imdclient 0.1.2__py3-none-any.whl → 0.1.4__py3-none-any.whl

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.
Files changed (50) hide show
  1. imdclient/{IMDREADER.py → IMD.py} +5 -4
  2. imdclient/IMDClient.py +118 -15
  3. imdclient/IMDProtocol.py +1 -0
  4. imdclient/data/gromacs/md/gromacs_v3_nst1.mdp +3 -3
  5. imdclient/data/gromacs/md/gromacs_v3_nst8.mdp +58 -0
  6. imdclient/data/lammps/md/{lammps_v3.in → lammps_v3_nst_1.in} +3 -3
  7. imdclient/data/lammps/md/lammps_v3_nst_8.in +71 -0
  8. imdclient/data/namd/md/{namd_v3.namd → namd_v3_nst_1.namd} +17 -5
  9. imdclient/data/namd/md/namd_v3_nst_8.namd +59 -0
  10. imdclient/tests/base.py +179 -45
  11. imdclient/tests/conftest.py +0 -39
  12. imdclient/tests/datafiles.py +33 -10
  13. imdclient/tests/docker_testing/docker.md +25 -0
  14. imdclient/tests/hpc_testing/gromacs/README.md +112 -0
  15. imdclient/tests/hpc_testing/gromacs/gmx_gpu_test.mdp +58 -0
  16. imdclient/tests/hpc_testing/gromacs/gmx_gpu_test.top +11764 -0
  17. imdclient/tests/hpc_testing/gromacs/struct.gro +21151 -0
  18. imdclient/tests/hpc_testing/gromacs/validate_gmx.sh +90 -0
  19. imdclient/tests/hpc_testing/lammps/README.md +62 -0
  20. imdclient/tests/hpc_testing/lammps/lammps_v3_nst_1.in +71 -0
  21. imdclient/tests/hpc_testing/lammps/topology_after_min.data +8022 -0
  22. imdclient/tests/hpc_testing/lammps/validate_lmp.sh +66 -0
  23. imdclient/tests/hpc_testing/namd/README.md +73 -0
  24. imdclient/tests/hpc_testing/namd/alanin.params +402 -0
  25. imdclient/tests/hpc_testing/namd/alanin.pdb +77 -0
  26. imdclient/tests/hpc_testing/namd/alanin.psf +206 -0
  27. imdclient/tests/hpc_testing/namd/namd_v3_nst_1.namd +59 -0
  28. imdclient/tests/hpc_testing/namd/validate_namd.sh +71 -0
  29. imdclient/tests/server.py +2 -11
  30. imdclient/tests/test_gromacs.py +32 -10
  31. imdclient/tests/test_imdclient.py +69 -0
  32. imdclient/tests/test_imdreader.py +74 -1
  33. imdclient/tests/test_lammps.py +57 -12
  34. imdclient/tests/test_manual.py +223 -65
  35. imdclient/tests/test_namd.py +101 -14
  36. imdclient/tests/test_stream_analysis.py +1 -1
  37. imdclient/tests/utils.py +0 -1
  38. imdclient-0.1.4.dist-info/LICENSE +5 -0
  39. imdclient-0.1.4.dist-info/METADATA +132 -0
  40. imdclient-0.1.4.dist-info/RECORD +57 -0
  41. {imdclient-0.1.2.dist-info → imdclient-0.1.4.dist-info}/WHEEL +1 -1
  42. imdclient/data/gromacs/md/gromacs_v3_nst1.tpr +0 -0
  43. imdclient/data/gromacs/md/gromacs_v3_nst1.trr +0 -0
  44. imdclient/data/lammps/md/lammps_trj.h5md +0 -0
  45. imdclient/data/namd/md/alanin.dcd +0 -0
  46. imdclient-0.1.2.dist-info/LICENSE +0 -674
  47. imdclient-0.1.2.dist-info/METADATA +0 -795
  48. imdclient-0.1.2.dist-info/RECORD +0 -42
  49. {imdclient-0.1.2.dist-info → imdclient-0.1.4.dist-info}/AUTHORS.md +0 -0
  50. {imdclient-0.1.2.dist-info → imdclient-0.1.4.dist-info}/top_level.txt +0 -0
@@ -0,0 +1,132 @@
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+ Metadata-Version: 2.1
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+ Name: imdclient
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+ Version: 0.1.4
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+ Summary: Receiver for IMD v2 and v3 data from simulation engines like Gromacs, LAMMPS, and NAMD
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+ Author-email: Lawson <ljwoods2@asu.edu>
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+ Maintainer-email: Lawson <ljwoods2@asu.edu>
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+ License: Copyright 2024 Lawson Woods
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+
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+ Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
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+
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+ The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
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+ Keywords: molecular simulations
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+ Requires-Python: >=3.9
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+ Description-Content-Type: text/markdown
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+ License-File: LICENSE
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+ License-File: AUTHORS.md
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+ Requires-Dist: MDAnalysis>=2.7.0
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+ Provides-Extra: test
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+ Requires-Dist: pytest>=6.0; extra == "test"
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+ Requires-Dist: pytest-xdist>=2.5; extra == "test"
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+ Requires-Dist: pytest-cov>=3.0; extra == "test"
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+ Requires-Dist: MDAnalysisTests>=2.7.0; extra == "test"
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+ Requires-Dist: docker-py; extra == "test"
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+ Provides-Extra: doc
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+ Requires-Dist: sphinx; extra == "doc"
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+ Requires-Dist: sphinx_rtd_theme; extra == "doc"
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+
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+ IMDClient
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+ ==============================
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+ [//]: # (Badges)
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+
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+ | **Latest release** | [![Last release tag][badge_release]][url_latest_release] ![GitHub commits since latest release (by date) for a branch][badge_commits_since] [![Documentation Status][badge_docs]][url_docs]|
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+ | :----------------- | :------- |
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+ | **Status** | [![GH Actions Status][badge_actions]][url_actions] [![codecov][badge_codecov]][url_codecov] |
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+ | **Community** | [![License: MIT][badge_license]][url_license] [![Powered by MDAnalysis][badge_mda]][url_mda]|
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+
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+ [badge_actions]: https://github.com/becksteinlab/imdclient/actions/workflows/gh-ci.yaml/badge.svg
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+ [badge_codecov]: https://codecov.io/gh/becksteinlab/imdclient/branch/main/graph/badge.svg
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+ [badge_commits_since]: https://img.shields.io/github/commits-since/becksteinlab/imdclient/latest
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+ [badge_docs]: https://readthedocs.org/projects/imdclient/badge/?version=latest
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+ [badge_license]: https://img.shields.io/badge/License-MIT-blue.svg
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+ [badge_mda]: https://img.shields.io/badge/powered%20by-MDAnalysis-orange.svg?logoWidth=16&logo=data:image/x-icon;base64,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+ [badge_release]: https://img.shields.io/github/release-pre/becksteinlab/imdclient.svg
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+ [url_actions]: https://github.com/becksteinlab/imdclient/actions?query=branch%3Amain+workflow%3Agh-ci
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+ [url_codecov]: https://codecov.io/gh/becksteinlab/imdclient/branch/main
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+ [url_docs]: https://imdclient.readthedocs.io/en/latest/?badge=latest
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+ [url_latest_release]: https://github.com/becksteinlab/imdclient/releases
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+ [url_license]: https://opensource.org/license/mit
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+ [url_mda]: https://www.mdanalysis.org
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+
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+ Receiver for [IMDv3 protocol](https://imdclient.readthedocs.io/en/latest/protocol_v3.html) from simulation engines like Gromacs, LAMMPS, and NAMD.
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+
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+ IMDClient is bound by a [Code of Conduct](https://github.com/becksteinlab/imdreader/blob/main/CODE_OF_CONDUCT.md).
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+
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+ ### Installation
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+
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+ IMDClient is available via PyPi and can be installed with pip:
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+ ```bash
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+ pip install imdclient
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+ ```
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+
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+ To build IMDClient from source,
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+ we highly recommend using virtual environments.
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+ If possible, we strongly recommend that you use
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+ [Anaconda](https://docs.conda.io/en/latest/) as your package manager.
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+ Below we provide instructions both for `conda` and
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+ for `pip`.
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+
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+ #### With conda
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+
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+ Ensure that you have [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html) installed.
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+
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+ Create a virtual environment and activate it:
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+
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+ ```
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+ conda create --name imdclient
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+ conda activate imdclient
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+ ```
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+
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+ <!-- Install the development and documentation dependencies:
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+
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+ ```
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+ conda env update --name imdreader --file devtools/conda-envs/test_env.yaml
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+ conda env update --name imdreader --file docs/requirements.yaml
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+ ``` -->
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+
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+ Build this package from source:
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+
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+ ```
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+ pip install -e .
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+ ```
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+
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+ If you want to update your dependencies (which can be risky!), run:
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+
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+ ```
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+ conda update --all
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+ ```
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+
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+ And when you are finished, you can exit the virtual environment with:
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+
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+ ```
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+ conda deactivate
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+ ```
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+
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+ #### With pip
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+
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+ To build the package from source, run:
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+
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+ ```
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+ pip install .
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+ ```
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+
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+ If you want to create a development environment, install
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+ the dependencies required for tests and docs with:
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+
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+ ```
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+ pip install ".[test,doc]"
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+ ```
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+
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+ ### Copyright
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+
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+ The IMDClient source code is hosted at https://github.com/becksteinlab/imdclient
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+ and is available under the MIT license (see the file [LICENSE](https://github.com/becksteinlab/imdclient/blob/main/LICENSE)).
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+
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+ Copyright (c) 2024, Lawson
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+
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+
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+ #### Acknowledgements
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+
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+ Project based on the
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+ [MDAnalysis Cookiecutter](https://github.com/MDAnalysis/cookiecutter-mda) version 0.1.
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+ <!-- Please cite [MDAnalysis](https://github.com/MDAnalysis/mdanalysis#citation) when using IMDReader in published work. -->
@@ -0,0 +1,57 @@
1
+ imdclient/IMD.py,sha256=QkYU0OUxrrjKVxumeEju3Jcewkj46K7DBk_J3vO5m1E,3842
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+ imdclient/IMDClient.py,sha256=9AMKniQaCNDgWO2esF_SXEgdf3fp_4pcZ5fUNpzewcY,34349
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+ imdclient/IMDProtocol.py,sha256=wePIuFlKGIULWXHJPCmzRVWBGlBiyDOJXgjxyQb7ssY,4063
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+ imdclient/__init__.py,sha256=Pa5h6Fjyvyxf3ECzO43pcmLm3Vk-vOuEb5Gi6TDWhds,339
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+ imdclient/backends.py,sha256=QmHjwYbmvFVHz-uFgpSOA0UmZTZqiMGqWMO7B8wr1zs,10368
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+ imdclient/results.py,sha256=2MyjFdQMW7BfiHhG5X6wQwMVrF_0mKYFnv907lgLMas,9920
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+ imdclient/streamanalysis.py,sha256=Qq0h_WPO-wb0_lP8jTRHe0HX7UDZNgJFA6C4PZdUmK8,38385
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+ imdclient/streambase.py,sha256=rwhdyC2V3_9pSz_6rNwjSc4MNToI9S318OH7AH0arHA,6176
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+ imdclient/utils.py,sha256=VWxk4vQ6hzxoYRu-8Ge8fJG-EitJwgJR93wOWCvzY-0,3308
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+ imdclient/data/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ imdclient/data/gromacs/md/gromacs_struct.gro,sha256=kt4vE10iF_1RbeyTogmYmIY9yKJacofrzNT-hPHGyL8,1459301
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+ imdclient/data/gromacs/md/gromacs_v3.top,sha256=AXFEDjvz5Qqq-VECffimdeEvhD6L-H0SFPILW-6Sums,348329
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+ imdclient/data/gromacs/md/gromacs_v3_nst1.mdp,sha256=VFAS3uM0oifxuX5WLz85vvRlwmzR-BhQbMCzjweaJcU,3040
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+ imdclient/data/gromacs/md/gromacs_v3_nst8.mdp,sha256=CYz5gKFApeJMrJyCmd3kgPFzRjahgaLRNyIomuVyY0w,3053
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+ imdclient/data/lammps/md/lammps_topol.data,sha256=u4osSkn7yG9p2Egz9ovLW4eVmdaThPxeZ0L218J3-V0,172948
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+ imdclient/data/lammps/md/lammps_v3_nst_1.in,sha256=AcvkgNNDtTkB7RlFZwpUEKKp6W_7o_UFgrX_LwC3HXI,2586
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+ imdclient/data/lammps/md/lammps_v3_nst_8.in,sha256=gpdAp1dDhJbG06wZVDtBGUs6biJNz8EStV341S0uJ2s,2594
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+ imdclient/data/namd/md/alanin.params,sha256=zWw-UfqYD3-xpdA_8R8T-0OYBbUM6py7jKAq_uyu8HE,17389
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+ imdclient/data/namd/md/alanin.pdb,sha256=eccDD-ledUXjbB2s1fxY40lmAKWWDpxkxANbsOkqjHc,5615
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+ imdclient/data/namd/md/alanin.psf,sha256=VhCZeGFhpUa8yN5iEL19zlVjqIJg2JIdPzhazpRForY,12953
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+ imdclient/data/namd/md/namd_v3_nst_1.namd,sha256=EZU7PGyytZdGixrBnmpAcwonN0n_JTk9U-Q82FoqO7k,983
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+ imdclient/data/namd/md/namd_v3_nst_8.namd,sha256=WJmwj0E4nJVhYRr_ALBlTax6kyNkdRE1krPsmY-QFLM,984
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+ imdclient/tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ imdclient/tests/base.py,sha256=gbu39CpII5mc9-rDSEZoQNv8JmNFwW1vviYkfOQmbD4,8043
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+ imdclient/tests/conftest.py,sha256=Xqz9ZjBXpnViSryR4CXjJdOyqZ1MOCAjuA0sRVwAVfk,31
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+ imdclient/tests/datafiles.py,sha256=0wAg1q5oB3Ve6XnSfnB6oGzbh7JvVpSGpj-ba0H2Z5w,1515
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+ imdclient/tests/server.py,sha256=x3IY5FDDS4z99_UyuuRe56CHd_XtfINJRolGbkNyOl8,6629
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+ imdclient/tests/test_gromacs.py,sha256=rXkabRB40xX7LRdF2_nrPgeNpfFF9J7m-5LeRNMA5TM,1454
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+ imdclient/tests/test_imdclient.py,sha256=FQwuNbJwOLgK33v5mFmbhaGaPSqXA8byTWFtYCpYyJo,7716
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+ imdclient/tests/test_imdreader.py,sha256=-DEFcwef87CZPXut45I2gpZPg_K3XXPFFreBqsW3ciE,25433
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+ imdclient/tests/test_lammps.py,sha256=hwZBVvhclN1mtPuYLyODUaWjlaZaAkhAFqX-mpQvWk4,2244
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+ imdclient/tests/test_manual.py,sha256=t5NeT1oPit9EMGxH4yG7hxnKQ24UEzZtR-vC1WOQAkc,8118
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+ imdclient/tests/test_namd.py,sha256=dFOJUQl9ByekuuYgUOIirf6qFj5_qaKfgQq4Qimtotw,3671
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+ imdclient/tests/test_stream_analysis.py,sha256=qqsm_Bv8qCXyNwgdSKZM8bLyiEO5nlpqJ-XtEn-YKew,1723
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+ imdclient/tests/utils.py,sha256=_x1gVQ3AmhaMurpcEPLKBG5BTGu4ZMy5EGUpr0P6D6g,854
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+ imdclient/tests/docker_testing/docker.md,sha256=SxHEpSA1mXAvzYzsxL0EesGqPCVC8qdRMbvxGz5R0Yo,840
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+ imdclient/tests/hpc_testing/gromacs/README.md,sha256=2SHVtIu5EyS8bwCMeWTZFgQoh1mmOwcBFjijzYDkj6k,2847
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+ imdclient/tests/hpc_testing/gromacs/gmx_gpu_test.mdp,sha256=BZl554WoHVi0bQq-Eb8UeYrdfum2TBHhtWFj4DxReCY,3050
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+ imdclient/tests/hpc_testing/gromacs/gmx_gpu_test.top,sha256=AXFEDjvz5Qqq-VECffimdeEvhD6L-H0SFPILW-6Sums,348329
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+ imdclient/tests/hpc_testing/gromacs/struct.gro,sha256=uT_Je8Jc37-o8gfkhFRH0PWcg3LOGkQj4ErSCkLMk00,1459301
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+ imdclient/tests/hpc_testing/gromacs/validate_gmx.sh,sha256=dszRgiWu-_9b4DxQP4u5x4Hi1liedjMG2YXQNURZQsQ,1938
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+ imdclient/tests/hpc_testing/lammps/README.md,sha256=Ek5z8H3gSxCoHg-gymMfmqKqi1URFvgRH4dYZuaC8Ro,1594
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+ imdclient/tests/hpc_testing/lammps/lammps_v3_nst_1.in,sha256=AcvkgNNDtTkB7RlFZwpUEKKp6W_7o_UFgrX_LwC3HXI,2586
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+ imdclient/tests/hpc_testing/lammps/topology_after_min.data,sha256=6CXJTFiVnnK6rKGK541sFYZ_6xjlkjebeWu0KPQl8Gc,172948
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+ imdclient/tests/hpc_testing/lammps/validate_lmp.sh,sha256=gqNFUvxLojBM1yrUHloL4FJm8pl4CNjTvgSYwh11pTc,1402
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+ imdclient/tests/hpc_testing/namd/README.md,sha256=fNnhQPcVS-wkG4aCtj7ru2CpoIMmxJFA9-9bGa9NQ2o,2103
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+ imdclient/tests/hpc_testing/namd/alanin.params,sha256=zWw-UfqYD3-xpdA_8R8T-0OYBbUM6py7jKAq_uyu8HE,17389
48
+ imdclient/tests/hpc_testing/namd/alanin.pdb,sha256=eccDD-ledUXjbB2s1fxY40lmAKWWDpxkxANbsOkqjHc,5615
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+ imdclient/tests/hpc_testing/namd/alanin.psf,sha256=VhCZeGFhpUa8yN5iEL19zlVjqIJg2JIdPzhazpRForY,12953
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+ imdclient/tests/hpc_testing/namd/namd_v3_nst_1.namd,sha256=EZU7PGyytZdGixrBnmpAcwonN0n_JTk9U-Q82FoqO7k,983
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+ imdclient/tests/hpc_testing/namd/validate_namd.sh,sha256=oMZNkY2p13q_4TJwepS5WjlT4xwxCoaZbDiWfLIWIvs,1543
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+ imdclient-0.1.4.dist-info/AUTHORS.md,sha256=R4JTI7mrgL1WYgfyuAv4quw0e0oLQGVjWcMQa-UXJlE,652
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+ imdclient-0.1.4.dist-info/LICENSE,sha256=28aS5DC2LCwcOVe3VN0g2L-Dooqof34T9TMGJ6jqMig,593
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+ imdclient-0.1.4.dist-info/METADATA,sha256=Uu9wpmeThDtEKtLPeqElgkG9R_DZSyxsIxzQUOjchds,6531
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+ imdclient-0.1.4.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
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+ imdclient-0.1.4.dist-info/top_level.txt,sha256=40W62GWiXUT2CbDm-No7GTeJG160wyIMpk1hBNrdkkE,10
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+ imdclient-0.1.4.dist-info/RECORD,,
@@ -1,5 +1,5 @@
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  Wheel-Version: 1.0
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- Generator: setuptools (75.2.0)
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+ Generator: setuptools (75.6.0)
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  Root-Is-Purelib: true
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  Tag: py3-none-any
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