Release History
Releases follow versioning as described in PEP440, where
major
increments denote a change that may break API compatibility with previousmajor
releasesminor
increments add features but do not break API compatibilitymicro
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.
0.3.18 - 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 toto_openmm
, overriding a default value inherited from old versions of the OpenFF Toolkit.#827 Adds
to_openmm_system
methods, which alias existingto_openmm
methods that createopenmm.System
s. 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 supportBondCharge
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 makesSMIRNOFFElectrostaticsCollection.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 theinclude_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 withopenmm.TwoParticleAverageSite
.#791 Conventional four-site water models using
DivalentLonePair
virtual sites, like TIP4P and its variants, are now implemented in OpenMM withopenmm.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 inopenmm.NonbondedForce.NoCutoff
when the topology is non-periodic andvdWHandler.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 ofInterchange.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
andInterchange.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 fromInterchangeException
which itself inherits fromException
.#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
Collection
s.#746 Fixes #745 in which
get_amber_energies
did not properly turn off the switching function.#746 Fixes #736 in which
get_openmm_energies
ignoredopenmm.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 aTopology
.#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 throughInterchange.to_openmm
.#697 Wires
combine_nonbonded_forces
argument throughget_summary_data
andget_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 submoduleopenff.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 multipleParameterHandler
s.#654 Adds a module
openff.interchange.common
containing base classes for different types ofCollection
s.#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
toopenff.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 forCollection
.Interchange.handlers
is deprecated forInterchange.collections
.PotentialHandler.slot_map
is deprecated forCollection.key_map
.Classes found in
openff.interchange.components.smirnoff
are now inopenff.interchange.smirnoff
.Some arguments with
handler
in their names are replaced withcollection
.
#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
SMIRNOFFCollection
s 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/orjaxlib
.#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 usescombine_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 OpenFFTopology
objects, includingWBO-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
foropenmm.System
objectsInterchange.to_openmm_topology
foropenmm.app.Topology
objects
Exports to GROMACS files:
Interchange.to_top
for.top
topology filesInterchange.to_gro
for.gro
coordinate files
Exports to AMBER files (EXPERIMENTAL):
Interchange.to_prmtop
for.prmtop
parameter/topology filesInterchange.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 aPotentialHandler
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 termsInterchange.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 anmdtraj.Topology
passed through themdtop
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 usePotentialKey
objects as keys instead ofPotential
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.