Deoxy results in skipped numbers in output files.

GLYCAM-Web / gmml

Glycam Molecular Modeling Library

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Deoxy results in skipped numbers in output files. #166

Closed gitoliver closed 5 months ago

gitoliver commented 7 months ago

Having a deoxy in the sequence triggers a deletion, so in DGlcp[3Me,4D] the 4D gets parsed by the sequence parser as a derivative, but in the 3D structure it just triggers an atom deletion then disappears. Except I forgot to update the atom numbering and residue numbering so they would skip numbers in the output, and the 3Me would be residue number 6.

To reproduce: DGlcp[4D,3Me]b1-2DManp[6H]a1-OH

gitoliver commented 6 months ago

Fix coming when the juggle_testBranchFreeze gets merged in.

gitoliver commented 5 months ago

Fix in gmml-test.