chemiscope 0.8.3

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 with jupyter notebooks.

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 frames using ase
# frames can also be stk objets, e.g.
# frames = [stk.BuildingBlock(smiles="NCCN")]
frames = 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", frames=frames, properties=properties)

To display a chemiscope widget inside a jupyter notebook:

import chemiscope
import ase.io

# read frames using ase
# frames can also be stk objets, e.g.
# frames = [stk.BuildingBlock(smiles="NCCN")]
frames = ase.io.read("structures.xyz", ":")

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

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