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.

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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 votes
1 answer
69 views

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 votes
1 answer
107 views

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
102 views

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 ...
6 votes
1 answer
83 views

Orientation of the molecules in MoleculePlot

Why the plot of the molecules with similar structures is not in the same orientation? ...
1 vote
1 answer
45 views

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
135 views

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: ...
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4 votes
1 answer
72 views

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 ...
4 votes
2 answers
172 views

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 ...
5 votes
1 answer
88 views

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 votes
0 answers
47 views

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
130 views

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 votes
0 answers
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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 ...
3 votes
2 answers
258 views

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
191 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
415 views

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 votes
0 answers
139 views

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
161 views

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 votes
0 answers
50 views

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
56 views

"MoleculeFeatures" in FeatureExtractor

"MoleculeFeatures" is one possible Feature Extractor method. What molecule properties does "MoleculeFeatures" entail?
3 votes
1 answer
58 views

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 votes
0 answers
43 views

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
105 views

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
98 views

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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3 votes
1 answer
48 views

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 ...
1 vote
0 answers
38 views

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 views

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 answers
86 views

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 votes
0 answers
141 views

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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1 vote
2 answers
160 views

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 ...
1 vote
1 answer
32 views

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 votes
1 answer
97 views

MoleculeModify[{"DeleteAtom", a}] behaving strangely

I am encountering a strange error with the following molecule: ...
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0 votes
0 answers
80 views

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, ...
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4 votes
0 answers
232 views

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
197 views

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: ...
2 votes
1 answer
81 views

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
181 views

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
37 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 votes
0 answers
149 views

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 ...
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5 votes
2 answers
171 views

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 views

Included hydrogens not always included in Molecule adjacency matrix?

Bug fixed in 13.0.0 Consider the following molecule, specified by a SMILES string: ...
5 votes
0 answers
90 views

MoleculePlot is completely unfunctional when DefaultStyleDefinitions sets to ReverseColor.nb [duplicate]

If you set the DefaultStyleDefinitions sets to ReverseColor.nb then when you try to execute the example from the MoleculePlot document, your MoleculePlot will have blank result like even if you ...
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1 vote
0 answers
98 views

Show distances, angles, and torsions with MoleculePlot3D

I would like to display some bond lengths, bond angles, and torsion angles of a molecule with MoleculePlot3D. For the example ...
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3 votes
1 answer
108 views

Label the atoms of a molecule imported from an XYZ file

I would like to label the atoms of a molecule imported from an XYZ file. The only example that I found is the following (How to label with numbers atoms when MoleculePlot3D): ...
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5 votes
2 answers
243 views

MoleculePlot always returns an empty plot

Bug introduced in 12.1.0, persisting through 13.0 and fixed in 13.1 MoleculePlot@Molecule["O=C(C1CCC1)S[C@@H]1CCC1(C)C"] This is a documented example ...
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1 vote
1 answer
193 views

Density of water at a given temperature and pressure

In Wolfram|Alpha if I write: density water at 500°C and 100 atm instantly I read: 30.92 kg/m^3 (kilograms per cubic meter) ...
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1 vote
1 answer
48 views

Enter an object into a FormPage

I am currently trying to make a FormPage that plots a Molecule and I try to add a possibility to input a custom Molecule. Entering the data for a Molecule makes Mathematica crash. Code: FormPage["...
1 vote
0 answers
228 views

NDSolve Error test failure at t == 5082.429032772312`; unable to continue

I am quite new to Mathematica, please help me struggling out of this question. I want to know how the HNO3 and HNO2 change in the system. first, I put the kinetics of some reactions: ...
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1 vote
0 answers
103 views

obabel_mod.exe not found [closed]

I don't know if this question has any connection to this question about TCP sockets. I encountered the problem after I was able to run my code base again following the resolution to that question. My ...
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