overreact
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geem-lab
βοΈπ Create and analyze chemical microkinetic models built from computational chemistry data. Crafted at the @geem-lab.
Adding some references here: https://doi.org/10.5194/acp-21-18351-2021 *I'm able to provide help, if wanted
Something like using [piccolomo/plotext](https://github.com/piccolomo/plotext).
Often we want to sum concentrations among different conformational structures or solvated ones. Instead of requiring post-processing, one would only need to add some unique IDs shared among some species...
It is a common use case, most of the concentrations in a complex reaction network will be zero. So assume them zero if some are missing. https://github.com/geem-lab/overreact/blob/ae55264300b8d0e13626f8c6fb6000e16f48fa45/overreact/simulate.py#L58-L60
[The whole thing](https://github.com/geem-lab/overreact/blob/main/overreact/_constants.py).
```console β― overreact model.k Traceback (most recent call last): File "/home/schneider/.local/bin/overreact", line 5, in from overreact._cli import main File "/home/schneider/.local/lib/python3.9/site-packages/overreact/_cli.py", line 15, in import matplotlib.pyplot as plt ModuleNotFoundError: No module...
Say, ``` $scheme A(w) -> B(w) [...] ``` and then ```console $ overreact model.k "A:1" # should have been "A(w):1" ``` Recipe for trouble π π½