Questions tagged [chemistry]
For questions related to chemical concepts such as solving equations related to reaction kinetics, graphically visualizing molecules, and using the chemistry-related curated data sets.
265
questions
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Is there a way to make Mathematica support Chemmacros of LaTeX?
On Mathematica 13 or later version, the ChemicalFormula and ChemicalReaction functions helpe a lot to deal with chemical formula ...
- 283
4
votes
1
answer
86
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How can the units of the "AtomCoordinates" in a Molecule be changed while keeping the resulting MoleculePlot3D consistent?
Mathematica provides the Molecule function that can be visualized with MoleculePlot3D since version 12.0. Before, importing "XYZ" files would produce a ...
- 43
5
votes
1
answer
74
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How to export SD file with metadata?
Despite the fact that Mathematica (V13.2) is able to import an SD file with corresponding metadata for each structure, e.g.
...
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3
votes
1
answer
97
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Are there plans to support multiple molecules in the Molecule function?
I am playing around with Molecule to run simple optimization on several water molecules in a single frame. The Molecule function only seems to create coordinates for a single molecule to use in
...
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0
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36
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Create a hollow polymer structure and simulate its mechanical strength under compression [closed]
I want to create a hollow cylinder structure surrounded by 13 cross-sections (structure details refer to https://elifesciences.org/articles/34695#s1). Each cross-section is connected by same spherical ...
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2
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1
answer
96
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Plotting the molecular isosurface electrostatic potential map
After performing Gaussian calculation, cube files can be obtained. The distributions are the potential cube and esp cube, both of which contain volume data. What I want to do now is to project the ...
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3
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1
answer
215
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Drawing of a cube file [closed]
The following is a description of a typical cube file
Based on the above instructions, I wrote the following mathematica code：
...
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1
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2
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133
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1
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0
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72
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Generating molecules using a GAN in Mathematica
I have been unable to find any tutorials or examples of creating molecules using a Generative Adversarial Network (GAN) in the Wolfram language. It appears that the Selfies paclet was created to ...
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3
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1
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75
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How to change atom sizes and colors in MoleculePlot3D? [duplicate]
I would like to use an individual size and color for each atom in a molecule (independently of the atom types). Could you please help me how to achive this? My MWE is the following:
...
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3
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1
answer
135
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Problems with plotting spherical harmonics
I have tried to graph the real angular functions of the px and py atomic orbitals, using the Mathematica command SphericalHarmonicY, but for some reason, in both ...
2
votes
1
answer
107
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Zoom MolecularPlot on protein region
When I import protein and ligand from two PDB files and display them together using Show I cannot see the ligand since it is tiny in comparison with protein. How can I zoom the MoleculePlot on ligand ...
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6
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1
answer
88
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Orientation of the molecules in MoleculePlot
Why the plot of the molecules with similar structures is not in the same orientation?
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1
vote
1
answer
46
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VEHICLe dataset - aromatic ring counts problem
I was recently exploring the VEHICLe data set and seem to have run into an inconsistency. The dataset is described as,
The VEHICLe database, short for Virtual Exploratory heterocyclic library, ...
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3
votes
2
answers
141
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Using different colors for the same type of atoms in MoleculePlot3D
I would like to plot a molecule in 3D and use different colors for the same atom type in the molecule. For example, by using:
...
- 347
4
votes
1
answer
80
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Getting Molecular Weight for Stoichiometry Calculations
I love the units system in Mathematica, it's an extremely useful addition to the language. Unfortunately there are still some sharp corners that I run into on a daily basis. For example, if I want to ...
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4
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2
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175
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How to chain/compose multiple ChemicalReaction?
v13 added some interesting-sounding chemical species functions like ChemicalReaction. But they don't seem to have any operations.
For example the most common operation would be adding / composing ...
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5
votes
1
answer
88
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FindIsomers produces disconnected fragments
I was playing around with FindIsomers and got this strange result,
FindIsomers[Molecule["butane"]]
output
This seems unexpected in the sense that you ...
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3
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0
answers
47
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How can I find the Solution properties in water like "Solubility"?
The official documentation of function ChemicalData says it can find solution properties in water below:
But I have made several attempts, none of them have ...
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6
votes
1
answer
131
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Graph Convolution Network, molecule activity
I am trying to translate an example code for graph convolution network from Deep Learning for Physical Scientists: Accelerating Research with Machine Learning.
Edward O. Pyzer-Knapp et. al. They have ...
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5
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0
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55
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Can the Wolfram Language perform conversions between organic compounds?
My question is straightforward - if I have a starting organic compound, say chlorobenzene and an ending organic compound, say aniline, can Wolfram give me a set of equations to go from chlorobenzene ...
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3
votes
2
answers
265
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Aligning two molecules in XYZ format, before v12.3
I have two molecules in "XYZ" format and I want to align them.
As I am using Mathematica version 12.0, which does not have this ...
11
votes
0
answers
202
views
Produce the same color scheme as IboView
I can use the following command to produce the HOMO (highest occupied molecular orbital) in chemistry:
...
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9
votes
2
answers
423
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How can I rotate and reflect a molecule plot?
Consider:
MoleculePlot[Molecule[Entity["Chemical", "Theobromine"]]]
How can I rotate and reflect it? This is my current method:
...
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7
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0
answers
142
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MoleculeModify not working in Mathematica 13.1
This question is related to an older question, which was acknowledged to have uncovered a bug.
Unlike in the previous question, this time I am not trying to delete a hydrogen atom. But in ...
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11
votes
1
answer
171
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protein visualization: display a residue in balls and sticks over the structure
I am trying to visualize a cytochrome c protein and display one of the residues in ball and sticks over it.
I am using the PDB file 1AKK for it (https://www.rcsb.org/structure/1akk). The Import ...
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0
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55
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3D Cylinder with uniform distribution in volume
I would like to draw a figure in 3D where I have a cylinder (or ellipsoid) and some spheres in volume with fixed distenced between.
I understand how to build a cylinder or Random spheres in cube, but ...
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4
votes
1
answer
58
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"MoleculeFeatures" in FeatureExtractor
"MoleculeFeatures" is one possible Feature Extractor method. What molecule properties does "MoleculeFeatures" entail?
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3
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1
answer
58
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GraphDiameter for molecule graphs error [closed]
I was looking into GraphDiameter for molecules and ended up on this [page][1], which gives examples in various modalities to calculate the graph diameter for this molecule.'CC(C)C(C(=O)NC(=O)C1CCCN1C(=...
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0
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46
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Identifying and tracking cluster elements in ClusterClassify for multiple time-steps of data
I have multiple time-steps of {x,y,z}coordinates data for some atoms. I would like to cluster the data for each frame and later identify how cluster compositions change and how each atom changes from ...
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3
votes
1
answer
112
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Extremely slow import of mx files with Molecule objects [closed]
Version: 13.0.1 on Linux
Hello,
I recently found a collection of 39,361 SMILES strings that I converted to Molecule format with Mathematica. I then exported the resulting list of Molecule objects into ...
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5
votes
0
answers
99
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Chemistry context in Mathematica 13
Version: 13.0.1 on Linux
Hello,
I am curious about the Chemistry` context in Mathematica. I noticed some new things; however, there doesn't seem to be documentation on them. I wonder if anyone here ...
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1
answer
50
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How to convert PQR Entity to Mathematica Molecule format
I am using the Pitt Quantum Repository and am trying to convert the format from Entity to Molecule, so that I can get the MoleculeValue Properties of the PQR chemicals in addition to the EntityValue ...
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0
answers
43
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How to compute the electronic energy reported by Gaussian from the AlphaOrbitalEnergies
I followed the instructions on https://reference.wolfram.com/language/ref/format/FCHK.html to analyze the fchk file.
Ran an energy calculation on Gaussian , converted the results to .fchk files. The ....
3
votes
1
answer
61
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Does MoleculeValue use a non-standard definition of bridgehead atoms?
According to many sources (e.g., this), there should be four bridgehead atoms in phenanthrene. But MoleculeValue returns an empty list.
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1
vote
0
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91
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Gaussian 16 fchk and log file import in mathematica
I am working with Gaussian log files and fchk files imported into Mathematica and I noticed a few things.
The ExampleData in documentation for these files use Gaussian 03 output files, while the ...
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2
votes
1
answer
71
views
Molecule fingerprint MorganConnectivity
I am looking for a way to calculate the MorganConnectivity finger print for molecule object in Mathematica. v12.1 seemed to have an undocumented function MoleculeFingerprint
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0
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156
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How to plot Energy line diagram
how to plot like this picture，In chemistry the ''Energy line diagram'' is important.
I can use "chemdraw",but I have to manually adjust the data and everything, which is a hassle, right.
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2
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How to get x and y values and function of xy pairs (H[x,y]) from Histogramlist?
So I have generated a set of random data points as shown below
sample1 = RandomVariate[BinormalDistribution[{0, 0.4}, {1.2, 1.2}, 0], 250];
From the sample, I ...
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1
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1
answer
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MoleculeValue option IncludeHydrogens does not work everywhere?
The coordination number property of a molecule seems to ignore the IncludeHydrogens flag. Adjacency matrix, on the other hand, seems to respect it.
...
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5
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1
answer
99
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MoleculeModify[{"DeleteAtom", a}] behaving strangely
I am encountering a strange error with the following molecule:
...
- 4,957
0
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0
answers
81
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Gay-Berne potential in Mathematica
Cross-posting from Physics SE.
I am trying to make a plot of the Gay-Berne potential using Mathematica. I am following this paper and I am trying to recreate Fig. 2. This is figure 2:
To save time, ...
- 101
4
votes
0
answers
238
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How do I generate SMILES using machine learning in Mathematica
I am wondering if anyone has experience with generating molecules using machine learning in Mathematica. There are a bunch of papers these days with such applications/developments. For example, https:/...
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3
votes
2
answers
213
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Animating Particle Motion Using Parametric Plot and Animate
I am attempting to animate my parametric plot and add a particle to move on the line but I am having difficulties.
Here is my graph for the trajectory:
...
- 41
2
votes
1
answer
83
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Does anyone know how to fix the issue not having the hydrogen atoms accounted for when converting to a .mol file?
Hi I am using moleculeRecognize function to upload structures from images and I am attempting to convert the structures in .mol files. However every time I convert to .mol files the hydrogen atoms in ...
7
votes
1
answer
186
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Molecule fingerprint functions v13
I am looking for calculation of molecular fingerprints (FingerprintFunction) in v13 of Mathematica. There was a WTC talk around v12.2 showing this functionality, however, I can't seem to find this in ...
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1
vote
1
answer
39
views
ServiceExecute for PubChem error when CID not found
I am trying to download properties of compounds from PubChem using ServiceExecute. However, I only possess names of compounds as strings. It appears that ServiceExecute exits completely even if the ...
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0
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0
answers
160
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How to calculate torsion angles (phi and psi) from ResidueCoordinates of protein?
I am trying to compute the torsion angles (phi, psi) from coordinates of protein (using pdb file in Mathematica). I am following the approach explained here.
The output values are in the range of -180 ...
- 1
5
votes
2
answers
172
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Select behaving differently with Dataset and List
I have just encountered what I would term an unexpected disagreement in behaviour between Dataset and List. Consider the ...
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4
votes
1
answer
92
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Included hydrogens not always included in Molecule adjacency matrix?
Bug fixed in 13.0.0
Consider the following molecule, specified by a SMILES string:
...
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