Enhanced Stereochemistry canonicalization errors

[tadhurst-cdd]

Reference Issue

Enhanced Stereochemistry canonicalization errors

What does this implement/fix? Explain your changes.

Many compounds can be formulated as smiles with different enhanced stereochemistry specification but are actually the same compound. For example:

N[C@H]1CC[C@@H](O)CC1 |a:1,4|
N[C@H]1CC[C@@H](O)CC1 |o1:1,4|
N[C@H]1CC[C@@H](O)CC1 |&1:1,4|
N[C@@H]1CC[C@H](O)CC1 |a:1,4|
N[C@@H]1CC[C@H](O)CC1 |o1:1,4|
N[C@@H]1CC[C@H](O)CC1 |&1:1,4

These are all the same, but without the new code, generate different canonical smiles

These are also the same:

C[C@@H](Cl)C[C@H](C)Cl |a:1,4,|
C[C@@H](Cl)C[C@H](C)Cl |o1:1,4,|
C[C@H](Cl)C[C@@H](C)Cl |a:1,4,|
C[C@@H](Cl)C[C@H](C)Cl |&1:1,4,|

Any other comments?

[mc-robinson]

@tadhurst-cdd this looks like a very nice change. It looks like this may go towards fixing an issue I recently reported #7266

[tadhurst-cdd]

Addressed changes to fix errors in tests provided by Greg Landrum. There were a couple of fixes, and the code now does NOT throw an error is the enhanced procedure does not work, but simply calls the old canonicalization method