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Recent Releases of https://github.com/becksteinlab/mdpow

https://github.com/becksteinlab/mdpow - release 0.9.0

New release 0.9.0 (after almost 2 years...)

  • new features (dihedral ensemble analysis workflow)
  • dropping support for old Python versions (sorry, too difficult to maintain and keep up with the Python eco system)
  • GROMACS 4.6.5 to 2024.3 tested
  • bug fixes and various quality-of-life improvements (e.g. black formatting, automated deployment, ...)

See CHANGES for the concise summary and below for list of merged PRs.

What's Changed

  • changed dihedral atom group selection strings in test_dihedral.py by @cadeduckworth in https://github.com/Becksteinlab/MDPOW/pull/218
  • CI updates by @orbeckst in https://github.com/Becksteinlab/MDPOW/pull/220
  • Update em_charmm.mdp by @VOD555 in https://github.com/Becksteinlab/MDPOW/pull/210
  • use new micro mamba action by @orbeckst in https://github.com/Becksteinlab/MDPOW/pull/221
  • developing back end run methods by @cadeduckworth in https://github.com/Becksteinlab/MDPOW/pull/216
  • Support toluene solvent by @VOD555 in https://github.com/Becksteinlab/MDPOW/pull/224
  • Support cgenff toluene by @VOD555 in https://github.com/Becksteinlab/MDPOW/pull/228
  • Fix setup and support toluene in mdpow-solvationenergy by @VOD555 in https://github.com/Becksteinlab/MDPOW/pull/230
  • Use AutoMBAR instead of MBAR by @VOD555 in https://github.com/Becksteinlab/MDPOW/pull/234
  • Automated Dihedral Analysis by @cadeduckworth in https://github.com/Becksteinlab/MDPOW/pull/217
  • Periodic Angle Padding by @cadeduckworth in https://github.com/Becksteinlab/MDPOW/pull/242
  • Workflows Base Module by @cadeduckworth in https://github.com/Becksteinlab/MDPOW/pull/229
  • update banner logging by @orbeckst in https://github.com/Becksteinlab/MDPOW/pull/247
  • Update statistical inefficiency calculation with statistical_inefficiency in alchemlyb 2.1.0 by @VOD555 in https://github.com/Becksteinlab/MDPOW/pull/250
  • drop python 3.7 and testing improvements by @orbeckst in https://github.com/Becksteinlab/MDPOW/pull/249
  • test on GROMACS 2022 and 2023 by @orbeckst in https://github.com/Becksteinlab/MDPOW/pull/255
  • use relative imports inside MDPOW by @orbeckst in https://github.com/Becksteinlab/MDPOW/pull/257
  • update to mamba-org/setup-micromamba by @orbeckst in https://github.com/Becksteinlab/MDPOW/pull/258
  • Dihedral Plots: RDKit Mol Object by @cadeduckworth in https://github.com/Becksteinlab/MDPOW/pull/243
  • Review all kwargs and consistency in top-level function calls by @cadeduckworth in https://github.com/Becksteinlab/MDPOW/pull/263
  • initialize guess_atoms function PR by @cadeduckworth in https://github.com/Becksteinlab/MDPOW/pull/264
  • Black formatting by @a-ws-m in https://github.com/Becksteinlab/MDPOW/pull/269
  • remove logger for SI in mdpow.fep by @VOD555 in https://github.com/Becksteinlab/MDPOW/pull/276
  • Use OOP forcefields by @a-ws-m in https://github.com/Becksteinlab/MDPOW/pull/267
  • replace scipy.integrate.simps with simpson by @orbeckst in https://github.com/Becksteinlab/MDPOW/pull/282
  • update versioneer by @orbeckst in https://github.com/Becksteinlab/MDPOW/pull/287
  • Update .readthedocs.yaml by @orbeckst in https://github.com/Becksteinlab/MDPOW/pull/284
  • change Python support to 3.10 - 3.12 by @orbeckst in https://github.com/Becksteinlab/MDPOW/pull/290
  • auto-deploy GHA workflow by @orbeckst in https://github.com/Becksteinlab/MDPOW/pull/292
  • Fix stage checking by @a-ws-m in https://github.com/Becksteinlab/MDPOW/pull/278

New Contributors

  • @a-ws-m made their first contribution in https://github.com/Becksteinlab/MDPOW/pull/269

Full Changelog: https://github.com/Becksteinlab/MDPOW/compare/release-0.8.0...release-0.9.0

- Python
Published by orbeckst over 1 year ago

https://github.com/becksteinlab/mdpow - release 0.9.0 (release candidate 3)

Pre-release for the new 0.9.0 * new features (dihedral ensemble analysis workflow) * dropping support for old Python versions (sorry, too difficult to maintain and keep up with the Python eco system) * GROMACS 4.6.5 to 2024.3 tested

What's Changed

  • change Python support to 3.10 - 3.12 by @orbeckst in https://github.com/Becksteinlab/MDPOW/pull/290
  • auto-deploy GHA workflow by @orbeckst in https://github.com/Becksteinlab/MDPOW/pull/292
  • changed dihedral atom group selection strings in test_dihedral.py by @cadeduckworth in https://github.com/Becksteinlab/MDPOW/pull/218
  • CI updates by @orbeckst in https://github.com/Becksteinlab/MDPOW/pull/220
  • Update em_charmm.mdp by @VOD555 in https://github.com/Becksteinlab/MDPOW/pull/210
  • use new micro mamba action by @orbeckst in https://github.com/Becksteinlab/MDPOW/pull/221
  • developing back end run methods by @cadeduckworth in https://github.com/Becksteinlab/MDPOW/pull/216
  • Support toluene solvent by @VOD555 in https://github.com/Becksteinlab/MDPOW/pull/224
  • Support cgenff toluene by @VOD555 in https://github.com/Becksteinlab/MDPOW/pull/228
  • Fix setup and support toluene in mdpow-solvationenergy by @VOD555 in https://github.com/Becksteinlab/MDPOW/pull/230
  • Use AutoMBAR instead of MBAR by @VOD555 in https://github.com/Becksteinlab/MDPOW/pull/234
  • Automated Dihedral Analysis by @cadeduckworth in https://github.com/Becksteinlab/MDPOW/pull/217
  • Periodic Angle Padding by @cadeduckworth in https://github.com/Becksteinlab/MDPOW/pull/242
  • Workflows Base Module by @cadeduckworth in https://github.com/Becksteinlab/MDPOW/pull/229
  • update banner logging by @orbeckst in https://github.com/Becksteinlab/MDPOW/pull/247
  • Update statistical inefficiency calculation with statistical_inefficiency in alchemlyb 2.1.0 by @VOD555 in https://github.com/Becksteinlab/MDPOW/pull/250
  • drop python 3.7 and testing improvements by @orbeckst in https://github.com/Becksteinlab/MDPOW/pull/249
  • test on GROMACS 2022 and 2023 by @orbeckst in https://github.com/Becksteinlab/MDPOW/pull/255
  • use relative imports inside MDPOW by @orbeckst in https://github.com/Becksteinlab/MDPOW/pull/257
  • update to mamba-org/setup-micromamba by @orbeckst in https://github.com/Becksteinlab/MDPOW/pull/258
  • Dihedral Plots: RDKit Mol Object by @cadeduckworth in https://github.com/Becksteinlab/MDPOW/pull/243
  • Review all kwargs and consistency in top-level function calls by @cadeduckworth in https://github.com/Becksteinlab/MDPOW/pull/263
  • initialize guess_atoms function PR by @cadeduckworth in https://github.com/Becksteinlab/MDPOW/pull/264
  • Black formatting by @a-ws-m in https://github.com/Becksteinlab/MDPOW/pull/269
  • remove logger for SI in mdpow.fep by @VOD555 in https://github.com/Becksteinlab/MDPOW/pull/276
  • Use OOP forcefields by @a-ws-m in https://github.com/Becksteinlab/MDPOW/pull/267
  • replace scipy.integrate.simps with simpson by @orbeckst in https://github.com/Becksteinlab/MDPOW/pull/282
  • update versioneer by @orbeckst in https://github.com/Becksteinlab/MDPOW/pull/287
  • Update .readthedocs.yaml by @orbeckst in https://github.com/Becksteinlab/MDPOW/pull/284

New Contributors

  • @a-ws-m made their first contribution in https://github.com/Becksteinlab/MDPOW/pull/269

Full Changelog: https://github.com/Becksteinlab/MDPOW/compare/release-0.8.0...release-0.9.0rc3

- Python
Published by orbeckst over 1 year ago

https://github.com/becksteinlab/mdpow - release 0.9.0 (release candidate 1)

Pre-release for the new 0.9.0 * new features (dihedral ensemble analysis workflow) * dropping support for old Python versions (sorry, too difficult to maintain and keep up with the Python eco system)

What's Changed

  • changed dihedral atom group selection strings in test_dihedral.py by @cadeduckworth in https://github.com/Becksteinlab/MDPOW/pull/218
  • CI updates by @orbeckst in https://github.com/Becksteinlab/MDPOW/pull/220
  • Update em_charmm.mdp by @VOD555 in https://github.com/Becksteinlab/MDPOW/pull/210
  • use new micro mamba action by @orbeckst in https://github.com/Becksteinlab/MDPOW/pull/221
  • developing back end run methods by @cadeduckworth in https://github.com/Becksteinlab/MDPOW/pull/216
  • Support toluene solvent by @VOD555 in https://github.com/Becksteinlab/MDPOW/pull/224
  • Support cgenff toluene by @VOD555 in https://github.com/Becksteinlab/MDPOW/pull/228
  • Fix setup and support toluene in mdpow-solvationenergy by @VOD555 in https://github.com/Becksteinlab/MDPOW/pull/230
  • Use AutoMBAR instead of MBAR by @VOD555 in https://github.com/Becksteinlab/MDPOW/pull/234
  • Automated Dihedral Analysis by @cadeduckworth in https://github.com/Becksteinlab/MDPOW/pull/217
  • Periodic Angle Padding by @cadeduckworth in https://github.com/Becksteinlab/MDPOW/pull/242
  • Workflows Base Module by @cadeduckworth in https://github.com/Becksteinlab/MDPOW/pull/229
  • update banner logging by @orbeckst in https://github.com/Becksteinlab/MDPOW/pull/247
  • Update statistical inefficiency calculation with statistical_inefficiency in alchemlyb 2.1.0 by @VOD555 in https://github.com/Becksteinlab/MDPOW/pull/250
  • drop python 3.7 and testing improvements by @orbeckst in https://github.com/Becksteinlab/MDPOW/pull/249
  • test on GROMACS 2022 and 2023 by @orbeckst in https://github.com/Becksteinlab/MDPOW/pull/255
  • use relative imports inside MDPOW by @orbeckst in https://github.com/Becksteinlab/MDPOW/pull/257
  • update to mamba-org/setup-micromamba by @orbeckst in https://github.com/Becksteinlab/MDPOW/pull/258
  • Dihedral Plots: RDKit Mol Object by @cadeduckworth in https://github.com/Becksteinlab/MDPOW/pull/243
  • Review all kwargs and consistency in top-level function calls by @cadeduckworth in https://github.com/Becksteinlab/MDPOW/pull/263
  • initialize guess_atoms function PR by @cadeduckworth in https://github.com/Becksteinlab/MDPOW/pull/264
  • Black formatting by @a-ws-m in https://github.com/Becksteinlab/MDPOW/pull/269
  • remove logger for SI in mdpow.fep by @VOD555 in https://github.com/Becksteinlab/MDPOW/pull/276
  • Use OOP forcefields by @a-ws-m in https://github.com/Becksteinlab/MDPOW/pull/267
  • replace scipy.integrate.simps with simpson by @orbeckst in https://github.com/Becksteinlab/MDPOW/pull/282
  • update versioneer by @orbeckst in https://github.com/Becksteinlab/MDPOW/pull/287
  • Update .readthedocs.yaml by @orbeckst in https://github.com/Becksteinlab/MDPOW/pull/284

New Contributors

  • @a-ws-m made their first contribution in https://github.com/Becksteinlab/MDPOW/pull/269

Full Changelog: https://github.com/Becksteinlab/MDPOW/compare/release-0.8.0...release-0.9.0rc1

- Python
Published by orbeckst over 1 year ago

https://github.com/becksteinlab/mdpow - Release 0.8.0

New release of MDPOW with new functionality; dropped support for legacy Python versions.

Important changes and fixes

  • support Python 3.7 – 3.9 (3.10 probably works but is currently not tested)
  • new ensemble analysis framework (#168) with two ensemble tools
    • dihedral analysis #190
    • solvation shell analysis #195
  • removed deprecated mdpow-ghyd script: use mdpow-solvationenergy (#183)
  • various fixes in the config file parser

All changes

See the CHANGES file for release 0.8.0.

- Python
Published by orbeckst about 4 years ago

https://github.com/becksteinlab/mdpow - Release 0.7.1

Important bug fixes and documentation updates - fixes installation issues with Python 2.7 due to alchemlyb update - fixed some of the mdpow scripts failing - fixed the fep.p_transfer() function - additional online documentation for the runinput file, forcefield handling, and for the contents of the doc/examples directory in the form of docs/examples/README.rst

See CHANGES for more details.

- Python
Published by orbeckst over 4 years ago

https://github.com/becksteinlab/mdpow - Release 0.7.0

Major release of MDPOW as used for SAMPL7, see

  • Precise force-field-based calculations of octanol-water partition coefficients for the SAMPL7 molecules. Shujie Fan, Hristo Nedev,  Ranjit Vijayan, Bogdan I. Iorga, Oliver Beckstein. Journal of Computer-Aided Molecular Design 2021, doi: 10.1007/s10822-021-00407-4
  • Becksteinlab/SAMPL7logPdata

The package was renamed from "POW" to "MDPOW". Install with bash pip install mdpow

Supported platforms

  • Python 2.7 and Python 3.6–3.9
  • GROMACS 4.6.5, 2018, 2020, 2021 (tested and confirmed), 5, 2016, 2019 (should work)
  • Linux and macOS (tested), Windows (might work)

Highlights

For details see CHANGES

- Python
Published by orbeckst over 4 years ago

https://github.com/becksteinlab/mdpow - Release 0.6.1

Bug fix release.

  • works with Gromas 4.6.x, 5.1.x, 2016.x (just source your preferred GMXRC)
  • bug fixes (see CHANGES for details)
  • improved tests
  • internally, we use EDR files as the primary storage format for energy data; XVG.bz2 files are generated when needed but this should not affect users

- Python
Published by orbeckst almost 9 years ago

https://github.com/becksteinlab/mdpow - Release 0.6.0

Major update since 0.5.1 with a lot of new functionality and backwards incompatible changes (eg the runinput file format was changed but a conversion script is available).

- Python
Published by orbeckst over 9 years ago