kekule-clj
v0.7.0
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A Kekule widget for Common Lisp Jupyter
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kekule-clj
A common-lisp-jupyter widget for kekule.js.
Installation
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)
Usage
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.