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For API consistency, when creating a Universe from a PDB file that doesn't have a CONECT record, accessing u.atoms.bonds should raise a NoDataError as it's the case for other file formats.
Actual behavior
u.atoms.bonds will return a TopologyGroup with 0 bonds.
Which version are you using? (run python -c "import MDAnalysis as mda; print(mda.__version__)")
2.0.0-dev0
Which version of Python (python -V)?
Python 3.6.10
Which operating system?
Ubuntu 18.04.4 LTS through a VM (WSL2)
The text was updated successfully, but these errors were encountered:
cbouy
changed the title
Empty u.atoms.bonds attribute for PDB files without a CONECT record
Empty u.atoms.bonds for PDB files without a CONECT record
Jul 9, 2020
Expected behavior
For API consistency, when creating a Universe from a PDB file that doesn't have a CONECT record, accessing
u.atoms.bonds
should raise aNoDataError
as it's the case for other file formats.Actual behavior
u.atoms.bonds
will return a TopologyGroup with 0 bonds.Code to reproduce the behavior
Current version of MDAnalysis
python -c "import MDAnalysis as mda; print(mda.__version__)"
)2.0.0-dev0
python -V
)?Python 3.6.10
Ubuntu 18.04.4 LTS through a VM (WSL2)
The text was updated successfully, but these errors were encountered: