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This is the kekule-clj Reference Manual, version 0.4.0, generated automatically by Declt version 3.0 "Montgomery Scott" on Wed Nov 04 13:59:34 2020 GMT+0.
| • Introduction | What kekule-clj is all about | |
| • Systems | The systems documentation | |
| • Modules | The modules documentation | |
| • Files | The files documentation | |
| • Packages | The packages documentation | |
| • Definitions | The symbols documentation | |
| • Indexes | Concepts, functions, variables and data types |
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+ or "smi"+kekule-json-format+ or "Kekule-JSON"+kekule-xml-format+ or "Kekule-XML"+mdl-mol-2000-format+ or "mol"+mdl-mol-3000-format+ or "mol3k"+mdl-structure-data-format+ or "sd"+mdl-reaction-2000-format+ or "rxn"+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.
Next: Modules, Previous: Introduction, Up: Top [Contents][Index]
The main system appears first, followed by any subsystem dependency.
| • The kekule-clj system |
Tarn W. Burton
MIT
A Kekule widget for Common Lisp Jupyter
0.4.0
kekule-clj.asd (file)
src (module)
Modules are listed depth-first from the system components tree.
| • The kekule-clj/src module |
kekule-clj (system)
src/
Files are sorted by type and then listed depth-first from the systems components trees.
| • Lisp files |
| • The kekule-clj.asd file | ||
| • The kekule-clj/src/packages.lisp file | ||
| • The kekule-clj/src/version.lisp file | ||
| • The kekule-clj/src/widget.lisp file |
Next: The kekule-clj/src/packages․lisp file, Previous: Lisp files, Up: Lisp files [Contents][Index]
kekule-clj.asd
kekule-clj (system)
Next: The kekule-clj/src/version․lisp file, Previous: The kekule-clj․asd file, Up: Lisp files [Contents][Index]
Next: The kekule-clj/src/widget․lisp file, Previous: The kekule-clj/src/packages․lisp file, Up: Lisp files [Contents][Index]
packages.lisp (file)
src (module)
src/version.lisp
Previous: The kekule-clj/src/version․lisp file, Up: Lisp files [Contents][Index]
version.lisp (file)
src (module)
src/widget.lisp
chem-widget (class)
Next: Definitions, Previous: Files, Up: Top [Contents][Index]
Packages are listed by definition order.
| • The kekule package |
packages.lisp (file)
common-lisp
Definitions are sorted by export status, category, package, and then by lexicographic order.
| • Exported definitions | ||
| • Internal definitions |
Next: Internal definitions, Previous: Definitions, Up: Definitions [Contents][Index]
| • Exported special variables | ||
| • Exported functions | ||
| • Exported generic functions | ||
| • Exported classes |
Next: Exported functions, Previous: Exported definitions, Up: Exported definitions [Contents][Index]
Kekule native JSON format tag
widget.lisp (file)
Kekule specific XML format tag
widget.lisp (file)
MDL Molfile V2000 format tag
widget.lisp (file)
MDL Molfile V3000 format tag
widget.lisp (file)
MDL Reaction V2000 format tag
widget.lisp (file)
MDL Reaction V3000 format tag
widget.lisp (file)
MDL Structure Data format tag
widget.lisp (file)
Simplified molecular-input line-entry system format tag
widget.lisp (file)
Next: Exported generic functions, Previous: Exported special variables, Up: Exported definitions [Contents][Index]
Fit view to current structures.
widget.lisp (file)
Load molecular data into an existing widget.
widget.lisp (file)
Load molecular data from a file into an existing widget.
widget.lisp (file)
Load molecular data from a url into an existing widget.
widget.lisp (file)
Next: Exported classes, Previous: Exported functions, Up: Exported definitions [Contents][Index]
Data to be displayed by the widget.
widget.lisp (file)
Whether to allow interaction with the molecule or not.
widget.lisp (file)
Whether to allow a popup editor to be shown or not.
widget.lisp (file)
Whether to show the toolbar or not.
widget.lisp (file)
Format tag of data. Current allowed values are smi, Kekule-JSON, Kekuule-XML, mol, mol3k, sd, rxn and rxn3k.
widget.lisp (file)
Whether the diagram is resizable or not.
widget.lisp (file)
A list of the names of buttons to show in the toolbar.
widget.lisp (file)
Previous: Exported generic functions, Up: Exported definitions [Contents][Index]
A widget that edits molecular data.
widget.lisp (file)
chem-widget (class)
| Initarg | Value |
|---|---|
| :%model-name | "kekulecomposermodel" |
| :%view-name | "kekulecomposerview" |
A widget that displays molecular data.
widget.lisp (file)
chem-widget (class)
Whether to show the toolbar or not.
boolean
:enable-toolbar
enable-toolbar (generic function)
(setf enable-toolbar) (generic function)
Whether to allow interaction with the molecule or not.
boolean
:enable-direct-interaction
t
enable-direct-interaction (generic function)
(setf enable-direct-interaction) (generic function)
Whether to allow a popup editor to be shown or not.
boolean
:enable-edit
t
enable-edit (generic function)
(setf enable-edit) (generic function)
A list of the names of buttons to show in the toolbar.
list
:tool-buttons
(list "loaddata" "savedata" "moldisplaytype" "molhidehydrogens" "zoomin" "zoomout" "rotateleft" "rotateright" "rotatex" "rotatey" "rotatez" "reset" "openeditor" "config")
tool-buttons (generic function)
(setf tool-buttons) (generic function)
Whether the diagram is resizable or not.
boolean
:resizable
resizable (generic function)
(setf resizable) (generic function)
| Initarg | Value |
|---|---|
| :%model-name | "kekulediagrammodel" |
| :%view-name | "kekulediagramview" |
Previous: Exported definitions, Up: Definitions [Contents][Index]
| • Internal special variables | ||
| • Internal classes |
Next: Internal classes, Previous: Internal definitions, Up: Internal definitions [Contents][Index]
version.lisp (file)
version.lisp (file)
Previous: Internal special variables, Up: Internal definitions [Contents][Index]
Base widget used by the diagram and composer widgets.
widget.lisp (file)
dom-widget (class)
Data to be displayed by the widget.
:data
"untitled document"
data (generic function)
(setf data) (generic function)
Format tag of data. Current allowed values are smi, Kekule-JSON, Kekuule-XML, mol, mol3k, sd, rxn and rxn3k.
string
:format-id
kekule:+mdl-reaction-2000-format+
format-id (generic function)
(setf format-id) (generic function)
| Initarg | Value |
|---|---|
| :%model-module | kekule::+module-name+ |
| :%model-module-version | kekule::+module-version+ |
| :%view-module | kekule::+module-name+ |
| :%view-module-version | kekule::+module-version+ |
| :layout | (make-instance (quote jupyter-widgets:layout) :width "100%" :height "480px") |
Previous: Definitions, Up: Top [Contents][Index]
| • Concept index | ||
| • Function index | ||
| • Variable index | ||
| • Data type index |
Next: Function index, Previous: Indexes, Up: Indexes [Contents][Index]
| Jump to: | F K L M |
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Next: Variable index, Previous: Concept index, Up: Indexes [Contents][Index]
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D E F G L M R T |
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D E F G L M R T |
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Next: Data type index, Previous: Function index, Up: Indexes [Contents][Index]
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D E F R S T |
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D E F R S T |
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Previous: Variable index, Up: Indexes [Contents][Index]
| Jump to: | C D K P S |
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