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.layout() call runs "forever" even if timeout is specified #724

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flc opened this issue May 3, 2022 · 1 comment · May be fixed by #790
Open

.layout() call runs "forever" even if timeout is specified #724

flc opened this issue May 3, 2022 · 1 comment · May be fixed by #790
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@flc
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flc commented May 3, 2022

The problem can be reproduced with the following code:

import indigo

ind = indigo.Indigo()
ind.setOption('timeout', 1000)
ind.setOption('layout-max-iterations', 1)
ind.setOption('smart-layout', False)

smiles = "O=[W]12345678(=O)(=O)(=O)(=O)(=O)(=O)(=O)(=O)(=O)(=O)(=O)(=O)(=O)(=O)(=O)(=O)(=O)(=O)(=O)(=O)(=O)(=O)(=O)(=O)(=O)(=O)(=O)(=O)(=O)(=O)(=O)[W][W]1[W]2[W]3[W]4[W]5[W]6[W]7[W]8"

imol = ind.loadMolecule(smiles)
imol.layout()
# and now we wait forever...

Python version:
Python 3.9.12

Indigo version:
1.6.1.0-g5dbb0c0f4-x86_64-linux-gnu-10.2.1

I know this is a really silly structure/SMILES but we actually encountered it. :)

Thank you!

@flc flc added the Bug label May 3, 2022
@mkviatkovskii mkviatkovskii self-assigned this May 4, 2022
@mkviatkovskii mkviatkovskii added this to the indigo-1.7 milestone May 4, 2022
@mkviatkovskii mkviatkovskii removed this from the indigo-1.7 milestone May 19, 2022
@khyurri khyurri linked a pull request Jul 19, 2022 that will close this issue
@flc
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flc commented Oct 28, 2024

just adding one more SMILES entry here for which the layout call takes 'forever', but even worse that it eats up all the memory:
C123[C@H](O)[C@]4([C@@](CO)(C(OC)=O)[C@]1(CC[N+]2(C)CC(C4)=CC)C1=C(C=CC=C1)N3)[H]

bug is still present in indigo 1.24.0

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