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 Mon Feb 26 16:50:19 2024 GMT+0.

Table of Contents


1 Introduction


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.


3.1 kekule-clj/src

Source

kekule-clj.asd.

Parent Component

kekule-clj (system).

Child Components

4 Files

Files are sorted by type and then listed depth-first from the systems components trees.


4.1 Lisp


4.1.1 kekule-clj/kekule-clj.asd

Source

kekule-clj.asd.

Parent Component

kekule-clj (system).

ASDF Systems

kekule-clj.


4.1.2 kekule-clj/src/packages.lisp

Source

kekule-clj.asd.

Parent Component

src (module).

Packages

kekule.


4.1.3 kekule-clj/src/version.lisp

Dependency

packages.lisp (file).

Source

kekule-clj.asd.

Parent Component

src (module).

Internals

4.1.4 kekule-clj/src/widget.lisp

Dependency

version.lisp (file).

Source

kekule-clj.asd.

Parent Component

src (module).

Public Interface
Internals

chem-widget (class).


4.1.5 kekule-clj/src/register-widgets.lisp

Dependency

widget.lisp (file).

Source

kekule-clj.asd.

Parent Component

src (module).

Public Interface

4.2 Other


4.2.1 kekule-clj/kekule-clj.lab-extension

Source

kekule-clj.asd.

Parent Component

kekule-clj (system).


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
InitargValue
:%model-namekekulecomposermodel
:%view-namekekulecomposerview
Class: diagram

A widget that displays molecular data.

Package

kekule.

Source

widget.lisp.

Direct superclasses

chem-widget.

Direct methods
Direct Default Initargs
InitargValue
:%model-namekekulediagrammodel
:%view-namekekulediagramview
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


6.2.1 Special variables

Special Variable: +module-name+
Package

kekule.

Source

version.lisp.

Special Variable: +module-version+
Package

kekule.

Source

version.lisp.


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
InitargValue
:%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.1 Concepts


A.2 Functions

Jump to:   (  
D   E   F   G   L   M   R   T  
Index Entry  Section

(
(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

Jump to:   +  
D   E   F   R   S   T  
Index Entry  Section

+
+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