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chirality not being used in atom ranks for chiral spiro four-ring linkage #3490

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greglandrum opened this issue Oct 13, 2020 · 0 comments
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greglandrum commented Oct 13, 2020

There's some order-dependence problem in the calculation of canonical atom ranks here:

from rdkit.Chem import Draw
m2a = Chem.MolFromSmiles('C([C@H](C)C1)[C@]12CCN2')
m2b = Chem.MolFromSmiles('C[C@H](C1)C[C@]12CCN2')
aranks = Chem.CanonicalRankAtoms(m2a,breakTies=False)
branks = Chem.CanonicalRankAtoms(m2b,breakTies=False)
for i,rnk in enumerate(aranks):
    m2a.GetAtomWithIdx(i).SetProp("atomNote",str(rnk))
for i,rnk in enumerate(branks):
    m2b.GetAtomWithIdx(i).SetProp("atomNote",str(rnk))
Draw.MolsToGridImage((m2a,m2b))

Here's the drawing of the two molecules with the atom ranks shown as atom annotations:
image

The original form of this was found and reported by @ptosco

@greglandrum greglandrum added this to the 2020_09_1 milestone Oct 13, 2020
@greglandrum greglandrum changed the title non-canonical atom ranks for chiral spiro four-ring linkage chirality not being used in atom ranks for chiral spiro four-ring linkage Oct 13, 2020
@greglandrum greglandrum modified the milestones: 2020_09_1, 2021_03_1 Oct 20, 2020
@greglandrum greglandrum modified the milestones: 2021_03_1, 2021_09_1 Mar 17, 2021
@greglandrum greglandrum modified the milestones: 2021_09_1, 2022_03_1 Oct 19, 2021
@greglandrum greglandrum removed this from the 2022_03_1 milestone Mar 28, 2022
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