asyncmd 0.3.2__py3-none-any.whl → 0.4.0__py3-none-any.whl

asyncmd-0.3.2.dist-info/METADATA

@@ -1,179 +0,0 @@
-Metadata-Version: 2.2
-Name: asyncmd
-Version: 0.3.2
-Summary: asyncmd is a library to write concurrent code to run and analyze molecular dynamics simulations using pythons async/await synthax.
-Author-email: Hendrik Jung <hendrik.jung@biophys.mpg.de>
-Maintainer-email: Hendrik Jung <hendrik.jung@biophys.mpg.de>
-Project-URL: Repository, https://github.com/bio-phys/asyncmd.git
-Project-URL: Issues, https://github.com/bio-phys/asyncmd/issues
-Keywords: molecular dynamics,molecular-dynamics,MD,high performance computing,HPC,slurm,SLURM,gromacs,GROMACS
-Classifier: Development Status :: 4 - Beta
-Classifier: Intended Audience :: Science/Research
-Classifier: Natural Language :: English
-Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
-Classifier: Operating System :: OS Independent
-Classifier: Programming Language :: Python
-Classifier: Programming Language :: Python :: 3
-Classifier: Topic :: Scientific/Engineering
-Classifier: Topic :: Scientific/Engineering :: Chemistry
-Classifier: Topic :: Scientific/Engineering :: Physics
-Classifier: Topic :: Software Development :: Libraries :: Python Modules
-Requires-Python: >=3.10
-Description-Content-Type: text/markdown
-License-File: LICENSE
-Requires-Dist: aiofiles
-Requires-Dist: mdanalysis
-Requires-Dist: numpy
-Provides-Extra: docs
-Requires-Dist: sphinx; extra == "docs"
-Provides-Extra: tests
-Requires-Dist: pytest; extra == "tests"
-Requires-Dist: pytest-asyncio; extra == "tests"
-Provides-Extra: tests-all
-Requires-Dist: asyncmd[tests]; extra == "tests-all"
-Requires-Dist: h5py; extra == "tests-all"
-Requires-Dist: coverage; extra == "tests-all"
-Requires-Dist: pytest-cov; extra == "tests-all"
-Provides-Extra: dev
-Requires-Dist: asyncmd[docs,tests-all]; extra == "dev"
-
-# asyncmd
-
-## Synopsis
-
-asyncmd is a library to write **concurrent** code to run and analyze molecular dynamics simulations using pythons **async/await** synthax.
-
-## Motivation
-
-Molecular dynamics simulations are fun and we can learn a lot about the simulated system. Running many molecular dynamics simulations of the same system concurrently is tedious, error-prone and boring but we can learn even more about the simulated system and are more efficient in doing so.
-This library addresses the tedious, error-prone and boring part of setting up many similar simulations, but it leaves you with the fun part of understanding the simulated system.
-
-## Code Example
-
-Run `N` gromacs engines concurently from configurations randomly picked up along a trajectory (`traj.trr`) for `n_steps` integration steps each, drawing random Maxwell-Boltzmann velocities for each configuration on the way. Finally turn the python function `func` (which acts on `Trajectory` objects) into an asyncronous and cached function by wrapping it and apply it on all generated trajectories concurrently:
-
-```python
-import asyncio
-import numpy as np
-import asyncmd
-import asyncmd.gromacs as asyncgmx
-
-in_traj = asyncmd.Trajectory(trajectory_files="traj.trr", structure_file="conf.gro")
-# get a random number generator and draw N random frames (with replacement)
-rng = np.default_rng()
-frame_idxs = rng.choice(len(in_traj), size=N)
-# use the RandomVelocitiesFrameExtractor to directly get the frames with MB-vels
-extractor = asyncmd.trajectory.convert.RandomVelocitiesFrameExtractor(T=303)
-mdps = [asyncgmx.MDP("config.mdp") for _ in range(N)]
-# MDConfig objects (like MDP) behave like dictionaries and are easy to modify
-for i, mdp in enumerate(mdps):
-    # here we just modify the output frequency for every engine separately
-    # but you can set any mdp option like this
-    # Note how the values are in the correct types? I.e. that they are ints?
-    mdp["nstxout"] *= (i + 1)
-    mdp["nstvout"] *= (i + 1)
-# create N gromacs engines
-engines = [asyncgmx.GmxEngine(mdp=mdp, gro_file="conf.gro", top_file="topol.top",
-                              # optional (can be omited or None), however naturally without an index file
-                              # you can not reference custom groups in the .mdp-file or MDP object
-                              ndx_file="index.ndx",
-                              )
-           for mdp in mdps]
-# extract starting configurations with MB-vels and save them to current directory
-start_confs = await asyncio.gather(*(extractor.extract_async(
-                                          outfile=f"start_conf{i}.trr",
-                                          traj_in=in_traj, idx=idx)
-                                     for i, idx in enumerate(frame_idxs)))
-# prepare the MD (for gromacs this is essentially a `grompp` call)
-await asyncio.gather(*(e.prepare(starting_configuration=conf,
-                                 workdir=".", deffnm=f"engine{i}")
-                       for i, (conf, e) in enumerate(zip(start_confs, engines))
-                       )
-                     )
-# and run the molecular dynamics
-out_trajs = await asyncio.gather(*(e.run_steps(nsteps=n_steps) for e in engines))
-# wrapp `func` and apply it on all output trajectories concurrently
-wrapped_func = asyncmd.trajectory.PyTrajectoryFunctionWrapper(function=func)
-cv_vals = await asyncio.gather(*(wrapped_func(traj) for traj in out_trajs))
-```
-
-Note that running via the [SLURM] queueing system is as easy as replacing the `GmxEngine` with a `SlurmGmxEngine` and the `PyTrajectoryFunctionWrapper` with a `SlurmTrajectoryFunctionWrapper` (and suppling them both with sbatch script skeletons).
-
-For an in-depth introduction see also the `examples` folder in this repository which contains jupyter notebooks on various topics.
-
-## Installation
-
-### pip install directly from the repository
-
-Please note that you need to have [git-lfs] (an open source git extension) setup to get all input files needed to run the notebooks in the `examples` folder. However, no [git-lfs] is needed to get a working version of the library.
-
-```bash
-git clone https://github.com/bio-phys/asyncmd.git
-cd asyncmd
-pip install .
-```
-
-## API Reference
-
-The documentation can be build with [sphinx], use e.g. the following to build it in html format:
-
-```bash
-cd asyncmd  # Need to be at the top folder of the repository for the next line to work
-sphinx-build -b html docs/source docs/build/html
-```
-
-Use ```pip install .\[docs\]``` to install the requirements needed to build the documentation.
-
-## Tests
-
-Tests use [pytest]. To run them just install asycmd with the test requirements
-
-```bash
-git clone https://github.com/bio-phys/asyncmd.git
-cd asyncmd
-pip install .\[tests\]
-```
-
-And then run the tests (against the installed version) as
-
-```bash
-pytest
-```
-
-## Contribute
-
-If you discover any issues or want to propose a new feature please feel free to open an [issue](https://github.com/bio-phys/asyncmd/issues) or a [pull request](https://github.com/bio-phys/asyncmd/pulls)!
-
-### Developer install
-
-For the developer install I recommend:
-
-```bash
-git clone https://github.com/bio-phys/asyncmd.git
-cd asyncmd
-pip install -e .\[dev\]
-```
-
-This will in addition to the requirements to run the tests and to build the documentation install [coverage] and its [pytest-cov] plugin such that you have an idea of the test coverage for your newly added code. To get a nice html coverage report you can run the tests as
-
-```bash
-pytest --cov=asyncmd --cov-report=html
-```
-
-### Contributors
-
-This project was originally conceived and started by Hendrik Jung in 2021/2022. For more check the `pyproject.toml` file. When you contribute code dont forget to add your name there to claim the credit for your work!
-
-## License
-
-asyncmd is under the terms of the GNU general public license version 3 or later, i.e. SPDX identifier "GPL-3.0-or-later".
-
----
-<sub>This README.md is printed from 100% recycled electrons.</sub>
-
-[coverage]: https://pypi.org/project/coverage/
-[git-lfs]: https://git-lfs.com/
-[pytest]: https://docs.pytest.org/en/latest/
-[pytest-cov]: https://pypi.org/project/pytest-cov/
-[SLURM]: https://slurm.schedmd.com/documentation.html
-[sphinx]: https://www.sphinx-doc.org/en/master/index.html

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