Questions tagged [chemistry]

For questions related to chemical concepts such as solving equations related to reaction kinetics, graphically visualizing molecules, and using the chemistry-related curated data sets.

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Exporting as .PDB extension

I am working with the 3-D coordinates of proteins. The file format I import and modify coordinates of is in the .PDB format, and the string to import is also in this same format. Currently, when I try ...
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0answers
648 views

Generating a function which outputs possible chemical reactions

I want to make a list of chemical reactions and I write them down in a $\require{mhchem}\LaTeX$ format. They are of the following form $$NA_n^i+MB_m^j \rightarrow \hat NA_{\hat n}^{\hat i}+\hat MA_{\...
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1answer
690 views

Find elements in a decay chain using IsotopeData

I am trying to write a program using the Mathematica function IsotopeData, but am finding the code troublesome. Due to my (relative) familiarity with Python, I am ...
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1answer
3k views

Efficient implementation of cubic equation of state

...In this case the Peng Robinson Equation of State. Equations of state are empirical equations with parameters derived from experimental data. They are used to predict pure component and mixture ...
3
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1answer
493 views

Efficiently importing XPM matrix data into Mathematica

The XPM file format is an image file format. Although it is primarily intended for icon pixmaps, it can also be used to store matrix data. For example, the GROMACS chemical simulation package uses ...
5
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1answer
381 views

Noticeable slowdown in graphical performance when using manipulate

I have been making these mathematica 3D objects that involve a molecule with some sort of surface displayed above them. This is done fairly easily by: ...
15
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1answer
627 views

Automatic formatting of isotope symbols in a text cell

InputAutoReplacements is an obvious choice for formatting isotope names in text cells. I'd like to be able to type "1H", for ...
31
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1answer
687 views

How to save ChemicalData queries so that they are available immediately on notebook load?

If I put some viscosity (or density, ...) lookups in my notebook, such as: ...
4
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1answer
852 views

NDSolve Problem

I am trying to solve a chemical equilibrium ODE with NDSolve where one function is the argument to another. I.E. My equations look like: ...

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