Depth-First: Tag aesthetics

Waldorf Salad

Rich Apodaca — Wed, 11 Jul 2007 09:36:00 +0000

One thing that really irritates me is badly drawn ChemDraw structures (maybe I should get out more...). ... Simple really... so why do a lot of ChemDraw structures that appear in papers or on slides at conferences look like a six-year old has drawn them with a crayon (and I mean a particularly untalented six-year old at that - one that probably wouldn't even win a Blue Peter drawing competition)? I think it’s just people being lazy...

-Stuart Cantrill, Badly Drawn Bonds

Chemical structures are a language. Like any language, grammar and spelling convey meaning and become "standardized" over time. But as native speakers of any language will tell you, languages also take on important cultural nuances that are difficult to convey to non-native speakers. Chemical structures are no different, as Stuart Cantrill's comments show.

Just about every chemist I've met has opinions on the "right way" to draw chemical structures that go beyond "grammar" and "spelling." These opinions come out most clearly in interdisciplinary environments, where non-chemists create chemical structures. Features such as "unconventional" line proportions, bond angles, or atom label proportions don't affect meaning. But they do violate conventions subconsciously learned over years of training. They look weird and because of this they distract attention and annoy audiences.

Not every badly-drawn structure is the result of laziness. Rather, it's more likely that: (1) the author didn't know there was a problem; (2) the author did know, but underestimated the benefit of correcting the problem; or (3) the author did know but wasn't using a tool that made it possible to correct the problem.

The increasing importance of computers in generating, manipulating, transmitting, and rendering chemical structures means that software developers now face the same choices as individual chemists with respect to quality. Before discounting structure aesthetics as irrelevant, it's worth considering that chemists can and do apply the same judgments to software as they apply to their fellow chemists.

Structure Diagram Generation

Rich Apodaca — Wed, 11 Apr 2007 10:20:00 +0000

Given a molecule with no 2D coordinates, how would you render a human-readable view? This problem arises in many situations, but most commonly in the context of interpreting line notations such as IUPAC nomenclature, SMILES, or InChI. Whatever the solution you come up with, you'll come face-to-face with the structure diagram generation (SDG) problem.

Generating 2D molecular coordinates is a fundamental (and remarkably difficult) problem in cheminformatics. Discussions in the primary literature date back to at least the 1970s with Chemical Abstract Service's pioneering large-scale efforts. A recent article from Chemical Computing Group (CCG) described the design and implementation of an advanced SDG system. To my knowledge, the only open source implementation of an SDG system is found in the Chemistry Development Kit, and by extension Ruby CDK.

The SDG problem plays an important role in the aesthetics of chemical structure diagrams, as mentioned by two readers. To render a molecule aesthetically, 2D coordinates must minimize confusing atom overlaps, unconventional orientations, and unusual bond angles.

The role of SDG in cheminformatics can only continue to increase in importance, especially as more and more structures are automatically generated through mining the primary literature, the Internet, old PDFs, and other sources. With all of these new computer-generated structures will come the need to make them readily understandable to a chemist through SDG.

The Aesthetics of Chemical Structure Diagrams

Rich Apodaca — Fri, 30 Mar 2007 10:21:00 +0000

Quick - name your favorite tool for thinking and talking about chemistry. Many of them have become so refined and integral to the practice of chemistry that they no longer seem like mere tools. The atomic model, the periodic table, octet theory, and electronegativity all fall into this category. So do chemical structure diagrams.

Two-dimensional chemical structure diagrams are a language with both grammar and aesthetics. For example, if you draw pentavalent carbon, you've probably made a grammatical mistake. Aesthetics come into play when a grammatically-correct structure doesn't readily make sense because it uses unfamiliar drawing conventions such as strange bond angles, random bond lengths, unusual orientations, or atom labels that are too small. If you've ever worked in an interdisciplinary environment where non-chemists draw structures (god bless 'em for trying), you've probably experienced the importance of structure aesthetics.

Two recent publications attempt to formalize the aesthetic qualities of good chemical structure diagrams. One deals with chemical structures in general, and the other focuses specifically on stereochemistry. The first document is a draft recommendation on which comments will be accepted until June 30, 2007.

Two long-term trends are raising the importance of standards in this area: (1) structures are increasingly being generated by software without any human guidance, as in the case of chemical nomenclature translation; and (2) in a flat chemical information world in which new scientific publishing models come into being, journal editors will no longer have the final say in how structures are rendered.

The best tools don't just solve a technical problem - they make their users happy. Although aesthetic qualities can be difficult to define, they matter at least as much as technical correctness. Chemical structure diagrams are no exception.

Image Credit: Marshlight