OEFF TK 2.3.0

Fall 2020

New features

• A new generic set of force field potential classes has been added to simplify implementing new force fields in OEFF TK:

  • OEFFPotential
  • OEStretchPotential
  • OEBendPotential
  • OETorsionPotential
  • OEOutOfPlanePotential
  • OENonBondPotBase
  • OENonBondPotential
  • OEVdwPotential
  • OECoulombPotential
  • OEInterNonBondPotBase
  • OEInterNonBondPotential
  • OEInterVdwPotential
  • OEInterCoulombPotential

• With the introduction of the new generic force field potential classes in OEFF TK, several previously existing classes have been deprecated. The following table shows the deprecated classes and their replacements:

  Deprecated Class	New Class
  OEMolPotential::OEStretchBase	OEStretchPotential
  OEMolMMFF::OEMMFFStretch
  OEMolSmirnoff::OESmirnoffStretch
  OEMolMMFF::OEMMFFBend	OEBendPotential
  OEMolSmirnoff::OESmirnoffBend
  OEMolMMFF::OEMMFFTorsion	OETorsionPotential
  OEMolSmirnoff::OESmirnoffTorsion
  OEMolSmirnoff::OESmirnoffOutOfPlane	OEOutOfPlanePotential
  OEMolPotential::OENonBondBase	OENonBondPotBase
  OEMolMMFF::OEMMFFVdw	OEVdwPotential
  OEMolSmirnoff::OESmirnoffVdw
  OEMolMMFF::OEMMFFCoulomb	OECoulombPotential
  OEMolSmirnoff::OESmirnoffCoulomb
  OEMolMMFF::OEMMFFInterVdw	OEInterVdwPotential
  OEMolMMFF::OEMMFFInterVdwNN
  OEMolSmirnoff::OESmirnoffInterVdw
  OEMolMMFF::OEMMFFInterCoulomb	OEInterCoulombPotential

• New OpenFF parameters parsley_1.2.1 have been added as built-in parameters and can be used in the construction of an OESmirnoff object.

• Two new classes, OEParsleyParams and OEParsley, have been added that work with the latest versions of available OpenFF Parsley force fields.

• New FF14SB ([Maier-2015]) protein force field parameters have been implemented. These parameters are accessible through the following parameter and force field classes.

  • OEFF14SBSmirnoffParams: an FF14SB for proteins with custom OESmirnoffParams for cofactor and/or ligand
  • OEFF14SBParsleyParams: an FF14SB for proteins with OEParsleyParams for cofactor and/or ligand
  • OEFF14SBSmirnoff: a force field for proteins with OEFF14SBSmirnoffParams
  • OEFF14SBParsley: a force field for proteins with OEFF14SBParsleyParams
  • OEFF14SBSmirnoffComplex: a force field for protein-ligand complexes with OEFF14SBSmirnoffParams
  • OEFF14SBParsleyComplex: a force field for protein-ligand complex with OEFF14SBParsleyParams

• A new class, OEMMFFAmberComplex, has been added that allows protein-ligand optimization with protein flexibility. Accordingly, OEFF::OEMMFFAmber has been deprecated.

• A new preliminary class, OEComplexFFParameter, has been added as part of the extended set of OEParameter classes. The new parameter class works with predefined complex force fields using an OEComplexFF object.

• The methods OEFF::OEComplexFF::PrepMol and OEFF::OEComplexFF::PrepHost have been removed from the preliminary API OEComplexFF as they are no longer required to setup an OEComplexFF.

• A new class, OEComplexEnergies, has been added that represents energy components of a protein-ligand complex.

• A new overload of GetFComponents has been added that provides the energy components in the form of an OEComplexEnergies.

Documentation changes

• All the OEFF TK examples have been reorganized to reflect the modified API behavior.