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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Solver for chemical equilibrium
Is there libraries (or software callable) to achieve the computation of chemical equilibrium (in particular for liquid and solid phases) ?
(From Python, or through a wrapper i can write)
For example, given a solution of ions and solids, i would like…
Xavier R.
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votes
3 answers
How to parse chemical formula to get atom component?
My data set is stored in a single column table named "Formula" which looks like this:
row.identity..main.ID.
C5H6O2N3
C10H12N
C5H6O2N3S
I want to extend the current table, where in each column the letters are written and in the line below the…
janb
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4
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2 answers
How do I get molecular structural information from SMILES
My question is: is there any algorithm that can convert a SMILES structure into a topological fingerprint? For example if glycerol is the input the answer would be 3 x -OH , 2x -CH2 and 1x -CH.
I'm trying to build a python script that can predict…
Berkay
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4
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2 answers
How to Correctly Add Perspective to a Gnuplot 3D connected Point Cloud Representing a Molecule?
I don't know about you people but I love me some Gnuplot. Properly used, that software produces beautiful images, charming in their simplicity and clarity, that I am very fond of.
For no particular reason, one day I caught myself thinking how good…
urquiza
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5 answers
Going from a list of elements to chemical formula
I have a list of elemental compositions, each element in it's own row. Sometimes these elements have a zero.
C H N O S
1 5 5 0 0 0
2 6 4 1 0 1
3 4 6 2 1 0
I need to combine them so that they read, e.g. C5H5, C6H4NS, C4H6N2O.
This means that…
HarD
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5 answers
How to render chemical reactions in Windows Forms?
How can I represent chemical reactions in windows form? I am using c# language. It is possible to represent mathematical formulas using mimetxt.dll, but what about chemical reactions?
In short, I want to represent on win forms 2H2 + O2 = 2H2O and…
Red Swan
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LaTeX for Chemistry on my website
I am programming a website on the subject of chemistry and for obvious reasons I also have to include structural and molecular formulas on that site. I want to have as few images as possible on the side and would therefore like to know how I can…
Sam
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3 answers
solve linear equations given variables and uncertainties: scipy-optimize?
I'd like to minimize a set of equations where the variables are known with their uncertainties. In essence I'd like to test the hypothesis that the given measured variables conform to the formula constraints given by the equations. This seems like…
srmulcahy
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Application of Machine Learning Techniques to Chemistry
I am a computer science student and i have to choose the theme of my future research work. I really want to solve some scientific problems in chemistry(or maybe biology) using computers. Also I have huge interest in machine learning sphere.
I have…
mr_borsch
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Would it be possible to use regular expressions to interpret IUPAC names of branched alkanes in Excel?
I need to work out information about the structure of branched alkanes using the IUPAC (International Union of Pure and Applied Chemistry) name in Excel. I have broken the problem into steps, and I have included examples for each step. Help with any…
Daniel
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1 answer
Finding the relative position of molecular substructures with RDKit
I have a collection of fatty acid molecules (in SMILES format) in which I would like to find the positions of the C=C double bonds. Position meaning: count how many carbons away the double bond is from the first carbon, which is the carbon of the…
jonas87
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2 answers
How can i chose the Atom for a branch in Chemfig?
\documentclass[11pt,a4paper]{report}
\usepackage{chemfig}
\usepackage{chemmacros}
\chemsetup{modules={all}}
\chemsetup{formula =…
TheChemist
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3
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2 answers
Counting the number of elements in a molecular compound with Python (recursion if possible)?
So I'm trying to code something to tell me the number of elements in any given compound. I'm not even sure where to start: I tried coding something but then realized that it only worked for simple compounds (or did not work at all). Here's an…
Codeman
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How to save RDKit conformer object into a sdf file?
I generated a bunch of conformers for a molecule. For each conformed, I want to save the coordinates in a SDF file. I tried the following, but the coordinates in the sdf file is different from that of the conformer.
from rdkit import Chem
from…
Zhen Liu
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3
votes
1 answer
How to extract a visible scatterplot matrix from Rstudio when you have many variables?
I'm doing the chemical analysis and trying to make a scatterplot matrix based on my chemistry data. I was able to create a matrix that I wanted but each scatterplot is not visible enough to read on my screen. I am planning to print this matrix on a…
Hazel
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