PyFraME 0.5.0__tar.gz → 0.5.1__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- {pyframe-0.5.0 → pyframe-0.5.1}/CHANGELOG.md +5 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/CITATION +3 -3
- {pyframe-0.5.0 → pyframe-0.5.1}/CITATION.cff +5 -5
- {pyframe-0.5.0 → pyframe-0.5.1}/PKG-INFO +3 -2
- {pyframe-0.5.0 → pyframe-0.5.1}/PyFraME.egg-info/PKG-INFO +3 -2
- {pyframe-0.5.0 → pyframe-0.5.1}/PyFraME.egg-info/requires.txt +1 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/README.md +1 -1
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/__init__.py +3 -3
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/version.py +1 -1
- {pyframe-0.5.0 → pyframe-0.5.1}/pyproject.toml +2 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/CONTRIBUTORS +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/LICENSE +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/MANIFEST.in +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/PyFraME.egg-info/SOURCES.txt +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/PyFraME.egg-info/dependency_links.txt +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/PyFraME.egg-info/top_level.txt +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/common/__init__.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/common/arrays.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/common/constants.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/common/elements.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/common/lennard_jones.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/common/log.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/common/potential_document.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/common/simulation_box.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/common/tensor_components.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/common/tests/constants_test.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/common/tests/elements_test.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/common/tests/lennard_jones_test.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/common/tests/log_test.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/common/tests/simulation_box_test.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/common/tests/tensor_components_test.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/common/units.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/construction/__init__.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/construction/atoms.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/construction/data/alep.csv +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/construction/data/cp3.csv +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/construction/data/ff03.csv +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/construction/data/ff94.csv +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/construction/data/lipid14.csv +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/construction/data/lipid17.csv +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/construction/data/sep.csv +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/construction/data/tip3p.csv +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/construction/exact_coordinates.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/construction/fragments.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/construction/from_system.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/construction/potential_builder.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/construction/potentials.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/construction/project.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/construction/readers.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/construction/regions.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/construction/system.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/construction/task_farming.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/construction/tests/atoms_test.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/construction/tests/conftest.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/construction/tests/data/README.md +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/construction/tests/data/precision_water.gro +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/construction/tests/data/precision_water.trr +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/construction/tests/data/precision_water.xtc +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/construction/tests/data/precision_water_double.trr +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/construction/tests/data/trajectory.gro +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/construction/tests/data/trajectory.mdp +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/construction/tests/data/trajectory.top +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/construction/tests/data/trajectory.tpr +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/construction/tests/data/trajectory.xtc +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/construction/tests/exact_coordinates_test.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/construction/tests/fragments_test.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/construction/tests/from_system_test.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/construction/tests/parameter_sets_test.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/construction/tests/potential_builder_test.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/construction/tests/potentials_test.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/construction/tests/readers_test.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/construction/tests/regions_test.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/construction/tests/system_test.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/construction/tests/task_farming_test.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/construction/tests/trajectory_test.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/construction/tests/utilities_test.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/construction/tests/writers_test.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/construction/trajectory.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/construction/utilities.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/construction/writers.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/__init__.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/combination_rules.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/dispersion_interactions.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/electrostatic_interactions.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/engine/computation.cpp +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/engine/computation.h +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/engine/engine.cpp +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/engine/global.cpp +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/engine/global.h +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/engine.pyi +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/fragment.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/induction_interactions.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/integral_driver_template.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/interaction_tensor.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/model.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/options.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/particle.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/polytensor.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/read_input.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/repulsion_interactions.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/solvers.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/subsystem.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/tensor_tools.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/tests/conftest.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/tests/data/HF.json +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/tests/data/Ne_test.json +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/tests/data/acrolein_wat_test.json +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/tests/data/act_wat_2.json +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/tests/data/act_wat_big.json +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/tests/data/act_wat_mid.json +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/tests/data/act_wat_small.json +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/tests/data/act_wat_test.json +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/tests/data/butadiene_water.json +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/tests/data/missing_classical_fragments_two_atoms_test.json +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/tests/data/missing_nuclei_two_atoms_test.json +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/tests/data/no_subsystems.json +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/tests/data/two_atom_test.json +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/tests/data/two_oxygen_nine_six_test.json +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/tests/data/two_oxygen_split_lj_test.json +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/tests/data/two_oxygen_test.json +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/tests/data/two_wat_test.json +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/tests/data/wat_in_wat_missing_lj_test.json +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/tests/data/wat_in_wat_split_lj_test.json +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/tests/data/wat_in_wat_test.json +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/tests/data/wat_in_wat_zero_lj_test.json +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/tests/dispersion_interactions_test.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/tests/electrostatic_interactions_test.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/tests/engine_arguments_test.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/tests/engine_stub_test.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/tests/engine_test.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/tests/fragment_test.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/tests/induction_interactions_test.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/tests/induction_mpi_worker.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/tests/induction_parallel_test.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/tests/integral_driver_template_test.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/tests/interaction_tensor_test.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/tests/lj_characterization_test.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/tests/lj_mpi_worker.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/tests/lj_parallel_test.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/tests/minimum_image_test.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/tests/model_test.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/tests/options_test.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/tests/particle_test.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/tests/performance.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/tests/polytensor_test.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/tests/read_input_test.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/tests/repulsion_interactions_test.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/tests/serial_test.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/tests/solvers_test.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/tests/subsystem_test.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/tests/tensor_tools_test.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/tests/totals_test.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/totals.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/py.typed +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/tests/api_test.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/pyframe/tests/layering_test.py +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/setup.cfg +0 -0
- {pyframe-0.5.0 → pyframe-0.5.1}/setup.py +0 -0
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<!-- How to write an entry: see the "Changelog" section of CONTRIBUTING.md. -->
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## [0.5.1] 2026-10-20
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## [0.5.0] 2026-10-13
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- Embedding calculations. The new embedding module computes the interaction of a quantum region with its environment
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@misc{pyframe:0.5.1,
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author = {Olsen, J. M. H. and Reinholdt, P. and Vester, J. and Heegaard, T. N. and Berger, G.},
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title = {{PyFraME}: {P}ython framework for {F}ragment-based {M}ultiscale {E}mbedding (version 0.5.
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title = {{PyFraME}: {P}ython framework for {F}ragment-based {M}ultiscale {E}mbedding (version 0.5.1)},
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year = {2026},
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doi = {10.5281/zenodo.23496949},
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note = {See https://gitlab.com/pyframe-project/pyframe}}
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message: If you use PyFraME, please cite the version you used as below.
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title: "PyFraME: Python framework for Fragment-based Multiscale Embedding"
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type: software
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date-released: "2026-10-
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version: 0.5.1
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date-released: "2026-10-20"
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doi: 10.5281/zenodo.23496949
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description: This version, 0.5.
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value: 10.5281/zenodo.23496949
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description: This version, 0.5.1.
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description: All versions, resolving to the latest.
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Version: 0.5.1
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Summary: PyFraME: Python framework for Fragment-based Multiscale Embedding
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Author-email: PyFraME Developers <pyframe-devs@pm.me>
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Maintainer-email: Jógvan Magnus Haugaard Olsen <pyframe-devs@pm.me>
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J. M. H. Olsen, P. Reinholdt, J. Vester, T. N. Heegaard, and G. Berger, *PyFraME: Python framework for Fragment-based
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Multiscale Embedding (version 0.5.1)*, **2026**. DOI: 10.5281/zenodo.23496949.
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where the version and DOI should correspond to the actual version that was
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Name: PyFraME
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Version: 0.5.
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Version: 0.5.1
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Summary: PyFraME: Python framework for Fragment-based Multiscale Embedding
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Author-email: PyFraME Developers <pyframe-devs@pm.me>
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Maintainer-email: Jógvan Magnus Haugaard Olsen <pyframe-devs@pm.me>
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@@ -35,6 +35,7 @@ Requires-Dist: h5py>=3.6
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Requires-Dist: MDAnalysis>=2.10
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Requires-Dist: mpi4py>=4.1
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Requires-Dist: numpy>=1.23.2
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Requires-Dist: pint!=0.26.2
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Requires-Dist: qcelemental>=0.26
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Requires-Dist: scikit-learn>=1.0.2
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Requires-Dist: scipy>=1.8
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@@ -136,7 +137,7 @@ How to cite
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To cite PyFraME please use a format similar to the following:
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J. M. H. Olsen, P. Reinholdt, J. Vester, T. N. Heegaard, and G. Berger, *PyFraME: Python framework for Fragment-based
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Multiscale Embedding (version 0.5.
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Multiscale Embedding (version 0.5.1)*, **2026**. DOI: 10.5281/zenodo.23496949.
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See https://gitlab.com/pyframe-project/pyframe.
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where the version and DOI should correspond to the actual version that was
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To cite PyFraME please use a format similar to the following:
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J. M. H. Olsen, P. Reinholdt, J. Vester, T. N. Heegaard, and G. Berger, *PyFraME: Python framework for Fragment-based
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Multiscale Embedding (version 0.5.
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Multiscale Embedding (version 0.5.1)*, **2026**. DOI: 10.5281/zenodo.23496949.
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See https://gitlab.com/pyframe-project/pyframe.
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where the version and DOI should correspond to the actual version that was
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@@ -101,11 +101,11 @@ def __dir__() -> list[str]:
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__version__ = version
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__copyright__ = 'Copyright (C) 2017-2026 PyFraME Contributors'
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CITATION = """@misc{pyframe:0.5.
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CITATION = """@misc{pyframe:0.5.1,
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author = {Olsen, J. M. H. and Reinholdt, P. and Vester, J. and Heegaard, T. N. and Berger, G.},
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title = {{PyFraME}: {P}ython framework for {F}ragment-based {M}ultiscale {E}mbedding (version 0.5.
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title = {{PyFraME}: {P}ython framework for {F}ragment-based {M}ultiscale {E}mbedding (version 0.5.1)},
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year = {2026},
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doi = {10.5281/zenodo.
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doi = {10.5281/zenodo.23496949},
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note = {See https://gitlab.com/pyframe-project/pyframe}}"""
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LICENSE = """Mozilla Public License Version 2.0
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"MDAnalysis>=2.10",
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"mpi4py>=4.1",
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"numpy>=1.23.2",
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# qcelemental cannot build its unit registry with pint 0.26.2, and pyframe.construction then fails to import.
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"pint!=0.26.2",
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"qcelemental>=0.26",
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"scikit-learn>=1.0.2",
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{pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/tests/data/missing_nuclei_two_atoms_test.json
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{pyframe-0.5.0 → pyframe-0.5.1}/pyframe/embedding/tests/data/wat_in_wat_missing_lj_test.json
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