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Materials Chempy

Python tools to analyze, simulate and plot results of chemical inorganic materials.

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eduardotcampos@usp.br [2023]

Package not yet available in Pypi and conda repos

Informations

  • The codes in this repository are still in the early stages of developement, not being yet suited for general use.

  • Initial focus in certain imaging and spectroscopy techniques.

  • Developement mostly in python, matplotlib, pandas DataFrames and Qt backends, suited for using in jupyter notebooks for example

  • Example notebooks of in progress work will be updated to the repository /notebooks folder

  • Visualization and other analysis techniques are considered with a focus in nanoparticles and MOFs compounds class.

Fluorescence emission

  • wavelength x CPS (counts per second)

Dependencies

Plotting

python -m pip install numpy pandas pytz six distinctipy astropy

Format parsing

python -m pip install pyyaml yaml pandas parse_binary_file

Articles Database Analysis

  • PubMed NCBI Databasedata analysis and visualization script.

  • Elsevier Escopus Database analysis and visualization script.

  • This modules consists on fetching the number of published articles presenting a specific keyword, in each database, in every month from a user defined year range.

  • It allows to save the queryied results to a csv file for later analysis.

  • The obtained results can be plotted as a bar plot, to demonstrate this specific subject interest evolution, over the time.

UV-Vis absorption

Electron microscopy

  • Tensorflow automatic identification and measure of nanoparticles.

  • Model still needs to be finished and optimized.

Mass spectrometry

  • Accepts data from .mzML and .ascii files

  • Plots the data, filtering from number of most intense peaks the user prefers to plot

  • Allows custom labeling specifc peaks, as well as automatic labeling the n highest peaks, with their corresponding m/z value

Structures simulation and visualization

  • Examples of molecular structures simulation and visualization.

  • Initially only in an example notebook, using the ase package

Documentation

  • The documentation present in docs folder is not yet available on the internet, however it can be build locally.

  • The docs folder contains a single html and a pdf version of the current early developement stages of the project.

TODO

  • Implement ase notebook examples in the package client module.

  • Finish tensorflow TEM image training

  • Implement mass spectrometry fragmentations plotting

  • Implement more complex data normalization and correction in spectrophotometry

  • Implement a github building workflow to the project.

  • Create a pypi releasing workflow