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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
23 stars 1 forks source link

A few updates and fixes #85

Closed xiaoruiDong closed 6 months ago

xiaoruiDong commented 6 months ago

This may not be ideal, but given my limited time, I still have to open compound PRs...

  1. Thanks to @am2145's recent attempts to use GeoMol with RDMC, RDMC and my fork of GeoMol received a few updates. With the change in this PR, once someone has installed the GeoMol environment, using the GeoMol conformer embedder should be issue-free (I hope). The new updates also give users options to run the GeoMol embedder on CPU or CUDA GPU. Relevant GeoMol changes can be found at https://github.com/xiaoruiDong/GeoMol
  2. I also tested out the downstream step of embedder, optimization, and found that the new xTB has some drastic changes regarding IO from version 6.4 to the recent 6.6 or 6.7. A few updates were made to ensure that the workflow also works with the newer xTB.
  3. The Conformer generation notebook was updated with a slightly better instruction now.
  4. One thing still missing for using conformer generation is how to set up the environment.
  5. A few other minor fixes were also made to the log parser and notebooks.
codecov[bot] commented 6 months ago

Codecov Report

Attention: Patch coverage is 12.06897% with 51 lines in your changes are missing coverage. Please review.

Project coverage is 49.08%. Comparing base (c0c7242) to head (9dd1869).

Files Patch % Lines
rdmc/external/xtb_tools/opt.py 0.00% 38 Missing :warning:
rdmc/external/logparser/base.py 15.38% 10 Missing and 1 partial :warning:
rdmc/view.py 66.66% 2 Missing :warning:
Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #85 +/- ## ========================================== - Coverage 49.37% 49.08% -0.29% ========================================== Files 39 39 Lines 4721 4759 +38 Branches 1234 1247 +13 ========================================== + Hits 2331 2336 +5 - Misses 2255 2287 +32 - Partials 135 136 +1 ```

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