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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
22 stars 1 forks source link

Update of xyz2mol #49

Closed xiaoruiDong closed 1 year ago

xiaoruiDong commented 1 year ago

Previously, we added xyz2mol to external to provide a second way of perceiving molecules from cartesian coordinates besides using Openbabel. RDkit's recent updates (2022.09.1) implemented the xyz2mol algorithm in the RDKit, written in C++. The developers also wrote a nice blog for this function.

In this PR,

  1. Update the xyz2mol.py in the external directory with the changes people implemented after Dec 2020 (the time I added this).
  2. Enable the use of RDKit built-in implementation, while keeping users still accessible to RDMC's implementation
  3. Add an unit test for parse_xyz_using_jensen