XMDS experiments: quantities, metrics and SVG

editexperiment8The XMDS molecular datasheet editor is steadily marching forward in terms of functionality: the reaction scheme editor has been complemented by separate display panels showing the quantities of each component in blocks, which can be opened up and edited. The green chemistry metrics (PMI, E-factor, atom economy) are also calculated and shown. In the interests of making the data useful for presentations, bitmapped or vector representations can be dragged directly into a graphics package (e.g. Pages, Word, PowerPoint, Keynote, etc.), and generation of SVG images is now supported, so reactions and molecules can be easily touched-up with a vector graphics editor like Inkscape. The XMDS app (for Mac OS X) is still in long beta, so you are welcome to try it out (just ask nicely).

Editing and viewing of experiments in the XMDS app is done using a framework for aspect extensions to datasheets. The datasheets themselves are relatively boring: they are spreadsheet-like grids with rows and columns, where each column is strongly typed (molecule, string, integer, real or boolean). The addition of aspect metadata provides a way for software to provide a higher order interpretation of these basic units of data. The Experiment aspect collects together a whole lot of columns (and sometimes multiple rows) for representing one-or-more reaction steps: molecules for the structures of the components, strings for the names, numbers for the stoichiometry, etc. Beyond the basic data model, the Experiment aspect plugs into the XMDS app by reserving its personal collection of columns, so that they don’t show up in the molecular spreadsheet editor. In their place are several manufactured meta-columns: header, scheme, quantity and metrics. Each of these synthesized columns has its own way of displaying its data within the overall spreadsheet view:


In editing mode, each of them has its own take-over panel for editing. The most advanced of these is the scheme editor:


It looks quite clean and straightforward, but there is a whole lot going on under the hood. It is designed to make drawing out a scheme as fast and ergonomic as possible. For the record, I am eating my own dogfood and going through an entire textbook full of organic chemistry reactions, and drawing out all of them, including structures for all reagents, fully balanced, atom-mapped and with quantities included. At this point I’m 10% of the way through, and by the time I get to the end, the editing efficiency will be very high indeed: anything that is annoying, inconvenient, glitchy or just plain ugly will get dealt with in order of how severely it is slowing me down.

More recently, the panel for showing reaction quantities has been added. This is both viewable and editable:


This panel is basically an alternate take on the reaction scheme, which shows all of the components, with an emphasis on the quantities rather than their place in the reaction. Component quantities can be provided within the scheme editor or in the quantity panel, so there is an element of redundancy: the choice of viewing mode is a matter of preference.

The green chemistry metrics panel is read-only:


These are the same calculations that are found in the Green Lab Notebook app. For each of the products (other than those marked as waste), the process mass intensity (PMI), E-factor and atom economy are calculated, as long as the requisite information is available. Calculating these numbers and making them always visible is a key angle for increasing the awareness of green chemistry within a regular day’s work at the bench, since the metrics provide another way to contemplate a reaction’s efficacy. Using XMDS or GLN, this requires no additional work.

The XMDS app has enabled dragging graphics figures into presentation software since an early incarnation, and now the aspect plugin mechanism has caught up, i.e. the reaction schemes, quantity blocks and green metrics can all be used as fodder for graphics creation. There are now 3 supported graphics formats:


PDF is the preferred format when pushing graphics into a word processor or presentation package, especially using software from Apple: their products have excellent support for using the PDF vector graphics format as inline figures, which preserve their quality at any resolution, and through many filetype conversions. PNG is the format of choice when vector rendering isn’t supported adequately well, such as when creating figures from the web, but it is important to keep in mind that rendering quality is resolution dependent, and it will not print well.

The most recently added format is SVG (Scalable Vector Graphics) which is an open vector graphics format. The format has its pros and cons: it is quite well supported within the open source community and within web browsers, but basically not at all within document creation software packages. Its main advantage is that it is designed to be edited post-creation (unlike PDF, which was designed to be the end-of-the-line). My favourite editing tool is Inkscape:


The user interface is a bit ornery, and it’s a pain to have to use X11 on the Mac, but it runs on all 3 relevant desktop platforms (Win/Lin/Mac), it’s incredibly powerful once you get used to it, and it also has a command line invocation which is fantastic for script-building large collections of icons. Being able to export molecules and reactions to SVG means that there is a pathway for modifying some of the layout decisions made by the originating software, or adding annotations of your own (e.g. highlights or explanatory text).

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