Same as #30 but the PR is opened from upstream repository instead of fork#32

Merged

siddharth7113 merged 68 commits into

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siddharth/pr-clean

Mar 20, 2026

Commits on Jan 22, 2026

Adding new entries in gitignore which needs to be mmodified before release
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Changes in maws2023.py to reduce the number of pdb files created during iteration loops
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Minor correction
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Added docstirngs for tools
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Removed kernels.py since only CenterofMass was being used from this script and moved the function to helpers.py and removed the use of numba jit, if the algorithm slows down, we can reintroduce but…
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Reduce verbose dostrings and added simplified explanation
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Adding docstrings to all shape attributes and minor correction in numpy apis to the latest version
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Removing unused routines and adding docstrings in functions and making internal fucntions private
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Removing incorrect doctest for tools.py
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Adding doctests and moving the center of mass function in helpers.py used to caclulate center of mass
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Added docstrings and removed the delegated rotate_global and translated_gloabl function
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Added intial docs to explain the repository structure
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Reduce convoluted docstrings from complex.py added wrapper functions to help in understanding the workflow of the program
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Calling modified wrapper function from complex.py to increase code reability
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This is the first version of public facing API and how the user would be interacting with MAWS algorithm.
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Modification in init related to run.py
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Adding 110 test, 1 test requires GPU to run, and these tests were AI generated but manually verified and tested locally on CPU, responsibility for correctness of test lies with @siddharth7113
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Adding a basic ci.yml file
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Updating environment.yml
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Need to be modified and verified for correct information
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Added gpu workflow
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Remove LIG.lib
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putting correct notebook
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latest code in maws2023
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correction in maws2023 function calls
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Update ci.yml

fkiraly
authored and
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modification in ci.yaml
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Modifications in ci.yml
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ruff corrections
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adding 1BRQ.pdb to data and removing old pdbs not being used and remvoving unnecessary files from gitignore
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Commits on Feb 2, 2026