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mzLib#1415 stops shipping Data/PSI-MOD.obo.xml. Its formal charges, the only part MetaMorpheus used, now ship as Data/PsiModFormalCharges.tsv and are read with ModificationLoader.ReadFormalChargesDictionary. - GlobalVariables.LoadModifications reads the table. PsiModDeserialized and the obo alias had no other reader and are removed. - The installer ships PsiModFormalCharges.tsv in place of PSI-MOD.obo.xml (new component GUID, since the component's file changed). Needs the first mzLib release that contains smith-chem-wisc#1415. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Draft. Do not merge before smith-chem-wisc/mzLib#1415 is merged and released. This branch does not build against any released mzLib: it calls
ModificationLoader.ReadFormalChargesDictionary, which smith-chem-wisc#1415 adds. Once the release is out, this goes to smith-chem-wisc/MetaMorpheus together with the mzLib version bump.What changed and why
mzLib#1415 stops shipping
Data/PSI-MOD.obo.xml, a 4.4 MB 2014 conversion of PSI-MOD. MetaMorpheus used it only for its formal charges, which now ship asData/PsiModFormalCharges.tsv(86 charges, derived from PSI-MOD.obo 1.039.0). A MetaMorpheus build against that mzLib without this change fails in two places:GlobalVariables.LoadModificationsloadsData\PSI-MOD.obo.xml. It now reads the table withModificationLoader.ReadFormalChargesDictionary.PsiModDeserialized, and theoboalias that existed only for it, had no other reader and are removed.MetaMorpheusSetup/Product.wxslistsData\PSI-MOD.obo.xml, so WiX fails withWIX0103: Cannot find the File file ...\Data\PSI-MOD.obo.xml. This is the failure in Revamp meta draw smith-chem-wisc/MetaMorpheus#1415'sintegrationcheck. The component now shipsPsiModFormalCharges.tsv, with a new component GUID because its file changed.What users see
The charges are the same, plus one more: MOD:01982 (N,N,N-trimethylglycine, 1+), which the 2014 file lacked. Together with smith-chem-wisc#1415's refreshed
unimod.xmlandptmlist.txt, some modification masses change. smith-chem-wisc#1415's description lists every change.🤖 Generated with Claude Code