A common-lisp-jupyter widget for kekule.js.
The Jupyter Lab frontend code should be installed using the following command:
jupyter-labextension install kekule-clj
Once the extension has been installed then widget can be loaded in a notebook using Quicklisp.
(ql:quickload :kekule-clj)For sample notebooks please see the examples directory. There are two main
widgets exported by kekule-clj. The diagram widget displays a molecular
diagram using a data source and format id. The composer widget allows editing
of the attached data. Both share a set of common slots data and format-id.
The accepted formats are:
- Smiles format via
+smiles-format+or"smi" - Kekule native JSON format via
+kekule-json-format+or"Kekule-JSON" - Kekule specific XML format via
+kekule-xml-format+or"Kekule-XML" - MDL Molfile V2000 format via
+mdl-mol-2000-format+or"mol" - MDL Molfile V3000 format via
+mdl-mol-3000-format+or"mol3k" - MDL Structure Data format via
+mdl-structure-data-format+or"sd" - MDL Reaction V2000 format via
+mdl-reaction-2000-format+or"rxn" - MDL Reaction V3000 format via
+mdl-reaction-3000-format+or"rxn3k"
The default format is MDL Molfile V2000 hence the following will display a file in the diagram widget and display a toolbar in addition.
(make-instance 'kekule:diagram
:enable-toolbar t
:data (alexandria:read-file-into-string "chemFiles/2D/aromaticRings.mol"))More options are available on the various widgets and can be seen in the source code.