chemiscope 1.1.0

Helpers to work with the chemiscope interactive structure/property explorer for materials and molecules

Python helpers for chemiscope

This package contains Python code to help generate input files for the chemiscope default visualizer, and integrate chemiscope as an interactive widget in notebook environments (Jupyter, JupyterLab, marimo, and Google Colab).

Installation

You should use pip to install this package:

pip install chemiscope

This installs both a chemiscope-input command line tool, and the chemiscope package.

Usage

To create a new chemiscope input file:

import chemiscope
import ase.io

# read structures using ase. You can also use other structure providers such as
# stk, MDAnalysis, …
structures = ase.io.read("structures.xyz", ":")

# add additional properties to display
properties = {
    "<property name>": {
        target: "atom",
        values: [3, 4, 2, 8, 9, 10],
    }
}

chemiscope.write_input(
    "my-input.json.gz", structures=structures, properties=properties
)

To display a chemiscope widget inside a notebook:

import chemiscope
import ase.io

structures = ase.io.read("structures.xyz", ":")

properties = {
    "<property name>": [3, 4, 2, 8, 9, 10],
}

chemiscope.show(structures=structures, properties=properties)