29
votes
Accepted
visualizing a normal mode vibration of a molecule in mathematica
Using a few undocumented functions that have been discussed here on the stack exchange before,
...
- 70.2k
18
votes
Accepted
Minimum energy path of a potential energy surface
Smooth Equations
Let $\varphi \colon \mathbb{R}^d \to \mathbb{R}$ denote a potential function (e.g., from OP's data file).
We attempt to solve the system
$$
\left\{
\begin{aligned}
\gamma(0) &...
- 110k
17
votes
What's the principle behind the new MoleculeRecognize function?
Using ResourceFunction["PrintDefinitions"][MoleculeRecognize], one can determine that the source implementation is MolVec. The specific source code is:
...
- 13.2k
16
votes
Plot 3D model of DNA in Mathematica
Here is a function that can wrap a double helix around any (sufficiently smooth) parameterized curve. Among other things, the function below computes a Bishop frame along the curve; twisting it leads ...
- 110k
16
votes
Accepted
Chemical data of Lactic acid
I've struggled with How Mathematica expects the end-user to interact with knowledge databases for quite some time. While this solution is likely not universal, it has been reasonably successful for ...
- 19.8k
16
votes
Accepted
Why does `Molecule` return a molecule for an incorrect SMILES string?
This is a bug, the most basic manifestation of which is
...
- 70.2k
15
votes
ChemistryData — where is specific gravity?
Specific gravity is not on the property list of curated chemical properties, so you can't get it directly. However, here is a function that will compute it.
...
- 108k
15
votes
Minimum energy path of a potential energy surface
Interesting problem. Decided to treat it as a graph problem, rather than fitting an InterpolatingFunction to it and getting descent directions from there. If I knew ...
- 7,213
14
votes
Computing the surface area and volume of molecules
I can offer a solution by discretization to ElementMesh with external meshing software Gmsh. Currently it produces better quality mesh on curved surfaces that built-...
- 6,553
14
votes
What's the principle behind the new MoleculeRecognize function?
I am one of the authors of Molvec. It was designed in a classical approach using various image processing heuristics to guess the structure. While it's on my todo list, we still haven't published a ...
- 241
14
votes
Mass Transport Model
OK. Let me extend my comments to an answer. First of all, I'd like to point out why OP's attempt doesn't work:
"NDSolveValue should return a list with three ...
- 68.4k
13
votes
Accepted
Plot polygonal surface
(grabbing a lot of code from this answer)
This is just to get you started, adding in colors to the final GraphicsComplex should be pretty easy.
...
- 70.2k
13
votes
How to apply different equations to different parts of a geometry in PDE?
Denote the disk by $\varOmega$ and its boundary by $\varGamma = \partial \varOmega$. I'd prefer to denote the function residing on the boundary by $u \colon \varGamma \to \mathbb{R}$; the function on ...
- 110k
13
votes
Computing the surface area and volume of molecules
The paper Fast Calculation of van der Waals Volume as a Sum of Atomic and Bond Contributions and Its Application to Drug Compounds, pointed out by theorist gives an approximate formula for the ...
- 70.2k
13
votes
MoleculePlot3D - how to replace spheres?
How to replace the spheres in the plot with other 3d figures, say "N" with a Cylinder, "O" with a Cuboid, and "H" with a sphere.
This answer takes points from the ...
- 38k
12
votes
Accepted
Connectivity in a molecule and permutations
Getting the graph from the XYZ file
You have only a set of coordinates and atom types in an XYZ file. When you import it in Mathematica you can import 3 elements: the 3D plot, the coordinates, and ...
- 70.2k
12
votes
Accepted
Maxwell construction problem with FindRoot
Good job on describing your problem.
Copying your definitions from your question
...
- 14.5k
12
votes
Accepted
Molecule fingerprint functions v13
edit: For direct access to the underlying fingerprint functions behind FeatureExtraction for molecules, see the Molecule Fingerprints paclet in the new paclet ...
- 70.2k
11
votes
Accepted
Proteins, ProteinData, WolframAlpha
Here's a workaround that directly queries the PDB search API and returns the first num search results as a Dataset[]. The ...
11
votes
Accepted
ChemicalData returns the correct result for "Sulfuric" but an empty list for "Sulfuric Acid". Why?
Consider using a dedicated search pattern making function.
Here is an example.
...
- 38k
11
votes
DFT for Helium atom
Here's what I mentioned in the comments. Life is better with NDEigensystem and NDSolve:
...
- 47.1k
11
votes
Accepted
How to apply different equations to different parts of a geometry in PDE?
Since I have the code to solve the original problem described in the article GDI-Mediated Cell Polarization in Yeast Provides Precise Spatial and Temporal Control of Cdc42 Signaling, I will give here ...
- 48.8k
11
votes
When looking at a chemical's bond lengths, which bonds do they represent?
There must be a better way, but here is a first pass. This method is based on [Experimental] functions, two of which are new in MMA 12, BondList and ...
- 12.8k
10
votes
How to apply different equations to different parts of a geometry in PDE?
What about:
Noting that equations 1 and 3 form a complete set, and solve them first, treating the remaining equation 2 for m afterwards.
Noting that your imposed ...
- 341
10
votes
Accepted
Chemical formulas with Mathematica
ClearAll["Global`*"]
Assuming that you are starting with a chemical formula
...
- 163k
10
votes
Accepted
MoleculePlot draws sucrose benzoate with overlapping bonds
Mathematica uses a number of libraries for generating 2D structure diagram coordinates. The automatic method produces a suboptimal result for this molecule. Probably the system should try to check ...
- 70.2k
9
votes
9
votes
How to plot Compressibility factor Z vs Pressure P using ParametricPlot?
The plot you were trying to reproduce is a plot of the reduced van der Waals equation; that is, it is using the reduced pressure $P_r=\frac{P}{P_c}$ and reduced temperature $T_r=\frac{T}{T_c}$ as the ...
9
votes
Constructing Icosahedral Fullerene Graphs
Jason B gave a hint to the tool buckygen. This tool is easily downloaded, unpacked and compiled (by running make in the unpacked ...
- 110k
9
votes
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