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Right now it seems like the connectivity rearrangement error is giving less-than-informative results. A user recently reported:
for one molecule with the error, i get "the following connections were expected but not found: {(28, 29)}\nThe following connections were found but not expected: {(3,29)}" . For another molecule, i get "the following connections were expected but not found: {(23,27)}\nThe following connections were found but not expected {(3,27)}". The weird thing is that in both those molecules, there is no atom in the smiles mapped to index 3.
The "no atom in the smiles mapped to index 3" issue probably arises from the difference between the (fragment to parent) atom map and the (fragment to itself) atom map. The user was seeing the former, while the indices in the error were referring to the latter. This error could be improved by including the fragment's CMILES in the error message.
The text was updated successfully, but these errors were encountered:
Right now it seems like the connectivity rearrangement error is giving less-than-informative results. A user recently reported:
The "no atom in the smiles mapped to index 3" issue probably arises from the difference between the (fragment to parent) atom map and the (fragment to itself) atom map. The user was seeing the former, while the indices in the error were referring to the latter. This error could be improved by including the fragment's CMILES in the error message.
The text was updated successfully, but these errors were encountered: