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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.

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Is there a Python package that can trace a curve with a Gaussian lineshape over several x and y values?

My apologies for my ignorance in advance; I've only been learning Python for about two months. Every example question that I've seen on Stack Overflow seems to discuss a single distribution over a series of data, but not one distribution per data…
ninth_account
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How to use MDAnalysis to principal_axes and moment_of_inertia with a group of atoms?

I am trying to use MDAnalysis (MDAnalysis.__version__ == 0.17.0) API functions principal_axes() and moment_of_inertia() to calculate these matrices for a group of selected atoms as described in the doc: import MDAnalysis from…
0x90
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AMBER16: running in parallel through job submission not working

I am trying to run AMBER16 on a cluster but it is not working when the job is submitted through the scheduler, using the "qsub" command. However, the job does work when running locally on the front node. I have all of the PATHS set correctly in the…
Astronomer
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Chemical balancer in Java

I'm making an app for a chemical formula, and I have made it so that it returns double coefficients. For example, C6H12O6 + O2 = CO2 + H2O returns .166666667, 1.0, 1.0, and 1.0. I want to write code so that it is 1, 6, 6, and 6 (integers). Also, for…
Upas
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Best practices when using an API (Apache Chemistry for Alfresco)

Okay so I'm using this API https://github.com/donbalon4/API_Alfresco to upload files to Alfresco from some other PHP site of another service. I don't have any code issue, it's just that as I was using it, some doubts on how to correctly use an API…
Miquel Perez
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How to label chemical structure (images) with continuing numbers in a docbook text?

In the chemical literature structure images are usually labelled with numbers according to the appearance in the text independently of figures. These numbers are then used to refer to the chemicals. Please point me to instructions how to do this…
Bernhard Kleine
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Can InChI be used for chemical structure search instead of fingerprints

I think Using InChI's Main Layer, Charge Layer and Stereochemical layer (InChI String), We can still compare the chemical molecules Structure search (Similarity and Substructure search), But why do most of the applications go for chemical…
Wiki
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Using Python to download specific .pdb files from Protein Data Bank

I have been trying to download .pdb files from the Protein Data Bank. I have written the following block of code to extract these files however I the files being downloaded instead contain the web page. #Sector C - Processing…
James
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ChemSpider refuses to accept the .MOL file I present it

I converted a .pdb file to a .MOL file through BABEL (Converter Software). I do get the .MOL file, but when I submit the file online for a similar structure search It doesn't even load the file in ChemSpider. To use PubChem's database you need…
SweetJD14
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Process GC-MS data in batch

Here is my question. My lab has a GC-MS(Gas Chromatography-Mass Spectrometer) equipment which detect the concentration of volatile organic coumpounds(VOCs) per hour. So, as the time accumulated, I have so many hourly data(.qgd format.)…
Han Zhengzu
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C++ calculate line of best fit using chi squared arrhenius

so i'm looking at this web page at the moment - its a chemistry /maths question that gives you data for rate vs temp to calculate the activation energy of the substance - the data is on the page & in the…
Jack
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Superscript/subscript in multiple text labels (table) in R

plot(x,y,type="h",...) text(x,y,labels=columnL) This seems very simple: I have a (histogram) plot and use the text function to label the points. In the data table, I have rows containing the x, y and label names (columnL, each point has a…
MHelf
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Analyze a chemical equation, multiply sub-indexes outside parenthesis in Python

So I'm kind of new to Python. Right now I'm making a chemical equation balancer and I've got stuck because what I want to do right now is that if you receive a compound in parenthesis, with a subindex outside (like this: (NaCl)2), I want to expand…
brolius
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Cycles and complex cycles. How to find them in a graph?

I have actually a molecule in cif format. I don't think that the format is really important, but provide it for those who are interested. This file has lots of data inside. What is most important (as this part of file actually describes molecule as…
Anna-Lischen
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Conversion of standard InChI to InChI with fixed-hydrogen-layer

Good evening, I am trying to convert a standard InChI string to a non-standard InChI string with fixed-hydrogen-layer: Example: Standard inChI for Uracil: InChI=1S/C4H4N2O2/c7-3-1-2-5-4(8)6-3/h1-2H,(H2,5,6,7,8) Desired…
Loddi
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