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All of this is true. The word "close" was chosen very, very deliberately. Though the Game of Life is surely simpler than the Reality of Life... if one were to

All of this is true. The word "close" was chosen very, very deliberately. Though the Game of Life is surely simpler than the Reality of Life... if one were to flat out name the core concept as "godel numbers for chemical formations", it's certainly possible, don't you think? InChI isn't it, I agree; just wanted to toss the seed of the idea out there, with an example that's a lot "closer" to the target semiotics than a bunch of unnormalized floating point coordinates drifting around in xml. "good enough is the enemy of good" can apply in spades here, so I appreciate your thorough analysis of specific weak points in InChI.

dalke 11y ago
InChI is not closer but actually further than SMILES or SD files for many of the use cases you wanted. It is not a supported capability to turn an InChI into a structure, which makes it hard to generate, say, a fingerprint for a Tanimoto search system. (Yes, the command-line tools and its wrappers support that, but the InChI developers do not condone its use. Even if you do so, the output may differ from your input structure in ways you disagree with.) InChI is only closer for the classical purpose of chemical documentation - record association and text-based search. That is not a bad thing, but given the entirety of your goals, it is equally correct to use "close" for SMILES, SLN, SD, Mol2, etc.