Recent Releases of https://github.com/cnpem/atompacker
https://github.com/cnpem/atompacker - AtomPacker v0.5.1
AtomPacker
AtomPacker is a Python package for packing nanoclusters into supramolecular cages. It includes tools for detecting cavities in molecular structures, identifying openings, packing nanoclusters into these cavities, summarizing cluster characteristics (e.g., diameters, number of atoms), and exporting the structures of cavities and clusters.
What's Changed
- Bump pytest from 8.4.1 to 8.4.2 by @dependabot[bot] in https://github.com/cnpem/AtomPacker/pull/69
- Handle maximum diameter calculation for different cluster sizes
Full Changelog: https://github.com/cnpem/AtomPacker/compare/0.5.0...0.5.1
- Python
Published by jvsguerra 9 months ago
https://github.com/cnpem/atompacker - AtomPacker v0.5.0
AtomPacker
AtomPacker is a Python package for packing nanoclusters into supramolecular cages. It includes tools for detecting cavities in molecular structures, identifying openings, packing nanoclusters into these cavities, summarizing cluster characteristics (e.g., diameters, number of atoms), and exporting the structures of cavities and clusters.
Full Changelog: https://github.com/cnpem/AtomPacker/compare/0.4.4...0.5.0
- Python
Published by jvsguerra 10 months ago
https://github.com/cnpem/atompacker - AtomPacker v0.4.4
AtomPacker
AtomPacker is a Python package for packing nanoclusters into supramolecular cages. It includes tools for detecting cavities in molecular structures, identifying openings, packing nanoclusters into these cavities, summarizing cluster characteristics (e.g., diameters, number of atoms), and exporting the structures of cavities and clusters.
Full Changelog: https://github.com/cnpem/AtomPacker/compare/0.4.3...0.4.4
- Python
Published by jvsguerra 10 months ago
https://github.com/cnpem/atompacker - AtomPacker v0.4.3
AtomPacker
AtomPacker is a Python package for packing nanoclusters into supramolecular cages. It includes tools for detecting cavities in molecular structures, identifying openings, packing nanoclusters into these cavities, summarizing cluster characteristics (e.g., diameters, number of atoms), and exporting the structures of cavities and clusters.
Full Changelog: https://github.com/cnpem/AtomPacker/compare/0.4.2...0.4.3
- Python
Published by jvsguerra 10 months ago
https://github.com/cnpem/atompacker - AtomPacker v0.4.2
AtomPacker
AtomPacker is a Python package for packing nanoclusters into supramolecular cages. It includes tools for detecting cavities in molecular structures, identifying openings, packing nanoclusters into these cavities, summarizing cluster characteristics (e.g., diameters, number of atoms), and exporting the structures of cavities and clusters.
Full Changelog: https://github.com/cnpem/AtomPacker/compare/0.4.1...0.4.2
- Python
Published by jvsguerra 10 months ago
https://github.com/cnpem/atompacker - AtomPacker v0.4.1
AtomPacker
AtomPacker is a Python package for packing nanoclusters into supramolecular cages. It includes tools for detecting cavities in molecular structures, identifying openings, packing nanoclusters into these cavities, summarizing cluster characteristics (e.g., diameters, number of atoms), and exporting the structures of cavities and clusters.
Full Changelog: https://github.com/cnpem/AtomPacker/compare/0.4.0...0.4.1
- Python
Published by jvsguerra 10 months ago
https://github.com/cnpem/atompacker - AtomPacker v0.4.0
AtomPacker
AtomPacker is a Python package for packing nanoclusters into supramolecular cages. It includes tools for detecting cavities in molecular structures, identifying openings, packing nanoclusters into these cavities, summarizing cluster characteristics (e.g., diameters, number of atoms), and exporting the structures of cavities and clusters.
What's Changed
- Update AtomPacker to v0.4.0 by @jvsguerra in https://github.com/cnpem/AtomPacker/pull/67
- Bump flake8 from 7.1.1 to 7.3.0 by @dependabot[bot] in https://github.com/cnpem/AtomPacker/pull/66
Full Changelog: https://github.com/cnpem/AtomPacker/compare/0.3.1...0.4.0
- Python
Published by jvsguerra 10 months ago
https://github.com/cnpem/atompacker - AtomPacker v0.3.1
AtomPacker
AtomPacker is a Python package for packing nanoclusters into supramolecular cages. It includes tools for detecting cavities in molecular structures, packing nanoclusters into these cavities, summarizing cluster characteristics (e.g., diameters, number of atoms), and exporting the structures of cavities and clusters.
What's Changed
- Bump flake8 from 7.1.0 to 7.1.1 by @dependabot in https://github.com/cnpem/AtomPacker/pull/45
- Bump black from 24.4.2 to 24.8.0 by @dependabot in https://github.com/cnpem/AtomPacker/pull/46
- Bump sphinx from 8.1.0 to 8.1.3 by @dependabot in https://github.com/cnpem/AtomPacker/pull/58
- Bump sphinx-rtd-theme from 3.0.1 to 3.0.2 by @dependabot in https://github.com/cnpem/AtomPacker/pull/59
- Add bounding box to packing by @jvsguerra in https://github.com/cnpem/AtomPacker/pull/65
- Bump ase from 3.23.0 to 3.24.0 by @dependabot in https://github.com/cnpem/AtomPacker/pull/62
- Bump pytest from 8.3.3 to 8.3.4 by @dependabot in https://github.com/cnpem/AtomPacker/pull/61
- Bump mdanalysis from 2.7.0 to 2.8.0 by @dependabot in https://github.com/cnpem/AtomPacker/pull/60
Full Changelog: https://github.com/cnpem/AtomPacker/compare/0.3.0...0.3.1
- Python
Published by jvsguerra 11 months ago
https://github.com/cnpem/atompacker - AtomPacker v0.3.0
AtomPacker
AtomPacker is a Python package for packing nanoclusters into supramolecular cages. It includes tools for detecting cavities in molecular structures, packing nanoclusters into these cavities, summarizing cluster characteristics (e.g., diameters, number of atoms), and exporting the structures of cavities and clusters.
What's Changed
- Bump biopython from 1.83.0 to 1.84 by @dependabot in https://github.com/cnpem/AtomPacker/pull/32
- Add grid-search optimization for rotation and translation, and filter clashing atoms in nanocluster by @jvsguerra in https://github.com/cnpem/AtomPacker/pull/43
Full Changelog: https://github.com/cnpem/AtomPacker/compare/0.2.1...0.3.0
- Python
Published by jvsguerra almost 2 years ago
https://github.com/cnpem/atompacker - AtomPacker v0.2.1
AtomPacker
AtomPacker is a Python package for packing nanoclusters into supramolecular cages. It includes tools for detecting cavities in molecular structures, packing nanoclusters into these cavities, summarizing cluster characteristics (e.g., diameters, number of atoms), and exporting the structures of cavities and clusters.
Full Changelog: https://github.com/cnpem/AtomPacker/compare/0.2.0...0.2.1
- Python
Published by jvsguerra almost 2 years ago
https://github.com/cnpem/atompacker - AtomPacker v0.2.0
AtomPacker
AtomPacker is a Python package for packing nanoclusters into supramolecular cages. It includes tools for detecting cavities in molecular structures, packing nanoclusters into these cavities, summarizing cluster characteristics (e.g., diameters, number of atoms), and exporting the structures of cavities and clusters.
What's Changed
- Bump black from 23.12.1 to 24.4.2 by @dependabot in https://github.com/cnpem/AtomPacker/pull/7, https://github.com/cnpem/AtomPacker/pull/9, https://github.com/cnpem/AtomPacker/pull/11, https://github.com/cnpem/AtomPacker/pull/17, https://github.com/cnpem/AtomPacker/pull/20, https://github.com/cnpem/AtomPacker/pull/22
- Bump pandas from 2.2.0 to 2.2.2 by @dependabot in https://github.com/cnpem/AtomPacker/pull/13, https://github.com/cnpem/AtomPacker/pull/19
- Bump pykvfinder from 0.6.12 to 0.6.14 by @dependabot and @jvsguerra in https://github.com/cnpem/AtomPacker/pull/24, https://github.com/cnpem/AtomPacker/pull/31
- Bump pytest from 7.4.4 to 8.2.2 by @dependabot in https://github.com/cnpem/AtomPacker/pull/8, https://github.com/cnpem/AtomPacker/pull/14, https://github.com/cnpem/AtomPacker/pull/15, https://github.com/cnpem/AtomPacker/pull/16, https://github.com/cnpem/AtomPacker/pull/23, https://github.com/cnpem/AtomPacker/pull/25, https://github.com/cnpem/AtomPacker/pull/27
- Integrate ASE package to AtomPacker by @jvsguerra in https://github.com/cnpem/AtomPacker/pull/31
New Contributors
- @dependabot made their first contribution in https://github.com/cnpem/AtomPacker/pull/7
Full Changelog: https://github.com/cnpem/AtomPacker/compare/v0.1.0...0.2.0
- Python
Published by jvsguerra almost 2 years ago
https://github.com/cnpem/atompacker - AtomPacker v0.2.0
AtomPacker
AtomPacker is a Python package for packing nanoclusters into supramolecular cages. It includes tools for detecting cavities in molecular structures, packing nanoclusters into these cavities, summarizing cluster characteristics (e.g., diameters, number of atoms), and exporting the structures of cavities and clusters.
What's Changed
- Bump black from 23.12.1 to 24.4.2 by @dependabot in https://github.com/cnpem/AtomPacker/pull/7, https://github.com/cnpem/AtomPacker/pull/9, https://github.com/cnpem/AtomPacker/pull/11, https://github.com/cnpem/AtomPacker/pull/17, https://github.com/cnpem/AtomPacker/pull/20, https://github.com/cnpem/AtomPacker/pull/22.
- Bump pytest from 7.4.4 to 8.2.2 by @dependabot in https://github.com/cnpem/AtomPacker/pull/8, https://github.com/cnpem/AtomPacker/pull/14, https://github.com/cnpem/AtomPacker/pull/15, https://github.com/cnpem/AtomPacker/pull/16, https://github.com/cnpem/AtomPacker/pull/23, https://github.com/cnpem/AtomPacker/pull/25, https://github.com/cnpem/AtomPacker/pull/27
- Bump pandas from 2.2.0 to 2.2.2 by @dependabot in https://github.com/cnpem/AtomPacker/pull/13, https://github.com/cnpem/AtomPacker/pull/19
- Bump pykvfinder from 0.6.12 to 0.6.14 by @dependabot and @jvsguerra in https://github.com/cnpem/AtomPacker/pull/24, https://github.com/cnpem/AtomPacker/pull/31
- Integrate ASE package to AtomPacker by @jvsguerra in https://github.com/cnpem/AtomPacker/pull/31
New Contributors
- @dependabot made their first contribution in https://github.com/cnpem/AtomPacker/pull/7
Full Changelog: https://github.com/cnpem/AtomPacker/compare/v0.1.0...v0.2.0
- Python
Published by jvsguerra almost 2 years ago
https://github.com/cnpem/atompacker - AtomPacker v0.1.0
AtomPacker
AtomPacker is a Python package designed for efficiently packing nanoparticle atoms into supramolecular cages. This release introduces two pipelines for packing nanoparticle atoms inside a supramolecular cage:
- Freely Packing and Filtering: Utilize Packmol to pack nanoparticle atoms freely and filter them inside the cavity.
- Boundary-Constrained Packing and Filtering: Employ Packmol within a boundary to pack nanoparticle atoms and filter them inside the cavity.
What's Changed
- New api by @jvsguerra in https://github.com/jvsguerra/AtomPacker/pull/1
New Contributors
- @jvsguerra made their first contribution in https://github.com/jvsguerra/AtomPacker/pull/1
Full Changelog: https://github.com/jvsguerra/AtomPacker/commits/v0.1.0
- Python
Published by jvsguerra over 2 years ago