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Recent Releases of molify: Molecular Structure Interface

molify: Molecular Structure Interface - v0.2.2

What's Changed

  • Add tests for graph modification workflow (ASE → networkx → modify → ASE/rdkit) by @Copilot in https://github.com/zincware/molify/pull/90
  • Add DeepWiki badge to README by @PythonFZ in https://github.com/zincware/molify/pull/91
  • Remove --recursive by @PythonFZ in https://github.com/zincware/molify/pull/92
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/zincware/molify/pull/88
  • Bump version from 0.2.1 to 0.2.2 by @PythonFZ in https://github.com/zincware/molify/pull/95
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/zincware/molify/pull/94
  • JOSS manuscript by @PythonFZ in https://github.com/zincware/molify/pull/48
  • add CITATION.cff by @PythonFZ in https://github.com/zincware/molify/pull/96

New Contributors

  • @Copilot made their first contribution in https://github.com/zincware/molify/pull/90

Full Changelog: https://github.com/zincware/molify/compare/v0.2.1...v0.2.2

- Python
Published by PythonFZ 6 months ago

molify: Molecular Structure Interface - v0.2.1

What's Changed

  • use packmol from PyPI by @PythonFZ in https://github.com/zincware/molify/pull/87

Full Changelog: https://github.com/zincware/molify/compare/v0.2.0...v0.2.1

- Python
Published by PythonFZ 7 months ago

molify: Molecular Structure Interface - v0.2.0

What's Changed

  • Update README.md by @PythonFZ in https://github.com/zincware/molify/pull/67
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/zincware/molify/pull/66
  • update README to include all requried import statemtns by @PythonFZ in https://github.com/zincware/molify/pull/70
  • improve julia / packmol detection by @PythonFZ in https://github.com/zincware/molify/pull/74
  • improve pack by @PythonFZ in https://github.com/zincware/molify/pull/75
  • fix: automatically handle None bond orders in ase2rdkit by @PythonFZ in https://github.com/zincware/molify/pull/77
  • rename rdkit2ase to molify by @PythonFZ in https://github.com/zincware/molify/pull/79
  • update documentation by @PythonFZ in https://github.com/zincware/molify/pull/80
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/zincware/molify/pull/76
  • release preperation by @PythonFZ in https://github.com/zincware/molify/pull/85
  • Update README links for molify project by @PythonFZ in https://github.com/zincware/molify/pull/86

Full Changelog: https://github.com/zincware/molify/compare/v0.1.13...v0.2.0

- Python
Published by PythonFZ 7 months ago

molify: Molecular Structure Interface - molify v0.0.1a2

What's Changed

  • Update README.md by @PythonFZ in https://github.com/zincware/rdkit2ase/pull/67
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/zincware/rdkit2ase/pull/66
  • update README to include all requried import statemtns by @PythonFZ in https://github.com/zincware/rdkit2ase/pull/70
  • improve julia / packmol detection by @PythonFZ in https://github.com/zincware/rdkit2ase/pull/74
  • improve pack by @PythonFZ in https://github.com/zincware/rdkit2ase/pull/75
  • fix: automatically handle None bond orders in ase2rdkit by @PythonFZ in https://github.com/zincware/rdkit2ase/pull/77
  • rename rdkit2ase to molify by @PythonFZ in https://github.com/zincware/rdkit2ase/pull/79
  • update documentation by @PythonFZ in https://github.com/zincware/rdkit2ase/pull/80

Full Changelog: https://github.com/zincware/rdkit2ase/compare/v0.1.13...v0.0.1a2

- Python
Published by PythonFZ 7 months ago

molify: Molecular Structure Interface - v0.1.13

What's Changed

  • ensure select atoms grouped is in order by @PythonFZ in https://github.com/zincware/rdkit2ase/pull/65

Full Changelog: https://github.com/zincware/rdkit2ase/compare/v0.1.12...v0.1.13

- Python
Published by PythonFZ 10 months ago

molify: Molecular Structure Interface - v0.1.12

What's Changed

  • getcenterof_mass by @PythonFZ in https://github.com/zincware/rdkit2ase/pull/56
  • Generics in connectivity by @PythonFZ in https://github.com/zincware/rdkit2ase/pull/58
  • add selection example for boxes by @PythonFZ in https://github.com/zincware/rdkit2ase/pull/60
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci[bot] in https://github.com/zincware/rdkit2ase/pull/51
  • Add advanced atom selection and visualization functions by @PythonFZ in https://github.com/zincware/rdkit2ase/pull/63

Full Changelog: https://github.com/zincware/rdkit2ase/compare/v0.1.11...v0.1.12

- Python
Published by PythonFZ 10 months ago

molify: Molecular Structure Interface - v0.1.11

What's Changed

  • v0.1.11 by @PythonFZ in https://github.com/zincware/rdkit2ase/pull/55

Full Changelog: https://github.com/zincware/rdkit2ase/compare/v0.1.10...v0.1.11

- Python
Published by PythonFZ 11 months ago

molify: Molecular Structure Interface - v0.1.10

What's Changed

  • Add test for partial suggestions by @PythonFZ in https://github.com/zincware/rdkit2ase/pull/52
  • add vesin and pbc flag by @PythonFZ in https://github.com/zincware/rdkit2ase/pull/53

Full Changelog: https://github.com/zincware/rdkit2ase/compare/v0.1.9...v0.1.10

- Python
Published by PythonFZ 11 months ago

molify: Molecular Structure Interface - v0.1.9

What's Changed

  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/zincware/rdkit2ase/pull/41
  • Improve bond guess by @PythonFZ in https://github.com/zincware/rdkit2ase/pull/50

Full Changelog: https://github.com/zincware/rdkit2ase/compare/v0.1.8...v0.1.9

- Python
Published by PythonFZ 11 months ago

molify: Molecular Structure Interface - v0.1.8

What's Changed

  • introduce separate argument for substructure matching by @PythonFZ in https://github.com/zincware/rdkit2ase/pull/42
  • Docs by @PythonFZ in https://github.com/zincware/rdkit2ase/pull/45
  • documentation update by @PythonFZ in https://github.com/zincware/rdkit2ase/pull/47

Full Changelog: https://github.com/zincware/rdkit2ase/compare/v0.1.7...v0.1.8

- Python
Published by PythonFZ 11 months ago

molify: Molecular Structure Interface - v0.1.7

What's Changed

  • add compress and get_substructures by @PythonFZ in https://github.com/zincware/rdkit2ase/pull/37
  • rename get_substructure to get_substructures by @PythonFZ in https://github.com/zincware/rdkit2ase/pull/38
  • Update README.md by @PythonFZ in https://github.com/zincware/rdkit2ase/pull/39

Full Changelog: https://github.com/zincware/rdkit2ase/compare/v0.1.6...v0.1.7

- Python
Published by PythonFZ about 1 year ago

molify: Molecular Structure Interface - v0.1.6

What's Changed

  • add test case by @PythonFZ in https://github.com/zincware/rdkit2ase/pull/31
  • remove uffoptimize by @PythonFZ in https://github.com/zincware/rdkit2ase/pull/32
  • support connectivity as numpy data by @PythonFZ in https://github.com/zincware/rdkit2ase/pull/34
  • keep initial charge information by @PythonFZ in https://github.com/zincware/rdkit2ase/pull/35
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/zincware/rdkit2ase/pull/29
  • bump to v0.1.6 by @PythonFZ in https://github.com/zincware/rdkit2ase/pull/36

Full Changelog: https://github.com/zincware/rdkit2ase/compare/v0.1.5...v0.1.6

- Python
Published by PythonFZ about 1 year ago

molify: Molecular Structure Interface - v0.1.5

What's Changed

  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/zincware/rdkit2ase/pull/15
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/zincware/rdkit2ase/pull/16
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/zincware/rdkit2ase/pull/20
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/zincware/rdkit2ase/pull/21
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/zincware/rdkit2ase/pull/22
  • support packmol.jl by @PythonFZ in https://github.com/zincware/rdkit2ase/pull/26
  • keep bond information in ase by @PythonFZ in https://github.com/zincware/rdkit2ase/pull/28
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/zincware/rdkit2ase/pull/24

Full Changelog: https://github.com/zincware/rdkit2ase/compare/v0.1.4...v0.1.5

- Python
Published by PythonFZ about 1 year ago

molify: Molecular Structure Interface - v0.1.4

What's Changed

  • Add seed to packmol and rdkit by @PythonFZ in https://github.com/zincware/rdkit2ase/pull/12
  • Use pdb instead of xyz files by @PythonFZ in https://github.com/zincware/rdkit2ase/pull/13
  • [pre-commit.ci] pre-commit autoupdate by @pre-commit-ci in https://github.com/zincware/rdkit2ase/pull/6

New Contributors

  • @pre-commit-ci made their first contribution in https://github.com/zincware/rdkit2ase/pull/6

Full Changelog: https://github.com/zincware/rdkit2ase/compare/v0.1.3...v0.1.4

- Python
Published by PythonFZ almost 2 years ago

molify: Molecular Structure Interface - v0.1.3

What's Changed

  • pack by @PythonFZ in https://github.com/zincware/rdkit2ase/pull/5
  • V 0.1.3 by @PythonFZ in https://github.com/zincware/rdkit2ase/pull/9

Full Changelog: https://github.com/zincware/rdkit2ase/commits/v0.1.3

- Python
Published by PythonFZ almost 2 years ago