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Comment by andrepd | Hacker News Reader

That at least has a logical meaning, and you really can't simplify it because the thing it represents is that complicated. Using a complicated system of strange words to represent numbers is incomparably worse.

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Meh...it's more of a relic of a weird transition point when chemists had the tools to discover complete structures but didn't have the tools to communicate them robustly other than "in words". These days most non-trivial chemicals are described using their "common name" (e.g. Cholesterol), and if you need a robust way of communicating structure there's SMILES (e.g. C[C@H](CCCC(C)C)[C@H]1CC[C@@H]2[C@@]1(CC[C@H]3[C@H]2CC=C4[C@@]3(CC[C@@H](C4)O)C)C for Cholesterol).

Almost no one will attempt to parse SMILES for non-trivial molecules by hand, but almost every computational package can easily parse them.

That's a tree based molecule language with the parens right? This must be for organic molecules mostly then because you can repeat atoms as in, i.e. crystal molecules?

SMILES is usable for any molecule (i.e. any compound with covalent bonds; crystals are generally not considered molecules), though it's most common use is for organic molecules. Parens indicate branching, and cycles are conceptually treated as branches that revisit the same atom twice.

Yes and no. Yes the system is logical and systematic. However, there are tons of named groups and then there are groups of groups and they all have different and arbitrary priority rules. It's actually quite a clusterfuck for what it does and doesn't really have any real purpose on mildly complex molecules.

Nobody in it's right mind will ever call it by it's real name except maybe to sound more intelligent. Most important molecule have short names either based on the standard or given names.

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