ipyspeck 0.6.0

Speck Jupyter Widget

ipyspeck

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Speck

Speck is a molecule renderer with the goal of producing figures that are as attractive as they are practical. Express your molecule clearly and with style.

ipypeck

Ipyspeck is a ipywidget wrapping speck to be used on a Jupyter notebook as a regular widget.

Usage

The ipyspeck widget renders xyz molecules.

import ipyspeck

H2O='''3
Water molecule
O          0.00000        0.00000        0.11779
H          0.00000        0.75545       -0.47116
H          0.00000       -0.75545       -0.47116'''
h2o = ipyspeck.speck.Speck(data=H2O)
h2o

Ideally it should be used as part of a container widget (such as Box, VBox, Grid, ...)

import ipywidgets as w
c = w.Box([h2o], layout=w.Layout(width="600px",height="400px"))
c

The visualization parameters can be modified

#Modify atoms size
h2o.atomScale = 0.3
#change bonds size
h2o.bondScale = 0.3
#highlight borders
h2o.outline = 0

To render molecules on different formats openbabel can be used to translate them as xyz

import openbabel
import requests
url = "https://files.rcsb.org/ligands/view/CO2_ideal.sdf"
r = requests.get(url)
obConversion = openbabel.OBConversion()
obConversion.SetInAndOutFormats("sdf", "xyz")
mol = openbabel.OBMol()
obConversion.ReadString(mol, r.text)
co2 = obConversion.WriteString(mol)
ipyspeck.speck.Speck(data=co2)

Installation

To install use pip:

$ pip install ipyspeck
$ jupyter nbextension enable --py --sys-prefix ipyspeck

To install for jupyterlab

$ jupyter labextension install ipyspeck

For a development installation (requires npm),

$ git clone https://github.com//denphi//speck.git
$ cd speck/widget/ipyspeck
$ pip install -e .
$ jupyter nbextension install --py --symlink --sys-prefix ipyspeck
$ jupyter nbextension enable --py --sys-prefix ipyspeck
$ jupyter labextension install js

When actively developing your extension, build Jupyter Lab with the command:

$ jupyter lab --watch

This takes a minute or so to get started, but then automatically rebuilds JupyterLab when your javascript changes.

Note on first jupyter lab --watch, you may need to touch a file to get Jupyter Lab to open.