The kekule-clj Reference Manual
This is the kekule-clj Reference Manual, version 0.4.0,
generated automatically by Declt version 4.0 beta 2 "William Riker"
on Sun Dec 15 06:33:02 2024 GMT+0.
2 Systems
The main system appears first, followed by any subsystem dependency.
2.1 kekule-clj
A Kekule widget for Common Lisp Jupyter
- Author
Tarn W. Burton
- License
MIT
- Version
0.4.0
- Defsystem Dependency
jupyter-lab-extension
(system).
- Dependency
common-lisp-jupyter
(system).
- Source
kekule-clj.asd
.
- Child Components
-
3 Modules
Modules are listed depth-first from the system components tree.
4 Files
Files are sorted by type and then listed depth-first from the systems
components trees.
5 Packages
Packages are listed by definition order.
5.1 kekule
- Source
packages.lisp
.
- Use List
common-lisp
.
- Public Interface
-
- Internals
-
6 Definitions
Definitions are sorted by export status, category, package, and then by
lexicographic order.
6.1 Public Interface
6.1.1 Special variables
- Special Variable: +kekule-json-format+ ¶
-
Kekule native JSON format tag
- Package
kekule
.
- Source
widget.lisp
.
- Special Variable: +kekule-xml-format+ ¶
-
Kekule specific XML format tag
- Package
kekule
.
- Source
widget.lisp
.
- Special Variable: +mdl-mol-2000-format+ ¶
-
MDL Molfile V2000 format tag
- Package
kekule
.
- Source
widget.lisp
.
- Special Variable: +mdl-mol-3000-format+ ¶
-
MDL Molfile V3000 format tag
- Package
kekule
.
- Source
widget.lisp
.
- Special Variable: +mdl-reaction-2000-format+ ¶
-
MDL Reaction V2000 format tag
- Package
kekule
.
- Source
widget.lisp
.
- Special Variable: +mdl-reaction-3000-format+ ¶
-
MDL Reaction V3000 format tag
- Package
kekule
.
- Source
widget.lisp
.
- Special Variable: +mdl-structure-data-format+ ¶
-
MDL Structure Data format tag
- Package
kekule
.
- Source
widget.lisp
.
- Special Variable: +smiles-format+ ¶
-
Simplified molecular-input line-entry system format tag
- Package
kekule
.
- Source
widget.lisp
.
6.1.2 Ordinary functions
- Function: fit (instance) ¶
-
Fit view to current structures.
- Package
kekule
.
- Source
widget.lisp
.
- Function: load-data (instance data format-id) ¶
-
Load molecular data into an existing widget.
- Package
kekule
.
- Source
widget.lisp
.
- Function: load-file (instance path) ¶
-
Load molecular data from a file into an existing widget.
- Package
kekule
.
- Source
widget.lisp
.
- Function: load-url (instance url) ¶
-
Load molecular data from a url into an existing widget.
- Package
kekule
.
- Source
widget.lisp
.
- Function: make-composer (&rest initargs &key comm-id on-close layout tabbable tooltip data format-id &allow-other-keys) ¶
-
- Package
kekule
.
- Source
register-widgets.lisp
.
- Function: make-diagram (&rest initargs &key comm-id on-close layout tabbable tooltip data format-id enable-toolbar enable-direct-interaction enable-edit tool-buttons resizable &allow-other-keys) ¶
-
- Package
kekule
.
- Source
register-widgets.lisp
.
6.1.3 Generic functions
- Generic Reader: data (object) ¶
-
- Generic Writer: (setf data) (object) ¶
-
- Package
kekule
.
- Methods
- Reader Method: data ((chem-widget
chem-widget
)) ¶
-
- Writer Method: (setf data) ((chem-widget
chem-widget
)) ¶
-
Data to be displayed by the widget.
- Source
widget.lisp
.
- Target Slot
data
.
- Generic Reader: enable-direct-interaction (object) ¶
-
- Generic Writer: (setf enable-direct-interaction) (object) ¶
-
- Package
kekule
.
- Methods
- Reader Method: enable-direct-interaction ((diagram
diagram
)) ¶
-
- Writer Method: (setf enable-direct-interaction) ((diagram
diagram
)) ¶
-
Whether to allow interaction with the molecule or not.
- Source
widget.lisp
.
- Target Slot
enable-direct-interaction
.
- Generic Reader: enable-edit (object) ¶
-
- Generic Writer: (setf enable-edit) (object) ¶
-
- Package
kekule
.
- Methods
- Reader Method: enable-edit ((diagram
diagram
)) ¶
-
- Writer Method: (setf enable-edit) ((diagram
diagram
)) ¶
-
Whether to allow a popup editor to be shown or not.
- Source
widget.lisp
.
- Target Slot
enable-edit
.
- Generic Reader: enable-toolbar (object) ¶
-
- Generic Writer: (setf enable-toolbar) (object) ¶
-
- Package
kekule
.
- Methods
- Reader Method: enable-toolbar ((diagram
diagram
)) ¶
-
- Writer Method: (setf enable-toolbar) ((diagram
diagram
)) ¶
-
Whether to show the toolbar or not.
- Source
widget.lisp
.
- Target Slot
enable-toolbar
.
- Generic Reader: format-id (object) ¶
-
- Generic Writer: (setf format-id) (object) ¶
-
- Package
kekule
.
- Methods
- Reader Method: format-id ((chem-widget
chem-widget
)) ¶
-
- Writer Method: (setf format-id) ((chem-widget
chem-widget
)) ¶
-
Format tag of data. Current allowed values are smi, Kekule-JSON, Kekuule-XML, mol, mol3k, sd, rxn and rxn3k.
- Source
widget.lisp
.
- Target Slot
format-id
.
- Generic Reader: resizable (object) ¶
-
- Generic Writer: (setf resizable) (object) ¶
-
- Package
kekule
.
- Methods
- Reader Method: resizable ((diagram
diagram
)) ¶
-
- Writer Method: (setf resizable) ((diagram
diagram
)) ¶
-
Whether the diagram is resizable or not.
- Source
widget.lisp
.
- Target Slot
resizable
.
- Generic Reader: tool-buttons (object) ¶
-
- Generic Writer: (setf tool-buttons) (object) ¶
-
- Package
kekule
.
- Methods
- Reader Method: tool-buttons ((diagram
diagram
)) ¶
-
- Writer Method: (setf tool-buttons) ((diagram
diagram
)) ¶
-
A list of the names of buttons to show in the toolbar.
- Source
widget.lisp
.
- Target Slot
tool-buttons
.
6.1.4 Classes
- Class: composer ¶
-
A widget that edits molecular data.
- Package
kekule
.
- Source
widget.lisp
.
- Direct superclasses
chem-widget
.
- Direct Default Initargs
Initarg | Value |
:%model-name | kekulecomposermodel |
:%view-name | kekulecomposerview |
- Class: diagram ¶
-
A widget that displays molecular data.
- Package
kekule
.
- Source
widget.lisp
.
- Direct superclasses
chem-widget
.
- Direct methods
-
- Direct Default Initargs
Initarg | Value |
:%model-name | kekulediagrammodel |
:%view-name | kekulediagramview |
- Direct slots
- Slot: enable-toolbar ¶
-
Whether to show the toolbar or not.
- Type
boolean
- Initargs
:enable-toolbar
- Readers
enable-toolbar
.
- Writers
(setf enable-toolbar)
.
- Slot: enable-direct-interaction ¶
-
Whether to allow interaction with the molecule or not.
- Type
boolean
- Initform
t
- Initargs
:enable-direct-interaction
- Readers
enable-direct-interaction
.
- Writers
(setf enable-direct-interaction)
.
- Slot: enable-edit ¶
-
Whether to allow a popup editor to be shown or not.
- Type
boolean
- Initform
t
- Initargs
:enable-edit
- Readers
enable-edit
.
- Writers
(setf enable-edit)
.
- Slot: tool-buttons ¶
-
A list of the names of buttons to show in the toolbar.
- Type
list
- Initform
(list "loaddata" "savedata" "moldisplaytype" "molhidehydrogens" "zoomin" "zoomout" "rotateleft" "rotateright" "rotatex" "rotatey" "rotatez" "reset" "openeditor" "config")
- Initargs
:tool-buttons
- Readers
tool-buttons
.
- Writers
(setf tool-buttons)
.
- Slot: resizable ¶
-
Whether the diagram is resizable or not.
- Type
boolean
- Initargs
:resizable
- Readers
resizable
.
- Writers
(setf resizable)
.
6.2 Internals
6.2.2 Classes
- Class: chem-widget ¶
-
Base widget used by the diagram and composer widgets.
- Package
kekule
.
- Source
widget.lisp
.
- Direct superclasses
dom-widget
.
- Direct subclasses
-
- Direct methods
-
- Direct Default Initargs
Initarg | Value |
:%model-module | +module-name+ |
:%model-module-version | +module-version+ |
:%view-module | +module-name+ |
:%view-module-version | +module-version+ |
:layout | (make-instance (quote layout) width 100% height 480px) |
- Direct slots
- Slot: data ¶
-
Data to be displayed by the widget.
- Initform
"untitled document"
- Initargs
:data
- Readers
data
.
- Writers
(setf data)
.
- Slot: format-id ¶
-
Format tag of data. Current allowed values are smi, Kekule-JSON, Kekuule-XML, mol, mol3k, sd, rxn and rxn3k.
- Type
string
- Initform
kekule:+mdl-reaction-2000-format+
- Initargs
:format-id
- Readers
format-id
.
- Writers
(setf format-id)
.
Appendix A Indexes
A.2 Functions
| |
|
( | | |
| (setf data) : | | Public generic functions |
| (setf data) : | | Public generic functions |
| (setf enable-direct-interaction) : | | Public generic functions |
| (setf enable-direct-interaction) : | | Public generic functions |
| (setf enable-edit) : | | Public generic functions |
| (setf enable-edit) : | | Public generic functions |
| (setf enable-toolbar) : | | Public generic functions |
| (setf enable-toolbar) : | | Public generic functions |
| (setf format-id) : | | Public generic functions |
| (setf format-id) : | | Public generic functions |
| (setf resizable) : | | Public generic functions |
| (setf resizable) : | | Public generic functions |
| (setf tool-buttons) : | | Public generic functions |
| (setf tool-buttons) : | | Public generic functions |
|
D | | |
| data : | | Public generic functions |
| data : | | Public generic functions |
|
E | | |
| enable-direct-interaction : | | Public generic functions |
| enable-direct-interaction : | | Public generic functions |
| enable-edit : | | Public generic functions |
| enable-edit : | | Public generic functions |
| enable-toolbar : | | Public generic functions |
| enable-toolbar : | | Public generic functions |
|
F | | |
| fit : | | Public ordinary functions |
| format-id : | | Public generic functions |
| format-id : | | Public generic functions |
| Function, fit : | | Public ordinary functions |
| Function, load-data : | | Public ordinary functions |
| Function, load-file : | | Public ordinary functions |
| Function, load-url : | | Public ordinary functions |
| Function, make-composer : | | Public ordinary functions |
| Function, make-diagram : | | Public ordinary functions |
|
G | | |
| Generic Function, (setf data) : | | Public generic functions |
| Generic Function, (setf enable-direct-interaction) : | | Public generic functions |
| Generic Function, (setf enable-edit) : | | Public generic functions |
| Generic Function, (setf enable-toolbar) : | | Public generic functions |
| Generic Function, (setf format-id) : | | Public generic functions |
| Generic Function, (setf resizable) : | | Public generic functions |
| Generic Function, (setf tool-buttons) : | | Public generic functions |
| Generic Function, data : | | Public generic functions |
| Generic Function, enable-direct-interaction : | | Public generic functions |
| Generic Function, enable-edit : | | Public generic functions |
| Generic Function, enable-toolbar : | | Public generic functions |
| Generic Function, format-id : | | Public generic functions |
| Generic Function, resizable : | | Public generic functions |
| Generic Function, tool-buttons : | | Public generic functions |
|
L | | |
| load-data : | | Public ordinary functions |
| load-file : | | Public ordinary functions |
| load-url : | | Public ordinary functions |
|
M | | |
| make-composer : | | Public ordinary functions |
| make-diagram : | | Public ordinary functions |
| Method, (setf data) : | | Public generic functions |
| Method, (setf enable-direct-interaction) : | | Public generic functions |
| Method, (setf enable-edit) : | | Public generic functions |
| Method, (setf enable-toolbar) : | | Public generic functions |
| Method, (setf format-id) : | | Public generic functions |
| Method, (setf resizable) : | | Public generic functions |
| Method, (setf tool-buttons) : | | Public generic functions |
| Method, data : | | Public generic functions |
| Method, enable-direct-interaction : | | Public generic functions |
| Method, enable-edit : | | Public generic functions |
| Method, enable-toolbar : | | Public generic functions |
| Method, format-id : | | Public generic functions |
| Method, resizable : | | Public generic functions |
| Method, tool-buttons : | | Public generic functions |
|
R | | |
| resizable : | | Public generic functions |
| resizable : | | Public generic functions |
|
T | | |
| tool-buttons : | | Public generic functions |
| tool-buttons : | | Public generic functions |
|
A.3 Variables
| |
|
+ | | |
| +kekule-json-format+ : | | Public special variables |
| +kekule-xml-format+ : | | Public special variables |
| +mdl-mol-2000-format+ : | | Public special variables |
| +mdl-mol-3000-format+ : | | Public special variables |
| +mdl-reaction-2000-format+ : | | Public special variables |
| +mdl-reaction-3000-format+ : | | Public special variables |
| +mdl-structure-data-format+ : | | Public special variables |
| +module-name+ : | | Private special variables |
| +module-version+ : | | Private special variables |
| +smiles-format+ : | | Public special variables |
|
D | | |
| data : | | Private classes |
|
E | | |
| enable-direct-interaction : | | Public classes |
| enable-edit : | | Public classes |
| enable-toolbar : | | Public classes |
|
F | | |
| format-id : | | Private classes |
|
R | | |
| resizable : | | Public classes |
|
S | | |
| Slot, data : | | Private classes |
| Slot, enable-direct-interaction : | | Public classes |
| Slot, enable-edit : | | Public classes |
| Slot, enable-toolbar : | | Public classes |
| Slot, format-id : | | Private classes |
| Slot, resizable : | | Public classes |
| Slot, tool-buttons : | | Public classes |
| Special Variable, +kekule-json-format+ : | | Public special variables |
| Special Variable, +kekule-xml-format+ : | | Public special variables |
| Special Variable, +mdl-mol-2000-format+ : | | Public special variables |
| Special Variable, +mdl-mol-3000-format+ : | | Public special variables |
| Special Variable, +mdl-reaction-2000-format+ : | | Public special variables |
| Special Variable, +mdl-reaction-3000-format+ : | | Public special variables |
| Special Variable, +mdl-structure-data-format+ : | | Public special variables |
| Special Variable, +module-name+ : | | Private special variables |
| Special Variable, +module-version+ : | | Private special variables |
| Special Variable, +smiles-format+ : | | Public special variables |
|
T | | |
| tool-buttons : | | Public classes |
|
A.4 Data types
| |
|
C | | |
| chem-widget : | | Private classes |
| Class, chem-widget : | | Private classes |
| Class, composer : | | Public classes |
| Class, diagram : | | Public classes |
| composer : | | Public classes |
|
D | | |
| diagram : | | Public classes |
|
F | | |
| File, kekule-clj.asd : | | The kekule-clj/kekule-clj․asd file |
| File, kekule-clj.lab-extension : | | The kekule-clj/kekule-clj․lab-extension file |
| File, packages.lisp : | | The kekule-clj/src/packages․lisp file |
| File, register-widgets.lisp : | | The kekule-clj/src/register-widgets․lisp file |
| File, version.lisp : | | The kekule-clj/src/version․lisp file |
| File, widget.lisp : | | The kekule-clj/src/widget․lisp file |
|
K | | |
| kekule : | | The kekule package |
| kekule-clj : | | The kekule-clj system |
| kekule-clj.asd : | | The kekule-clj/kekule-clj․asd file |
| kekule-clj.lab-extension : | | The kekule-clj/kekule-clj․lab-extension file |
|
M | | |
| Module, src : | | The kekule-clj/src module |
|
P | | |
| Package, kekule : | | The kekule package |
| packages.lisp : | | The kekule-clj/src/packages․lisp file |
|
R | | |
| register-widgets.lisp : | | The kekule-clj/src/register-widgets․lisp file |
|
S | | |
| src : | | The kekule-clj/src module |
| System, kekule-clj : | | The kekule-clj system |
|
V | | |
| version.lisp : | | The kekule-clj/src/version․lisp file |
|
W | | |
| widget.lisp : | | The kekule-clj/src/widget․lisp file |
|