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RDKit atropisomers - #1212

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egonw merged 5 commits into
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rdkit-atropisomers
Aug 19, 2025
Merged

RDKit atropisomers#1212
egonw merged 5 commits into
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rdkit-atropisomers

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@johnmay

@johnmay johnmay commented Aug 19, 2025

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RDKit support atropisomer from SMILES using a custom extension and abusing wedges in CXSMILES where there no coordinates. I'm not a massive fan of this approach but I don't have anything better and so Roger convinced me to add support.

You can therefore now depict and test CIP rules on atropisomers in CDK depict.

Some examples from Roger:

Cc1c(C)c(C)c(-c2c(C)c(C)c(C)c(C)c2Br)c(Br)c1C |wU:6.5|  ABEFET
Oc1ccc2ccccc2c1-c1c(O)ccc2ccccc12 |wU:10.10|    (S)-(−)-1,1′-Bi(2-napthol)
Oc1ccc2ccccc2c1-c1c(O)ccc2ccccc12 |wU:10.11|    (R)-(+)-1,1'-Bi(2-napthol)
Oc1ccc2ccccc2c1-c1c(O)ccc2ccccc12 |wU:10.10|    (S)-BINOL
Oc1ccc2ccccc2c1-c1c(O)ccc2ccccc12 |wU:10.11|    (R)-BINOL
O=C(O)CSc1nnc(Br)n1-c1ccc(C2CC2)c2ccccc12 |wU:10.10|    TIPQER01
O=C(O)CSc1nnc(Br)n1-c1ccc(C2CC2)c2ccccc12 |wU:10.9|     TIPQER03
O=C(O)CSc1nnc(Br)n1-c1ccc(C2CC2)c2ccccc12 |wU:10.9|     (+)-lesinurad
O=C(O)CSc1nnc(Br)n1-c1ccc(C2CC2)c2ccccc12 |wU:10.10|    (-)-lesinurad
C=CC(=O)N1CCN(c2nc(=O)n(-c3c(C)ccnc3C(C)C)c3nc(-c4c(O)cccc4F)c(F)cc23)[C@@H](C)C1 |wU:12.23|    (m)-sotorasib
C=CC(=O)N1CCN(c2nc(=O)n(-c3c(C)ccnc3C(C)C)c3nc(-c4c(O)cccc4F)c(F)cc23)[C@@H](C)C1 |wU:12.11|    (p)-sotorasib
Cc1c(-c2c(-c3ccc(F)o3)sc3ncnc(O[C@H](Cc4ccccc4OCc4ccnn4CC(F)(F)F)C(=O)O)c23)ccc(OCCN2CCN(C)CC2)c1Cl |wU:17.18|  S-63845




@johnmay

johnmay commented Aug 19, 2025

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Oh and there is also some tweaks to the 2D perception to ensure:
image
(from Wikipedia) is interpreted correctly.

@egonw egonw self-assigned this Aug 19, 2025
@johnmay

johnmay commented Aug 19, 2025

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I had previously not allowed >N- in atropisomers systems, specifically it is sometimes tetrahedral... but if it's not one of the special cases we consider it as tricoorinate like an Sp2 atom.

@sonarqubecloud

sonarqubecloud Bot commented Aug 19, 2025

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Quality Gate Passed Quality Gate passed

Issues
15 New issues
0 Accepted issues

Measures
0 Security Hotspots
62.6% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

@egonw
egonw merged commit 6304d81 into main Aug 19, 2025
10 of 11 checks passed
@johnmay
johnmay deleted the rdkit-atropisomers branch March 3, 2026 13:54
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@johnmay @egonw