v4.0.3

Application to do rigid body fitting of atomic structures like proteins in cryo-electron microscopy density maps

What's Changed

• Report coloring by @sverhoeven in #98

Full Changelog: v4.0.2...v4.0.3

v4.0.2

Application to do rigid body fitting of atomic structures like proteins in cryo-electron microscopy density maps.

What's Changed

• Removed dead code and unused scripts in #39
• Add linter/formatter in #35

Full Changelog: v4.0.1...v4.0.2

v4.0.1

Application to do rigid body fitting of atomic structures like proteins in cryo-electron microscopy density maps.

What's Changed

• Fix sigma diff calc by @sverhoeven in #92

Full Changelog: v4.0.0...v4.0.1

v4.0.0

Application to do rigid body fitting of atomic structures like proteins in cryo-electron microscopy density maps.

Breaking change

Powefit now by default uses laplace pre-filter and uses core-weighted local cross-correlation score.

What's Changed

• Report table by @sverhoeven in #86
• Add powerfit_many function by @BSchilperoort in #83
• Add support for gzipped template files by @sverhoeven in #85
• Allow for gzipped target files by @BSchilperoort in #88
• Invert --laplace and --core-weighted cli arguments to --no-laplace and --no-core-weighted by @sverhoeven in #90

Full Changelog: v3.1.0...v4.0.0

v3.1.0

Application to do rigid body fitting of atomic structures like proteins in cryo-electron microscopy density maps.

What's Changed

• Added --report that generates a report.html with Mol* visualizing fitted models by @sverhoeven in #68

Full Changelog: v3.0.6...v3.1.0

v3.0.6

Application to do rigid body fitting of atomic structures like proteins in cryo-electron microscopy density maps.

This release features improved GPU and CPU performance. Disable the progressbar with --no-progressbar to speed up searches.

Additionally, there are now instructions on running powerfit on (Intel) integrated graphics, with improved performance and energy efficiency compared to CPU.

Benchmark

Search time has been benchmarked on the same template structure and target as in the reference paper (Table 2, Fine & T + R), with
powerfit EMD-1046.map 20 9a2g.pdb -a 4.71 -l --no-progressbar.

Using a AMD Ryzen 7 7700 8-Core Processor and a AMD Radeon RX 7800 XT (16GB DDR6) GPU.

Time for search, as reported by powerfit;

Version	GPU	CPU	CPU (8 threads)
v3.0.6	13s	1m51s	18s
v3.0.5	16s	2m09s	25s
v3.0.4	19s	2m09s	26s
v3.0.3	37s	2m09s	25s

What's Changed

• Refactor GPU correlator by @BSchilperoort in #58
• Refactor CPU correlator by @BSchilperoort in #66
  • Move to single precision for faster computation
• Use importlib.resources instead of __file__, #67 by @BSchilperoort in #74
• Working importlib.resources in python <3.13 by @sverhoeven in #78
• When progressbar is disabled, don't wait for queue or counter lock by @BSchilperoort in #75
• Add notes on iGPU by @BSchilperoort in #79

Full Changelog: v3.0.5...v3.0.6

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/em_prepare.ipynb
with time powerfit emd_33292-7xm9-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 #55

Full Changelog: v3.0.4...v3.0.5

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 #48
• Reuse rotate_image3d kernel, remove redundant queue .finish() by @BSchilperoort in #50
• Fix multi processor, cif and chain by @sverhoeven in #53

New Contributors

• @BSchilperoort made their first contribution in #50

Full Changelog: v3.0.3...v3.0.4

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 powerfit in #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: v3.0.2...v3.0.3

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

• Correct link to pypi (#43)
• Make sure non python files are in wheels and sdist (#45)

Full Changelog: v3.0.1...v3.0.2