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Reimplement Clar Optimization with Scipy MILP #2623

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Commits on Mar 5, 2024

  1. Refactoring clar optimization and utilize scipy MILP

    1. Replace lpsolve APIs with the scipy milp APIs. The new implementation potentially have a slightly better performance (due to vectorization, less data transfer, comparable solver performance, etc.) and improved readability.
    2. Decouple the MILP solving step (as _solve_clar_milp ) from the MILP formulation step. The motivation is to avoid unnecessary computation. The original approach includes molecule analysis (specifically `get_aromatic_rings`) into the recursive calls. However, this is not necessary, as molecules are just copied and not modified at all. Therefore analyzing once is enough.
    xiaoruiDong committed Mar 5, 2024
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  5. Fix list style in clar optimization

    Co-authored-by: Hao-Wei Pang <45482070+hwpang@users.noreply.github.com>
    xiaoruiDong and hwpang authored Mar 5, 2024
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Commits on Mar 6, 2024

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Commits on Jun 11, 2024

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