAdaptor

Attention

This API is currently available in C++ and Python.

class OETorAdaptor : public OEMolAdaptor

The OETorAdaptor class provides the ability to optimize torsion angles of a molecule while holding bond lengths and bond angles fixed. OEMolFunc1 derived classes typically require Cartesian coordinates for function evaluation. OETorAdaptor transforms a set of torsions into Cartesian coordinates, passes the resultant coordinates to the internally stored OEMolFunc1 type function, and transforms the Cartesian gradients back into torsion gradients. Additional facilities are provided for excluding invariant molecule function interactions, controlling the definition of a rotatable bond, and fixing atomic positions during coordinate transformation.

The following methods are publicly inherited from OEAdaptor:

• AdaptVar

• GetVar

The following methods are publicly inherited from OEFunc0:

• operator()

• GetFComponents

• NumVar

The following methods are publicly inherited from OEFunc1:

• operator()

The following methods are publicly inherited from OEMolFunc:

• Clear

• ClearPredicates

• GetInteractions

• Setup

The following methods are publicly inherited from OEMolAdaptor:

• SetMolFunc

The OETorAdaptor class defines the following public methods:

• AdaptGrad

• Set

Constructors

OETorAdaptor(OEMolFunc1 &, bool own=false, bool excludeInteract=true)

Default and copy constructors.

Constructs an OETorAdaptor instance. The molecule function used for function evaluation must be provided as the first argument to the constructor. The second argument specifies whether the OETorAdaptor object takes ownership of the memory of the molecule function instance. By default the OETorAdaptor instance does not take ownership of the molecule function, so the OETorAdaptor destructor does not delete the molecule function instance. If ownership of the molecule function is transferred to the OETorAdaptor instance, the molecule function’s delete operator will be called in the OETorAdaptor destructor. The third argument controls the inclusion of invariant molecule function interactions. By default, interactions which remain constant during the torsion minimization are excluded from calculation (for example bond stretch interactions). If the third calling argument is false then all interactions will be computed during every function evaluation.

AdaptGrad

bool AdaptGrad(double *torGrad, const double *grads) const

Takes a set of Cartesian gradients of a conformer (second argument), and transforms them into angular torsion gradients (first argument).

Set

bool Set(const OESystem::OEUnaryPredicate<OEChem::OEAtomBase>&)
bool Set(const OESystem::OEUnaryPredicate<OEChem::OEBondBase>&)

The first method assigns an atom predicate which is used to specify atoms which are to be held fixed in their starting positions during an optimization. The second method assigns a bond predicate which is used to determine which bonds of a molecule are to be rotated during an optimization. Both the Set methods must be called before the Setup for it to be effective.