Foyer 0.4.0

• Performance

  • Atomtype by "residue" (#138)
    • Previously, each "residue" (e.g. unique molecule) in a system would be atomtyped even if an identical residue was previously found. Foyer's functionality has been updated so that subgraph isomorphisms are performed only for each unique molecule prototype. Duplicate "residues" are now atomtyped by referring to the atomtypes assigned to the residue prototype.
  • Slice out "rules" for elements not found in a system (#133)
  • Limit ring finding to sizes of eight atoms or less (prior behavior scaled poorly atomtyping surfaces) (#134)

• Misc.

  • Housekeeping for OPLS-aa forcefield XML (#127, #141)
  • Provide verbose option in Forcefield.apply when encountering missing atomtypes (#143)
  • Minor Travis CI fixes (#144, #147)
  • Syntax updates for backwards and forwards compatibility with NetworkX v1 and v2 (#148)

Foyer 0.3.1

Bump version to 0.3.1

Foyer 0.3.0

Merge pull request #126 from mattwthompson/add-improper-xsd

Add Improper in xsd

Foyer 0.2.3

Foyer 0.2.3

Foyer 0.2.2

Tag 0.2.1

Foyer 0.2.1

Tag 0.2.1

Foyer 0.2.0

Merge pull request #61 from ctk3b/master

Update mbuild version

Initial concept

Proof of concept implementation using Python decorators for rules.

The current code works as a proof of concept but is being supplanted by the smarts branch.