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The serialization of porphyrin to mol format introduces some double bonds with bond stereo 3/either #7306
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Here's what's happening: The solution is to modify the mol block writer to keep track of which bonds were originally aromatic and not write stereo tags for them. It's an easy fix. |
Do not cross bonds which were previously aromatic
commit 295eb87 Merge: 7e1f881 d6171aa Author: Riccardo Vianello <riccardo.vianello@gmail.com> Date: Mon Jun 17 00:33:21 2024 +0200 Merge branch 'master' into fix/github7306 commit 7e1f881 Author: greg landrum <greg.landrum@gmail.com> Date: Sun Jun 9 07:21:07 2024 +0200 revert one of the test changes commit ddb982b Author: greg landrum <greg.landrum@gmail.com> Date: Sun Jun 9 05:52:45 2024 +0200 Fixes rdkit#7306 Do not cross bonds which were previously aromatic
resolved in #7510 |
Thank you, @greglandrum |
* Fixes rdkit#7306 Do not cross bonds which were previously aromatic * revert one of the test changes * change in response to review --------- Co-authored-by: Riccardo Vianello <riccardo.vianello@gmail.com>
Describe the bug
Loading a structure containing a porphyrin into an RDKit molecule instance and rewriting it to mol format introduces some double bonds with bond stereo 3/either
To Reproduce
input.zip
Configuration (please complete the following information):
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