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SketchEl
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Disambiguation: this article refers to the molecule drawing program, rather than the line of artistic satchels. SketchEl is a molecule editor, which allows 2D chemical structures to be viewed, edited and presented. It also features a datasheet editor, which is a table containing molecules, numbers and text, which can be edited with a spreadsheet-like interface. It uses its own file formats by default, but also supports the major industry standards. There are several options for producing presentation quality graphics output. The program is written in pure Java, and supports an applet mode which can be embedded in web pages. SketchEl was created by Dr. Alex M. Clark in 2005, and continues to be actively maintained. Molecule Editor The chemical diagram sketching part is quite conventional, with a toolbar for the most commonly used features, and a menu bar which is comprehensive. The primary tools are similar to other popular editor such as Symyx Draw, ChemDraw, ACD/Sketch, MarvinSketch, JChemPaint, and many others. Although SketchEl uses its own data format by default, it can read and write the ubiquitous industry standard MDL MOL files, as well as some dialects of CML (Chemical Markup Language). Editing Tools Tools for selecting, panning, rotating, deleting, setting atom labels, defining bond orders and bond stereochemistry, adjusting ionic charge or selecting templates can be accessed by selecting the appropriate toolbar icon or corresponding menu entry. Other features such as vertical/horizontal flip and bond length normalisation are available only from the menu. The list of atoms and bonds can be edited by way of a popup dialog box, which allows properties to be specifically edited, e.g. setting atom charge, X and Y position, etc. Selected atoms can be moved around by dragging with the mouse cursor, with keyboard modifier combinations, or they can be nudged by small increments by using the cursor keys. Chirality can be explicitly selected (R or S), which will cause the wedge bonds to be updated appropriately. Templates A collection of small ring templates is included as part of the package. To use a template, it is necessary to click on one of its atoms or bonds. This selection will be used to guide the fusion of the template when it is added to an existing fragment. View Modes The default viewing mode shows all elements, except for carbon atoms in most cases, in black & white. The display can be switched to show all atoms, or show other properties instead of atoms: numeric indices, mapping numbers, ring IDs or CIP priorities (used to calculate stereochemistry). Stereolabels can optionally be displayed (R/S for chirality, E/Z for alkene-like stereochemistry). At any given time, the molecular structure is displayed according to a rendering policy, which controls properties such as font size, bond line width, default sizing, and colours. Rendering policies can be added and modified using a configuration panel. Defining multiple rendering policies is useful when preparing presentation graphics, e.g. one preferred style for viewing molecules onscreen, and another for preparing diagrams for publication. Hydrogens Like most molecule sketchers, implicit hydrogens are calculated automatically for common heavy atoms, such as carbon, nitrogen, oxygen, etc. However, the list of atoms and circumstances where the number of implied hydrogens is more than zero is much more conservative than for most cheminformatics software. The default hydrogen status for all explicit atoms is auto, which means that the number will be calculated. It may be changed to a specific number, e.g. set to 0 to disable implicit hydrogens, or set to non-zero to force a specific value. The hydrogen status is stored in the native data format used by SketchEl, but unfortunately will be lost when interconverting with other formats such as MDL MOL. Clipboard Molecules and fragments can be transferred to and from the system clipboard. When the only format available is text, the fragment is copied as a conglomeration of MDL MOL and SketchEl native molecule format. MDL MOL is listed first, so most third party software which can read a MOL file from the clipboard can parse the fragment. When reading from the clipboard, the SketchEl native portion is used preferentially, if available. On Unix-based systems, it is possible to provide any number of clipboard encodings, each with its own MIME type. SketchEl makes as many export formats available as possible, including its own molecule format, MDL MOL, CML, SVG, OpenDocument and PNG bitmaps. When another program is reading the clipboard data provided by SketchEl, it is free to select whichever format it wants. Multiple formats are also made available on the Windows clipboard, but the mechanism is different. The ability of third party programs to make use of strongly-typed molecular data or vector graphics is currently quite limited, since there is a chicken-and-egg problem of limited supply and demand. DataSheet Editor SketchEl can be used to view and edit datasheets, which are tables of data, where each column has a specific type. The editor is very similar to the spreadsheet-like programs used to edit typed tables such as results from an SQL database, the main difference being that one of the available datatypes is used to store molecules. Molecules are shown in their respective cells, and when they are edited, a sketcher window pops up, allowing the molecule to be interactively modified. By default, datasheets use a dialect of XML as a file format, but can also interconvert with industry standard MDL SD files. The datasheet editor can be used as an SD file viewer and editor. Graphics Output SketchEl can output molecules as raster graphics images, using the PNG format. It can be used to generate SVG (Scalable Vector Graphics) files, which can be scaled to arbitrarily high resolution or printed without losing any quality. The SVG output files use path-embedding for fonts, which means that the graphics will still render well when the target software does not properly support font rendering, which is the vast majority of SVG display devices. Graphics can be exported in a variety of OpenDocument dialects: ODG ( OpenDocument Graphics) for individual molecules; ODT (OpenDocument Text) and ODS (OpenDocument Spreadsheet) for datasheets. The OpenDocument graphics formats are similar to SVG. OpenDocument graphics can be transferred into OpenOffice documents by mouse-dragging, or via the clipboard. SVG and OpenDocument output files contain embedded copies of the original molecule or datasheet, which can be reopened by SketchEl. Applet Mode The same Java archive which is used to run SketchEl in standard desktop mode can be used to embed the molecule editor in a web page as a Java applet. Although the applet cannot read or write files, it can interact with the web page by function calls which are made available to JavaScript. A demonstration of the applet mode can be found on the SourceForge page. Licensing & Availability SketchEl is available under the terms of the GNU public license version 2.0. It is regularly updated, and hosted on SourceForge. Interoperability SketchEl has import and export filters for convenient use of MDL MOL and SD file formats as well as CML for single molecules. The native formats used by SketchEl for storing molecules and datasheets are also used by MMDS (Mobile Molecular DataSheet). 
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