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[Python 3.9] Reimplement Clar Optimization with Scipy MILP #2694
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Commits on Jul 24, 2024
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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.
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Fix list style in clar optimization
Co-authored-by: Hao-Wei Pang <45482070+hwpang@users.noreply.github.com>
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Commits on Jul 25, 2024
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add back the cclib version restriction
we are not compatible with the latest version, will be resolved in this PR: #2639
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Commits on Jul 26, 2024
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Merge pull request #2695 from ReactionMechanismGenerator/feat/isodesm…
…ic_scipy [Python 3.9] Improve isodesmic and add element balance constraints
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Commits on Aug 21, 2024
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