'Fragment' object has no attribute 'is_atom_in_cycle' error#2400
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'Fragment' object has no attribute 'is_atom_in_cycle' error#2400
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@@ Coverage Diff @@
## main #2400 +/- ##
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+ Coverage 48.24% 48.29% +0.04%
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Files 110 110
Lines 30626 30649 +23
Branches 7986 7995 +9
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+ Hits 14776 14802 +26
+ Misses 14306 14304 -2
+ Partials 1544 1543 -1
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I agree that inherit from Molecule is easier for maintainability. We have this separate PR addressing this issue #2360 |
lily90502
approved these changes
Mar 21, 2023
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Related to #2395
Another issue with the
Fragmentclass was encountered. It takes time for these errors to pop (in my experience, only in an advanced stage of an RMG run after a few hundred species were added into the core).I got the following trace:
I'm not fluent in the purpose of the
Fragmentobject, and one of the questions to be asked is whether the behavior that we see (here and in the previous PR) that a call inside statmech.py ofmolecule.is_atom_in_cycle(atom)is treating aFragmentinstance instead of aMoleculeinstance is desired. PerhapsFragmentobjects are not supposed to be processed by statmech at all? If so, then we need a more fundamental fix rather than these patches.(I didn't specifically asked in the input file to use fragments)
This patch PR addresses the specific error in the above trace. We may encounter additional similar instances in the future since the
Fragmentclass by design does not implement all the methods of theMoleculeobject. Perhaps a possible solution would be to inherit fromMoleculeinstead of fromGraph? E.g.,class Fragment(Molecule)? I don't feel I have a thorough understanding of theFragmentobject though to go ahead and implement this.