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.

0.3.4 - 2023-05-14

Bugfixes

#721 Fixes #720 in which units were not checked when writing [ settles ] in GROMACS files.

0.3.3 - 2023-05-08

#703 Clarifies the experimental state of some features, which require opt-in to use.

Behavior changes

#706 Updates pack_box to return a Topology.
#716 Removes InterMol and ParmEd conversions, which were untested and not part of the public API.

Bugfixes

#705 Fixes #693 in which 1-4 vdW interactions were not scaled when using Interchange.to_openmm(combine_nonbonded_forces=False)
#702 Fixes #701 in which Interchange was needlessly re-exported in the high-level module.

Documentation improvements

#673 Adds a vectorized representation example.
#703 Adds a section to the user guide on accessing experimental functionality.
#706 Updates the mixed solvent example.
#708 Updates the protein-ligand example.
#708 Updates the ligand-in-water example.

0.3.2 - 2023-05-02

Behavior changes

#677 Replaces .constraints with .potentials in constraint collections.
#677 Unifies parameters in Ryckaert-Bellemans torsions around lowercase values (c0, c1, etc.).

New features

#671 Adds Interchange.to_gromacs which writes both GROMACS topology and coordinate files at once.
#677 Improves support for Ryckaert-Bellemans torsions in parsers, writers, and drivers.
#681 Ports a PACKMOL wrapper from OpenFF Evaluator.
#692 Tags some features as experimental, requiring opt-in to access.
#697 Wires add_constrained_forces argument through Interchange.to_openmm.
#697 Wires combine_nonbonded_forces argument through get_summary_data and get_all_energies.

Bugfixes

#680 Fixes #678 in which, in some cases, text wrapping in Amber files was mangled.
#680 Fixes #679 in which atom exclusion lists in Amber files were written incorrectly.
#685 Fixes #682 in which some 1-4 interactions in Amber files were counted incorrectly.
#695 Fixes #694 in which systems with no electrostatics did not check for plugins.

0.3.1 - 2023-04-19

Behavior changes

#639 Drops support for Python 3.8, following NEP 29.
#635 Moves and re-organizes the contents of openff.interchange.interop.internal.gromacs to a new submodule openff.interchange.interop.gromacs.
#662 Moves tests and un-tested modules from the public API to pseudo-private.

Bugfixes

#655 Fixes #652 by avoiding writing a blank RESIDUE_LABEL section in Amber files.

New features

#635 Adds a dedicated class GROMACSSystem to represent GROMACS state.
#635 Adds parsing and exporting between GROMACS files and GROMACSSystem objects.
#651 Adds support for SMIRNOFFCollection plugins that depend on multiple ParameterHandlers.
#654 Adds a module openff.interchange.common containing base classes for different types of Collections.
#659 Improves testing for from_openmm.
#649 Removes the use of pkg_resources, which is deprecated.
#660 Moves the contents of openff.interchange.components.foyer to openff.interchange.foyer while maintaining existing import paths.
#663 Improves the performance of Interchange.to_prmtop.
#665 Properly write [ settles ] directive in GROMACS files.

0.3.0 - 2023-04-10

Behavior changes

#566 Refactors EnergyReport to more explicitly handle comparisons.
#583, #588, #603 Change some code paths of internal objects.
- PotentialHandler is deprecated for Collection.
- Interchange.handlers is deprecated for Interchange.collections.
- PotentialHandler.slot_map is deprecated for Collection.key_map.
- Classes found in openff.interchange.components.smirnoff are now in openff.interchange.smirnoff.
- Some arguments with handler in their names are replaced with collection.
#583 Refactors the internals of Interchange.from_smirnoff away from the chain-of-responsibility pattern.
#601 Groups GROMACS improper torsion energies in the "Torsions" key.

Bugfixes

#593 Fixes #592 in which OpenMM exports fail to create multiple non-bonded forces without a vdW handler.
#601 Fixes #600 in which some parameters were rounded to 6 digits in Interchange.to_top.
#598 Fixes #597 in which residue names were incorrectly written to Amber files for single-residue systems.
#618 Fixes #616 in which positions of multiple molecules were mangled with to_openmm_positions.
#618 Fixes #617 in which the return type of to_openmm_positions was inconsistent.
#582 Allows OpenMM version to change in regression tests.
#622 Fixes passing some settings to OpenMM’s GBSA forces.

New features

#569 Allows for quick importing from openff.interchange import Interchange.
#558 Removes a safeguard against a long-since fixed toolkit bug when looking up rmin_half.
#574 Adds more specific subclasses of TopologyKey.
#589 For convenience, per-parameter variables are now stored on SMIRNOFFCollection.potential_parameters and its subclasses.
#591 Adds custom SMIRNOFFCollections via a plugin interface.
#614 Adds support for GBSA parameters in SMIRNOFF force fields.
#586 #591 #605 #609 #613 Support custom SMIRNOFF sections with OpenMM.

Documentation improvements

#634 Improves documentation for SMIRNOFF plugins.
#610 Adds duplicate documentation on how to covert to OpenMM-styled unit/quantity objects.
#699 Updates the project’s README.

Maintenance

#400 Adds Python 3.10 to testing.
#561 #564 #572 #577 #580 #581 #590 #625 Update pre-commit configuration.
#562 Removes the use of python setup.py.
#565 Removes duplicate code in favor of openff-models.
#575 #576 Avoid installing old, incompatible versions of jax and/or jaxlib.
#578 Updates some type annotations.
#619 Removes duplicate OpenMM virtual site construction code.

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.