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Recent Releases of openff-interchange

openff-interchange - 0.4.5

What's Changed

  • Fix JSON deserialization with preset charges by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1274
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/openforcefield/openff-interchange/pull/1285
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/openforcefield/openff-interchange/pull/1292
  • Bump actions/checkout from 4 to 5 by @dependabot[bot] in https://github.com/openforcefield/openff-interchange/pull/1293
  • Fix box_shape docstring by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1294
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/openforcefield/openff-interchange/pull/1303
  • Bump OpenEye Toolkits to 2025 line by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1305
  • Handle NAGLCharges by @j-wags in https://github.com/openforcefield/openff-interchange/pull/1206
  • Make padding argument optional, avoid over-specifying inputs by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1302
  • Finalize 0.4.5 release notes by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1307

Full Changelog: https://github.com/openforcefield/openff-interchange/compare/v0.4.4...v0.4.5

- Python
Published by mattwthompson 10 months ago

openff-interchange - 0.4.4

What's Changed

  • Remove obsolete warnings of experimental/unstable status by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1259
  • Remove importlib_metadata backport when loading plugins by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1263
  • Skip molecules with zero count in Packmol wrapper by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1272
  • Implement SLTCAP in solvate_topology by @chapincavender in https://github.com/openforcefield/openff-interchange/pull/1273
  • Finalize 0.4.4 release notes by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1277

New Contributors

  • @chapincavender made their first contribution in https://github.com/openforcefield/openff-interchange/pull/1273

Full Changelog: https://github.com/openforcefield/openff-interchange/compare/v0.4.3...v0.4.4

- Python
Published by mattwthompson 11 months ago

openff-interchange - v0.4.3

What's Changed

  • Make protein-ligand example charge-neutral by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1175
  • Drop "v0.4 changes" section by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1173
  • Add smirnoff-plugins back to CI by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1176
  • Always use openmm.LangevinMiddleIntegrator by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1137
  • Do not assume molecules are grouped by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1186
  • Update Interchange.combine warning by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1183
  • Test on Python 3.13 by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1174
  • Match toolkit behavior when writing PDB files by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1192
  • Add CODEOWNERS file by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1199
  • Fix improper atom ordering in LAMMPS by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1200
  • LAMMPS improper atom order by @benjamindjensen in https://github.com/openforcefield/openff-interchange/pull/1195
  • Add example loading and comparing energy evaluations of prepared SAMPL6 system by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1187
  • Drop Python 3.10 by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1194
  • Remove hybrid pair styles by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1205
  • Add (optional) type labels to LAMMPS export by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1216
  • LAMMPS type labels by @benjamindjensen in https://github.com/openforcefield/openff-interchange/pull/1208
  • Support importing (some) virtual sites in Interchange.from_openmm by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1081
  • Do not treat topology argument as optional by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1215
  • Improve errors when parsing GROMACS files by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1224
  • Treat asterisks as comments in GROMACS topology files by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1225
  • Document how to control GROMACS molecule names by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1241
  • Use pyedr instead of panedr by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1243
  • Improve detailed energy reporting by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1229
  • Add simple charge array getter by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1219
  • Allow Interchange.combine when cutoffs differ by tiny amount by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1250
  • Have get_charge_array fail when virtual sites are present by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1255
  • Set positions from .gro files by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1220
  • Finalize release v0.4.3 by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1253

New Contributors

  • @benjamindjensen made their first contribution in https://github.com/openforcefield/openff-interchange/pull/1195

Full Changelog: https://github.com/openforcefield/openff-interchange/compare/v0.4.2...v0.4.3

- Python
Published by mattwthompson 11 months ago

openff-interchange - 0.4.2

What's Changed

  • Read GROMACS topology files split into .itp files by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1120
  • Add center-of-mass motion remover in OpenMM export by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1133
  • Cache some charge increment calculations by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1126
  • Handle OpenMM version parsing in regression tests by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1140
  • Document why tolerance is removed from box edges by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1159
  • Document sharp edge of charges and Interchange.combine by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1155
  • Error when non-bonded 1-4 scaling factors differ significantly by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1153
  • Fixing some packmol interface docs. by @IAlibay in https://github.com/openforcefield/openff-interchange/pull/1163
  • Update experimental tag on examples, tests, experimental docs by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1150
  • Finalize 0.4.2 release notes by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1171

New Contributors

  • @IAlibay made their first contribution in https://github.com/openforcefield/openff-interchange/pull/1163

Full Changelog: https://github.com/openforcefield/openff-interchange/compare/v0.4.1...v0.4.2

- Python
Published by mattwthompson over 1 year ago

openff-interchange - 0.4.1

What's Changed

  • Log charge assignment by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1053
  • Handle some edge cases with preset charges by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1070
  • Switch CI to use macos-latest by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1092
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/openforcefield/openff-interchange/pull/1094
  • Constrain openmm =8.1.2 in tests by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1100
  • Switch version handling to to versioningit by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1097
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/openforcefield/openff-interchange/pull/1099
  • Fix RTD build by @Yoshanuikabundi in https://github.com/openforcefield/openff-interchange/pull/1103
  • Defer some third-party imports for quicker high-level imports by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1085
  • Allow HMR with virtual sites in OpenMM by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1080
  • Bump codecov/codecov-action from 4 to 5 by @dependabot in https://github.com/openforcefield/openff-interchange/pull/1108
  • Revert "Bump codecov/codecov-action from 4 to 5" by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1112
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/openforcefield/openff-interchange/pull/1113
  • Discard other conformers when packing by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1111
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/openforcefield/openff-interchange/pull/1116
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/openforcefield/openff-interchange/pull/1117
  • Document Pydantic/Pint helpers by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1105
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/openforcefield/openff-interchange/pull/1121
  • Bump mamba-org/setup-micromamba from 1 to 2 by @dependabot in https://github.com/openforcefield/openff-interchange/pull/1072
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/openforcefield/openff-interchange/pull/1128
  • Test JSON roundtrip after Interchange.from_openmm by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1089
  • Update CI by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1123
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/openforcefield/openff-interchange/pull/1129
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/openforcefield/openff-interchange/pull/1130
  • Update beta workflow by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1131
  • Optionally write GROMACS topologies as multiple .itp files by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1119
  • Create blank collections when importing only water by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1134
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/openforcefield/openff-interchange/pull/1138
  • Improve testing of GROMACS import by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1118
  • More consistently use existing charge caching by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1115
  • Improve performance of Interchange.from_smirnoff on polymers by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1122
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/openforcefield/openff-interchange/pull/1147
  • Consolidate Python config files by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1104
  • Finalize 0.4.1 release notes by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1148

Full Changelog: https://github.com/openforcefield/openff-interchange/compare/v0.4.0...v0.4.1

- Python
Published by mattwthompson over 1 year ago

openff-interchange - 0.4.0

This release includes several new features, bug fixes, documentation improvements, and some behavior changes. Some features previously tagged as experimental are now, with some limitations, in the public API.

For more, see the 0.4.0 release notes, installation instructions, or full documentation.

What's Changed

  • Migrate to Pydantic v2 by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/964
  • Make Interchange.topology a required field by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/995
  • Collection ergonomics by @Yoshanuikabundi in https://github.com/openforcefield/openff-interchange/pull/990
  • Improve documentation of from_openmm and related features by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1008
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/openforcefield/openff-interchange/pull/1025
  • Simplify access to Pydantic v1 API by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1026
  • Migrate formatting to ruff by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1032
  • Convenience methods for producing run input files by @Yoshanuikabundi in https://github.com/openforcefield/openff-interchange/pull/1027
  • Do not write vacuum simulations to GROMACS files by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1034
  • API cleanup by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1043
  • Add amber example by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1046
  • Add to_amber convenience method by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1041
  • Fix default .charges by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1066
  • Use update instead of assignment to set _charges by @ntBre in https://github.com/openforcefield/openff-interchange/pull/1069
  • Log packing failures by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1067
  • Error if HMR results in negative particle mass by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1065
  • Clarify to_openmm_simulation docstring and rename to_lammps(file_path) arg to prefix by @Yoshanuikabundi in https://github.com/openforcefield/openff-interchange/pull/1042
  • Fix regression tests by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1073
  • Add high-level positions getter, exclude virtual sites by default by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1074
  • Export positions with virtual sites by default by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1078
  • Decrease default density in Packmol wrappers by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1068
  • Update topology/system particle bookkeeping in OpenMM by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1051
  • Document that topology charges are ignored by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1064

New Contributors

  • @ntBre made their first contribution in https://github.com/openforcefield/openff-interchange/pull/1069

Full Changelog: https://github.com/openforcefield/openff-interchange/compare/v0.3.29...v0.4.0rc1

- Python
Published by mattwthompson over 1 year ago

openff-interchange - v0.4.0rc1

What's Changed

  • Migrate to Pydantic v2 by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/964
  • Make Interchange.topology a required field by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/995
  • Collection ergonomics by @Yoshanuikabundi in https://github.com/openforcefield/openff-interchange/pull/990
  • Improve documentation of from_openmm and related features by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1008
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/openforcefield/openff-interchange/pull/1025
  • Simplify access to Pydantic v1 API by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1026
  • Migrate formatting to ruff by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1032
  • Convenience methods for producing run input files by @Yoshanuikabundi in https://github.com/openforcefield/openff-interchange/pull/1027
  • Do not write vacuum simulations to GROMACS files by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1034
  • API cleanup by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1043
  • Add amber example by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1046
  • Add to_amber convenience method by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1041
  • Fix default .charges by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1066
  • Use update instead of assignment to set _charges by @ntBre in https://github.com/openforcefield/openff-interchange/pull/1069
  • Log packing failures by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1067
  • Error if HMR results in negative particle mass by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1065
  • Clarify to_openmm_simulation docstring and rename to_lammps(file_path) arg to prefix by @Yoshanuikabundi in https://github.com/openforcefield/openff-interchange/pull/1042
  • Fix regression tests by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1073
  • Add high-level positions getter, exclude virtual sites by default by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1074
  • Export positions with virtual sites by default by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1078
  • Decrease default density in Packmol wrappers by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1068
  • Update topology/system particle bookkeeping in OpenMM by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1051
  • Document that topology charges are ignored by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1064

New Contributors

  • @ntBre made their first contribution in https://github.com/openforcefield/openff-interchange/pull/1069

Full Changelog: https://github.com/openforcefield/openff-interchange/compare/v0.3.29...v0.4.0rc1

- Python
Published by mattwthompson over 1 year ago

openff-interchange - v0.4.0beta2

What's Changed

  • Migrate to Pydantic v2 by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/964
  • Make Interchange.topology a required field by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/995
  • Collection ergonomics by @Yoshanuikabundi in https://github.com/openforcefield/openff-interchange/pull/990
  • Improve documentation of from_openmm and related features by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1008
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/openforcefield/openff-interchange/pull/1025
  • Simplify access to Pydantic v1 API by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1026
  • Migrate formatting to ruff by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1032
  • Convenience methods for producing run input files by @Yoshanuikabundi in https://github.com/openforcefield/openff-interchange/pull/1027
  • Do not write vacuum simulations to GROMACS files by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1034
  • API cleanup by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1043
  • Add amber example by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1046
  • Add to_amber convenience method by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1041
  • Fix default .charges by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1066
  • Use update instead of assignment to set _charges by @ntBre in https://github.com/openforcefield/openff-interchange/pull/1069
  • Log packing failures by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1067
  • Error if HMR results in negative particle mass by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1065
  • Clarify to_openmm_simulation docstring and rename to_lammps(file_path) arg to prefix by @Yoshanuikabundi in https://github.com/openforcefield/openff-interchange/pull/1042
  • Fix regression tests by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1073
  • Add high-level positions getter, exclude virtual sites by default by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1074

New Contributors

  • @ntBre made their first contribution in https://github.com/openforcefield/openff-interchange/pull/1069

Full Changelog: https://github.com/openforcefield/openff-interchange/compare/v0.3.29...v0.4.0beta2

- Python
Published by mattwthompson over 1 year ago

openff-interchange - v0.4.0beta1

What's Changed

  • Migrate to Pydantic v2 by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/964
  • Make Interchange.topology a required field by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/995
  • Collection ergonomics by @Yoshanuikabundi in https://github.com/openforcefield/openff-interchange/pull/990
  • Improve documentation of from_openmm and related features by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1008
  • Migrate formatting to ruff by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1032
  • Convenience methods for producing run input files by @Yoshanuikabundi in https://github.com/openforcefield/openff-interchange/pull/1027
  • Do not write vacuum simulations to GROMACS files by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1034
  • API changes by @mattwthompson in https://github.com/openforcefield/openff-interchange/pull/1043
  • Remove openff-models dependency in d35a4b53a9399b3c5f312cc7dfeda1990038b398

Full Changelog: https://github.com/openforcefield/openff-interchange/compare/v0.3.29...v0.4.0beta1

- Python
Published by mattwthompson almost 2 years ago

openff-interchange - 0.3.29

0.3.29 GROMACS export performance improements and bugfixes

For the complete release notes, please see the release history.

For help installing Interchange, the installation instructions.

Please report bugs, request features, or ask questions through our issue tracker.

Please note that there may still be some changes to the API prior to a stable 1.0.0 release.

- Python
Published by mattwthompson almost 2 years ago

openff-interchange - 0.3.28

0.3.28 Interoperability bugfixes

For the complete release notes, please see the release history.

For help installing Interchange, the installation instructions.

Please report bugs, request features, or ask questions through our issue tracker.

Please note that there may still be some changes to the API prior to a stable 1.0.0 release.

- Python
Published by mattwthompson almost 2 years ago

openff-interchange - 0.3.27

0.3.27 Interoperability improvements and bugfixes

For the complete release notes, please see the release history.

For help installing Interchange, the installation instructions.

Please report bugs, request features, or ask questions through our issue tracker.

Please note that there may still be some changes to the API prior to a stable 1.0.0 release.

- Python
Published by mattwthompson about 2 years ago

openff-interchange - 0.3.26

0.3.26 Interoperability and documentation improvements

This release drops support for Python 3.9, updates some notebooks, and some experimental features

For the complete release notes, please see the release history.

For help installing Interchange, the installation instructions.

Please report bugs, request features, or ask questions through our issue tracker.

Please note that there may still be some changes to the API prior to a stable 1.0.0 release.

- Python
Published by mattwthompson about 2 years ago

openff-interchange - 0.3.25

0.3.25 Virtual site improvements

This release updates two example notebooks and fixes a bug in which virtual site parameters sometimes clashed and.

For the complete release notes, please see the release history.

For help installing Interchange, the installation instructions.

Please report bugs, request features, or ask questions through our issue tracker.

Please note that there may still be some changes to the API prior to a stable 1.0.0 release.

- Python
Published by mattwthompson about 2 years ago

openff-interchange - 0.3.24

0.3.24 Interoperability improvements

This release fixes two bugs adjacent to Interchange.from_openmm and improves testing with it and Interchange.combine.

For the complete release notes, please see the release history.

For help installing Interchange, the installation instructions.

Please report bugs, request features, or ask questions through our issue tracker.

Please note that there may still be some changes to the API prior to a stable 1.0.0 release.

- Python
Published by mattwthompson about 2 years ago

openff-interchange - 0.3.23

0.3.23 Interoperability improvements

This release includes performances improvements with large LAMMPS systems, fixes some bugs with virtual sites an non-standard functional forms, and adds warnings to the user when an engine cannot wholly implement a SMIRNOFF force field.

For the complete release notes, please see the release history.

For help installing Interchange, the installation instructions.

Please report bugs, request features, or ask questions through our issue tracker.

Please note that there may still be some changes to the API prior to a stable 1.0.0 release.

- Python
Published by mattwthompson over 2 years ago

openff-interchange - 0.3.22

0.3.22 GROMACS rigid water bugfix

This release fixes a bug in which rigid water geometries were sometimes incorrectly written to GROMACS files.

For the complete release notes, please see the release history.

For help installing Interchange, the installation instructions.

Please report bugs, request features, or ask questions through our issue tracker.

Please note that there may still be some changes to the API prior to a stable 1.0.0 release.

- Python
Published by mattwthompson over 2 years ago

openff-interchange - 0.3.21

0.3.21 Virtual site exclusions bugfix

This release fixes a bug in which, in many cases, exclusions between virtual sites were not correctly added to the relevant OpenMM force.

For the complete release notes, please see the release history.

For help installing Interchange, the installation instructions.

Please report bugs, request features, or ask questions through our issue tracker.

Please note that there may still be some changes to the API prior to a stable 1.0.0 release.

- Python
Published by mattwthompson over 2 years ago

openff-interchange - 0.3.20

0.3.20 Hydrogen mass repartitioning

This release adds hydrogen mass repartitioning (HMR) to the OpenMM and GROMACS exports. To apply HMR, the hydrogen_mass argument to the relevant Interchange.to_x method.

For the complete release notes, please see the release history.

For help installing Interchange, the installation instructions.

Please report bugs, request features, or ask questions through our issue tracker.

Please note that there may still be some changes to the API prior to a stable 1.0.0 release.

- Python
Published by mattwthompson over 2 years ago

openff-interchange - 0.3.19

0.3.19 Interoperability improvements

This release includes several changes to better support importing from OpenMM objects, visualizing Interchanges, and improves some existing operations when virtual sites are present.

For the complete release notes, please see the release history.

For help installing Interchange, the installation instructions.

Please report bugs, request features, or ask questions through our issue tracker.

Please note that there may still be some changes to the API prior to a stable 1.0.0 release.

- Python
Published by mattwthompson over 2 years ago

openff-interchange - 0.3.18

0.3.18 Bugfix release

This release fixes a rare bug involving atom ordering potentially disrupting caching used in the bookkeeping of partial charges.

For the complete release notes, please see the release history.

For help installing Interchange, the installation instructions.

Please report bugs, request features, or ask questions through our issue tracker.

Please note that there may still be some changes to the API prior to a stable 1.0.0 release.

- Python
Published by mattwthompson over 2 years ago

openff-interchange - 0.3.17

0.3.17 Improved OpenMM virtual site implementation

This release reverts some previous changes away from the use of openmm.LocalCoordinatesSite, which is the only strictly proper way to handle SMIRNOFF-style virtual sites in OpenMM.

For the complete release notes, please see the release history.

For help installing Interchange, the installation instructions.

Please report bugs, request features, or ask questions through our issue tracker.

Please note that there may still be some changes to the API prior to a stable 1.0.0 release.

- Python
Published by mattwthompson over 2 years ago

openff-interchange - 0.3.16

0.3.16 Improved virtual site support

This release exposes an ewald_tolerance argument to OpenMM methods and refactors how OpenMM virtual site objects, and positions of systems containing virtual sites, are constructed

For the complete release notes, please see the release history.

For help installing Interchange, the installation instructions.

Please report bugs, request features, or ask questions through our issue tracker.

Please note that there may still be some changes to the API prior to a stable 1.0.0 release.

- Python
Published by mattwthompson over 2 years ago

openff-interchange - 0.3.15

0.3.15 Bugfix release

This release fixes four bugs with no common theme.

For the complete release notes, please see the release history.

For help installing Interchange, the installation instructions.

Please report bugs, request features, or ask questions through our issue tracker.

Please note that there may still be some changes to the API prior to a stable 1.0.0 release.

- Python
Published by mattwthompson over 2 years ago

openff-interchange - 0.3.14

0.3.14 Bugfix release and improved virtual site support

This release fixes a bug with charge assignment when virtual sites are present and improves virtual site support in GROMACS, including BondCharge virtual sites and four-site water models.

For the complete release notes, please see the release history.

For help installing Interchange, the installation instructions.

Please report bugs, request features, or ask questions through our issue tracker.

Please note that there may still be some changes to the API prior to a stable 1.0.0 release.

- Python
Published by mattwthompson almost 3 years ago

openff-interchange - 0.3.13

0.3.13 Bugfix release

This release fixes a bug with BondCharge virtual sites, improves visualization of and computing positions of virtual sites, and refactors the OpenMM export to use more standard virtual site types.

For the complete release notes, please see the release history.

For help installing Interchange, the installation instructions.

Please report bugs, request features, or ask questions through our issue tracker.

Please note that there may still be some changes to the API prior to a stable 1.0.0 release.

- Python
Published by mattwthompson almost 3 years ago

openff-interchange - 0.3.12

0.3.12 Minor feature release

This release makes OpenMM an optional dependency at runtime. Installing the conda package openff-interchange-base, or installing from source, is required.

For the complete release notes, please see the release history.

For help installing Interchange, the installation instructions.

Please report bugs, request features, or ask questions through our issue tracker.

Please note that there may still be some changes to the API prior to a stable 1.0.0 release.

- Python
Published by mattwthompson almost 3 years ago

openff-interchange - 0.3.11

0.3.11 Minor feature release

This release updates some internal components and Interchange.to_openmm to use 0.4 version of vdWHandler.

For the complete release notes, please see the release history.

For help installing Interchange, the installation instructions.

Please report bugs, request features, or ask questions through our issue tracker.

Please note that there may still be some changes to the API prior to a stable 1.0.0 release.

- Python
Published by mattwthompson almost 3 years ago

openff-interchange - 0.3.10

0.3.10 Minor feature release

This release includes some updates to the Foyer compatibility layer, installation-level compatibility with Pydantic 2, and support for the future 0.4 version of vdWHandler.

For the complete release notes, please see the release history.

For help installing Interchange, the installation instructions.

Please report bugs, request features, or ask questions through our issue tracker.

Please note that there may still be some changes to the API prior to a stable 1.0.0 release.

- Python
Published by mattwthompson almost 3 years ago

openff-interchange - 0.3.9

0.3.9 Bugfix release

This release makes Interchange.from_openmm a class method, which it was always intended to be, as a shortcut to the wrapped function.

For the complete release notes, please see the release history.

For help installing Interchange, the installation instructions.

Please report bugs, request features, or ask questions through our issue tracker.

Please note that there may still be some changes to the API prior to a stable 1.0.0 release.

- Python
Published by mattwthompson almost 3 years ago

openff-interchange - 0.3.8

0.3.8 Bugfix release

This release improves handling of positions in some exporters when virtual sites are present.

For the complete release notes, please see the release history.

For help installing Interchange, the installation instructions.

Please report bugs, request features, or ask questions through our issue tracker.

Please note that there may still be some changes to the API prior to a stable 1.0.0 release.

- Python
Published by mattwthompson almost 3 years ago

openff-interchange - 0.3.7

0.3.7 Bugfix release

This release updates example notebooks and adds support for the geometric mixing rule in the OpenMM export.

For the complete release notes, please see the release history.

For help installing Interchange, the installation instructions.

Please report bugs, request features, or ask questions through our issue tracker.

Please note that there may still be some changes to the API prior to a stable 1.0.0 release.

- Python
Published by mattwthompson almost 3 years ago

openff-interchange - 0.3.6

0.3.6 Bugfix release

This release fixes a bug in exception handling and improves support for non-rectangular boxes.

For the complete release notes, please see the release history.

For help installing Interchange, the installation instructions.

Please report bugs, request features, or ask questions through our issue tracker.

Please note that there may still be some changes to the API prior to a stable 1.0.0 release.

- Python
Published by mattwthompson almost 3 years ago

openff-interchange - 0.3.5

0.3.5 Bugfix release

This release fixes bugs in Interchange.to_gromacs and improves JSON serialization/deserialization.

For the complete release notes, please see the release history.

For help installing Interchange, the installation instructions.

Please report bugs, request features, or ask questions through our issue tracker.

Please note that there may still be some changes to the API prior to a stable 1.0.0 release.

- Python
Published by mattwthompson about 3 years ago

openff-interchange - 0.3.4

0.3.4 Bugfix release

This release fixes a bug in Interchange.to_gromacs (and Interchange.to_top) in which [ settles ] directives may be written with incorrect unit conversions.

For the complete release notes, please see the release history.

For help installing Interchange, the installation instructions.

Please report bugs, request features, or ask questions through our issue tracker.

Please note that there may still be some changes to the API prior to a stable 1.0.0 release.

- Python
Published by mattwthompson about 3 years ago

openff-interchange - 0.3.3

0.3.3 Bugfix release

This release fixes a bug in Interchange.to_openmm with combine_nonbonded_forces=False.

For the complete release notes, please see the release history.

For help installing Interchange, the installation instructions.

Please report bugs, request features, or ask questions through our issue tracker.

Please note that there may still be some changes to the API prior to a stable 1.0.0 release.

- Python
Published by mattwthompson about 3 years ago

openff-interchange - 0.3.2

0.3.2 Bugfix release

This release fixes some issues with non-bonded exclusions in Interchange.to_prmtop.

For the complete release notes, please see the release history.

For help installing Interchange, the installation instructions.

Please report bugs, request features, or ask questions through our issue tracker.

Please note that there may still be some changes to the API prior to a stable 1.0.0 release.

- Python
Published by mattwthompson about 3 years ago

openff-interchange - 0.3.1

0.3.1 Bugfix release

This release fixes a regression in and improves the performance of Interchange.to_prmtop.

Following NEP 29, this release supports Python 3.9+.

For the complete release notes, please see the release history.

For help installing Interchange, the installation instructions.

Please report bugs, request features, or ask questions through our issue tracker.

Please note that there may still be some changes to the API prior to a stable 1.0.0 release.

- Python
Published by mattwthompson about 3 years ago

openff-interchange - 0.3.0

0.3.0 SMIRNOFF Plugins and Internal Refactors

This release adds support for SMIRNOFF plugins and GBSA parameters along with several reliability and usability improvements.

For the complete release notes, please see the release history.

For help installing Interchange, the installation instructions.

Please report bugs, request features, or ask questions through our issue tracker.

Please note that there may still be some changes to the API prior to a stable 1.0.0 release.

- Python
Published by mattwthompson about 3 years ago

openff-interchange - 0.2.3 Interoperability Improvements

0.2.3 Interoperability Improvements

This release includes assorted interoperability improvements.

For the complete release notes, please see the release history.

For help installing Interchange, the installation instructions.

Please report bugs, request features, or ask questions through our issue tracker.

Please note that there may still be some changes to the API prior to a stable 1.0.0 release.

- Python
Published by mattwthompson over 3 years ago

openff-interchange - 0.2.2 Improved Metadata Handling in Amber Exporter

0.2.2 Improved Metadata Handling in Amber Exporter

This release includes fixes in how metadata is handled in the Amber exporter.

For the complete release notes, please see the release history.

For help installing Interchange, the installation instructions.

Please report bugs, request features, or ask questions through our issue tracker.

Please note that there may still be some changes to the API prior to a stable 1.0.0 release.

- Python
Published by mattwthompson over 3 years ago

openff-interchange - 0.2.1 Performance Improvements In Exporters

0.2.1 Performance Improvements In Exporters

This release includes significant performance improvements in GROMACS (Interchange.to_top) and OpenMM (Interchange.to_openmm) exporters.

For the complete release notes, please see the release history.

For help installing Interchange, the installation instructions.

Please report bugs, request features, or ask questions through our issue tracker.

Please note that there may still be some changes to the API prior to a stable 1.0.0 release.

- Python
Published by mattwthompson almost 4 years ago

openff-interchange - 0.2.0 Biopolymer Support and Toolkit Adoption

0.2.0 Biopolymer Support and Toolkit Adoption

This release targets biopolymer support alongside version of 0.11.0 of the OpenFF Toolkit. Interchange now serves as the backend for OpenMM System creation in ForceField.create_openmm_system as part of the toolkit API, which also added ForceField.create_interchange. For more details on changes to the toolkit, see the OpenFF Toolkit release notes.

For the complete release notes, please see the release history.

For help installing Interchange, the installation instructions.

Please report bugs, request features, or ask questions through our issue tracker.

Please note that there may still be some changes to the API prior to a stable 1.0.0 release.

- Python
Published by mattwthompson almost 4 years ago

openff-interchange - 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.

- Python
Published by mattwthompson over 4 years ago

openff-interchange - 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.

- Python
Published by mattwthompson over 4 years ago

openff-interchange - 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.

- Python
Published by mattwthompson over 4 years ago

openff-interchange - 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.

- Python
Published by mattwthompson almost 5 years ago

openff-interchange - 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.

- Python
Published by mattwthompson almost 5 years ago

openff-interchange - 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.

- Python
Published by mattwthompson over 5 years ago