Support/Jupyter - Revision history

Perrim at 17:17, 11 September 2021

2021-09-11T17:17:20Z

2021-09-11T17:16:49Z

2021-09-11T17:15:53Z

2021-09-11T17:04:40Z

2021-09-11T17:04:07Z

2021-09-11T17:00:58Z

2021-08-24T18:48:53Z

Jupyter notebooks

2021-08-24T18:45:44Z

Jupyter notebooks

New page

= Running JSmol in Jupyter notebooks =

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 Wayne Decatur has setup a [https://mybinder.org/v2/gist/fomightez/c6c0954414a8e576c5c2611c64163790/HEAD?filepath=1%20-%20Basic%20usage.ipynb Binder container] to demonstrate usage
-ChemCompute has jupyter-jsmol preinstalled in its Jupyter notebooks.  ChemCompute is a free website for students to run Computational Chemistry jobs.  Through ChemCompute's Jupyter Notebook you can run a calculation with [https://psicode.org/ Psi4] and view the output in JSmol.
+[https://chemcompute.org ChemCompute] has jupyter-jsmol preinstalled in its Jupyter notebooks.  ChemCompute is a free website for students to run Computational Chemistry jobs.  Through ChemCompute's Jupyter Notebook you can run a calculation with [https://psicode.org/ Psi4] and view the output in JSmol.
 # Go to [https://chemcompute.org ChemCompute] and login or register at the top right.  You can likely login with your institutional login.
 # Access an [https://chemcompute.org/jupyterhub_internal/user-redirect/notebooks/experiments/05%20-%20H2%20MOs%20STO-3G.ipynb example Jupyter Notebook]

@@ Line 25: / Line 25: @@
 Wayne Decatur has setup a [https://mybinder.org/v2/gist/fomightez/c6c0954414a8e576c5c2611c64163790/HEAD?filepath=1%20-%20Basic%20usage.ipynb Binder container] to demonstrate usage
-ChemCompute has jupyter-jsmol preinstalled in its Jupyter notebooks.  ChemCompute is a free website for students to run Computational Chemistry jobs.  Through ChemCompute's Jupyter Notebook you can run a calculation with Psi4 and view the output in JSmol.
+ChemCompute has jupyter-jsmol preinstalled in its Jupyter notebooks.  ChemCompute is a free website for students to run Computational Chemistry jobs.  Through ChemCompute's Jupyter Notebook you can run a calculation with [https://psicode.org/ Psi4] and view the output in JSmol.
 # Go to [https://chemcompute.org ChemCompute] and login or register at the top right.  You can likely login with your institutional login.
 # Access an [https://chemcompute.org/jupyterhub_internal/user-redirect/notebooks/experiments/05%20-%20H2%20MOs%20STO-3G.ipynb example Jupyter Notebook]

@@ Line 4: / Line 4: @@
 JSmol may be implemented in a Jupyter Notebook through [https://towardsdatascience.com/jupyter-notebook-extensions-517fa69d2231 Jupyter Notebook Extensions], which blend javascript with the notebook environment.  One extension is [https://github.com/fekad/jupyter-jsmol jupyter-jsmol] by Adam Fekete.  Jupyter-jsmol provides a python wrapper to the JSmol widget.
 Jupyter-jsmol can be installed with pip in your notebook virtual environment.  (Note the use of the underscore in the pip package)
@@ Line 17: / Line 19: @@
 <code>jupyter labextension install @jupyter-widgets/jupyterlab-manager</code>
+ChemCompute has jupyter-jsmol preinstalled in its Jupyter notebooks.  ChemCompute is a free website for students to run Computational Chemistry jobs.  Through ChemCompute's Jupyter Notebook you can run a calculation with Psi4 and view the output in JSmol.
+# Go to [https://chemcompute.org ChemCompute] and login or register at the top right.  You can likely login with your institutional login.
+# Access an [https://chemcompute.org/jupyterhub_internal/user-redirect/notebooks/experiments/05%20-%20H2%20MOs%20STO-3G.ipynb example Jupyter Notebook]

@@ Line 10: / Line 10: @@
 Old versions of Jupyter Notebooks require you to enable the extension:
 <code>jupyter nbextension enable --py [--sys-prefix|--user|--system] jupyter_jsmol</code>
 If you use JupyterLab you'll have to install the extension:
 <code>jupyter labextension install @jupyter-widgets/jupyterlab-manager</code>

← Older revision		Revision as of 17:04, 11 September 2021
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	<code>pip install jupyter_jsmol</code>		<code>pip install jupyter_jsmol</code>
		+
		+	Old versions of Jupyter Notebooks require you to enable the extension:
		+	<code>jupyter nbextension enable --py [--sys-prefix\|--user\|--system] jupyter_jsmol</code>
		+
		+	If you use JupyterLab you'll have to install the extension:
		+	<code>jupyter labextension install @jupyter-widgets/jupyterlab-manager</code>
		+

@@ Line 3: / Line 3: @@
 The [https://jupyter.org/ Jupyter Notebook] is an open-source web application that allows you to create and share documents that contain live code, equations, visualizations and narrative text.
-JSmol may be implemented in a Jupyter Notebook
+JSmol may be implemented in a Jupyter Notebook through [https://towardsdatascience.com/jupyter-notebook-extensions-517fa69d2231 Jupyter Notebook Extensions], which blend javascript with the notebook environment.  One extension is [https://github.com/fekad/jupyter-jsmol jupyter-jsmol] by Adam Fekete.  Jupyter-jsmol provides a python wrapper to the JSmol widget.
-''(more information to follow)''

← Older revision		Revision as of 18:48, 24 August 2021
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	= Running JSmol in Jupyter notebooks =		= Running JSmol in Jupyter notebooks =

−	...	+	The [https://jupyter.org/ Jupyter Notebook] is an open-source web application that allows you to create and share documents that contain live code, equations, visualizations and narrative text.
		+
		+	JSmol may be implemented in a Jupyter Notebook
		+	''(more information to follow)''
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		+
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