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Add hydrogens works too slow (>10 minutes) for Ozempic (Semaglutide) #1810

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AlexeyGirin opened this issue Mar 14, 2024 · 1 comment
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@AlexeyGirin
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AlexeyGirin commented Mar 14, 2024

Steps to Reproduce

  1. Put on the canvas following SMILES:
    CC[C@H](C)[C@@H](C(=O)N[C@@H](C)C(=O)N[C@@H](Cc1c[nH]c2c1cccc2)C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](C(C)C)C(=O)N[C@@H](CCCNC(=N)N)C(=O)NCC(=O)N[C@@H](CCCNC(=N)N)C(=O)NCC(=O)O)NC(=O)[C@H](Cc3ccccc3)NC(=O)[C@H](CCC(=O)O)NC(=O)[C@H](CCCCNC(=O)COCCOCCNC(=O)COCCOCCNC(=O)CC[C@@H](C(=O)O)NC(=O)CCCCCCCCCCCCCCCCC(=O)O)NC(=O)[C@H](C)NC(=O)[C@H](C)NC(=O)[C@H](CCC(=O)N)NC(=O)CNC(=O)[C@H](CCC(=O)O)NC(=O)[C@H](CC(C)C)NC(=O)[C@H](Cc4ccc(cc4)O)NC(=O)[C@H](CO)NC(=O)[C@H](CO)NC(=O)[C@H](C(C)C)NC(=O)[C@H](CC(=O)O)NC(=O)[C@H](CO)NC(=O)[C@H]([C@@H](C)O)NC(=O)[C@H](Cc5ccccc5)NC(=O)[C@H]([C@@H](C)O)NC(=O)CNC(=O)[C@H](CCC(=O)O)NC(=O)C(C)(C)NC(=O)[C@H](Cc6cnc[nH]6)N
  2. Press Add/Remove explicit hydrogens button to fold hydrogens
    image

Actual behavior
System rise the spinner but it took too much time to got the result

Expected behavior
Folding hydrogens works same fast as unfold hydrogens.
Try it with following SMILES:
C([H])([H])([H])C([H])([H])[C@@]([H])([C@]([H])(N([H])C([C@@]([H])(N([H])C([C@@]([H])(N([H])C([C@@]([H])(N([H])C([C@@]([H])(N([H])C([C@]([H])(N([H])C([C@@]([H])(N([H])C(C([H])([H])N([H])C([C@@]([H])(N([H])C([C@@]([H])(N([H])C([C@@]([H])(N([H])C([C@@]([H])(N([H])C([C@@]([H])(N([H])C([C@@]([H])(N([H])C([C@@]([H])(N([H])C([C@@]([H])(N([H])C([C@@]([H])(N([H])C([C@@]([H])(N([H])C([C@@]([H])(N([H])C(C([H])([H])N([H])C([C@@]([H])(N([H])C(C(N([H])C([C@]([H])(N([H])[H])C([H])([H])c1[n]([H])c([H])nc1[H])=O)(C([H])([H])[H])C([H])([H])[H])=O)C([H])([H])C([H])([H])C(O[H])=O)=O)=O)[C@]([H])(O[H])C([H])([H])[H])=O)C([H])([H])c1c([H])c([H])c([H])c([H])c1[H])=O)[C@]([H])(O[H])C([H])([H])[H])=O)C([H])([H])O[H])=O)C([H])([H])C(O[H])=O)=O)C([H])(C([H])([H])[H])C([H])([H])[H])=O)C([H])([H])O[H])=O)C([H])([H])O[H])=O)C([H])([H])c1c([H])c([H])c(O[H])c([H])c1[H])=O)C([H])([H])C([H])(C([H])([H])[H])C([H])([H])[H])=O)C([H])([H])C([H])([H])C(O[H])=O)=O)=O)C([H])([H])C([H])([H])C(N([H])[H])=O)=O)C([H])([H])[H])=O)C([H])([H])[H])=O)C([H])([H])C([H])([H])C([H])([H])C([H])([H])N([H])C(C([H])([H])OC([H])([H])C([H])([H])OC([H])([H])C([H])([H])N([H])C(C([H])([H])OC([H])([H])C([H])([H])OC([H])([H])C([H])([H])N([H])C(C([H])([H])C([H])([H])[C@]([H])(N([H])C(C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C(O[H])=O)=O)C(O[H])=O)=O)=O)=O)=O)C([H])([H])C([H])([H])C(O[H])=O)=O)C([H])([H])c1c([H])c([H])c([H])c([H])c1[H])=O)C(N([H])[C@]([H])(C(N([H])[C@@]([H])(C(N([H])[C@]([H])(C(N([H])[C@]([H])(C(N([H])[C@]([H])(C(N([H])C([H])([H])C(N([H])[C@]([H])(C(N([H])C([H])([H])C(O[H])=O)=O)C([H])([H])C([H])([H])C([H])([H])N([H])/C(/N([H])[H])=N/[H])=O)=O)C([H])([H])C([H])([H])C([H])([H])N([H])/C(/N([H])[H])=N/[H])=O)C([H])(C([H])([H])[H])C([H])([H])[H])=O)C([H])([H])C([H])(C([H])([H])[H])C([H])([H])[H])=O)C([H])([H])c1c2c([H])c([H])c([H])c([H])c2[n]([H])c1[H])=O)C([H])([H])[H])=O)C([H])([H])[H]

Ketcher version [e.g. v2.4.2].

@AlexeyGirin
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Duplicate as per @AlexanderSavelyev

@AlexeyGirin AlexeyGirin closed this as not planned Won't fix, can't repro, duplicate, stale Mar 21, 2024
@AlexeyGirin AlexeyGirin removed this from the Waiting for triage milestone Mar 28, 2024
@github-project-automation github-project-automation bot moved this to Done in Indigo Aug 27, 2024
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