0.1.4 Interoperability and documentation improvements

0.1.4 Interoperability and documentation improvements

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

This release supports Python 3.8 and 3.9; it may be compatible with other versions but older and newer versions are not tested and therefore compatibility 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.

See the documentation for more information.

Please report bugs, request features, or ask questions via the issue tracker.

Please note that there will likely be API changes prior to a stable 1.0.0 release.

0.1.3 Reliability and documentation improvements

0.1.3 Reliability and documentation improvements

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

See the documentation for more information.

Please report bugs, request features, or ask questions via the issue tracker.

Please note that there will likely be API changes prior to a stable 1.0.0 release.

0.1.2 - Preliminary support for exporting to Amber files and InterMol Interoperability

0.1.2 - Preliminary support for exporting to Amber files and InterMol Interoperability

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.

See the documentation for more information.

Please report bugs, request features, or ask questions via the issue tracker.

Please note that there will likely be API changes prior to a stable 1.0.0 release.

0.1.1 - Preliminary support for virtual sites and bond order-based parameter interpolation

0.1.1 - Preliminary support for virtual sites and bond order-based parameter interpolation

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.

See the documentation for more information.

Please report bugs, request features, or ask questions via the issue tracker.

Please note that there will likely be API changes prior to a stable 1.0.0 release.

0.1.0 - Initial Release

0.1.0 - Initial Release

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

See the documentation for more information.

Please report bugs, request features, or ask questions via the issue tracker.

Please note that there will likely be API changes prior to a stable 1.0.0 release.

0.0.1 Initial pre-alpha release

0.0.1 Initial pre-alpha release

The is an initial release in a pre-alpha phase.

Please note that this a pre-release in a pre-alpha testing phase and many API changes will come before a stable release.