The kekule-clj Reference Manual

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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 Wed Nov 04 13:59:34 2020 GMT+0.


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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:

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.


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2 Systems

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


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2.1 kekule-clj

Author

Tarn W. Burton

License

MIT

Description

A Kekule widget for Common Lisp Jupyter

Version

0.4.0

Dependencies
Source

kekule-clj.asd (file)

Component

src (module)


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3 Modules

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


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3.1 kekule-clj/src

Parent

kekule-clj (system)

Location

src/

Components

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4 Files

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


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4.1 Lisp


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4.1.1 kekule-clj.asd

Location

kekule-clj.asd

Systems

kekule-clj (system)


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4.1.2 kekule-clj/src/packages.lisp

Parent

src (module)

Location

src/packages.lisp

Packages

kekule


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4.1.3 kekule-clj/src/version.lisp

Dependency

packages.lisp (file)

Parent

src (module)

Location

src/version.lisp

Internal Definitions

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4.1.4 kekule-clj/src/widget.lisp

Dependency

version.lisp (file)

Parent

src (module)

Location

src/widget.lisp

Exported Definitions
Internal Definitions

chem-widget (class)


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5 Packages

Packages are listed by definition order.


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5.1 kekule

Source

packages.lisp (file)

Use List

common-lisp

Exported Definitions
Internal Definitions

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6 Definitions

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


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6.1 Exported definitions


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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)


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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)


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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)


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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
InitargValue
:%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
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
InitargValue
:%model-name"kekulediagrammodel"
:%view-name"kekulediagramview"

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6.2 Internal definitions


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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)


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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
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
InitargValue
:%model-modulekekule::+module-name+
:%model-module-versionkekule::+module-version+
:%view-modulekekule::+module-name+
:%view-module-versionkekule::+module-version+
:layout(make-instance (quote jupyter-widgets:layout) :width "100%" :height "480px")

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Appendix A Indexes


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A.1 Concepts

Jump to:   F   K   L   M  
Index Entry  Section

F
File, Lisp, kekule-clj.asd: The kekule-clj․asd file
File, Lisp, kekule-clj/src/packages.lisp: The kekule-clj/src/packages․lisp file
File, Lisp, kekule-clj/src/version.lisp: The kekule-clj/src/version․lisp file
File, Lisp, kekule-clj/src/widget.lisp: The kekule-clj/src/widget․lisp file

K
kekule-clj.asd: The kekule-clj․asd file
kekule-clj/src: The kekule-clj/src module
kekule-clj/src/packages.lisp: The kekule-clj/src/packages․lisp file
kekule-clj/src/version.lisp: The kekule-clj/src/version․lisp file
kekule-clj/src/widget.lisp: The kekule-clj/src/widget․lisp file

L
Lisp File, kekule-clj.asd: The kekule-clj․asd file
Lisp File, kekule-clj/src/packages.lisp: The kekule-clj/src/packages․lisp file
Lisp File, kekule-clj/src/version.lisp: The kekule-clj/src/version․lisp file
Lisp File, kekule-clj/src/widget.lisp: The kekule-clj/src/widget․lisp file

M
Module, kekule-clj/src: The kekule-clj/src module

Jump to:   F   K   L   M  

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A.2 Functions

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D   E   F   G   L   M   R   T  
Index Entry  Section

(
(setf data): Exported generic functions
(setf data): Exported generic functions
(setf enable-direct-interaction): Exported generic functions
(setf enable-direct-interaction): Exported generic functions
(setf enable-edit): Exported generic functions
(setf enable-edit): Exported generic functions
(setf enable-toolbar): Exported generic functions
(setf enable-toolbar): Exported generic functions
(setf format-id): Exported generic functions
(setf format-id): Exported generic functions
(setf resizable): Exported generic functions
(setf resizable): Exported generic functions
(setf tool-buttons): Exported generic functions
(setf tool-buttons): Exported generic functions

D
data: Exported generic functions
data: Exported generic functions

E
enable-direct-interaction: Exported generic functions
enable-direct-interaction: Exported generic functions
enable-edit: Exported generic functions
enable-edit: Exported generic functions
enable-toolbar: Exported generic functions
enable-toolbar: Exported generic functions

F
fit: Exported functions
format-id: Exported generic functions
format-id: Exported generic functions
Function, fit: Exported functions
Function, load-data: Exported functions
Function, load-file: Exported functions
Function, load-url: Exported functions

G
Generic Function, (setf data): Exported generic functions
Generic Function, (setf enable-direct-interaction): Exported generic functions
Generic Function, (setf enable-edit): Exported generic functions
Generic Function, (setf enable-toolbar): Exported generic functions
Generic Function, (setf format-id): Exported generic functions
Generic Function, (setf resizable): Exported generic functions
Generic Function, (setf tool-buttons): Exported generic functions
Generic Function, data: Exported generic functions
Generic Function, enable-direct-interaction: Exported generic functions
Generic Function, enable-edit: Exported generic functions
Generic Function, enable-toolbar: Exported generic functions
Generic Function, format-id: Exported generic functions
Generic Function, resizable: Exported generic functions
Generic Function, tool-buttons: Exported generic functions

L
load-data: Exported functions
load-file: Exported functions
load-url: Exported functions

M
Method, (setf data): Exported generic functions
Method, (setf enable-direct-interaction): Exported generic functions
Method, (setf enable-edit): Exported generic functions
Method, (setf enable-toolbar): Exported generic functions
Method, (setf format-id): Exported generic functions
Method, (setf resizable): Exported generic functions
Method, (setf tool-buttons): Exported generic functions
Method, data: Exported generic functions
Method, enable-direct-interaction: Exported generic functions
Method, enable-edit: Exported generic functions
Method, enable-toolbar: Exported generic functions
Method, format-id: Exported generic functions
Method, resizable: Exported generic functions
Method, tool-buttons: Exported generic functions

R
resizable: Exported generic functions
resizable: Exported generic functions

T
tool-buttons: Exported generic functions
tool-buttons: Exported generic functions

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D   E   F   G   L   M   R   T  

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A.3 Variables

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D   E   F   R   S   T  
Index Entry  Section

+
+kekule-json-format+: Exported special variables
+kekule-xml-format+: Exported special variables
+mdl-mol-2000-format+: Exported special variables
+mdl-mol-3000-format+: Exported special variables
+mdl-reaction-2000-format+: Exported special variables
+mdl-reaction-3000-format+: Exported special variables
+mdl-structure-data-format+: Exported special variables
+module-name+: Internal special variables
+module-version+: Internal special variables
+smiles-format+: Exported special variables

D
data: Internal classes

E
enable-direct-interaction: Exported classes
enable-edit: Exported classes
enable-toolbar: Exported classes

F
format-id: Internal classes

R
resizable: Exported classes

S
Slot, data: Internal classes
Slot, enable-direct-interaction: Exported classes
Slot, enable-edit: Exported classes
Slot, enable-toolbar: Exported classes
Slot, format-id: Internal classes
Slot, resizable: Exported classes
Slot, tool-buttons: Exported classes
Special Variable, +kekule-json-format+: Exported special variables
Special Variable, +kekule-xml-format+: Exported special variables
Special Variable, +mdl-mol-2000-format+: Exported special variables
Special Variable, +mdl-mol-3000-format+: Exported special variables
Special Variable, +mdl-reaction-2000-format+: Exported special variables
Special Variable, +mdl-reaction-3000-format+: Exported special variables
Special Variable, +mdl-structure-data-format+: Exported special variables
Special Variable, +module-name+: Internal special variables
Special Variable, +module-version+: Internal special variables
Special Variable, +smiles-format+: Exported special variables

T
tool-buttons: Exported classes

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D   E   F   R   S   T  

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A.4 Data types

Jump to:   C   D   K   P   S  
Index Entry  Section

C
chem-widget: Internal classes
Class, chem-widget: Internal classes
Class, composer: Exported classes
Class, diagram: Exported classes
composer: Exported classes

D
diagram: Exported classes

K
kekule: The kekule package
kekule-clj: The kekule-clj system

P
Package, kekule: The kekule package

S
System, kekule-clj: The kekule-clj system

Jump to:   C   D   K   P   S