https://github.com/rs-station/rs-booster

Useful scripts for analyzing diffraction
https://github.com/rs-station/rs-booster

crystallography diffraction python reciprocalspaceship xray xray-diffraction

Last synced: 25 days ago
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Useful scripts for analyzing diffraction

• Host: GitHub
• URL: https://github.com/rs-station/rs-booster
• Owner: rs-station
• License: mit
• Created: 2021-02-24T15:18:30.000Z (almost 5 years ago)
• Default Branch: main
• Last Pushed: 2025-05-04T19:54:47.000Z (9 months ago)
• Last Synced: 2025-09-29T12:06:39.461Z (4 months ago)
• Topics: crystallography, diffraction, python, reciprocalspaceship, xray, xray-diffraction
• Language: Python
• Homepage: https://rs-station.github.io/rs-booster/
• Size: 5.43 MB
• Stars: 3
• Watchers: 4
• Forks: 5
• Open Issues: 14
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# rs-booster

![Build](https://github.com/rs-station/rs-booster/workflows/Build/badge.svg)

[![PyPI](https://img.shields.io/pypi/v/rs-booster?color=blue)](https://pypi.org/project/rs-booster/)  

`rs-booster` contains commandline scripts for diffraction data analysis tasks.

This package can be viewed as a "booster rocket" for [`reciprocalspaceship`](https://github.com/rs-station/reciprocalspaceship).

### Installation

The fastest way to install `rs-booster` is using pip:

```bash

pip install rs-booster

```

If you are interested in getting access to new features that haven't yet made it into a release, you can install `rs-booster` from source:

```bash

git clone https://github.com/rs-station/rs-booster.git

cd rs-booster

python -m pip install -e .

```

### Design and usage

`rs-booster` is designed primarily as a command line interface. 

Applications from this package are prefixed with `rs.`.

Users can **list available commands** by typing `rs.` and double-pressing the `TAB` key. 

Each subprogram is documented using the [argparse library](https://docs.python.org/3/library/argparse.html).

To get usage info for a subprogram, use the `-h` or `--help` flag. 

For instance,

```bash

$ rs.find_peaks -h

```

will print the following

```bash

usage: rs.find_peaks [-h] -f STRUCTURE_FACTOR_KEY -p PHASE_KEY [-o CSV_OUT] [-z SIGMA_CUTOFF] [-w WEIGHT_KEY] [--sample-rate SAMPLE_RATE] [--min-volume MIN_VOLUME]

                           [--min-score MIN_SCORE] [--min-peak MIN_PEAK] [-d DISTANCE_CUTOFF] [--use-long-names]

                           mtz_file pdb_file

Search an electron density map for peaks in the vicinity of a structure.

positional arguments:

  mtz_file

  pdb_file

options:

  -h, --help            show this help message and exit

  -f STRUCTURE_FACTOR_KEY, --structure-factor-key STRUCTURE_FACTOR_KEY

                        column label of the structure factor you want to use.

  -p PHASE_KEY, --phase-key PHASE_KEY

                        column label of the phase you want to use.

  -o CSV_OUT, --csv-out CSV_OUT

                        output the report to a csv file

  -z SIGMA_CUTOFF, --sigma-cutoff SIGMA_CUTOFF

                        the z-score cutoff for voxels to be included in the peak search. the default is 1.5

  -w WEIGHT_KEY, --weight-key WEIGHT_KEY

                        column label of any weights you wish to apply to the map.

  --sample-rate SAMPLE_RATE

                        change fft oversampling from the default (3).

  --min-volume MIN_VOLUME

                        the minimum volume of peaks with default zero.

  --min-score MIN_SCORE

                        the minimum score of peaks with default zero.

  --min-peak MIN_PEAK   the minimum peak value with default zero.

  -d DISTANCE_CUTOFF, --distance-cutoff DISTANCE_CUTOFF

                        the distance cutoff of nearest neighbor search with default of 4 angstroms.

  --use-long-names      use more verbose column names in the peak report.

```