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xiaoruiDong / RDMC

Reaction Data and Molecular Conformers (RDMC) is a package dealing with reactions, molecules, conformers, majorly in 3D.
https://xiaoruidong.github.io/RDMC/
MIT License
21 stars 0 forks source link

bug fixes and mol_comparison #73

Closed xiaoruiDong closed 8 months ago

xiaoruiDong commented 8 months ago

This PR addresses bugs related to fixing molecules and adds features related to molecule/reaction comparison

  1. add molecule fixes for O2 and CO
  2. fix molecule fixing strategy for correcting "amine radical"
  3. Add element counts to RDKitMol and reaction
  4. fix resonance structure generation returning an empty list
  5. add functions to compare molecule complexes
codecov[bot] commented 8 months ago

Codecov Report

Attention: 68 lines in your changes are missing coverage. Please review.

Comparison is base (ee3663d) 36.51% compared to head (cc64388) 36.15%.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #73 +/- ## ========================================== - Coverage 36.51% 36.15% -0.36% ========================================== Files 31 34 +3 Lines 3618 3684 +66 Branches 924 942 +18 ========================================== + Hits 1321 1332 +11 - Misses 2228 2278 +50 - Partials 69 74 +5 ``` | [Files](https://app.codecov.io/gh/xiaoruiDong/RDMC/pull/73?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Xiaorui+Dong) | Coverage Δ | | |---|---|---| | [rdmc/fix.py](https://app.codecov.io/gh/xiaoruiDong/RDMC/pull/73?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Xiaorui+Dong#diff-cmRtYy9maXgucHk=) | `80.70% <ø> (-5.27%)` | :arrow_down: | | [rdmc/resonance/\_\_init\_\_.py](https://app.codecov.io/gh/xiaoruiDong/RDMC/pull/73?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Xiaorui+Dong#diff-cmRtYy9yZXNvbmFuY2UvX19pbml0X18ucHk=) | `100.00% <100.00%> (ø)` | | | [rdmc/mol.py](https://app.codecov.io/gh/xiaoruiDong/RDMC/pull/73?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Xiaorui+Dong#diff-cmRtYy9tb2wucHk=) | `65.41% <75.00%> (-3.95%)` | :arrow_down: | | [rdmc/resonance/resonance.py](https://app.codecov.io/gh/xiaoruiDong/RDMC/pull/73?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Xiaorui+Dong#diff-cmRtYy9yZXNvbmFuY2UvcmVzb25hbmNlLnB5) | `85.00% <85.00%> (ø)` | | | [rdmc/reaction.py](https://app.codecov.io/gh/xiaoruiDong/RDMC/pull/73?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Xiaorui+Dong#diff-cmRtYy9yZWFjdGlvbi5weQ==) | `58.41% <53.06%> (+0.11%)` | :arrow_up: | | [rdmc/mol\_compare.py](https://app.codecov.io/gh/xiaoruiDong/RDMC/pull/73?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Xiaorui+Dong#diff-cmRtYy9tb2xfY29tcGFyZS5weQ==) | `40.67% <40.67%> (ø)` | |

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