For programming questions that involve chemistry - such as questions about programmatically working with chemical formulae, simulating chemical processes, or using chemistry-related libraries and APIs. Non-programming questions about chemistry are off-topic here, but may be on-topic on chemistry.stackexchange.com.
Questions tagged [chemistry]
275 questions
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How to prevent the script from running the files it produced?
I'm writing a script to run AutoDock Vina. The script will look for all files with .pdbqt ending with ligand in front of it. When the script is run, it produces an output file with the same name of the file, but including _out.pdbqt on it. For…
Carlos Ventura
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2 answers
Molecular dynamics - particle interactions
I am trying to simulate noble gas interactions based on the Lennar Jones Potential.
And I ran into the problem that the interactions of the particles is apparently calculated in discrete steps so that the acceleration tends to either jump to…
Titus
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How to assign print output to a variable
moleculeparse = chemparse.parse_formula(molecule) #Parses the molecular formula to present the atoms and No. of atoms. Molecule here is 'C2H6O2'
print(moleculeparse) #Print the dictionary
for x,y in moleculeparse.items(): #For every key and value…
Jak
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How to plot Arrhenius Equation in Maple to obtain a linear plot?
For the Arrhenius equation in Maple, I have the following code:
A := 0.9e10;
Ea := 350;
R := 0.8314e-2;
lnk := ln(A)-Ea/(T*R);
plot(lnk, T = 1/100 .. 1/400);
that gives me the following plot:
but i am not getting a straight line plot like:
How…
Time Step
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Is there a way for modifying molecule in RDkit?
I have a branched molecule just like in the Image (left one).
I want to add COOH at the end of each branch like Image (right one)
Here is the SMILES format of my molecule in a simplified form with 4…
Aykut Elmas
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Balancing a System of Non-Linear equations for Chemical Reactions
I am trying to compute the final composition and temperature of a mixture of syn-gas and air. They enter in at 300 K and 600 K respectively. The syn-gas is a mixture of CO and H2 the proportions of which I am varying from 3:1 to 1:3. Later on, this…
Thomas Murdoch
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Problems encountered when using RDKIT to convert SMILES to mol
I want to get the molecules from the SMILES using rdkit in python. The SMILES I used was downloaded from the drugbank.
However, when I using the function Chem.MolFromSmiles, some SMILES would report but some wouldn't:
Explicit valence for atom # 0…
Great_cva
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1 answer
Formatting Custom Grid View to Periodic Table in Swift?
How can I reformat the code of GridStack in the view body so I may duplicate it per row, such as 1 row of 2 columns, 2 rows of 8 columns, 4 rows of 18 columns, 2 rows of 15 columns?, I am cutting out the holes with this Hypothesis to shape an…
user16933914
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PySpark, read multiline file (.sdf)
What is the most efficient way to read a collection of sdf files?
sdf is a chemical table file, containing both 3D information about molecules but also properties of said molecule. All of this information is stored in a multiline (gzipped) ASCII…
Helius185
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How do you find similarities and changes within strings in two data frames?
Hi I have a 2 large datasets and I'm trying to identify changes within molecular compositions. I have two dataframes... one that is pre-exposed to a reagent and another that has been exposed to this reagent (reagent = NaNO3).
The Formulas have a…
David
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RDKit: generate fingerprints from ZINC database for cluster analysis
I'm new to RDKit. I need to do a cluster analysis of a database of compounds.
I've downloaded 191K compounds from ZINC database in 3D mol2 format and now I need to obtain fingerprints using RDKit.
First, I don't understand if it's possible to…
Alice
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3 answers
How to make code that can read an .xyz file and calculate distances between atoms?
I want to make a python script that will load an xyz file. From the xyz parameters, I need to find the distance between atoms, angle and dihedral between atoms.I have a xyz coordinate in this matrix form:
60 Buckminsterfullerene (C60 Bucky Ball)
…
Jose Pinto
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Can Jmol show an arbitrary number of molecules at once?
I'm trying to display a group of dimers with Jmol, and can only seem to figure out how to display just one molecule at a time. Ideally, I would like to be able to load several molecules at once, and display each of them.
Is this actually possible…
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What is the best way to solve a non-linear kinetic problem using python?
I have a chemical kinetics problem which involves several species that can transfer electrons between each other. I can describe the kinetics using a system of five differential equations.
I am trying to fit the model to time-resolved spectroscopic…
Max
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Keras: feed multiple inputs to ONE input layer at a time and then sum results before the output
I'm trying to feed multiple inputs to a single input layer. To be precise, it is an atomic potential. So, the NN should predict the energy of a molecule based on atomic coordinates (atomic descriptors).
Let's take H2O. So, it has two H atoms and one…
maksim
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