PDBLoader: Remove assumption of continuously defined atoms. #19242
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Related: #19225
I'm not yet sure about the semantics of
TERrecords but at least the PR ensures that the mentioned file of the issue can be loaded.The problem was that
PDBLoaderassumed a continuous definition of atoms which is not always true because ofTERrecords. These records terminate a chain of atoms and can be present in a PDB file multiple times. The PR removed this assumption making the loader more generic.However, it was also necessary to remove the
json.bondsdata which was previously part of the loader's result since its indices refer to wrong atoms in thejson.atomsarray ifTERrecords are present.json.bondswas not used in the examples once and I think making it public does not provide real benefits.