7 votes
Accepted

Is it possible to obtain the atomic indices of a bond by clicking on a MoleculePlot?

First a few basic observations. Mousing over the diagram in the summary box shows tooltips with the atom indices. That also works with MoleculePlot. There is a WFR that lets one click on atoms in 3D ...
Vitaliy Kaurov's user avatar
7 votes
Accepted

Drawing of a cube file

The first issue you are having is this: In[262]:= ToExpression["1.06897E-03"] Out[262]= -0.0942383 It's unfortunate, but that string is interpreted as a ...
Jason B.'s user avatar
  • 68.4k
7 votes
Accepted

Chemistry context in Mathematica 13

The "Chemistry`" context contains mostly internal functions used by the built-in System Chemistry functionality. These functions are undocumented and may change from version to version. A ...
Jason B.'s user avatar
  • 68.4k
5 votes

How to export SD file with metadata?

When exporting multiple elements for a file, you want to include them all together in the first argument and not place some of them at the end like options. That's why your first ...
Jason B.'s user avatar
  • 68.4k
4 votes
Accepted

Are there plans to support multiple molecules in the Molecule function?

I don't quite agree with this statement Molecule function can create reasonable coordinates even for disconnected entities The individual fragments are embedded in 3D separately and then just ...
Jason B.'s user avatar
  • 68.4k
4 votes
Accepted

Is there a way to make Mathematica support Chemmacros of LaTeX?

Either do ...
Nasser's user avatar
  • 143k
4 votes
Accepted

How can the units of the "AtomCoordinates" in a Molecule be changed while keeping the resulting MoleculePlot3D consistent?

There are two issues here - first a bug that was introduced in version 13.1 and should be fixed in a future release, and secondly some confusion about the design of ...
Jason B.'s user avatar
  • 68.4k
3 votes
Accepted

Method of lines - Dirichlet and mixed BC

We can solve this problem using FDM and NDSolve as well to compare solutions. First code with FDM implementation ...
Alex Trounev's user avatar
  • 44.5k
3 votes

Extract coordinates from the Gaussian09 calculation file

...
Roland F's user avatar
  • 3,534
3 votes
Accepted

Extract coordinates from the Gaussian09 calculation file

We first search the positions of the horizontal dashed lines: ...
Daniel Huber's user avatar
  • 51.5k
2 votes
Accepted

Plotting the molecular isosurface electrostatic potential map

As mentioned in the comment above, the problem is strongly related to How can I convert a 3D contour plot into a region for use as a custom slice in ListSliceDensityPlot3D? And you don't need any ...
xzczd's user avatar
  • 66k
2 votes
Accepted

Import fails for Gaussian calculation output file

Until this is fixed, the following function should work to import the molecule geometry from a Gaussian output file. It does not work with charged fragments, nor does it import any other type of data....
Jason B.'s user avatar
  • 68.4k
2 votes
Accepted

Trace animation of spherical and $\pi$ atomic orbital

The local constants in Block were missing ...
Roland F's user avatar
  • 3,534
2 votes
Accepted

Newton Raphson apply to Van der Waal Equation

To find curve we can use this code ...
Alex Trounev's user avatar
  • 44.5k
1 vote

Chemdraw (CDX) import fails to yield complete molecules for implicit alkyl chains

ChemDraw can interpret the correct representation, even if this is not explicitly represented in the CDX file. So the idea is to remotely control ChemDraw to get the information, and to do that we ...
Joshua Schrier's user avatar
1 vote

How to enter chemical equations?

Now, with Mathematica 13 or above, you can do these. ChemicalFormula["SO4^2-"] get Or ...
Y. zeng's user avatar
  • 567
1 vote

Generating molecules using a GAN in Mathematica

You may be restricting yourself to overly complicated techniques in particular GANs. There are far simpler methods for generating molecules and in fact statistical models such as Markovian text ...
ChemMaster's user avatar

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