Psssssst @Jason

I'm trying to use ComplexPlot with PrimeZetaP but it just plots a blank canvas. Zeta works fine. Anyone know how to solve this?

@JasonB. your MoleculePlot3D ((did you head this one?)) function plots chiral structures in the exact same manner, I don't think it is supposed to do that! Any way I can get the chiral structure to be accentuated? One example is with + and - limonene

I'm probably dumb, but entering the entities in MoleculePlot3D and asking true or false for equivalency gives true

@gwr I'll say something to someone, not having any authority or standing, but I'm within reach of those who matter! I noticed it takes a bit, but they always get back to you.I'm still battling for an answer to the system-wide reformatting of notebooks issue I had earlier this month

While I'm here clogging up the feed, does anyone know how to automatically evaluate in place? I am making an educational notebook, and I figure that doing that instead of copying output is a lot more functional?

@CarlLange @C.E. if you want to go a pure Mathematica route you can also use the XMLGraph stuff I presented in that same question. I use this all the time for scraping these days. (I was just thinking about this because I was just using it...)

Forces you to use weird syntax though because I like the weird syntax

radiiXML =
  Import["https://en.wikipedia.org/wiki/Atomic_radii_of_the_elements_(data_\
page)", {"HTML", "XMLObject"}];

<< XMLGraph`

g = XMLGraph[radiiXML]

Values[g@"Children"[g@"Select"[".wikitable td"]]][[2 ;; ;; 9]]

{{"H"}, {"He"}, {"Li"}, {"Be"}, {"B"}, {"C"}, {"N"}, {"O"}, {"F"}, {"Ne"}, \
{"Na"}, {"Mg"}, {"Al"}, {"Si"}, {"P"}, {"S"}, {"Cl"}, {"Ar"}, {"K"}, {"Ca"}, \
{"Sc"}, {"Ti"}, {"V"}, {"Cr"}, {"Mn"}, {"Fe"}, {"Co"}, {"Ni"}, {"Cu"}, \
{"Zn"}, {"Ga"}, {"Ge"}, {"As"}, {"Se"}, {"Br"}, {"Kr"}, {"Rb"}, {"Sr"}, \

@b3m2a1 Oh, that's cool!

@CATrevillian Are you looking for selecting a region then shift-command-enter?

@CarlLange I think that's accurate, I forgot about that one! But so...hmm, that shouldn't result in anything much different than copy and pasting it? But yes, this is exactly what I was trying to remember! Ohhh the simple things, hey? I'm hoping my content doesn't get unformatted when I go to publish it, is all.

@CATrevillian Yes, sometimes I wish things like Quantity[5, "seconds"] would automatically get formatted nicely for readability, and then click-to-edit. 🤷‍♀️

@CarlLange Oh, that would be great! Nice idea. I'll mention something ;) But the select shift control/command enter works very nicely to keep a cleaner workspace. Thanks again for the reminder :))

@CATrevillian How are you building your limonene molecules? If doing so from entities, that is the issue. The "Chemical" entities need a major update.

If I create the molecules using their IUPAC names then you can see the stereochemistry

@JasonB. from chemical entities, yeah, I'm a bit inept in that area. Should I use some online model? Ahhhh okay I will use this method! I was surprised because the 2D diagrams were the best for comparison to each other (writing on chirality, and that's a great example to use that we enjoy in everyday life) but wow you rock :D:D:D:D:D:D:D

If you want to highlight any chiral atom, you can use Atom["AtomChirality" -> Except[None]] as a pattern

@JasonB. Yeah those ones plot out nicely using the entities also--I'll peek at the 3D ones real quick using the IUPAC names :) OOOOOOH yes dude yes that is exactly what I could benefit from!!!! Woo!

Also, lets say you have a molecule with no defined stereo,

mol = Entity["Chemical", "Dipentene"] // Molecule

you can see what atoms could be chiral with mol["PossibleStereocenters"]

Then something like

will make the R enantiomer

This does make it throw out the coordinates it had from the entity, but new 3D coordinates are easy to generate for this example

Wowwwwwwie wow wow man @JasonB. this is awesome :D thank you! What's an easy way to get ahold of an input-able IUPAC name? Possibly from an entity?

It looks like our entity for limonene is for the racemic mix, and so you don't have any stereo on the entity

If I only have a common name, I'll google it, the wikipedia page or the pubchem entry will usually have a SMILES string or parsable name

The ServiceConnect for pubchem works, so you could query it programmatically

@JasonB. presumably you also take SDF right? The PubChem ServiceConnect only returns 2D coordinate data, but you can chain a ServiceConnect request for an ID number with a secondary ping to the actual API to get SDF out.

@CATrevillian

That way you can just get some 3D coordinates directly from whatever PubChem has stored (which is probably no better or worse than Jason's 3D coordinate generator)

we do also import SDF

I should look at that ServiceConnect code and add a direct "Molecule" element

which would in turn just call Import on the SDF

Neither PrimeZetaP nor EllipticTheta works with ComplexPlot.

@user76284 To give you a hint: Look at PrimeZetaP[-1.0] and then re-check the region you wanted to plot.

@halirutan I’m only plotting Re(z) > 0.

@user76284 Still, there will be ComplexInfinity in it. Use e.g. Table[PrimeZetaP[x - I*y], {x, 0.1, 1, .1}, {y, -1, 1, .1}] to see this.

@user76284 Two things: First, you can use <<GeneralUtilities` and PrintDefinitions[PrimeZetaP] to see its implementation. Second, you can use a quick hack to filter all non-numeric results:

pzp[z_?NumericQ] := With[{result = PrimeZetaP[z]},
  If[NumericQ[result] && Head[result] =!= PrimeZetaP, result,  0.0]
  ];

ComplexPlot[
 PrimeZetaP[z],
 {z, 0.1 - I, 1 + I},
 ColorFunctionScaling -> False
 ]