Recent Releases of powerfit-em
powerfit-em - v3.0.5
Application to do rigid body fitting of atomic structures like proteins in cryo-electron microscopy density maps.
This version has improved GPU performance. It is 2 times faster than v3.0.3 and 1.5 times faster than v3.0.4.
Benchmark on files of https://github.com/haddocking/protein-detective/blob/main/docs/emprepare.ipynb with `time powerfit emd33292-7xm9-B-3.48.cheated.mrc 3.48 7xm9.B-reoriented.pdb ...` ran on AMD Radeon RX 7900 XTX and AMD 7800X3D
GPU Benchmarks
| Version | Wall Time | Rot/s | |---------|------------|-------| | v3.0.5 | 0m5.339s | 2319 | | v3.0.4 | 0m7.455s | 1535 | | v3.0.3 | 0m8.632s | 1172 |
CPU Benchmarks
Ran on 8 processor cores.
| Version | Wall Time | Rot/s | |---------|------------|-------| | v3.0.5 | 1m19.823s | 90 | | v3.0.4 | 1m20.042s | 89 | | v3.0.3 | 1m27.092s | 73 |
What's Changed
- Move to VkFFT instead of GpyFFT by @BSchilperoort in https://github.com/haddocking/powerfit/pull/55
Full Changelog: https://github.com/haddocking/powerfit/compare/v3.0.4...v3.0.5
- Python
Published by sverhoeven 7 months ago
powerfit-em - v3.0.4
Application to do rigid body fitting of atomic structures like proteins in cryo-electron microscopy density maps.
What's Changed
- Update version in docker commands by @sverhoeven in https://github.com/haddocking/powerfit/pull/48
- Reuse rotate_image3d kernel, remove redundant queue
.finish()by @BSchilperoort in https://github.com/haddocking/powerfit/pull/50 - Fix multi processor, cif and chain by @sverhoeven in https://github.com/haddocking/powerfit/pull/53
New Contributors
- @BSchilperoort made their first contribution in https://github.com/haddocking/powerfit/pull/50
Full Changelog: https://github.com/haddocking/powerfit/compare/v3.0.3...v3.0.4
- Python
Published by sverhoeven 8 months ago
powerfit-em - v3.0.3
Application to do rigid body fitting of atomic structures like proteins in cryo-electron microscopy density maps.
What's Changed
- Run powerfit from Python using
from powerfit_em.powerfit import powerfitin #46 - Nicer terminal output with rich in #46
- Configurable progressbar with tqdm in #46
- Allow to pick which gpu to use with
--gpu <platform>:<device>in #46 - Make version more visible #31
- Make runnable from dask #47
Full Changelog: https://github.com/haddocking/powerfit/compare/v3.0.2...v3.0.3
- Python
Published by sverhoeven 8 months ago
powerfit-em - v3.0.2
Application to do rigid body fitting of atomic structures like proteins in cryo-electron microscopy density maps.
The major change is that powerfit is now a Python3 package and can be run without having to install OS dependencies.
What's Changed
Full Changelog: https://github.com/haddocking/powerfit/compare/v3.0.1...v3.0.2
- Python
Published by sverhoeven 9 months ago
powerfit-em - v3.0.1
Application to do rigid body fitting of atomic structures like proteins in cryo-electron microscopy density maps.
The major change is that powerfit is now a Python3 package and can be run without having to install OS dependencies.
What's Changed
Full Changelog: https://github.com/haddocking/powerfit/compare/v3.0.0...v3.0.1
- Python
Published by sverhoeven 9 months ago
powerfit-em - v3.0.0
Application to do rigid body fitting of atomic structures like proteins in cryo-electron microscopy density maps.
The major change is that powerfit is now a Python3 package and can be run without having to install OS dependencies.
What's Changed
- Python 3 by @sverhoeven in https://github.com/haddocking/powerfit/pull/18
- rename package from powerfit to powerfit-em by @rvhonorato in https://github.com/haddocking/powerfit/pull/37
- Add link to rsd by @sverhoeven in https://github.com/haddocking/powerfit/pull/33
- code of conduct and contributing guidelines by @sverhoeven in https://github.com/haddocking/powerfit/pull/34
- Modernize packaging with pyproject.toml and src layout by @sverhoeven in https://github.com/haddocking/powerfit/pull/38
- Add Anna as author by @sverhoeven in https://github.com/haddocking/powerfit/pull/40
- Pypi publish CI job with binary wheels by @sverhoeven in https://github.com/haddocking/powerfit/pull/32
New Contributors
- @sverhoeven made their first contribution in https://github.com/haddocking/powerfit/pull/18
- @rvhonorato made their first contribution in https://github.com/haddocking/powerfit/pull/37
Full Changelog: https://github.com/haddocking/powerfit/compare/v2.1.1...v3.0.0
- Python
Published by sverhoeven 9 months ago
powerfit-em - v2.1.1
What's Changed
- Docker Container for PowerFit by @maurerv in https://github.com/haddocking/powerfit/pull/16
New Contributors
- @maurerv made their first contribution in https://github.com/haddocking/powerfit/pull/16
Full Changelog: https://github.com/haddocking/powerfit/compare/v2.1.0...v2.1.1
- Python
Published by rvhonorato over 1 year ago
powerfit-em - v2.1.0
What's Changed
- [Update] Check for spacegroup and box angles when reading in CCP4 den… by @schaarj in https://github.com/haddocking/powerfit/pull/1
- fix for gpu issue on Tesla K80 by @schaarj in https://github.com/haddocking/powerfit/pull/3
- Testing integration with INDIGO Jenkins by @orviz in https://github.com/haddocking/powerfit/pull/4
- INDIGO Jenkins integration test (do not merge) by @orviz in https://github.com/haddocking/powerfit/pull/5
- Minor fixes by @FloLangenfeld in https://github.com/haddocking/powerfit/pull/10
- Remove spacegroup requirement for input density files. by @latrocinia in https://github.com/haddocking/powerfit/pull/12
New Contributors
- @schaarj made their first contribution in https://github.com/haddocking/powerfit/pull/1
- @orviz made their first contribution in https://github.com/haddocking/powerfit/pull/4
- @FloLangenfeld made their first contribution in https://github.com/haddocking/powerfit/pull/10
- @latrocinia made their first contribution in https://github.com/haddocking/powerfit/pull/12
Full Changelog: https://github.com/haddocking/powerfit/compare/v2.0.0...v2.1.0
- Python
Published by rvhonorato over 2 years ago