zndraw 0.2.0a10

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ZnDraw

Install via pip install zndraw or pip install zndraw[webview] to open zndraw in a dedicated window.

CLI

You can use ZnDraw with the CLI zndraw atoms.xyz. Alternatively, you can use zndraw from within a Juypter Notebook

from zndraw import ZnDraw
import ase

zndraw = ZnDraw()

zndraw
# this will show you the molecule

# new cell
zndraw.socket.sleep(2) # give it some time to fully connect
zndraw[0] = ase.Atoms(
  "H2O", positions=[[0.75, -0.75, 0], [0.75, 0.75, 0], [0, 0, 0]]
  )

or a normal Python script using zndraw = ZnDraw(jupyter=False) to open a browser window.

ZnDraw is designed to work with your Python scripts. To interface you can inherit from zndraw.examples.UpdateScene or follow this base class:

import abc
from pydantic import BaseModel

class UpdateScene(BaseModel, abc.ABC):
    @abc.abstractmethod
    def run(self, atom_ids: list[int], atoms: ase.Atoms, **kwargs) -> list[ase.Atoms]:
        pass

The run method expects as inputs

• atom_ids: list[int], the ids of the currently selected atoms
• atoms: ase.Atoms, the configuration as ase.Atoms file where atom_ids where selected.
• kwargs: dict could be additional information from the scene

and as an output:

• list[ase.Atoms], a list of ase Atoms objects to display.

You can define the parameters using pydantic.Field which will be displayed in the UI.

class MyUpdateCls(UpdateScene):
    steps: int = Field(100, le=1000, ge=1)
    x: float = Field(0.5, le=5, ge=0)
    symbol: str = Field("same")

To add your method click on the + on the right side of the window. Your should be able to add your method from the working directory via module.MyUpdateCls as long as it can be imported via from module import MyUpdateCls.

Development

ZnDraw is developed using https://python-poetry.org/. Furthermore, the javascript packages have to be installed using https://www.npmjs.com/.

cd zndraw/static/
npm install