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:
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
OEMolMMFF::OEMMFFStretch
OEMolSmirnoff::OESmirnoffStretch
OEMolMMFF::OEMMFFBend
OEMolSmirnoff::OESmirnoffBend
OEMolMMFF::OEMMFFTorsion
OEMolSmirnoff::OESmirnoffTorsion
OEMolSmirnoff::OESmirnoffOutOfPlane
OEMolPotential::OENonBondBase
OEMolMMFF::OEMMFFVdw
OEMolSmirnoff::OESmirnoffVdw
OEMolMMFF::OEMMFFCoulomb
OEMolSmirnoff::OESmirnoffCoulomb
OEMolMMFF::OEMMFFInterVdw
OEMolMMFF::OEMMFFInterVdwNN
OEMolSmirnoff::OESmirnoffInterVdw
OEMolMMFF::OEMMFFInterCoulomb
New OpenFF parameters
parsley_1.2.1
have been added as built-in parameters and can be used in the construction of anOESmirnoff
object.Two new classes,
OEParsleyParams
andOEParsley
, 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 customOESmirnoffParams
for cofactor and/or ligandOEFF14SBParsleyParams
: an FF14SB for proteins withOEParsleyParams
for cofactor and/or ligandOEFF14SBSmirnoff
: a force field for proteins withOEFF14SBSmirnoffParams
OEFF14SBParsley
: a force field for proteins withOEFF14SBParsleyParams
OEFF14SBSmirnoffComplex
: a force field for protein-ligand complexes withOEFF14SBSmirnoffParams
OEFF14SBParsleyComplex
: a force field for protein-ligand complex withOEFF14SBParsleyParams
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 ofOEParameter
classes. The new parameter class works with predefined complex force fields using anOEComplexFF
object.The methods
OEFF::OEComplexFF::PrepMol
andOEFF::OEComplexFF::PrepHost
have been removed from the preliminary APIOEComplexFF
as they are no longer required to setup anOEComplexFF
.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 anOEComplexEnergies
.
Documentation changes¶
All the OEFF TK examples have been reorganized to reflect the modified API behavior.