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.
257
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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
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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:
...
- 232
3
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1
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107
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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
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1
answer
102
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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
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83
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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
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45
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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
135
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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
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1
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72
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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 ...
- 344
4
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2
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172
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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
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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
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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
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1
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130
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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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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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2
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258
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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
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0
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191
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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
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2
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415
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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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139
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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
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1
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161
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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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50
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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
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1
answer
56
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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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43
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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
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1
answer
105
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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
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0
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98
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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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48
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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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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
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86
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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
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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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141
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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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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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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
97
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MoleculeModify[{"DeleteAtom", a}] behaving strangely
I am encountering a strange error with the following molecule:
...
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0
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0
answers
80
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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
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0
answers
232
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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
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2
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197
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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:
...
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2
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1
answer
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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
181
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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
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1
answer
37
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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
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149
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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 ...
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5
votes
2
answers
171
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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
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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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5
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0
answers
90
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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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98
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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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1
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108
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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
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2
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243
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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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193
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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)
...
- 291
1
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1
answer
48
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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["...
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0
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228
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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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103
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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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