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Rewrite clean2d algorithm on Python See merge request cimm/public/chython!1
stsouko
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Dec 22, 2024
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| __all__ = ['Calculate2DMolecule', 'Calculate2DReaction'] | ||
| from .clean2d import Calculate2DMolecule, Calculate2DReaction No newline at end of file |
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fixed and additionally rechecked for operability
Clean2d python
Some property classes and properties that duplicate the existing functionality of the kayton were removed, and were made to improve the readability of the code, which allowed to optimize the algorithm The Vestor class for calculating coordinates and vectors was also improved, it was inherited from np.array and as a result a 2.5 times boost was obtained. Also some functions were improved, the changes were of the following nature - stylistic character - changes aimed at improving code readability - changes aimed at optimizing the algorithm (it was completely rewritten) - changes related to the replacement of property class analogs with the existing ones of the molecular container. - minor corrections of functions, in which calculation operations over coordinates and vectors took place, the same algorithm was rewritten, but adjusted to the optimized class already
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refactor clean2d on python See merge request cimm/public/chython!2
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Some property classes and properties that duplicate the existing functionality of the kayton were removed, and were made to improve the readability of the code, which allowed to optimize the algorithm The Vestor class for calculating coordinates and vectors was also improved, it was inherited from np.array and as a result a 2.5 times boost was obtained. Also some functions were improved, the changes were of the following nature
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All mentions of the old algorithm written in JavaScript have been removed. The file
chython/algorithms/calculate2d/clean2d.jshas been rewritten in Python, with new imports for the new algorithm, and moved tochython/algorithms/calculate2d/clean2d.py.All files containing JavaScript code have been deleted, and instead, new files have been added to the
chython/algorithms/calculate2d/folder.Calculate2d.pyis the main recursive algorithm that calculates the coordinates of the vertices of the molecular graph.KKLayout.pycontains the Kamada-Kaway algorithm, which is necessary for calculating the coordinates of bridged cyclic molecules.MathHelper.pyincludes auxiliary mathematical functions needed for calculations in the main algorithm, such as vectors and polygons (this will be completely replaced with an equivalent written using the NumPy library).Properties.pycontains auxiliary property classes for extending information about atoms, cycles, and bonds (this will soon be rewritten to reduce code repetition).