Rachel Walker

Greg, I know you mentioned a couple of other ideas for how to approach this issue. This PR is mostly a draft to see what you think. We noticed that...

**Describe the bug** Recently when we upgraded RDKit, I noticed that `MolFragmentToSmiles` was occasionally producing non-canonical SMILES. @ricrogz mentioned that there were some recent changes to the canonicalization code that...

Support writing CX extensions in reactions

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We are hoping to get support for writing CX extensions when writing to reaction SMILES/SMARTS. This is just a draft, I wanted to see if we think this would work....

Interface to build a monomer-based representation of a molecule

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This PR includes the following: - Interface to build a “MonomerMol” (in MonomerMol.cpp) - `toMonomeric` -- converts an atomistic structure with PDB residue information into a "MonomerMol" - `toAtomistic.` --...

#### What does this implement/fix? Explain your changes. This should allow https://github.com/rdkit/rdkit/pull/8981 to be read correctly, but I think we will need to do some further updates to the template...

Move some fields and methods from AtomPDBResidueInfo to base class

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#### What does this implement/fix? Explain your changes. Currently, information about monomers can be set on an atom using the `AtomMonomerInfo` class which is accessed and set by `get`/`setMonomerInfo`. Some...