Release History

Releases follow versioning as described in PEP440, where

  • major increments denote a change that may break API compatibility with previous major releases

  • minor increments add features but do not break API compatibility

  • micro increments represent bugfix releases or improvements in documentation

Please note that all releases prior to a version 1.0.0 are considered pre-releases and many API changes will come before a stable release.

Current development

0.2.3 - 2022-11-21

Behavior changes

  • #554 Interchange.to_openmm now uses combine_nonbonded_forces=True by default.

New features

  • #534 An openmm.Platform can be specified as an argument to the OpenMM driver.

Documentation improvements

  • #553 Adds a solvation example.

Bugfixes

  • #545 List the central atom first in CVFF style dihedrals in LAMMPS export

  • #551 Use Interchange.box to define periodicity when exporting to PDB files.

0.2.2 - 2022-10-12

This pre-release of Interchange includes improvements in metadata in the Amber export.

Behavior changes

  • #536 Use atom names provided by the toolkit, or element symbols if not provided, in Amber export

Bugfixes

  • #539 Fix case of single-molecule export to Amber with ambiguous residue information

Examples added

  • #533 Add experimental example using openmmforcefields to generate ligand parameters

  • #524 Add experimental example using from_openmm to import a system prepared with OpenMM tools

0.2.1 - 2022-09-02

This pre-release of Interchange includes performance improvements in exporters.

Performance improvements

  • #519 Improve runtime of Interchange.to_top by bypassing JAX broadcasting

  • #520 Improve runtime of Interchange.to_top by using a set to track constrained atom pairs

Behavior changes

  • #519 Exports to array representations no longer use jax.numpy by default

0.2.0 - 2022-08-29

The 0.2.x line of Interchange targets biopolymer support alongside version 0.11.0 of the OpenFF Toolkit. Due to the scope of changes, versions 0.2.0 and newer will not generally be compatible with the 0.1.x line or versions of the OpenFF Toolkit less than 0.11.0. In lieu of a changelog entry for this release, below is a brief summary of the current capabilities of Interchange. Future releases will continue with conventional changelog entries.

Imports from OpenFF Toolkit objects:

  • Interchange.from_smirnoff, consuming SMIRNOFF force fields and OpenFF Topology objects, including

    • WBO-based bond order interpolation of valence parameters

    • Virtual sites

  • See the Molecule Cookbook for information on preparing molecule inputs and Molecule API docs for more information.

Imports from MoSDeF objects:

  • Interchange.from_foyer Exports to OpenMM objects:

  • Interchange.to_openmm for openmm.System objects

  • Interchange.to_openmm_topology for openmm.app.Topology objects

Exports to GROMACS files:

  • Interchange.to_top for .top topology files

  • Interchange.to_gro for .gro coordinate files

Exports to AMBER files (EXPERIMENTAL):

  • Interchange.to_prmtop for .prmtop parameter/topology files

  • Interchange.to_inpcrd for .inpcrd coordinate files

Exports to LAMMPS files (EXPERIMENTAL):

  • Interchange.to_lammps for .data data files

Exports to JAX arrays:

  • Call .get_force_field_parameters or .get_system_parameters on a PotentialHandler subclass to get a JAX array of force field or “system” parameters associated with that handler.

Known issues and limitations:

  • Residue hierarchy information may not be preserved in GROMACS and AMBER exports

  • Some operations are slow and not yet optimized for performance, including

    • Interchange.from_smirnoff, particularly for large systems with many valence terms

    • Interchange.to_top, particularly for systems with polymers, including proteins

During development of this release, the default branch has been renamed from master to main.

0.1.4 - 2022-01-11

This pre-release of OpenFF Interchange includes interoperability and documentation improvements.

This release supports Python 3.8 and 3.9; it may be compatible with older and newer versions may but is not guaranteed.

New features

  • #355 Add Interchange.to_pdb

  • #357 Add more type annotations

Documentation improvements

  • #319 Add Foyer showcase (silica nanoparticle solvated in an organic species)

  • #358 Fix output.md

  • #352 Fix some typos in docstrings

Breaking changes

  • #357 The _OFFBioTop constructor now requires an mdtraj.Topology passed through the mdtop argumment.

  • #363 This project is no longer tested on Python 3.7

Bugfixes

  • #351 Fix setting byte order while processing bytes to NumPy arrays

  • #354 Fix positions processing in Interchange.__add__

  • e176033 Fixes nonbonded energies not being parsed while reporting energies from the OpenMM drver.

0.1.3 - 2021-11-12

This pre-release of OpenFF Interchange includes documentation improvements and some reliability and testing improvements.

New features

  • #317 Partially avoids parameter clashes in Interchange object combination

Documentation improvements

  • #234 Switch documentation them theme to openff-sphinx-theme

  • #309 Improves the user guide

  • #190 Adds parameter splitting example

  • #331 Restores autodoc_pydantic sphinx extension

Bugfixes

  • #332 Fixes export of multi-molecule systems to Amber files

Testing and reliability improvements

  • #324 Removes pmdtest module

  • #327 Skips unavailable drivers instead of erroring out

  • #246 Improves exports of non-bonded settings to Amber files

  • #333 Makes beta/RC tests run automatically

0.1.2 - 2021-10-26

This pre-release of the OpenFF Interchange adds preliminary support for exporting to some file formats used by the Amber suite of biomolecular simulation programs and some support for conversions from InterMol objects. Stability, reliability, and feature completeness of these new features is not guaranteed - please report bugs or any surprising behavior.

Features added

  • #310 Adds functions that run all energy drivers at once. See openff/interchange/drivers/all.py for details.

  • #312 Adds conversion from InterMol System objects.

  • #316 Adds an experimental GROMACS parser.

  • #230 Adds experimental exports to some Amber files (.inpcrd and .prmtop).

Bug Fixes

  • #308 Fixes a bug involving duck-types NumPy types.

  • #322 Fixes a bug in which the Amber driver would not work with some mainline OpenFF force fields.

0.1.1 - 2021-09-13

This pre-release of the OpenFF Interchange adds preliminary support for virtual sites and bond order-based parameter interpolation. Stability and reliability with these new features is not guaranteed - please report bugs or any surprising behavior.

Note: This release is not compatible with versions of OpenMM older than 7.6.

Features added

  • #252 Improves error handling in cases of unassigned valence terms.

  • #228 Adds support for bond-order based interpolation of harmonic bond parameters.

  • #263 Adds support for bond-order based interpolation of periodic torsion parameters.

  • #244 Adds preliminary support for internally storing virtual sites following the SMIRNOFF specification.

  • #253 Adds support for virtual sites modifying partial charges via charge increments.

  • #248 Adds preliminary support exporting systems with virtual sites to GROMACS.

  • #268 Adds preliminary support exporting systems with virtual sites to OpenMM.

  • #298 Adds PotentialHandler.set_force_field_parameters

  • #300 Adds a GROMACS .gro file reader.

Behavior changed

  • #298 Refactors PotentialHandler.get_mapping to use PotentialKey objects as keys instead of Potential objects.

Documentation improvements

  • #267 Adds docstrings for most functions and classes in the source code.

  • #285 Adds an example using a SMIRNOFF force field with a liquid-phase mixture of organic compounds.

  • #286 Updates the README file.

  • #271 Adds automatic API documentation via autosummary.

Testing and reliability improvements

  • #269 OpenEye toolkits are now used in automated testing by default.

  • #281 Refactors the test suite into unit tests, interoperability tests, and energy comparison tests.

  • #289 Improves the Amber energy driver.

  • #292 Improves some ParmEd conversions.

  • #232 Fixes mypy and updates its configuration.

0.1.0 - 2021-06-30

The is an initial pre-release of the OpenFF Interchange.