Cheer up your LaTeX with SMILES support II

In Part I, I showed how to embed PNGs, automatically generated from SMILES by obabel, into LaTeX documents. An alternative approach is to use the SVG output from obabel.

In a comment to my earlier post, Billy suggests running the SVG through Inkscape or rsvg-convert:

You can also embed the material as a vector graphic, of course. Inkscape doesn't seem to support pipes, and rsvg-convert gives ugly output, but I'm sure there's other options.

\immediate\write18{obabel -:'#1' -osvg -p | rsvg-convert -f pdf -o smilesimg\arabic{smilescounter}.pdf}

\immediate\write18{obabel -:'#1' -O smilesimg\arabic{smilescounter}.svg -p ; inkscape -f smilesimg\arabic{smilescounter}.svg -A smilesimg\arabic{smilescounter}.pdf}

Also, if you don't want to call these applications when the graphic files aren't out of date, then use the code snippet found at the top of the 3rd page from this article.

I found a third approach on the interwebs soon after writing the initial post. It's by Jakob Lykke Andersen who converts the SVG to PDF with ImageMagick's convert. If you download the file graphviz.tex from his website, you can just include it and use it as in the following example:
The resulting PDF looks better than the original (though it could be because I didn't handle the PNGs properly in the first PDF). A nice little touch in Jakob's version is that an error box appears in the PDF if there is a problem generating the image.

Exercise for the reader:
A bit more polish is needed before these methods can be used wholesale by others. If you know a bit about LaTeX, have a go at an obabel package for CTAN.

Molecular eye candy for IPython

IPython is an enhanced Python shell that does magic and is wonderful. Apart from me, everyone else uses it. You can install it with "easy_install IPython" on Windows, Linux, etc. Recent versions have a graphical console (start with "ipython-qtconsole") to which we can add some molecular eye candy. Greg Landrum has already done this for RDKit. Here's how to do it for Pybel.

First of all, here's the before picture:

Now, copy and paste the following into the console:

pybel.Molecule._repr_png_ = lambda x: x.write("png")

And here's how it looks after:

Greg has gone a bit further with RDKit, and has enhanced substructure matches, but that's where I'll draw the line for now.

Reduce, recycle and reuse bond closure symbols?

Time for a new poll. I'd like to know what you think about reusing bond closure symbols in SMILES strings. Simply put, when writing SMILES there is a choice between reusing the bond closure symbols or using a new number each time. That is, the following molecule with two rings could be written as:
C1CC1c1ccccc1 or
C1CC1c2ccccc2

Here are the pros and cons of choosing not to reuse bond closure symbols (anything missing?):

Pro:

• Easier to count up the number of rings
• Easier for a human to find corresponding bond openings and closures
• Easier to implement (but not a lot)
• Reuse of bond symbols can cause confusion

Con:

• Use of % notation for two-digit bond closures can cause confusion (people are not so familiar with it)
• Leads to syntax like C%1145, meaning that bonds 11, 4 and 5 close here (not very intuitive)
• Limits bond closures to 99 (but more than 99 is unlikely)
• Not as concise as alternative (for molecules with at least 10 bond closures)

See if you can answer this poll before checking what does software A do, or standard B suggest. What do you think should be the standard approach?

Update (17/04/2012): Poll results: 8 for reuse, 3 against

Cheer up your LaTeX with SMILES support

No-one likes an unhappy document preparation system, so let's add support for SMILES to LaTeX. LaTeX has already seen a lot of love from chemists - check out the list of chemistry packages at CTAN. Perhaps even more surprising is the fact that a couple of these packages are being actively maintained and updated (e.g. chemmacros and chemfig).

So, let's get down to business. This is a simple hack that will insert a 2D diagram of a molecule if you use the \smiles command. Here's the necessary code (at the top of the .tex file) and an example of use in the main body. The resulting PDF is here.

So how does this work? Well, it simply calls obabel at the command-line to create a .PNG file, and then adds an \includegraphics command (the idea is taken from texments). The only catch is that command-line calling of executables is only allowed if you run pdflatex with the -shell-escape option ("pdflatex -shell-escape myfile.tex"). (For the record, I did this all on Windows, with pdflatex provided by Cygwin.)

While this is, um, neat, to be honest you'd probably be better off creating the PNGs in advance if you have a lot of SMILES strings. A much cooler way to embed chemistry in LaTeX would be to write a QSAR paper using Sweave/R/CDK via Rajarshi's CDK/R packages. This is the idea of literate programming, where the document functions as a complete description of the analysis because it is the analysis; it is the ultimate in reproducible research. Has this been done? Any takers?

Share ami

Some time ago Google shut down the Share feature of Google Reader to push everyone onto Google Plus. Unfortunately, Google Plus is a bit of a walled garden (and also it sucks compared to FriendFeed, but that's not the issue here). Unlike Google Reader, it doesn't provide an RSS feed for shared items so there's no way I can list them in the sidebar of this blog (as I used to). Instead, this post contains a selection of items I shared on Google Plus since I joined in Nov last year.

I don't know if this is going to be a regular feature, so to follow me on Google Plus, check out my profile page.

The following items are listed somewhat chronologically, youngest first:

• Google summer of code with the CDK and Bioclipse
• CP2K paper
• Another javascript WebGL viewer for molecules.
• 64-bit compilation working on Windows with MSVC++ Express
• What chemistry journals will accept a manuscript from a preprint server? from Jan Jensen
• Video tutorial showing installation and use of Open Babel GUI on Windows... from OSDD
• Marcus has gotten Kinect integrated into Avogadro! at Kitware
• ESR weighs in on OA in Chemistry at PMR
• Nice to see mention of my docking work...
• In Which I Fix My Girlfriend’s Grandparents’ WiFi and Am Hailed as a Conquering Hero. Epic.
• Kitware Receives Phase II Funding for the Development of a Computational Chemistry Workbench
• Negative activation energies in molecular modeling: diagnosis and cures" at Jan Jensen
• How to include the ligand in GROMACS at Proteins and Wavefunctions
• Never thought of citations in terms of ethics before. If I promote my paper, am I shamelessly manipulating citations? at CHMINF-L
• Andrew parallelises chemfp. I think this is going to be fast. Very fast.
• Reflections on 2011: Open Source, Open Science and Open Chemistry by Marcus Hanwell
• IBM Donates Large Collection of Patent Chemical Structures to NIH/PubChem at Depth-First
• Chemical Name Pattern Searching (or even more on chemical Name Searching) at /chemical/structure Blog
• How to turn on Grimme's dispersion correction in Gaussian. at CCL.net
• CAS and InfoChem collaboration
• Jmol on Android Table at Henry Rzepa's blog
• Open Babel, SMARTS at Python in Chemistry
• Open Babel citations
• Substructure searching from NIH...code available... at Rajarshi's blog
• A compilation of NWChem under Cygwin at Computational Chemistry Software
• Rajarshi asks What are the founding principles of cheminformatics?
• create and use QSAR models online at OCHEM
• Transription of Andrew Dalke's interview with Paolo Tosco at Molecular Coding

Presentation on Solar Cells at Smart Surfaces 2012

Here are the slides of the talk I presented at Smart Surfaces 2012 last week. For background see this post. To see the animation on slide 14, check out this post.

Large-scale computational design and selection of polymers for solar cells

View more presentations from baoilleach

Accessing the CDK from Jython in Knime

I've been trying to find out how to use the CDK and/or Open Babel from Jython in Knime. Unfortunately, there's no documentation beyond a single example script. It's a bit strange, as having this working would enable a whole host of developers to write nodes, particularly in the area of chemistry where Python has made considerable inroads.

After asking and not receiving any answer, I've tried to hack something together. I haven't yet figured out how to do it properly, but at least I've learnt a bit, and the end result was that I was able to calculate the molecular weights with the CDK as in the following diagram:

Here's the code for the node. It was debugged by keeping the console log file open in gvim, and reloading (:edit) after every run. Also I had to configure the node by selecting the "Script Output" tab, choosing "Append columns to input table spec", and adding an Output column of type Double:

The way I did this was by hacking the source code for the Jython node itself. First I figured out how to compile it (YMMV). The source is available, but for some reason various files are missing that prevent it compiling out of the box (e.g. the plugin.xml). So I ran the Create Node Wizard (manipulator), copied over various files from the source, copied over various files from the binary (the files in lib and schema), added the lib/jython.jar (as described here), and installed the org.python.plugin node (not forgetting to remove the duplicate org.knime.ext.jython).

To add the CDK jar to the Classpath, I placed it in the lib directory, repeated the procedure described above for lib/jython.jar, and then added the following hack to PythonScriptNodeModel.execute:

classpath.append("/C:/workspace/Jython/lib/cdk-1.4.5.jar");

If there's someone from Knime reading this, please let me know the correct way of doing this. I know that there's an extension point for extending the Classpath of the Jython node, but how is this used?