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
0
votes
0 answers

Balance a chemical equation in C# / Unity

I have a problem with balancing equations in my unity program. So I wrote a script called "Equalizer" for balancing. My problem is that the equalizer doesn't work properly. Sometimes there are some "0" or overflow exceptions but I can't see through…
C. Rose
  • 1
  • 1
0
votes
3 answers

How to write formulas contained many constants in a function while keeping their names meaningful without using global variables?

I have a function which should be solved using ode solver. The problems is that it has many constants (say 100) and at the same time I don't want to put them in an array because it would be hard to understand the formulas (which are chemical stuff).…
Kamran Bigdely
  • 7,946
  • 18
  • 66
  • 86
0
votes
1 answer

Python: os.walk() placing files in unexpected locations

I have code that intends to iterate through a directory hierarchy, and, for every file at the bottom of the hierarchy, create a file. for currentDirectory, listOfSubDirectories, listOfStructures in os.walk(projectsLocation): #this says if we arent…
rictuar
  • 74
  • 6
0
votes
1 answer

fortran averaging columns frame by frame in specific format

I would like to average first column and last column shown here(that is my output). My code does several things such as compare specific atoms with the name "CA" for each frame (I have 1000 frames), exclude the nearest neighbours and depending on…
Vishal
  • 3
  • 3
0
votes
0 answers

Apache Chemistry Workbench support for Centos 7 Desktop

We are trying to install Apache Chemistry Workbench 1.1.0 on Centos 7 desktop. We are facing a blocker where we are not able to get the GUI for the application. Centos 7 environment has Java 1.8.161 installed. Please help me in understanding the…
sibh8
  • 53
  • 3
0
votes
1 answer

Coloring blank Unity3D mesh of molecular compound by element

My team is building an augmented reality chemistry app. We have successfully imported a 3D mesh of a molecule from wolfram mathematica using a special library...however, the way we are doing it only imports the mesh -- there are no colors on the…
kodiak3
  • 45
  • 5
0
votes
2 answers

Iterative calculations in Matlab

I'm looking to model the precipitation of a mineral through time at rate, r. As this mineral precipitates, it draws down the concentration of Fe(II) in solution, and this reduces the saturation state of the solution with respect to the mineral,…
Geochemist1
  • 3
  • 1
0
votes
0 answers

How to connect in parallel virtual machines in order to exploit all available resources?

I want to connect in parallel 40 virtual machines in order to run a quantum chemistry program in parallel. Each one of the virtual machines has a different inet6 address and all of them are connected to the internet. The reason that I need to…
python kindergarden developer
  • 48
  • 1
  • 14
0
votes
3 answers

Help with a Chemical Balancer? (Conversion from arraylists to matrix) in java

I am making a java application that balances chemical equations. I loop through each term and create two arraylists. In one arraylist, I have the set of all of the elements. For example (in the first term) if the equation is C6H12O6+O2=CO2+H2O, the…
Upas
  • 1
0
votes
1 answer

How to use the optimize.fmin function in python 2.7 with chemical reaction kinetics

I have an assignment to plot two consecutive first order reactions, then find the maximum concentration for reaction B. I've managed to plot a graph of the three functions, i'm struggling with finding the maximum value. My teacher told me to use…
George Sandle
  • 61
  • 1
  • 7
0
votes
2 answers

CMIS add custom type to cm:folder

I've one repository where I create some Site for store all documents and folders that my organization create. I've one web app that include this php library https://github.com/dkd/php-cmis-client (port of Apache Chemistry Java implementation). So I…
aivdev
  • 59
  • 7
0
votes
2 answers

Calculating shortest path from set node to all other nodes, with some nodes forbidden from path

I would like to implement the following in Python but not sure where to start. Are there good modules for shortest path problems of this type? I am trying to define the shortest path from a particular atom (node) to all other atoms (nodes) in a…
reid_indeed
  • 3
  • 3
0
votes
1 answer

Associating a combination's indices with a value

I am working on a program for which I need combinations of the distances between atoms, or various points in 3D space. Here's an example: A file 'test' contains the following information: Ti 1.0 1.0 1.0 O 0.0 2.0 0.0 O 0.0 0.0 0.0 Ti 1.0 3.0…
jd423
  • 13
  • 3
0
votes
1 answer

In PyMOL, how can I make the "resi" selection work with variables?

If I want to select a residue on a protein (let's say the tenth residue), when writing a PyMOL script, I can use the following code to assign it to a variable "pep" select pep, (resi 10) However, if I try to use a predefined variable in place of…
Isaac
  • 3
  • 4
0
votes
2 answers

FORTRAN counter loop returns multiple iterations of the same value

First of all I am a complete novice to FORTRAN. With that said I am attempting to "build" a box, then randomly generate x, y, z coordinates for 100 atoms. From there, the goal is to calculate the distance between each atom, which becomes the value…
Charles Butler
  • 42
  • 5
1 2 3
…
18 19