Stack Overflow
Stack Overflow

Questions tagged [chemistry]

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.

275 questions
1
vote
1 answer

Units of JMol XYZ

XYZ files specify atoms and their cartesian coordinates. Example XYZ file: [Number of atoms] Comment [Chemical symbol] [X] [Y] [Z] I was wondering what the units used were in JMol (i.e., Angstroms or Bohr radii)
mailmindlin
  • 616
  • 2
  • 7
  • 25
1
vote
3 answers

NetLogo- how to put balanced chemical equations into a model?

I was wondering if it was possible to put balanced chemical equations into a model - and if so, how to include state symbols in an existing NetLogo model. I have not seen any examples in the models library so was not sure if it was possible. I…
user286190
  • 41
  • 3
1
vote
1 answer

Turtle that has no effect on other turtles implementation but speeds up the reaction

I am using an existing model in netlogo called Chemical Equilibrium and am adding some more code. I want to add turtles (catalyst) which have no effect on the reaction/other turtles but speeds up the FORWARD reaction, which has been defined as…
user286190
  • 41
  • 3
1
vote
3 answers

replacing text in a chemical formula string

I'm having trouble writing a function that will take a chemical formula string such as "NiNFe(AsO2)2" and remove one of the elements. my current attempt is: pattern = new RegExp(symbol, "g") formula.replace(pattern, "") If the symbol is "N" and…
gaplus
  • 279
  • 4
  • 15
1
vote
1 answer

Molecular weight calculator in Lua

As my first real program in Lua, I'd like to create a molecular weight calculator (similar to the one here: http://www.lenntech.com/calculators/molecular/molecular-weight-calculator.htm ) I'd like some help with the first step of this program. My…
Far Zin
  • 121
  • 4
1
vote
0 answers

Trouble with the steepest descent algorithm

I am trying to write a program that minimizes the total energy of a 2-dimensional, 400 atom system using the steepest descent algorithm. The general idea of my program is the following: Get the atomic coordinates (x, y) Randomly choose an…
user3164457
  • 13
  • 2
1
vote
1 answer

Using VBA macro in Excel to retrieve images of chemical structures from the NCI Chemical Identifier Resolver

Based on the code given at this site (see below) I would like to adapt some VBA Excel macros to convert chemical names to chemical structures in Excel using the NCI Chemical Identifier Resolver at http://cactus.nci.nih.gov/chemical/structure In…
Tom Wenseleers
  • 7,535
  • 7
  • 63
  • 103
1
vote
1 answer

Importing data associated with a given CAS number from the NIST webbook web site into R

I would like to retrieve information associated with a given CAS registry number (Chemical Abstracts Service nr) from the NIST webbook web site in R, using the provided API. E.g. for cas nr. "19431-79-9" (Caryophylladienol II),…
Tom Wenseleers
  • 7,535
  • 7
  • 63
  • 103
1
vote
1 answer

Calculate diversity index (dissimilarity index) for a set of compounds in R

I want to calculate the diversity index for a given matrix. I have a dataset matrix (xmatrix.RData), which is a 986 * 881 matrix, indicating 986 compounds and 881 fingerprints descriptors. The formula to calculate the diversity index is explained…
BioChemoinformatics
  • 715
  • 4
  • 17
1
vote
2 answers

Algorithm to spread dots evenly on a circle (Shell Model - Chemistry)

I want to create an illustrator script that places dots around a circle. Let's say the shells are given, but I need a way to evenly spread out a n amount of dots (electrons) on a n-sized circle. For example 2 dots on the first circle, 8 on the…
SHDY
  • 33
  • 1
  • 4
1
vote
4 answers

Preventing double hash operation when trying to update value in a of type Dictionary

I am working on software for scientific research that deals heavily with chemical formulas. I keep track of the contents of a chemical formula using an internal Dictionary where Isotope is an object like "Carbon-13", "Nitrogen-14", and…
Moop
  • 3,414
  • 2
  • 23
  • 37
0
votes
3 answers

MySQL - selecting where all other columns = 0

Suppose you have a table with many property fields, such as: id datetime q a c d . . . (etc) where q,a,c,d etc denote an indefinite number of int fields whose names are generated (also created at runtime) How do you select with the constraint that…
ina
  • 19,167
  • 39
  • 122
  • 201
0
votes
2 answers

How to Debug Following Program in Xcode

I'm using Xcode 3.2.1 on OSX 10.6.8, and I want to study how Avogadro works by debugging its source code. There is a CMake guide here: https://web.archive.org/web/20160816105549/http://avogadro.cc/wiki/Compiling_on_Linux_and_Mac_OS_X that explains…
ejang
  • 3,982
  • 8
  • 44
  • 70
0
votes
0 answers

Cython quadrature problem : big array element access

My problem is that I want to to a 3d quadrature on some function. The objective is to compute electronic-integrals. The electron-electron potential integrals being the problem now. I am using 20 Gauss-Chebyshev integration points in each direction…
L Maxime
  • 82
  • 1
  • 8
0
votes
0 answers

How to include a functional JSME (chemical editor) widget in a Voila dashboard and run commands?

EDITED to (I hope) clarify I'm trying to enhance one of my tools by adding the JSME editor (https://jsme-editor.github.io/) in a ipynb that I render in a Voila dashboard. Working directly on the ipynb in JupyterHub, I manage to display the widget…
Pepimouth
  • 1
  • 1
1 2 3
…
18 19