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1:24 AM
@b3m2a1 @C.E. Nothing in the current Mathematica support of highlight.js is done decently.
It starts with the pattern for keywords which is '(\\$|\\b)' + hljs.IDENT_RE + '\\b'. Since hljs.IDENT_RE is defined as starting with a letter followed by \w* it means that _ are allowed in the middle of symbol names. The list of symbols is not up-to-date AFAIK. Our numbers are definitely not hljs.C_NUMBER_MODE, no pattern highlighting, etc..
I know that the list of symbols is huge for Mathematica. We could trim this down by converting it into a prefix tree.. and, oh god, someone already implemented this
3
It's kind of annoying that the SE company introduces changes without giving their sites a heads up. It's their money and we work for free. Is it too much to ask to just reach out? That's basically the main reason I haven't reacted yet.
3
Some things never change. Like when they decided to re-design all sites and we had to jump through hoops to get our fixes to their bugs implemented. Waiting several months for a simple switch of our logo that we fixed was a real downer for me.
 
2:13 AM
@bobthechemist - In your example you create a Molecule from a string in two very different ways. In Molecule[Entity["Chemical", mol]] you make an entity first then convert it to a molecule. It looks to the knowledge base for an entity with a given standard name, and uses EntityValue to get properties (like coordinates). But when you type Molecule[mol] it interprets the string locally.
It will actually interpret the name using the OPSIN parser so you can give it almost any valid chemical name and get a molecule back
I wish it was more intuitive, and obvious how that was happening.
So Molecule["Methylnitrene"]["PointGroup"] works, even though there is no chemical entity for methynitrene
 
 
9 hours later…
11:16 AM
@JasonB. Thanks for the clarification - is Molecule computing properties upon request or are values such as the point group in a lookup table? Also, tangentially related, how are we to know that "PointGroup" is a valid property when Molecule[mol]["Properties"] does not indicate as such? (Granted, in this case one can find "PointGroupString", but I see nothing that suggests that "PointGroup" would work.)
 
12:14 PM
Molecule computes everything as needed - so when you ask for Molecule["Methylnitrene"]["PointGroupString"] it uses the name to create a SMILES string, then makes a chemical graph from the SMILES, computes 3D coordinates using distance geometry embedding, then the MMFF force field to minimize the coordinates, then finds the point group from those coordinates.
"PointGroup" was the original name for the "PointGroupDisplay" property, but it was decided to use "PointGroupDisplay" and "PointGroupString" instead, as they are more descriptive about what is returned. I keep using "PointGroup", which is now just an alias for the display version, out of habit.
 
12:32 PM
Nice - The recent additions to the chemistry toolkit (for lack of a better term) in M have been really exciting. I haven't had time to think about their use in my classes, but it's definitely on my to do list.
 

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