0.13.0 Temporarily remove GAFFTemplateGenerator

0.13.0 Temporarily remove GAFFTemplateGenerator

This release temporarily removes GAFFTemplateGenerator because of packaging incompatibilities with
AmberTools 23. This functionality is planned to be re-introduced in 0.14.0.

This release is expected to work with Python 3.10-3.12.

Other changes include

• The default force field of SystemGenerator was updated from openff-1.0.0 (code name Parsley) to
  openff-2.0.0 (code name Sage).

What's Changed

• Merge dependabot changes by @mattwthompson in #307
• Update SMIRNOFF/OpenFF docs/examples by @mattwthompson in #305
• fix badges + readme updates by @mikemhenry in #309
• feat: Improve handling of NB 1-4 scaling factors by @LilDojd in #318
• Update partial charge assignment docs by @mattwthompson in #313
• Specify major version of checkout action by @mattwthompson in #314
• Do not generate conformers that will not be used by @mattwthompson in #315
• Temporarily remove GAFF because of parmchk2 issues by @mattwthompson in #329
• Add correct cutoffs to SMIRNOFF example by @mattwthompson in #324
• Bump codecov/codecov-action from 3 to 4 by @dependabot in #322
• Add uniform, automated linting by @mattwthompson in #319
• Remove code paths that use old OpenFF Toolkit API by @mattwthompson in #323
• linted all files by @mikemhenry in #332
• make a new excpetion for dropping gaff support by @mikemhenry in #333

New Contributors

• @LilDojd made their first contribution in #318

Full Changelog: 0.12.0...0.13.0

0.12.0 Release

What's Changed

Improvements

• Convert all amber ions (see openmm/openmm#3663 for more detail) one-to-one using Amber ion frcmod files (from AmberTools 22) into OpenMM xml files with the same names and the same contents. by @mattwthompson & @aizvorski in #242 & #239
• SystemGenerator should only add barostat if system is periodic. Solves #252 by @jchodera in #253
• Fix OPC3 bond length. In the Amber implementation of the OPC3 water model at ffxml/amber/opc3.xml, the H-O bond length was too large by a factor of 10. by @mattwthompson in #273
• raise ForceException if a custom force is found. by @mattwthompson in #292
• Allow an offxml string to be used as a small molecule force field for the SystemGenerator and SMIRNOFFTemplateGenerator for example:

"Try and load a OFFXML string into a system generator object"
from openmmforcefields.generators import SystemGenerator
from openff.toolkit.typing.engines.smirnoff import ForceField
from openff.toolkit.topology import Molecule
import openmm

# load the ff
ff = ForceField("openff-2.0.0.offxml")
# create a system generator
system_gen = SystemGenerator(
    forcefields=['amber/ff14SB.xml', 'amber/tip3p_standard.xml'],
    small_molecule_forcefield=ff.to_string()
)
mol = Molecule.from_smiles("CC")
system = system_gen.create_system(topology=mol.to_topology().to_openmm(), molecules=mol)
with open("system.xml", "w") as output:
    output.write(openmm.XmlSerializer.serialize(system))

by @jthorton in #288

• Support system and template generator for Espaloma 0.3.* (espaloma 0.2.* is no longer supported) by @ijpulidos in #293

CI

• Bump codecov/codecov-action from 3.1.0 to 3.1.1 by @dependabot in #238
• Switch to setup-micromamba by @mattwthompson in #274
• Scattered fixes to get CI running by @mattwthompson in #290

Docs

• Update docstrings, run in CI by @mattwthompson in #240

New Contributors

• @jthorton made their first contribution in #288

Full Changelog: 0.11.2...0.12.0

0.11.2 Bugfix Release (fix new openff toolkit support)

Quick Look

@mikemhenry bungled the support of the new OpenFF Toolkit. This release fixes that.

What's Changed

• add back in openeye toolkit by @mikemhenry in #226
• Tweak CI: Switch to Micromamba, pin to supported OpenFF Toolkit versions by @mattwthompson in #232
• Bump codecov/codecov-action from 2.1.0 to 3.1.0 by @dependabot in #197
• Bump actions/checkout from 2 to 3.0.2 by @dependabot in #196
• Fix toolkit tests by @mikemhenry in #227
• make sure we don't install the newest toolkit by mistake by @mikemhenry in #237

Full Changelog: 0.11.1...0.11.2

0.11.1 Bugfix Release - Add support for new openff-toolkit 0.11

Quick Look

This bug fix release mostly fixes regressions when introduced during development of 0.11.1, hence many of these bugs never made it into a release.
The main highlight is we now support the new openff-toolkit 0.11 and have backwards compatible support for older versions.
See changelog below for more details.

What's Changed

• Remove espaloma debug line by @mikemhenry in #201
• Remove debug prints. by @ijpulidos in #198
• Fix CI by @mikemhenry in #202
• Fix accidental elimination of torsions after 0.11.0 release by @jchodera in #208
• Fix #210: gaff atom type name is now correctly passed by @jchodera in #212
• Fix #211 : Use basename instead of full path for cache database table names by @jchodera in #213
• Update for upcoming OpenFF Toolkit API breaks by @mattwthompson in #191
• Remove oe license check by @mikemhenry in #220
• Fix #214: Leave temp dir before raising exceptions by @rosemary-cresset in #218
• Fix #216: Remove % sign from parmchk2 command by @rosemary-cresset in #217
• Fix #215: Copy gaff dat file to temp dir by @rosemary-cresset in #219

New Contributors

• @ijpulidos made their first contribution in #198
• @mattwthompson made their first contribution in #191
• @rosemary-cresset made their first contribution in #218

Full Changelog: 0.11.0...0.11.1

0.11.0 Experimental support for espaloma for small molecule parameter generation

This release adds experimental support for generating small molecule parameters with the graph convolutional model espaloma, which must be installed separately to use this capability. This feature is documented in the README.

Bugfixes:

• Some fixes to GLYCAM support (#180)

0.10.0

• Update imports and tests for OpenMM 7.6 #173
• Fix tests to test GLYCAM and use new way of importing for openmm #177
• Enable GLYCAM06j-1 forcefield conversion #156
• Bump codecov/codecov-action from 1 to 2.0.3 #171
• fix dependabot so it can see our secrets #167
• Testing CI #155

Updates for openforcefield 0.9.0 toolkit on conda-forge

This release utilizes the new openforcefield 0.9.0 toolkit now distributed through conda-forge.

This release contains updated CHARMM and AMBER force fields for use with OpenMM 7.5.0 and the new openforcefield 0.9.0 toolkit, both now distributed through conda-forge.

Amber force fields were updated to versions distributed with AmberTools 20.15
Added AMBER phosaa14SB parameters for phosphorylated amino acids
CHARMM force fields were updated to July 2020 CHARMM additive force field releaseThis release utilizes the new openforcefield 0.9.0 toolkit now distributed through conda-forge.

This release contains updated CHARMM and AMBER force fields for use with OpenMM 7.5.0 and the new openforcefield 0.9.0 toolkit, both now distributed through conda-forge.

• Amber force fields were updated to versions distributed with AmberTools 20.15
• Added AMBER phosaa14SB parameters for phosphorylated amino acids
• CHARMM force fields were updated to July 2020 CHARMM additive force field release

0.8.0 Updates for openforcefield 0.7.1 toolkit

• (PR #128) Update README for openff-1.2.0 and use openforcefield 0.7.1 toolkit API for identifying installed force fields

Bugfix release to ensure compatibility with openforcefield toolkit 0.7.0

Bugfixes:

• (PR #121) Add compatibility with openforcefield 0.7.0

Bugfix release: Compatibility with openforcefield toolkit 0.7.0 and auto-detection of installed openforcefield force fields

Bugfixes

• (PR #119) Handle None partial charges in openforcefield Molecule objects (needed in openforcefield toolkit 0.7.0)

Features

• (PR #120) Auto-detect installed SMIRNOFF force fields