The kekule-clj Reference Manual

Table of Contents

The kekule-clj Reference Manual

This is the kekule-clj Reference Manual, version 0.4.0, generated automatically by Declt version 3.0 "Montgomery Scott" on Mon Apr 19 16:33:27 2021 GMT+0.

1 Introduction

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.

2 Systems

The main system appears first, followed by any subsystem dependency.

2.1 kekule-clj

Author

Tarn W. Burton

License

MIT

Description

A Kekule widget for Common Lisp Jupyter

Version

0.4.0

Dependency

common-lisp-jupyter

Source

kekule-clj.asd (file)

Component

src (module)

3 Modules

Modules are listed depth-first from the system components tree.

3.1 kekule-clj/src

Parent

kekule-clj (system)

Location

src/

Components

• packages.lisp (file)
• version.lisp (file)
• widget.lisp (file)
• register-widgets.lisp (file)

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.asd

Location

kekule-clj.asd

Systems

kekule-clj (system)

4.1.2 kekule-clj/src/packages.lisp

Parent

src (module)

Location

src/packages.lisp

Packages

kekule

4.1.3 kekule-clj/src/version.lisp

Dependency

packages.lisp (file)

Parent

src (module)

Location

src/version.lisp

Internal Definitions

• +module-name+ (special variable)
• +module-version+ (special variable)

4.1.4 kekule-clj/src/widget.lisp

Dependency

version.lisp (file)

Parent

src (module)

Location

src/widget.lisp

Exported Definitions

• +kekule-json-format+ (special variable)
• +kekule-xml-format+ (special variable)
• +mdl-mol-2000-format+ (special variable)
• +mdl-mol-3000-format+ (special variable)
• +mdl-reaction-2000-format+ (special variable)
• +mdl-reaction-3000-format+ (special variable)
• +mdl-structure-data-format+ (special variable)
• +smiles-format+ (special variable)
• composer (class)
• data (method)
• (setf data) (method)
• diagram (class)
• enable-direct-interaction (method)
• (setf enable-direct-interaction) (method)
• enable-edit (method)
• (setf enable-edit) (method)
• enable-toolbar (method)
• (setf enable-toolbar) (method)
• fit (function)
• format-id (method)
• (setf format-id) (method)
• load-data (function)
• load-file (function)
• load-url (function)
• resizable (method)
• (setf resizable) (method)
• tool-buttons (method)
• (setf tool-buttons) (method)

Internal Definitions

chem-widget (class)

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

Dependency

widget.lisp (file)

Parent

src (module)

Location

src/register-widgets.lisp

Exported Definitions

• make-composer (function)
• make-diagram (function)

5 Packages

Packages are listed by definition order.

5.1 kekule

Source

packages.lisp (file)

Use List

common-lisp

Exported Definitions

• +kekule-json-format+ (special variable)
• +kekule-xml-format+ (special variable)
• +mdl-mol-2000-format+ (special variable)
• +mdl-mol-3000-format+ (special variable)
• +mdl-reaction-2000-format+ (special variable)
• +mdl-reaction-3000-format+ (special variable)
• +mdl-structure-data-format+ (special variable)
• +smiles-format+ (special variable)
• composer (class)
• data (generic function)
• data (method)
• (setf data) (method)
• (setf data) (generic function)
• diagram (class)
• enable-direct-interaction (generic function)
• enable-direct-interaction (method)
• (setf enable-direct-interaction) (method)
• (setf enable-direct-interaction) (generic function)
• enable-edit (generic function)
• enable-edit (method)
• (setf enable-edit) (method)
• (setf enable-edit) (generic function)
• enable-toolbar (generic function)
• enable-toolbar (method)
• (setf enable-toolbar) (method)
• (setf enable-toolbar) (generic function)
• fit (function)
• format-id (generic function)
• format-id (method)
• (setf format-id) (method)
• (setf format-id) (generic function)
• load-data (function)
• load-file (function)
• load-url (function)
• make-composer (function)
• make-diagram (function)
• resizable (generic function)
• resizable (method)
• (setf resizable) (method)
• (setf resizable) (generic function)
• tool-buttons (generic function)
• tool-buttons (method)
• (setf tool-buttons) (method)
• (setf tool-buttons) (generic function)

Internal Definitions

• +module-name+ (special variable)
• +module-version+ (special variable)
• chem-widget (class)

6 Definitions

Definitions are sorted by export status, category, package, and then by lexicographic order.

6.1 Exported definitions

6.1.1 Special variables

Special Variable: +kekule-json-format+

Kekule native JSON format tag

Package

kekule

Source

widget.lisp (file)

Special Variable: +kekule-xml-format+

Kekule specific XML format tag

Package

kekule

Source

widget.lisp (file)

Special Variable: +mdl-mol-2000-format+

MDL Molfile V2000 format tag

Package

kekule

Source

widget.lisp (file)

Special Variable: +mdl-mol-3000-format+

MDL Molfile V3000 format tag

Package

kekule

Source

widget.lisp (file)

Special Variable: +mdl-reaction-2000-format+

MDL Reaction V2000 format tag

Package

kekule

Source

widget.lisp (file)

Special Variable: +mdl-reaction-3000-format+

MDL Reaction V3000 format tag

Package

kekule

Source

widget.lisp (file)

Special Variable: +mdl-structure-data-format+

MDL Structure Data format tag

Package

kekule

Source

widget.lisp (file)

Special Variable: +smiles-format+

Simplified molecular-input line-entry system format tag

Package

kekule

Source

widget.lisp (file)

6.1.2 Functions

Function: fit INSTANCE

Fit view to current structures.

Package

kekule

Source

widget.lisp (file)

Function: load-data INSTANCE DATA FORMAT-ID

Load molecular data into an existing widget.

Package

kekule

Source

widget.lisp (file)

Function: load-file INSTANCE PATH

Load molecular data from a file into an existing widget.

Package

kekule

Source

widget.lisp (file)

Function: load-url INSTANCE URL

Load molecular data from a url into an existing widget.

Package

kekule

Source

widget.lisp (file)

Function: make-composer &rest INITARGS &key LAYOUT DATA FORMAT-ID &allow-other-keys

Package

kekule

Source

register-widgets.lisp (file)

Function: make-diagram &rest INITARGS &key LAYOUT DATA FORMAT-ID ENABLE-TOOLBAR ENABLE-DIRECT-INTERACTION ENABLE-EDIT TOOL-BUTTONS RESIZABLE &allow-other-keys

Package

kekule

Source

register-widgets.lisp (file)

6.1.3 Generic functions

Generic Function: data OBJECT

Generic Function: (setf data) NEW-VALUE OBJECT

Package

kekule

Methods

Method: data (CHEM-WIDGET chem-widget)

Method: (setf data) NEW-VALUE (CHEM-WIDGET chem-widget)

Data to be displayed by the widget.

Source

widget.lisp (file)

Generic Function: enable-direct-interaction OBJECT

Generic Function: (setf enable-direct-interaction) NEW-VALUE OBJECT

Package

kekule

Methods

Method: enable-direct-interaction (DIAGRAM diagram)

Method: (setf enable-direct-interaction) NEW-VALUE (DIAGRAM diagram)

Whether to allow interaction with the molecule or not.

Source

widget.lisp (file)

Generic Function: enable-edit OBJECT

Generic Function: (setf enable-edit) NEW-VALUE OBJECT

Package

kekule

Methods

Method: enable-edit (DIAGRAM diagram)

Method: (setf enable-edit) NEW-VALUE (DIAGRAM diagram)

Whether to allow a popup editor to be shown or not.

Source

widget.lisp (file)

Generic Function: enable-toolbar OBJECT

Generic Function: (setf enable-toolbar) NEW-VALUE OBJECT

Package

kekule

Methods

Method: enable-toolbar (DIAGRAM diagram)

Method: (setf enable-toolbar) NEW-VALUE (DIAGRAM diagram)

Whether to show the toolbar or not.

Source

widget.lisp (file)

Generic Function: format-id OBJECT

Generic Function: (setf format-id) NEW-VALUE OBJECT

Package

kekule

Methods

Method: format-id (CHEM-WIDGET chem-widget)

Method: (setf format-id) NEW-VALUE (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 (file)

Generic Function: resizable OBJECT

Generic Function: (setf resizable) NEW-VALUE OBJECT

Package

kekule

Methods

Method: resizable (DIAGRAM diagram)

Method: (setf resizable) NEW-VALUE (DIAGRAM diagram)

Whether the diagram is resizable or not.

Source

widget.lisp (file)

Generic Function: tool-buttons OBJECT

Generic Function: (setf tool-buttons) NEW-VALUE OBJECT

Package

kekule

Methods

Method: tool-buttons (DIAGRAM diagram)

Method: (setf tool-buttons) NEW-VALUE (DIAGRAM diagram)

A list of the names of buttons to show in the toolbar.

Source

widget.lisp (file)

6.1.4 Classes

Class: composer ()

A widget that edits molecular data.

Package

kekule

Source

widget.lisp (file)

Direct superclasses

chem-widget (class)

Direct Default Initargs

Initarg	Value
:%model-name	"kekulecomposermodel"
:%view-name	"kekulecomposerview"

Class: diagram ()

A widget that displays molecular data.

Package

kekule

Source

widget.lisp (file)

Direct superclasses

chem-widget (class)

Direct methods

• resizable (method)
• resizable (method)
• tool-buttons (method)
• tool-buttons (method)
• enable-edit (method)
• enable-edit (method)
• enable-direct-interaction (method)
• enable-direct-interaction (method)
• enable-toolbar (method)
• enable-toolbar (method)

Direct slots

Slot: enable-toolbar

Whether to show the toolbar or not.

Type

boolean

Initargs

:enable-toolbar

Readers

enable-toolbar (generic function)

Writers

(setf enable-toolbar) (generic function)

Slot: enable-direct-interaction

Whether to allow interaction with the molecule or not.

Type

boolean

Initargs

:enable-direct-interaction

Initform

t

Readers

enable-direct-interaction (generic function)

Writers

(setf enable-direct-interaction) (generic function)

Slot: enable-edit

Whether to allow a popup editor to be shown or not.

Type

boolean

Initargs

:enable-edit

Initform

t

Readers

enable-edit (generic function)

Writers

(setf enable-edit) (generic function)

Slot: tool-buttons

A list of the names of buttons to show in the toolbar.

Type

list

Initargs

:tool-buttons

Initform

(list "loaddata" "savedata" "moldisplaytype" "molhidehydrogens" "zoomin" "zoomout" "rotateleft" "rotateright" "rotatex" "rotatey" "rotatez" "reset" "openeditor" "config")

Readers

tool-buttons (generic function)

Writers

(setf tool-buttons) (generic function)

Slot: resizable

Whether the diagram is resizable or not.

Type

boolean

Initargs

:resizable

Readers

resizable (generic function)

Writers

(setf resizable) (generic function)

Direct Default Initargs

Initarg	Value
:%model-name	"kekulediagrammodel"
:%view-name	"kekulediagramview"

6.2 Internal definitions

6.2.1 Special variables

Special Variable: +module-name+

Package

kekule

Source

version.lisp (file)

Special Variable: +module-version+

Package

kekule

Source

version.lisp (file)

6.2.2 Classes

Class: chem-widget ()

Base widget used by the diagram and composer widgets.

Package

kekule

Source

widget.lisp (file)

Direct superclasses

dom-widget (class)

Direct subclasses

• diagram (class)
• composer (class)

Direct methods

• format-id (method)
• format-id (method)
• data (method)
• data (method)

Direct slots

Slot: data

Data to be displayed by the widget.

Initargs

:data

Initform

"untitled document"

Readers

data (generic function)

Writers

(setf data) (generic function)

Slot: format-id

Format tag of data. Current allowed values are smi, Kekule-JSON, Kekuule-XML, mol, mol3k, sd, rxn and rxn3k.

Type

string

Initargs

:format-id

Initform

kekule:+mdl-reaction-2000-format+

Readers

format-id (generic function)

Writers

(setf format-id) (generic function)

Direct Default Initargs

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")

Appendix A Indexes

A.1 Concepts

A.2 Functions

A.3 Variables

A.4 Data types