https://github.com/cmwoodley/kallisto

Efficiently calculate 3D-features for quantitative structure-activity relationship approaches.

https://github.com/cmwoodley/kallisto

Repository

Efficiently calculate 3D-features for quantitative structure-activity relationship approaches.

https://github.com/cmwoodley/kallisto/blob/master/

##

![PyPI - Python Version](https://img.shields.io/pypi/pyversions/kallisto)
[![Documentation](https://img.shields.io/badge/GitBook-Docu-lightgrey)](https://ehjc.gitbook.io/kallisto/)
[![Maturity Level](https://img.shields.io/badge/Maturity%20Level-Under%20Development-orange)](https://img.shields.io/badge/Maturity%20Level-Under%20Development-orange)
[![Tests](https://github.com/AstraZeneca/kallisto/workflows/Tests/badge.svg)](https://github.com/AstraZeneca/kallisto/actions?workflow=Tests)
[![codecov](https://codecov.io/gh/AstraZeneca/kallisto/branch/master/graph/badge.svg?token=HI0U0R96X8)](https://codecov.io/gh/AstraZeneca/kallisto)
[![status](https://joss.theoj.org/papers/16126cbcfb826bf4810d243a009a6b02/status.svg)](https://joss.theoj.org/papers/16126cbcfb826bf4810d243a009a6b02)

# Table of Contents

- Full Author List
- Introduction
- Installation
- Testing suite
- Reference

# Full Author List

- Developer [Eike Caldeweyher](https://scholar.google.com/citations?user=25n8C3wAAAAJ&hl)
- Developer [Rocco Meli](https://scholar.google.com/citations?hl=de&user=s8cVcvYAAAAJ)
- Developer [Philipp Pracht](https://scholar.google.com/citations?user=PJiGPk0AAAAJ&hl)

# Introduction

We developed the `kallisto` program for the efficient and robust calculation of atomic features using molecular geometries either in a `xmol` or a `Turbomole` format.
Furthermore, several modelling tools are implemented, e.g., to calculate root-mean squared deviations via quaternions (including rotation matrices), sorting of molecular geometries and many more. All features of `kallisto` are described in detail within our [documentation](https://ehjc.gitbook.io/kallisto/) ([GitBook repository](https://github.com/f3rmion/gitbook-kallisto)).

## Main dependencies

```bash
click 7.1.2 Composable command line interface toolkit
numpy 1.20.1 NumPy is the fundamental package for array computing with Python.
scipy 1.6.0 SciPy: Scientific Library for Python
 numpy >=1.16.5
```

For a list of all dependencies have a look at the pyproject.toml file.

## Installation from PyPI

To install `kallisto` via `pip` use our published PyPI package

```bash
pip install kallisto
```

## Installation from Source

Requirements to install `kallisto`from sources:

- [poetry](https://python-poetry.org/docs/#installation)
- [pyenv](https://github.com/pyenv/pyenv#installation) or [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html)
- python >=3.7

First check that `poetry` is running correctly (v1.0.10 at the time of writing)

```bash
> poetry --version
Poetry version 1.0.10
```

Create a virtual environment (via `pyenv` or `conda`) and activate it. Afterwards, clone the `kallisto` project from GitHub and install it using `poetry`

```bash
> git clone git@github.com:AstraZeneca/kallisto.git
> cd kallisto
> poetry install
```

## Testing suite

The `kallisto` project uses [nox](https://nox.thea.codes/en/stable/tutorial.html#installation) as an automated unit test suite, which is therefore an additional dependency.

### Default nox session

The default session includes: linting (lint), type checks (mypy, pytype), and unit tests (tests).

```bash
> nox
```

When everything runs smoothly through, you are ready to go! After one successful nox run, we can reuse the created virtual environment via the `-r` flag.

```bash
> nox -r
```

Different unit test sessions are implemented (check the noxfile.py). They can be called separately via the run session `-rs` flag.

### Tests

Run all unit tests that are defined in the /tests directory.

```bash
> nox -rs tests
```

### Lint

`kallisto` uses the [flake8](https://flake8.pycqa.org/en/latest/) linter (check the .flake8 config file).

```bash
> nox -rs lint
```

### Black

`kallisto` uses the [black](https://github.com/psf/black) code formatter.

```bash
> nox -rs black
```

### Safety

`kallisto` checks the security of dependencies via [safety](https://pyup.io/safety/).

```bash
> nox -rs safety
```

### Mypy

`kallisto` checks for static types via [mypy](https://github.com/python/mypy) (check the mypy.ini config file).

```bash
> nox -rs mypy
```

### Pytype

`kallisto` furthermore uses [pytype](https://github.com/google/pytype) for type checks.

```bash
> nox -rs pytype
```

### Coverage

Unit test [coverage](https://coverage.readthedocs.io/en/coverage-5.4/) can be checked as well.

```bash
> nox -rs coverage
```

## Reference

Always cite:

Eike Caldeweyher, J. Open Source Softw., _2021_, 6, 3050. DOI: [10.21105/joss.03050](https://doi.org/10.21105/joss.03050)

```
@article{Caldeweyher2021,
  doi = {10.21105/joss.03050},
  url = {https://doi.org/10.21105/joss.03050},
  year = {2021},
  volume = {6},
  number = {60},
  pages = {3050},
  author = {Eike Caldeweyher},
  title = {kallisto: A command-line interface to simplify computational modelling and the generation of atomic features},
  journal = {J. Open Source Softw.}
}
```

Owner

GitHub Events