Implementation of graph structure for some algorithms on ctab.
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Index
algorithm/kekule.graph.js
algorithm/kekule.structures.aromatics.js
Extension methods to perceive aromatic rings in molecule ctab.
algorithm/kekule.structures.canonicalizers.js
Canonicalizers for chemical structures, especially for ctab based ones.
The general process of canonicalization includes three phrases:
1. An indexer object is called and assign index to each node in structure.
2. An node sorter object is called and sort nodes according to canonicalization index
in previous step.
3. An connector sorter object is called to sort connectors according to sorted
nodes.
Different canonicalization method may requires different indexer or node sorter.
Connector sorter usually do not need to vary.
algorithm/kekule.structures.helpers.js
This file provides some essential helper classes for algorithms on chem structures.
algorithm/kekule.structures.ringSearches.js
Extension methods to perceive rings in molecule ctab.
algorithm/kekule.structures.searches.js
Methods about basic chem structures searching and matching.
algorithm/kekule.structures.standardizers.js
Standardization routines for chemical structures, especially for ctab based ones.
Standardization may include canonicalization, aromatic perception and so on.
algorithm/kekule.structures.stereos.js
Basic classes and methods related with stereo chemistry.
calculation/kekule.calc.base.js
Provides basic interface of calculation task.
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chemdoc/kekule.attachedMarkers.js
Implementation of property markers (e.g. charge mark, lone pair, etc.) binding to the chem object.
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chemdoc/kekule.commonChemMarkers.js
Implementation of some concrete property markers (e.g. charge mark, lone pair, etc.) binding to the chem object.
chemdoc/kekule.contentBlocks.js
Implementation of text/rich text block in 2D drawing.
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chemdoc/kekule.glyph.base.js
Defines glyphs used in 2D/3D drawing.
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chemdoc/kekule.glyph.chemGlyphs.js
Glyphs of some chem symbols.
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chemdoc/kekule.glyph.lines.js
Implementation of line based glyphs defined by a series of nodes and paths.
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chemdoc/kekule.glyph.pathGlyphs.js
Implementation of glyphs defined by a series of nodes and paths.
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core/kekule.chemUtils.js
Utils method about chem objects.
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core/kekule.common.js
Some global symbols used in Kekule library.
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core/kekule.configs.js
Classes used for store configurations.
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core/kekule.electrons.js
This file contains basic classes related with electrons (bond, lone pair...).
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core/kekule.elements.js
This file contains basic classes to represent an element or isotope.
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core/kekule.exceptions.js
This file is for exception and error handling in Kekule.
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core/kekule.reactions.js
This file contains basic classes about chemical reactions.
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core/kekule.structureBuilder.js
Classes and utils to help to build a chemical structure (such as molecule).
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core/kekule.structures.js
This file contains basic classes to represent structural objects in molecule.
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core/kekule.valences.js
This file helps to determine the valence of a neutral, anion(-) or cation(+) atom.
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html/kekule.nativeServices.js
Classes and functions related with native services (e.g., file picker dialog).
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html/kekule.predefinedResLoaders.js
Utils and classes to load chem resources embedded or linked in HTML page.
The chem resources (usually a formatted file (.mol, .cml...) or a formatted string)
can be embedded in <script> tag:
<script id="chem2" type="chemical/x-kekule-json" src="externalMol.kcj"></script>
<link id="chem3" type="chemical/x-cml" href="external.cml" /> Afterwards, user can ref to chem resource by ID directly in HTML code, such as:
<div data-kekule-role="Kekule.ChemWidget.Viewer2D" data-chem-obj="url(#chem1)" /> which will initialize a 2D viewer.
<script id="chem1" type="chemical/x-mdl-molfile"> Untitled Document-1 ChemDraw09151219572D 2 1 0 0 0 0 0 0 0 0999 V2000 -0.4125 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4125 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 M END </script>or linked in by <script> or <link> tag as the follows:
<script id="chem2" type="chemical/x-kekule-json" src="externalMol.kcj"></script>
<link id="chem3" type="chemical/x-cml" href="external.cml" /> Afterwards, user can ref to chem resource by ID directly in HTML code, such as:
<div data-kekule-role="Kekule.ChemWidget.Viewer2D" data-chem-obj="url(#chem1)" /> which will initialize a 2D viewer.
io/cml/kekule.io.cml.js
File for supporting CML (Chemical Markup Language), especially on read/write molecules and reactions.
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io/kekule.io.js
Abstract root classes for concrete strcuture reader/writers of different structure formats.
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io/mdl/kekule.io.mdl2000.js
File for supporting MDL CTAB/MOL/RXN V2000 data.
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io/mdl/kekule.io.mdl3000.js
File for supporting MDL CTAB/MOL/RXN V3000 data.
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io/mdl/kekule.io.mdlBase.js
Some common routines for both MOL/RXN 2000 and MOL/RXN 3000 files.
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io/mdl/kekule.io.mdlIO.js
Reader and Writer classes for MDL V2000 and V3000 formats.
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io/native/kekule.io.native.js
File to support read or write chemical data in JSON or XML format by built-in serializers.
The JSON data serialized directly from Kekule.ChemObject is called KCJ (Kekule Chem JSON),
while the XML data is called KCX (Kekule Chem XML).
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io/smiles/kekule.io.smiles.js
File for supporting reading/writing molecule to SMILES format.
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lan/classes.js
This file simulates the class-based inheritance, most of the code is
borrowed from Prototype lib. My own property system borrowed form WebShow framework
is also added here.
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lan/serializations.js
Classes and methods to support serialization of ObjectEx.
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lan/xmlJsons.js
Utilities to handle XML and JSON data. Borrowed from WebShow.XML and WebShow.JSON.
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render/2d/kekule.render.canvasRenderer.js
2D renderer using HTML5 canvas.
render/2d/kekule.render.glyphRender2D.js
A default implementation of 2D renderer to render small glyphs.
render/2d/kekule.render.raphaelRenderer.js
2D renderer using Raphael.js.
render/2d/kekule.render.renderer2D.js
A default implementation of 2D molecule renderer.
render/3d/kekule.render.renderer3D.js
A default implementation of 3D molecule renderer.
render/3d/kekule.render.threeRenderer.js
3D renderer using three.js library.
render/kekule.render.base.js
Base (abstract) class of 2D or 3D molecule renderers.
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render/kekule.render.baseTextRender.js
An abstract implementation of a rich text drawer.
render/kekule.render.boundInfoRecorder.js
This file contains a helper class to record all bound infos of basic object
during the rendering of chem object.
render/kekule.render.configs.js
Changable global configurations for renderers.
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render/kekule.render.extensions.js
Extend some core classes for displaying purpose.
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render/kekule.render.painter.js
This file contains classes to draw ChemSpace objects in 2D or 3D context.
Usually the user do not need to call renderer classes to draw, but use painter instances instead.
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render/kekule.render.renderColorData.js
Some predefined data used by 3D renderer.
render/kekule.render.utils.js
Utility classes and methods for rendering 2D or 3D molecule structures.
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utils/kekule.domHelper.js
Generally we can use getElementsByTagName, getAttribute to analysis a DOM tree. If the
DOM has namespaces, getElementsByTagNameNS and getAttributeNS should be used instead.
However, IE (and MSXML) does not support those NS methods. So this file is trying to
provide a cross-browser solution.
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utils/kekule.domUtils.js
Utility functions about DOM, Script and so on.
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utils/kekule.textHelper.js
Contains classes and functions help to analysis text format chemical data,
especially the line/column fixed ones such as MDL MOL/SDF/RXN.
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utils/kekule.utils.js
Some common utility functions.
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widgets/advCtrls/grids/kekule.widget.dataGrids.js
Implementation of a data-grid widget based on HTML table.
widgets/advCtrls/grids/kekule.widget.dataSets.js
DataProvider is a special class to provide part of large amount of data to other widgets (e.g., DataTable).
For example, suppose a database table is filled with 1000 records, the provider can fetch 100 items from it
first, then the next 100 ones.
widgets/advCtrls/kekule.widget.colorPickers.js
Implementation of a color picker panel.
widgets/advCtrls/kekule.widget.textEditors.js
Implementation of an advanced plain text editor.
widgets/advCtrls/kekule.widget.valueListEditors.js
Implementation of a value list editor (like object inspector in Delphi).
widgets/advCtrls/kekule.widget.widgetGrids.js
A grid to contain multiple float widgets.
widgets/advCtrls/objInspector/kekule.widget.objInspector.chemPropEditors.js
Implementation of some special property editor for chem objects.
widgets/advCtrls/objInspector/kekule.widget.objInspector.operations.js
Operations for property modifications in object inspector.
widgets/advCtrls/objInspector/kekule.widget.objInspector.propEditors.js
Implementation of some basic property editor for object inspector.
widgets/advCtrls/objInspector/kekule.widget.objInspectors.js
Implementation of object inspector.
widgets/chem/editor/kekule.chemEditor.actions.js
Implements of actions related with chem editor.
widgets/chem/editor/kekule.chemEditor.baseEditors.js
Base types and classes used by chem editor.
widgets/chem/editor/kekule.chemEditor.chemSpaceEditors.js
Editor for Kekule.ChemSpace.
widgets/chem/editor/kekule.chemEditor.composers.js
Implements an editor with essential UI.
widgets/chem/editor/kekule.chemEditor.configs.js
Configurations of base editors.
widgets/chem/editor/kekule.chemEditor.editorUtils.js
Util methods for chem editor.
widgets/chem/editor/kekule.chemEditor.extensions.js
Extend some core classes for editing purpose.
widgets/chem/editor/kekule.chemEditor.nexus.js
Containing a nexus class which can link all essential editor component
(including editor, structure tree view and object inspector) together.
widgets/chem/editor/kekule.chemEditor.objModifiers.js
Widgets to modify an chem object in a user friendly way in chem editor.
widgets/chem/editor/kekule.chemEditor.operations.js
Operations need to implement an editor.
widgets/chem/editor/kekule.chemEditor.repositories.js
Implementation of repository for editor.
widgets/chem/editor/kekule.chemEditor.repositoryData.js
Some predefined repository item data used by composer.
widgets/chem/editor/kekule.chemEditor.trackParser.js
Input chem structure by touch or mouse track.
widgets/chem/editor/kekule.chemEditor.utilWidgets.js
Small widgets used by chem editor.
widgets/chem/editor/modifiers/kekule.chemEditor.structureModifiers.js
Object modifier to change property of atoms (and other similar chem nodes) in chem editor.
widgets/chem/editor/modifiers/kekule.chemEditor.styleModifiers.js
Object modifier to change the render styles of objects in chem editor.
widgets/chem/editor/modifiers/kekule.chemEditor.textModifiers.js
Object modifier to change format of text, atom label, etc. in chem editor.
widgets/chem/kekule.chemWidget.base.js
Chem widget is widget related with chem tasks, such as chem object view/editor.
widgets/chem/kekule.chemWidget.chemObjDisplayers.js
Implemetation of base class involves in displaying chem object (such as viewer or editor).
widgets/chem/kekule.chemWidget.dialogs.js
Some common dialogs used by other chem widgets.
widgets/chem/periodicTable/kekule.chemWidget.periodicTables.js
Implementation of periodic table of elements.
widgets/chem/structureTreeView/kekule.chemWidget.structureTreeViews.js
A tree widget to display the internal structure of chem object (such as ChemSpace, Molecule and so on).
widgets/chem/uiMarker/kekule.chemWidget.uiMarkers.js
Class to store UI marker information and the renderer to draw them on context.
widgets/chem/viewer/kekule.chemWidget.chemObjInserters.js
A chem object setter widget based on Viewer.
This widget is mainly designed for extra web editor plugins or browser addons.
widgets/chem/viewer/kekule.chemWidget.viewerGrids.js
Base types and classes of chem viewer.
Viewer is a widget to show chem objects on HTML page.
widgets/chem/viewer/kekule.chemWidget.viewers.js
Related types and classes of chem viewer.
Viewer is a widget to show chem objects on HTML page.
widgets/commonCtrls/kekule.widget.buttons.js
Implementation of button widgets.
widgets/commonCtrls/kekule.widget.containers.js
Implementation of container that can hold a set of other widgets.
widgets/commonCtrls/kekule.widget.dialogs.js
Implementation of popup dialogs.
widgets/commonCtrls/kekule.widget.formControls.js
Implementation of textbox widgets.
widgets/commonCtrls/kekule.widget.images.js
Implementation of image related widgets.
widgets/commonCtrls/kekule.widget.menus.js
Implementation of menu widgets.
Unfinished yet.
widgets/commonCtrls/kekule.widget.movers.js
Enable widget or element to be movable by mouse or touch.
widgets/commonCtrls/kekule.widget.msgPanels.js
Implementation of a panel to display special informations.
widgets/commonCtrls/kekule.widget.nestedContainers.js
Base class of container that can hold a set of nested children (e.g., menu, tree view).
widgets/commonCtrls/kekule.widget.resizers.js
Implementation of resize gripper for other widgets or HTML elements.
widgets/commonCtrls/kekule.widget.tabViews.js
A tab widget.
widgets/commonCtrls/kekule.widget.treeViews.js
A tree widget.
widgets/kekule.widget.autoLaunchers.js
Utils and classes to identify and load Kekule Widget in HTML tag when a page is loaded.
Generally, the auto launcher will iterate through elements in document. If an element is
with a data-widget attribute, it will be regarded as a Kekule related one. Then a
specified Kekule widget will be created (according to data-widget attribute) on this tag.
Widget property will also be set from "data-XXX" attribute.
widgets/kekule.widget.base.js
Widget is a control embeded in HTML element and react to UI events (so it can interact with users).
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widgets/kekule.widget.clipboards.js
Support of an internal "clipboard" to transfer data between different widgets in one page.
widgets/kekule.widget.helpers.js
Some helper classes for widgets.
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widgets/kekule.widget.styleResources.js
Style resource is a special object that links to a CSS style selector (usually a CSS class).
User can appoint resource to a widget to change its style.
widgets/kekule.widget.sys.js
Some system functions of Kekule widget lib.
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widgets/operation/kekule.actions.js
The implementation of Action class.
Action is a type of class that can be associated with widget to do a specified job (like the corresponding
part in Delphi).
widgets/operation/kekule.operations.js
Implementation of command pattern.
widgets/operation/kekule.operHistoryTreeViews.js
A tree widget to display the internal structure of operation history.
widgets/sys/kekule.widget.sysMsgs.js
A special message panel group to display system exception informations.
widgets/transitions/kekule.widget.transitions.js
Implementation of different HTML transitions.
widgets/transitions/kekule.widget.transMgr.js
A helper unit to control the universal transition style (especially show/hide animation) of widgets.