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Bidentate ligand with linear geometry #240

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dbkchu opened this issue Jun 8, 2024 · 0 comments
Open

Bidentate ligand with linear geometry #240

dbkchu opened this issue Jun 8, 2024 · 0 comments

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@dbkchu
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dbkchu commented Jun 8, 2024

Bidentate ligands appear to crash structgen when combined with a linear geometry.

Example from #235:
molsimplify -cores Fe -lig '[N+](=O)([O-])[O-]' -smicat [[3, 4]] -coord 2 -ligocc 1 -spin 1

Traceback (most recent call last):
  File "/home/dbkchu/programs/miniconda3/envs/mols/bin/molsimplify", line 33, in <module>
    sys.exit(load_entry_point('molSimplify', 'console_scripts', 'molsimplify')())
  File "/home/dbkchu/programs/molSimplify/molSimplify/__main__.py", line 193, in main
    startgen(args, False, gui)
  File "/home/dbkchu/programs/molSimplify/molSimplify/Scripts/generator.py", line 255, in startgen
    emsg = multigenruns(rundir, args, write_files=write_files)
  File "/home/dbkchu/programs/molSimplify/molSimplify/Scripts/rungen.py", line 308, in multigenruns
    emsg = rungen(rundir, args, write_files=write_files)
  File "/home/dbkchu/programs/molSimplify/molSimplify/Scripts/rungen.py", line 615, in rungen
    args, rootdir, ligands, ligocc, mcount, write_files=write_files)
  File "/home/dbkchu/programs/molSimplify/molSimplify/Scripts/structgen.py", line 2970, in structgen
    args, ligands, ligoc)
  File "/home/dbkchu/programs/molSimplify/molSimplify/Scripts/structgen.py", line 2543, in mcomplex
    cpoint = m3D.getAtom(batoms[0])
IndexError: list index out of range
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