Ichiru Take

@gedeck Do you have any issue related to the module `TorsionFingerprints.py` at line 384-386. Does the algorithm should be `if len(nb1) > 1 and len(nb2) > 1:` instead of `if...

@greglandrum I have resolved the conflict in PR 5014

> For a rather complex multi-ring natural-product like compound, bond.IsInRing() does not correctly identify one of the bonds as ring bond. The compound has 3 non-ring bonds. RDKit identifies a...

> Hi Ichiru. I am not sure whether I understand you correctly. However, I do not think that if startAtom and endAtom are in a ring this is a sufficient...

@bp-kelley I have changed as requested, can you take a look?

The following code snipset described the idea ```python def prepareNeighborStack(mol: Mol, atomIdx: int, neighborStack: List[Tuple[int, int]], useHs: bool): coreAtom = mol.GetAtomWithIdx(atomIdx) for bond in coreAtom.GetBonds(): if useHs or bond.GetOtherAtom(coreAtom).GetAtomicNum() !=...

@greglandrum If you have time, can you take a look at it? It would be great. Although I can produce relatively good on Python with result, I don't understand where...

@greglandrum Thank you for your support. First I has switched it to std::unordered_map instead of boost::dynamic_bitset. It may cause a little bit of memory extra on small molecules, but on...

@greglandrum I have updated what we discussed in discussion #5162. I hope you can review it and give me some suggestion if need edited. Thank you.

In fact, if our molecular graph space is just one normal molecule (no fragment nor broken bond), we can set it to be particularly useful for any scenario that is...