search

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

V1.0 Refactoring other core modules #89

Closed xiaoruiDong closed 3 months ago

xiaoruiDong commented 3 months ago

In this PR, the modules under the rdmc folder gets cleaned.

  1. rdtools now is moved out of rdmc
  2. ts is refactored into modules of rdtools
  3. RDKitConf is not renamed as EditableConformer, and some functions are refactored and added into rdtools.conf
  4. rxn_compare is gone. The function is put into reaction
  5. moved a few methods related to reactions into rdtools.reaction. Add is_valid_habs_ts which is developed previously, but never formally added into RDMC.
  6. only kept conformer_generation, external, mathlib, conf, forcefield, plotter, mol, reaction, and utils in the rdmc folder in the end.
  7. Clean up all the imports
  8. Clean up the docs
  9. Clean up the logistic files.
codecov[bot] commented 3 months ago

Codecov Report

Attention: Patch coverage is 57.65550% with 354 lines in your changes are missing coverage. Please review.

Project coverage is 57.85%. Comparing base (0b8b815) to head (698ed6d). Report is 1 commits behind head on v1.0/dev.

Files Patch % Lines
rdmc/external/logparser/base.py 26.00% 104 Missing and 7 partials :warning:
rdtools/atommap.py 50.00% 66 Missing and 2 partials :warning:
rdmc/forcefield.py 41.07% 66 Missing :warning:
rdmc/external/logparser/utils.py 31.66% 28 Missing and 13 partials :warning:
rdtools/reaction/ts.py 68.75% 30 Missing and 10 partials :warning:
rdmc/reaction.py 66.66% 7 Missing and 3 partials :warning:
rdmc/conf.py 68.18% 6 Missing and 1 partial :warning:
rdtools/bond.py 91.11% 4 Missing :warning:
rdtools/reaction/stereo.py 88.88% 3 Missing and 1 partial :warning:
rdtools/view/base.py 25.00% 3 Missing :warning:
Additional details and impacted files ```diff @@ Coverage Diff @@ ## v1.0/dev #89 +/- ## ============================================ + Coverage 55.75% 57.85% +2.09% ============================================ Files 71 71 Lines 5183 5108 -75 Branches 1262 1247 -15 ============================================ + Hits 2890 2955 +65 + Misses 2166 2015 -151 - Partials 127 138 +11 ```

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.