Open Babel Error in OpenBabel::OBBuilder::GetFragmentCoord Rigid fragment C1CCCNC1 in rigid-fragments.txt has all zero coordinates

[StashOfCode]

• [x] I believe this to be a bug with Open Babel
• [ ] This is a feature request

Environment Information

Open Babel version: 3.1.0 Operating system and version: Windows 10

Expected Behavior

mol = pybel.readstring("smi", 'BrC/C=C/c1ccc(O[C@@H]2CCCNC2)cc1')
mol.make3D()

Actual Behavior

jupyter lab Kernel dies with this output in the cmd

Open Babel Error  in OpenBabel::OBBuilder::GetFragmentCoord
Rigid fragment C1CCCNC1 in rigid-fragments.txt has all zero coordinates

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[StashOfCode]

Try this one too. Babel hangs with it forever BrC/C=C/c1ccc(O[C@@H]2C[C@H]3CC[C@H]2NC3)cc1. "smilies to sdf" with "generate 3d coords" checked

[HuMuK]

Open Babel 3.1.1 has the same problem when generating 3d structure (does not matter the output format) from .smi files.

[PatReis]

Is there a at least a way to catch this error without resorting to subprocesses?

try:
    mol = pybel.readstring("smi", 'BrC/C=C/c1ccc(O[C@@H]2CCCNC2)cc1')
    mol.make3D()
except:
    print("failed")

This does not work

[PatReis]

okay you can check if BABEL_DATADIR is correctly set (assuming you have conda install). This worked for me (setting manually).

import os
os.environ["BABEL_DATADIR"] = "C:\Users\...\anaconda3\envs\...\share\openbabel"  # Adjust for your conda path
import openbabel
import openbabel.pybel as pybel
mol = pybel.readstring("smi", 'BrC/C=C/c1ccc(O[C@@H]2CCCNC2)cc1')
mol.make3D()
print("everything is fine.")