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Description:

flour 1.0.1

flour is a Python library for really fast chemical file reading and writing.

Table of contents

Installation
.cube files
Developer guide

Installation
pip install flour

.cube files
import numpy as np
import flour

# Write the cube file.
flour.write_cube(
path="molecule.cube",
title1="The first line of the cube file",
title2="The second line of the cube file",
# The atomic number of each atom.
atoms=np.array([1, 35], dtype=np.uint8),
# The charge on each atom.
charges=np.array([0., 0.]),
# The position matrix of the molecule.
positions=np.array([
[-0.5, 0., 0.],
[1., 0., 0.],
]),
# The origin of the voxel grid.
voxel_origin=np.array([-4.5, -4.5, -4.5]),
# The a, b, c vectors of a single voxel.
voxel_size=np.array(
[
[0.5, 0., 0.],
[0., 0.5, 0.],
[0., 0., 0.5],
],
),
# A 20 x 20 x 20 voxel grid.
voxels=np.random.rand(20, 20, 20),
)

# Read the cube file.
cube_data = flour.read_cube("molecule.cube")
cube_data.atoms # The atomic number of each atom.
cube_data.charges # The charge of each atom.
cube_data.positions # The position matrix of the molecule.
cube_data.grid.origin # The origin of the voxel grid.
cube_data.grid.voxel_size # The a, b, c vectors of a single voxel.
cube_data.grid.voxels # The voxel grid.

Developer guide
If you want to develop FLOUR there’s a couple of handy things you should know.
FLOUR is built using the excellent maturin library. This means that to build
the library you run
maturin develop --extras=dev --profile=release
and that’s more or less all there is to it. The only other thing to note is that we do have
a justfile, which contains commands you might find helpful for formatting and linting your code.
To use the justfile you should grab just.