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

Dates are given in YYYY-MM-DD format.

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.

0.3.26 - 2024-04-16

#952 Drops support for Python 3.9.
#853 Better support LJPME in some GROMACS tests.
#954 Fixes a broken link in plugin documentation.
#963 Removes pre-set partial charges from host-guest example.
#956 Adds another helper function for solvation in non-aqueous solvent.
#946 Adds support for GROMACS’s 3fad virtual sites.
#918 Improves storage of cosmetic attributes.
#880 Improves virtual site example notebook.

0.3.25 - 2024-03-29

#947 Fixes a bug in which virtual site parameters with identical SMIRKS would clash.
#948 Updates the GAFF example.
#950 Fixes a bug in which atom ordering was often incorrect in GROMACS .gro files when virtual sites were present.
#942 Fixes an errant internally-thrown DeprecationWarning.
#942 Recommends jupyter-lab over jupyer-notebook.

0.3.24 - 2024-03-19

#925 Adds documentation of upcoming v0.4 changes.
#933 Fixes #934 in which atom order was sometimes mangled in Interchange.from_openmm.
#932 Fixes #935 in which KeyError was sometimes raised after Interchange.combine.
#929 A warning is raised when positions are not passed to Interchange.from_openmm.
#930 Adds additional_forces argument to create_openmm_simulation.
#938 An error is raised when non-bonded settings do not match when using Interchange.combine.

0.3.23 - 2024-03-07

#923 An error is raised in Interchange.from_openmm when the topology and system are incompatible.
#912 A warning is raised when writing an input/run file (not data file) to an engine that does not implement a switching function described by SMIRNOFF.
#916 Some internal code paths are re-organized, including removing the openff.interchange.interop.internal submodule.
#916 Improves speed of Interchange.to_lammps, particularly for larger systems.
#920 Fixes a bug in which virtual site exclusions were incorrect when using split non-bonded forces.
#915 Deprecates Interchange.__add__ in favor of Interchange.combine.
#897 Improves energy evaluation with LAMMPS when some bonds are constrained.

0.3.22 - 2024-02-27

#912 Fixes a bug in which rigid water geometries were incorrectly written to GROMACS files.
#909 Fixes a bug in which numerical values such as scale_14 were lost when parsing JSON dumps.

0.3.21 - 2024-02-20

#906 Fixes a bug in which intramolecular interactions between virtual sites were not properly excluded with OpenMM.
#901 Interchange.from_openmm now requires the system argument.
#903 The Python API of LAMMPS is now internally used for LAMMPS energy calculations.

0.3.20 - 2024-02-12

#891 Adds support for hydrogen mass repartitioning (HMR) in GROMACS export. Note that this implementation never modifies masses in waters and requires the system contains no virtual sites.
#887 Adds support for hydrogen mass repartitioning (HMR) in OpenMM export. Note that this implementation never modifies masses in waters and requires the system contains no virtual sites.

0.3.19 - 2024-02-05

#867 Tags PotentialKey.virtual_site_type with the associated type provided by SMIRNOFF parameters.
#857 Tags PotentialKey.associated_handler when importing data from OpenMM.
#848 Raises a more useful error when Interchange.minimize is called while positions are not present.
#852 Support LJPME in OpenMM export.
#871 Re-introduces Foyer compatibility with version 0.12.1.
#883 Improve topology interoperability after importing data from OpenMM, using OpenFF Toolkit 0.15.2.
#883 Falls back to Topology.visualize in most cases.

Bugfixes

#848 Fixes a bug in which Interchange.minimize erroneously appended virtual site positions to the positions attribute.
#883 Using openff-models 0.1.2, fixes parsing box information from OpenMM data.
#883 Skips writing unnecessary PDB file during visualization.
#883 Preserves atom metadata when round-tripping topologies with OpenMM.

Documentation improvements

#864 Updates installation instructions.

0.3.18 - 2023-11-16

Bugfixes

#844 Fixes a bug in which charge assignment caching incorrect charges between similar molecules with different atom orderings.

Behavior changes

#845 Adds an exception when unimplemented virtual sites are present while writing to Amber files. Previously this was a silent error producing invalid files.

0.3.17 - 2023-11-02

New Features

#831 Adds Interchange.minimize and an underlying implementation with OpenMM.

Bugfixes

#830 #834 Updates versioneer configuration for Python 3.12 compatibility.

Behavior changes

#835 Most SMIRNOFF virtual site types are once again implemented in OpenMM with openmm.LocalCoordinatesSite as it is strictly the only proper option.

0.3.16 - 2023-10-18

New Features

#827 Adds the ewald_tolerance option to to_openmm, overriding a default value inherited from old versions of the OpenFF Toolkit.
#827 Adds to_openmm_system methods, which alias existing to_openmm methods that create openmm.Systems. Existing methods are not removed or currently deprecated.

Behavior changes

#828 Most virtual site types are implemented in OpenMM as types other than openmm.LocalCoordinatesSite for better human readability.

Documentation improvements

#828 Adds a notebook demonstrating, including visualization and running short simulations, several use cases of SMIRNOFF virtual sites.

Examples added

#825 Adds a host-guest example derived from the SAMPL6 challenge.

0.3.15 - 2023-10-06

New Features

#815 Most SMIRNOFF collections are now available via a public interface (from openff.interchange.smirnoff import ...).

Bugfixes

#814 Tracks scale_12 in non-bonded handlers.
#821 Fixes visualization issues described in #819.
#816 Ensures virtual sites are added at the end of an openmm.System, after all atoms (i.e. not interlaced with molecules).

0.3.14 - 2023-09-07

New Features

#798 Interchange.to_gromacs and related methods now support BondCharge virtual sites and four-site water models.

Bugfixes

#797 Fixes a bug in which virtual site charge increments were not properly applied.

Breaking changes

#797 SMIRNOFFElectrostaticsCollection now applies virtual site charge increments.
#797 Removes ElectrostaticsCollection.charges_without_virtual_sites, FoyerElectrostaticsHandler.charges_without_virtual_sites, and makes SMIRNOFFElectrostaticsCollection.charges_without_virtual_sites private.

Documentation improvements

#802 Fixes some typos in the vdWHandler down-conversion warning.

0.3.13 - 2023-08-22

New Features

#791 Interchange.visualize can now visualize virtual sites via the include_virtual_sites argument.
#791 get_positions_with_virtual_sites now supports more virtual site types.

Behavior changes

#791 BondCharge virtual sites are now implemented in OpenMM with openmm.TwoParticleAverageSite.
#791 Conventional four-site water models using DivalentLonePair virtual sites, like TIP4P and its variants, are now implemented in OpenMM with openmm.ThreeParticleAverageSite.

0.3.12 - 2023-08-14

New features

#782 OpenMM is now an optional dependency at runtime or if using the openff-interchange-base conda package.

0.3.11 - 2023-08-09

Behavior changes

#789 Internally use vdWHandler 0.4 when storing SMIRNOFF data and creating OpenMM forces.
#789 Using plugins that create openmm.NonbondedForce now results in openmm.NonbondedForce.NoCutoff when the topology is non-periodic and vdWHandler.nonperiodic_method == "no-cutoff"

0.3.10 - 2023-08-02

New features

#781 Adds support for version 0.4 of the SMIRNOFF vdW section.
#780 Adds compatibility with Pydantic v2, using the existing v1 API.

Behavior changes

#778 Interchange.from_foyer now infers positions from the input topology, matching the behavior of Interchange.from_smirnoff.

Documentation improvements

#778 Updates the Foyer migration guide.

0.3.9 - 2023-07-25

Bugfixes

#775 Makes Interchange.from_openmm a class method as originally intended.

0.3.8 - 2023-07-14

Behavior changes

#667 Clarifies lack of support for (hard) cut-off electrostatics in OpenMM.

New features

#763 Optionally adds virtual sites to Interchange.to_pdb and Interchange.visualize and refactors virtual site position fetching into a common module.

Bugfixes

#766 Fixes #765 in which the path to the GROMACS energy file argument was hard-coded in _parse_gmx_energy.

Maintenance

#759 Improves internal handling of non-bonded settings in OpenMM export.

0.3.7 - 2023-06-29

New features

#579 Adds support for using the geometric mixing rule in OpenMM export.

Documentation improvements

#756 Updates example notebooks using a more consistent structure.
#754 Fixes a call to pack_box in the protein-ligand example.

0.3.6 - 2023-06-20

Behavior changes

#748 Resolves #747 in which exceptions inherited from BaseException against recommended practice. Exceptions now inherit from InterchangeException which itself inherits from Exception.
#707 Overhauls the openff.interchange.components._packmol module.

New features

#731 Adds support for non-rectangular boxes in GROMACS export.
#707 Improves error handling when attempting to export non-rectangular boxes to Amber and LAMMPS.

0.3.5 - 2023-06-14

New features

#725 Adds Interchange.to_openmm_simulation.

Bugfixes

#724 Fixes #723 in which some parameters in GROMACS files were incorrectly written.
#728 Fixes #719 in which GROMACS coordinate files were written incorrectly when containing more than 100,000 atoms.
#741 Improves JSON (de)serialization, particularly while parsing Collections.
#746 Fixes #745 in which get_amber_energies did not properly turn off the switching function.
#746 Fixes #736 in which get_openmm_energies ignored openmm.RBTorsionForce.

Documentation improvements

#744 Removes binder links.

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 argument.
#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 non-bonded energies not being parsed while reporting energies from the OpenMM driver.

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.