OEFF TK 2.1.0

New features

• A new class, OESmirnoff, has been added that facilitates creating a SMIRNOFF force field (release 0.3), a small-molecule force field that uses extended SMARTS patterns for its chemical representation of parameters (https://openforcefield.org/). The following classes have also been added that define interaction functions using the functional forms in the SMIRNOFF force field:

  • OESmirnoffParams
  • OESmirnoffStretch
  • OESmirnoffBend
  • OESmirnoffTorsion
  • OESmirnoffOutOfPlane
  • OESmirnoffVdw
  • OESmirnoffInterVdw
  • OESmirnoffCoulomb

• The following classes, derived from the parent class OEInteractParams, have been added to create a set of force field parameters for a given molecule:

  • OEStretchParams
  • OEBendParams
  • OETorsionParams
  • OEVdwParams
  • OEOutOfPlaneParams

• The OEFFParam namespace has been expanded to support SMIRNOFF force field torsion potential.

• A new method, GetIterLimit, has been added that allows assessing the state of an OEOptimizer0.

• Two new methods, GetIterLimit and GetTolerance, have been added that allow assessing the state of an OEOptimizer1.

• Two new methods, GetIterLimit and GetTolerance, have been added that allow assessing the state of an OEOptimizer2.

Major bug fixes

• A memory leak in OEInterAdaptor has been fixed.
• A memory leak in OEAM1 has been fixed.

Documentation changes

• Theory documentation for SMIRNOFF has been added (see SMIRNOFF).
• A new program, Single ligand in vacuum, has been added that demonstrates calculating energy and optimizing a single ligand in vacuum.
• The following example programs have been corrected:
  • Single ligand in vacuum
  • Energy components of a single ligand in vacuum
  • MMFF interactions of a single ligand
  • Protein-ligand optimization with MMFF
  • Protein-ligand optimization with MMFFAmber
  • Optimizing a single ligand with fixed atoms
  • Optimizing a single ligand torsions
  • Optimizing rigid ligand in protein