Pandoc filters for chemistry

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One of the great things about pandoc is that it is very extensible through the use of filters. The best example of this is pandoc-citeproc, which is how references are processed in the native pandoc syntax. However, there are many other filters available, and they are fairly easy to write if you’re passingly familiar with any one of a number of different programming languages (although Haskell—pandoc’s native language—and Python appear to be most common).

As a chemist, this sort of extensibility is both tremendously useful and sometimes very necessary. There are, I’ve realized, some real idiosyncrasies to our writing (for example, our insistence on having at least two and sometimes three different categories of figures that are numbered separately). In LaTeX, these are taken care of with different packages, like mhchem. I like to use LaTeX for Supporting Info files and these sorts of packages are very useful. In pandoc, a lot of similar functionality can be added through short filters that are applied when the files are processed.

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A pandoc template for letterhead

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Yikes, been longer than I intended between posts. Alas for the uneven free time of an academic. In my defense, I’m trying to start up a new project in my group and I have a very energetic dog.

In the last post, I discussed my use of pandoc as a tool for writing in plain text and outputting to a variety of different formats. I use it as much as I possibly can because I just prefer writing in the simplest format possible and then “compiling” my final documents for distribution. Here, I’d like to share a simple template that I use to produce letters on Miami’s letterhead. I use this primarily for letters of recommendation.

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An example of a molecular animation in Blender

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To me, one of the great advantages of using Blender to visualize molecules is that it’s a unified platform for rendering both high quality stills and animations. Even though I haven’t explored the animation side all that deeply, simple videos of rotating molecules and the like are trivially simple. I use this all the time in my courses to jazz up my lectures as an alternative to yet another bond-line structure.

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A quick intro to importing molecular geometries into Blender through the blmol script

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In the last post, I talked about my experiences using Blender to visualize different aspects of my group’s research. In this post, I’ll give a quick introduction to the script I use to import geometries into Blender along with the template I import them into. The script brings in structures in PDB format files and can generate bond-line or space-filling models.

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Space-filling model of a stack of macrocycles, rendered in Blender.

Blender for chemists

Most of the work we do in my group focuses on molecules or systems with somewhat complicated three-dimensional structures. A few years back, I was working on a proposal and found myself spending the better portion of a day struggling to draw a single ChemDraw graphic; it was of a compound with a stacked architecture and I was trying to fudge in a sort of 3D perspective. The process was tedious and the end result was deeply unsatisfying. It started to become clear that the work we were doing really demanded some means of rendering decent images of 3D objects, both molecules and abstract cartoons. That led to a little poking around online and eventually to Blender, a free, open source, professional-grade package for rendering 3D images and animations.

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RSS feeds and the chemistry literature—A quick primer

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The last post went over pretty well, so I thought I’d follow-up with a quick how-to on RSS feeds for the uninitiated. Truthfully, this is a tremendously simple process. All that’s needed is a feed aggregator. For this purpose, I chose RSSOwl. This actually isn’t what I use (I use Reeder as a client for Feedbin, a cloud RSS reader), but RSSOwl is both free and multiplatform. The process shouldn’t be any more complicated with other clients. There are quite a number available for different PCs, smartphones, and tablets. Continue reading →

RSS feeds and the chemistry literature

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Honestly, there’s nothing particularly novel about the topic of this post: using RSS feeds to keep up with the scientific literature. The technology has been around for ages. Nature Chemistry actually has a nice editorial on this subject (among other things) from a couple of years ago, and many library websites offer advice. So file this post under “advice for new grad students in my group that could be of interest to others”. If you already have a good RSS workflow I’m not sure there will be a whole lot on offer here. However, if you don’t, you really owe it to yourself to consider switching over. Perhaps as part of a New Year’s resolution to better keep up with the literature?

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A Python script for grading partial credit multiple choice: Part 4—The script

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Here I thought I’d go through the script and explain its logic. The idea is that it could be modified to fit whatever format you get your MC output in or to change the information that it returns, hopefully even without a lot of programming experience.

Let me say at the outset that this was one of my first little Python projects. I make no claims that it’s particularly elegant or pythonic; in fact, I have plans for a newer version that will be a bit better organized. Criticisms always appreciated. That said, it does get the job done.

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