Re: Unambiguously describing molecules... and more

Hi,

  "H. S. Teoh" <hsteoh@...> wrote:  On Fri, Mar 16, 2007 at 08:21:40PM -0400, Leon Lin wrote:
  [...]
  >> Isomers. (see http://en.wikipedia.org/wiki/Isomer) So... basically
  >> what I'm asking (or thinking about) is how to describe molecules, not
  >> only by the atoms they contain, but also their structure (the bonds).
  >> Can you come up with anything better that SMILES (see
  >> http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html)?

  >It looks pretty solid to me already. What disadvantages do you see in it
  >that might need improvement?

 Perhaps this is more of an impossibility that a linguistic idea, but can
anyone think of an efficient way to describe the angles at which the bonds are?
This is probably not important or necessary except maybe with proteins, which
twist and bend even though they could be stretched out into a long sequence of
amino acids.

 Going back the graph thing, if I'm not mistaken, SMILES cannot tell if
something is on the inside or outside of something else. For example, if we had
a buckyball (see http://en.wikipedia.org/wiki/Buckyball) with some attachments,
you would have no idea whether these appendages were on the inside or outside
of the "ball". This difference affects how the molecule interacts with other
things.

 Also, if the language is a human conlang, then readability is an issue. A
"shortcut" option could be available for describing crystals or other things
that have a repeated pattern. For example, cubane could be described as
follows:

 Cubane is a molecule with 8 carbon atoms in the structure of a cube (with an
atom at each vertex). Each carbon atom is bonded to one hydrogen atom.

 In SMILES, cubane is C12C3C4C1C5C4C3C25. When in the midst of other
hydrocarbons, one could mistake this for another asymmetrical, branching,
molecule whose structure is difficult to remember. How complicated would a
description of a crystal be? Surely there is a way to describe symmetrical
chemical structures? I am not critisizing SMILES because I don't think it was
created for humans to read.

  -Leon

"H. S. Teoh" <hsteoh@...> wrote:  On Fri, Mar 16, 2007 at 08:21:40PM -0400, Leon Lin wrote:
[...]
> Isomers. (see http://en.wikipedia.org/wiki/Isomer) So... basically
> what I'm asking (or thinking about) is how to describe molecules, not
> only by the atoms they contain, but also their structure (the bonds).
> Can you come up with anything better that SMILES (see
> http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html)?
It looks pretty solid to me already. What disadvantages do you see in it
that might need improvement?


> In general, have any of you all included describing graphs (this kind of
> graph: http://en.wikipedia.org/wiki/Graph_%28mathematics%29) in your
> languages. Which traversal method is best?
Depends on the criteria you use to choose between them. "Best" is a
subjective measure.


T

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First Rule of History: History doesn't repeat itself -- historians
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