Friday, 23 September 2016

Open Babel 2.4.0 released

As announced by Geoff on the mailing list, Open Babel 2.4.0 is now available to download:
I'm pleased to announce that Open Babel 2.4.0 has finally been released.

This release represents a major update and should be a stable upgrade, strongly recommended for all users.

We intend to move to an annual major release every September, with bug fix releases as needed.

A sample of major new features:
  • Integration of the confab conformer generator
  • Improved partial charge models, including EEM methods, EQeq
  • ECFP radial fingerprints
  • Initial support for ring rotamer / conformer sampling
  • Improved GAFF atom typing and parameterization
  • New PHP scripting bindings
  • Many new file formats, features and bug fixes

For a full list of changes and to download:
https://github.com/openbabel/openbabel/releases
https://sourceforge.net/projects/openbabel/files/openbabel/2.4.0

Thanks to a cast of many for this release, including:
Alexandr Fonari, Anders Steen Christensen, Andreas Kempe, arkose, Benoit Leblanc, Björn Grüning, Casper Steinmann, Chris Morley, Christoph Willing, Craig James, Dagmar Lenk, David Hall, David Koes, David Lonie, David van der Spoel, Dmitriy Fomichev, Fulvio Ciriaco, Fredrik Wallner, Geoff Hutchison, Heiko Becker, Itay Zandbank, Jean-Noel Avila, Jeff Janes, Joaquin Peralta, Joshua Swamidass, Julien Nabet, Karol Langner, Karthik Rajagopalan, Katsuhiko Nishimra, Kevin Horan, Kirill Okhotnikov, Lee-Ping, Matt Harvey, Maciej Wójcikowski, Marcus Hanwell, Mathias Laurin, Matt Swain, Mohamad Mohebifar, Mohammad Ghahremanpour, Noel O'Boyle, Patrick Avery, Patrick Fuller, Paul van Maaren, Peng Bai, Philipp Thiel, Reinis Danne, Roger Sayle, Ronald Cohen, Scott McKechnie, Stefano Forli, Steve Roughley, Steffen Moeller, Tim Vandermeersch, Tomas Racek, Tomáš Trnka, Tor Colvin, Torsten Sachse, Yi-Shu Tu, Zhixiong Zhao

On a personal note, in particular I'd like to thank Stefano, Steve and Steffen for contributing; not to mention Matt, Matt, Mathias and Maciej and David, David, David and David. Without them, ordering the authors by first name would not have so richly paid off.

As Chris Morley has taken a step back from the project, I did the Windows release for the first time. One change is that now we have a 64-bit version along with the 32-bit. I've also moved to supporting "pip install openbabel" as the primary means of installing the Python bindings - there's already been some work on this for Mac/Linux by Matt Swain and others.

If you have any comments/criticisms or need help, the best place to go is to our mailing list (openbabel-discuss@lists.sf.net) or file bugs on Github (click the green "New Issue").

Sunday, 21 August 2016

My new thing - providing manuscript images as PDFs

My latest oeuvre (on the topic of which fingerprint is best) was published by J. Cheminf. a few weeks ago. For the first time, instead of providing the images as PNGs, I submitted them as PDFs.

You see, John had worked me over. At the start, I thought of a PDF as the bad boy of the journal publishing scene, the hamburger and not the cow. What appears at first as text arranged into sentences, is just a haphazard arrangement of glyphs which through some trickery of the eye coalesces into scientific discourse. To generate a PDF myself would be to add to this madness.

But the thing is, when you strip a PDF down to its essentials, it's a relative of a PostScript file (details omitted due to ignorance), a vector graphics format. A more popular vector graphics format is an SVG file, but this is not supported by most publishers and so I spend a lot of time calculating DPI and inches per column and then generating a PNG. But they do often support PDFs, and these can readily be generated (with a bit of care) from many different programs. And all other things being equal, the best quality images will be generated by providing a vector graphics format as the publisher can resize it without any loss of quality.

Below I provide details about how I generated the PDFs, but let's look at their handling by Journal of Cheminformatics. This journal provides three views of the paper, a HTML page, an ePUB (which I won't discuss further) and a PDF. The HTML version contains embedded PNGs, they are a little small for my taste (maybe my fault - I don't know) but they are readable. So somehow they were able to convert the PDFs to images of whatever size they wanted for the HTML page. The PDF is a bit more interesting, as the images are now included as vector graphics. That is, if you keep zooming in on an image in the PDF, the lines remain sharp (in contrast to the PNGs in the HTML version).

So, in short, there seems little downside to providing PDFs, and much to gain. I'd be interested in hearing the viewpoint of anyone involved with the publishing side of things.

Notes:
1. When using matplotlib to generate graphs, just give the file a .PDF extension, e.g. plt.savefig("overallperformance_%s.pdf" % benchmark, dpi=300)
2. When using Inkscape, save as PDF.
3. The hardest part was the chemical structures. I tried a variety of recipes with two different commercial programs. In the end, although ChemDraw's SVG export had the heteroatoms all over the place, the EMF export was openable by Inkscape and then I could save as PDF. (Apparently you can go direct to PDF from ChemDraw on a Mac.)

Tuesday, 2 August 2016

Open Source Cheminformatics Toolkits - they keep on coming

It has been just over three years since I last surveyed the world of open source cheminformatics toolkits. So what's new?

  • Kekule.js - This is a JavaScript toolkit by Chen Jiang with an associated publication in JCIM this year. JavaScript cheminformatics is still in its infancy, and it's good a see a new player in this area. It's currently at version 0.7. Interestingly, it appears to include in _extras, a JavaScript version of Open Babel created using Emscripten.
  • OpenChemLib - This Java toolkit was developed by Thomas Sander at Actelion, and is the engine behind Data Warrior. It has since been converted to JavaScript (using GWT) by Luc Patiny and used, for example, in the impressive Wikipedia Chemical Structure Explorer.
  • Lilly MedChem Rules - Strictly speaking, this is not obviously a toolkit, but a commandline Ruby application. However, there is a C++ cheminf toolkit sitting behind that application, which was developed by Ian Watson at Eli Lilly.

Let me know if I've missed anything. For a more comprehensive overview of Open Source Molecular Modelling see the very recent paper by Pirhadi et al, which has an associated Github repo for keeping the information up to date.

Monday, 18 July 2016

Your SD file will never be the same again...with ASCII depiction

A recent blog post showed how to depict a record in an SD file from within Vim. This of course is no help to those readers who have yet to successfully exit from a Vim session. But what if there was no need to create an ASCII depiction...because it was already there?

Yes, that's right, you have no clue what I'm talking about. What I'm saying is, why not bung in an ASCII depiction of the molecule in a property field? Well, apart from it being a bonkers idea that'll bloat the SD file to hitherto unimagined sizes (but think of the improved compression!), I can't think of any reason not to do this. It is my belief that this could finally unleash the untapped potential of ASCII depiction. And so I've added an option to the SD file writer in Open Babel to do exactly this.

John is fond of quoting Jurassic Park's "your scientists were so preoccupied with whether or not they could that they didn't stop to think if they should." I don't know why I just mentioned that.

Thursday, 14 July 2016

Even more molecular depiction in Vim

Previous posts focused on popping up an ASCII depiction in Vim, but what doing something with the PNG output from Open Babel? Is there any way this can be viewed from Vim? Aged readers may remember a previous blog post of mine that looked into PNG to ASCII conversion, and that would be one approach.

A more direct approach is to use Vim's built-in capabilities to view bitmap files. Well, to be exact, a specific type of old-skool bitmap called an XPM. This has a very simple format and so Vim can show the entire contents of the file and use syntax-highlighting to visualise it. The alleged use for this is to enable people to directly edit bitmaps - that's right, someone out there is using Vim as a bitmap editor.

The only problem is generating the XPM file in the first place. We could probably do this directly from Open Babel as the format is fairly simple (e.g. as an option to the PNG writer) but in a certain light that just might ("just might", mind you) be viewed as feature creep. So instead, we can use ImageMagick's convert to do the job (which is available cross-platform). As before the required script is shown below.

Once I got it working I got to thinking, "well, that's a 79x79 bitmap it's showing, which is pretty small but what if I reduce the font size? aha! - then I can show an arbitrary sized bitmap and show much better detail". At which point I realised that in any environment where I can change the font size in Vim, I should probably just pop up an image viewer to display the PNG (left as an exercise for the reader).

In the end, are these depictions better than the ASCII ones? Meh, probably not - which I think was one of the conclusions also from my previous foray into PNG to ASCII conversion. Oh well.

noremap <silent> <leader>d :call SmiToPng(77)<CR>
function! SmiToPng(width)
  let smiles = expand("<cWORD>")
  " Strip quotation marks and commas
  let smiles = substitute(smiles, "[\"',]", "", "g")
  " Handle escaped backslashes, e.g. in C++ strings
  let smiles = substitute(smiles, "\\\\", "\\", "g")

  botright new
  setlocal buftype=nofile bufhidden=wipe nobuflisted noswapfile nowrap
  let fname = tempname().'.png'
  call system('obabel -:'.smiles. ' -O '.fname.' -d -xm -xp '. a:width)
  execute '$read ! "C:\Program Files (x86)\ImageMagick-6.5.8-Q16\convert.exe" '.fname.' xpm:-'
  setlocal filetype=xpm
  execute "normal! ggd/pixels\<cr>dd"
  silent! g/\v^"(\S)\1+",?/d
  execute "normal! Gdd"
  setlocal nomodifiable
  1
endfunction

The 7th Joint Sheffield Conference on Chemoinformatics - a real tweet

Just back from the Sheffield meeting, which takes place every 3rd year. Great meeting as ever - tribute was paid to John Holliday for the lion's share of the organisation. I got to meet some old friends and some new. For the first time at a meeting I decided to live-tweet the talks, joining such Twitter luminaries as Wendy Warr, Mireille Krier, Nathan Brown, and Jérémy Besnard.

It worked out quite well, and kept me completely engaged and awake. When you are aware that what you write is instantly publicly visible, you really make an effort to follow method descriptions etc so that you can adequately describe what's going on. To speed things up I decided to avoid editorialising; if the author described their method/result as the best thing since sliced bread, I dutifully reported a major advance in the field of baked goods even if I was thinking "bread is dead, baby, bread is dead". I have since learned that this is referred to as journalism.

With about 750 tweets covering 27 talks (I missed one due to flat batteries), I averaged about 27 tweets per talk, which may be just over one per slide. Afterwards I asked on Twitter whether people were annoyed or found my avalanche of tweets useful; based on 13 respondents, the results were 3 to 1 in favour of the tweets. If I do a repeat performance, next time I'll give a heads-up so people can mute me if uninterested.

I don't like my efforts disappearing into the void, so I've archived the complete list of #ShefChem16 tweets from all attendees and remotes that used that hashtag. You can relive the build-up, the talks themselves, the scones/doughnuts, the conference dinner, not to mention the queuing for taxis to the station. The talks and posters are being made available by-and-by on the conference website so you might find it interesting to look at the tweets in combination with the slides.

Notes on creating the download of tweets:
I tried to do this the hi-tech route via the Twitter API, but I think it's impossible if there were more than 100 tweets in a day. The API is geared towards streaming not historical analysis. In the end, I went to the Twitter website, searched for #ShefChem16, hit "All tweets", zoomed out and kept hitting Page Down until all the conference tweets were shown. Next I saved the generated HTML via Firebug (right click on the <head> element and choose "save outer html" or so), and extracted the tweets with the following script. Unfortunately, although it's possible to know to whom a reply has been made, the corresponding tweet id does not seem to be available so I didn't bother handling replies in a special way.

# vim: set fileencoding=utf-8 :
from bs4 import BeautifulSoup as bs

soup = bs(open("shefchem16.html"), "lxml")

HANDLESIZE = 10

data = []
name = None
for tag in soup.find_all("div"):
    if not tag.get("class"):
        continue
    if "stream-item-header" in tag.get("class"):
        name = tag.a['href'][1:]
    if "js-tweet-text-container" in tag.get("class"):
        tweet = tag.get_text().encode("utf-8").replace(" …", "")
        data.append("%10s %s" % (name[:HANDLESIZE], tweet.strip().replace("\n", "\n"+" "*(HANDLESIZE+1))))

with open("tmp.txt", "w") as f:
    for d in reversed(data):
        f.write(d+"\n")

Image credit: Egon Willighagen on Twitter

Tuesday, 12 July 2016

Basic Graphviz input file generator in Python

Generating a Graphviz Dot input file is fairly simple, so I tend to code it up myself rather than use an existing library. However the need to normalise the node names complicates things a little bit. Here's a copy of the one I wrote today. Note that you may need to beef up the normalisation if your node names contain additional non-alphanumeric characters. (Note to future self: next time just autoincrement the node labels instead of trying to use a normalised form.)
class Graph:
    def __init__(self):
        self.lookup = {}
        self.edges = []
    def add_edge(self, x):
        if x in self.lookup: return
        nx = x
        for y in " -()[]":
            nx = nx.replace(y, "_") # normalise the label
        self.lookup[x] = nx
    def add(self, x, y):
        self.add_edge(x)
        self.add_edge(y)
        self.edges.append( (x, y) )
    def write(self):
        tmp = ["digraph {"]
        for x, y in self.edges:
            tmp.append( '%s -> %s;' % (self.lookup[x], self.lookup[y]))
        for x, y in self.lookup.iteritems():
            tmp.append('%s [label="%s"]' % (y, x))
        tmp.append("}")
        return "\n".join(tmp)