OEFF TK 2.0.0

Licensing

• OEFF TK is available to anyone with an OESzybki TK license. Visit https://www.eyesopen.com/contact if you need an OESzybki TK license.

OEFF functionality

This is the first official release of OEFF TK. The underlying functionality was previously released in C++ as part of the OESzybki TK advanced interface. This toolkit is currently available in C++ and Python. An overview of its capabilities is provided below.

OEFF TK provides access to powerful low-level functionality for advanced users to develop molecular modeling applications. With OEFF TK, users also have the ability to create variations of molecular interaction classes for energy evaluation and optimization, adding to the built-in interactions, if desired. OESzybki TK complements OEFF TK as the high-level API for molecular modeling functionalities.

Objective functions and molecular interactions

All molecular interactions are objective functions with additional API points for molecular definitions. A set of pure virtual classes that can be used to define new interactions are provided for both generic objective functions and molecule specific interaction functions. The following virtual base classes are available:

• OEFunc0

• OEFunc1

• OEFunc2

• OEMolFunc

• OEMolFunc0

• OEMolFunc1

• OEMolFunc2

Force fields

Force fields and components of force fields are defined as molecule objective functions and are derived from the above-specified base classes. The following force fields and components are available:

• OEMMFF

• OEMolMMFF::OEMMFFBend

• OEMolMMFF::OEMMFFStretch

• OEMMFFStretchBend

• OEMolMMFF::OEMMFFOutOfPlane

• OEMolMMFF::OEMMFFTorsion

• OEMolMMFF::OEMMFFVdw

• OEMolMMFF::OEMMFFInterVdw

• OEMolMMFF::OEMMFFInterVdwNN

• OEMolMMFF::OEMMFFCoulomb

• OEMolMMFF::OEMMFFInterCoulomb

• OEFF::OEMMFFAmber

• OEMMFFIEFF

• OESheffield

Optimizers

A powerful set of optimizers that can be used to optimize objective functions is now available:

• OEBFGSOpt

• OEConjGradOpt

• OEDFPOpt

• OEFletcherReevesOpt

• OENewtonOpt

• OERibierePolakOpt

• OESteepestDescentOpt

Adaptors

Adaptors that can be used to optimize molecule objective functions in transformed coordinate space are now available:

• OEInterAdaptor

• OEQuatAdaptor

• OESubsetAdaptor

• OETorAdaptor

• OETorQuatAdaptor

New features

• Two new intermolecular force fields, OEFF::OEMMFFAmber and OEMMFFIEFF, have been added to the force field suites for molecular interactions. Both force fields use OEMMFF for intermolecular interactions and more accurate components for intermolecular interactions.

• A new class, OEFF::OEMMFFAmberOptions, has been added that sets all options of the OEFF::OEMMFFAmber object during its construction.

• A new class, OEMMFFIEFFOptions, has been added that sets all options of the OEMMFFIEFF object during its construction.

• A new class, OESheffieldOptions, has been added that sets all options of the OESheffield object during its construction. All OESheffield methods with similar names as their OESheffieldOptions counterparts are now deprecated.

  The following table shows the older, deprecated functions and their new option replacements:

  Deprecated	New option-based
  OESheff::OESheffield::Set_A	OESheffieldOptions::SetA
  OESheff::OESheffield::Set_B	OESheffieldOptions::SetB
  OESheff::OESheffield::SetSoluteDielectricConstant	OESheffieldOptions::SetSoluteDielectricConstant
  OESheff::OESheffield::SetSolventDielectricConstant	OESheffieldOptions::SetSolventDielectricConstant
  OESheff::OESheffield::GetParameters	OESheffieldOptions::GetA OESheffieldOptions::GetB OESheffieldOptions::GetSoluteDielectricConstant OESheffieldOptions::GetSolventDielectricConstant