Commits on Aug 22, 2020

1. Towards #2468 (RDKit interoperability GSOC project) …

   * Overview of work done in PR
   
     This PR adds the `RDKitConverter` class which converts MDAnalysis
     `Universe`/`Atomgroup` objects to `RDKit rdchem.Mol` objects.
   
   * Limitations
     - Bonds and elements must be present (the former will be inferred if not
       present).
     - This converter mainly aims at supporting cases where explicit hydrogens
       are present.
   
   * Extra implementation details
     - Bond order and formal charges are inferred via atomic valencies & the
       number of unpaired electrons (see `_infer_bo_and_charges`).
     - In part due to the influence of atom read order on inferring, bond
       conjugation and functional groups are standardized using SMARTS
       reactions (see `_standardize_patterns`).
   
   *  Other changes
   
      Also includes some PEP8 changes and some cleaning up of the tests for the
      `RDKITReader`.
   
   * References
     For more information on the development process for this PR, see:
     1) https://cbouy.github.io/blog/2020/07/01/rdkit-converter
     2) https://cbouy.github.io/blog/2020/07/22/rdkit-converter-part2

   

   Cédric Bouysset authored and orbeckst committed Aug 22, 2020
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