0000320: Patch system fails to patch SER properly in 158 cases

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0000320

Rosetta

[All Projects] Bad Coding

public

2014-01-21 14:03

2014-01-21 14:20

Reporter

Labonte

Assigned To

Labonte

Priority

normal

Severity

minor

Reproducibility

always

Status

resolved

Resolution

fixed

Platform

OS Version

Product Version

Trunk

Fixed in Version

Trunk

Summary

0000320: Patch system fails to patch SER properly in 158 cases

Description

When the Tracer volume is turned up for core.chemical.PatchOperations.hh, it becomes clear that there are issues patching the SER ResidueType with the phosphorylated patch due to a missing HG atom.

Steps To Reproduce

Use the -out:levels core.chemical.PatchOperations.hh:400 flag.

Additional Information

Tracer Output:
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:CtermProteinFull_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:CtermProteinFull_p:NtermProteinFull_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:protein_cutpoint_upper_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:CtermProteinFull_p:protein_cutpoint_upper_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:protein_cutpoint_lower_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:protein_cutpoint_lower_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:protein_cutpoint_upper_p:protein_cutpoint_lower_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:CtermProteinFull_p:ProteinVirtBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:ProteinVirtBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:CtermProteinFull_p:NtermProteinFull_p:ProteinVirtBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:protein_cutpoint_upper_p:ProteinVirtBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:CtermProteinFull_p:protein_cutpoint_upper_p:ProteinVirtBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:protein_cutpoint_lower_p:ProteinVirtBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:protein_cutpoint_lower_p:ProteinVirtBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:protein_cutpoint_upper_p:protein_cutpoint_lower_p:ProteinVirtBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinShoveBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:CtermProteinFull_p:ProteinShoveBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:ProteinShoveBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:CtermProteinFull_p:NtermProteinFull_p:ProteinShoveBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:protein_cutpoint_upper_p:ProteinShoveBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:CtermProteinFull_p:protein_cutpoint_upper_p:ProteinShoveBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:protein_cutpoint_lower_p:ProteinShoveBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:protein_cutpoint_lower_p:ProteinShoveBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:protein_cutpoint_upper_p:protein_cutpoint_lower_p:ProteinShoveBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:ProteinShoveBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:CtermProteinFull_p:ProteinVirtBB_p:ProteinShoveBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:ProteinVirtBB_p:ProteinShoveBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:CtermProteinFull_p:NtermProteinFull_p:ProteinVirtBB_p:ProteinShoveBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:protein_cutpoint_upper_p:ProteinVirtBB_p:ProteinShoveBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:CtermProteinFull_p:protein_cutpoint_upper_p:ProteinVirtBB_p:ProteinShoveBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:protein_cutpoint_lower_p:ProteinVirtBB_p:ProteinShoveBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:protein_cutpoint_lower_p:ProteinVirtBB_p:ProteinShoveBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:protein_cutpoint_upper_p:protein_cutpoint_lower_p:ProteinVirtBB_p:ProteinShoveBB_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:VirtualNterm_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:CtermProteinFull_p:NtermProteinFull_p:VirtualNterm_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:protein_cutpoint_lower_p:VirtualNterm_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:ProteinVirtBB_p:VirtualNterm_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:CtermProteinFull_p:NtermProteinFull_p:ProteinVirtBB_p:VirtualNterm_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:protein_cutpoint_lower_p:ProteinVirtBB_p:VirtualNterm_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:ProteinShoveBB_p:VirtualNterm_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:CtermProteinFull_p:NtermProteinFull_p:ProteinShoveBB_p:VirtualNterm_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:protein_cutpoint_lower_p:ProteinShoveBB_p:VirtualNterm_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:ProteinVirtBB_p:ProteinShoveBB_p:VirtualNterm_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:CtermProteinFull_p:NtermProteinFull_p:ProteinVirtBB_p:ProteinShoveBB_p:VirtualNterm_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:protein_cutpoint_lower_p:ProteinVirtBB_p:ProteinShoveBB_p:VirtualNterm_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:Virtual_Protein_Residue_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:Virtual_Protein_Residue_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinShoveBB_p:Virtual_Protein_Residue_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:ProteinShoveBB_p:Virtual_Protein_Residue_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:protein_cutpoint_upper_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:protein_cutpoint_lower_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:protein_cutpoint_lower_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:protein_cutpoint_upper_p:protein_cutpoint_lower_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:ProteinVirtBB_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:protein_cutpoint_upper_p:ProteinVirtBB_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:protein_cutpoint_lower_p:ProteinVirtBB_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:protein_cutpoint_lower_p:ProteinVirtBB_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:protein_cutpoint_upper_p:protein_cutpoint_lower_p:ProteinVirtBB_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinShoveBB_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:ProteinShoveBB_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:protein_cutpoint_upper_p:ProteinShoveBB_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:protein_cutpoint_lower_p:ProteinShoveBB_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:protein_cutpoint_lower_p:ProteinShoveBB_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:protein_cutpoint_upper_p:protein_cutpoint_lower_p:ProteinShoveBB_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:ProteinShoveBB_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:ProteinVirtBB_p:ProteinShoveBB_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:protein_cutpoint_upper_p:ProteinVirtBB_p:ProteinShoveBB_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:protein_cutpoint_lower_p:ProteinVirtBB_p:ProteinShoveBB_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:protein_cutpoint_lower_p:ProteinVirtBB_p:ProteinShoveBB_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:protein_cutpoint_upper_p:protein_cutpoint_lower_p:ProteinVirtBB_p:ProteinShoveBB_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:VirtualNterm_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:protein_cutpoint_lower_p:VirtualNterm_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:ProteinVirtBB_p:VirtualNterm_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:protein_cutpoint_lower_p:ProteinVirtBB_p:VirtualNterm_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:ProteinShoveBB_p:VirtualNterm_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:protein_cutpoint_lower_p:ProteinShoveBB_p:VirtualNterm_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:ProteinVirtBB_p:ProteinShoveBB_p:VirtualNterm_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:protein_cutpoint_lower_p:ProteinVirtBB_p:ProteinShoveBB_p:VirtualNterm_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:Virtual_Protein_Residue_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:Virtual_Protein_Residue_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinShoveBB_p:Virtual_Protein_Residue_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:ProteinShoveBB_p:Virtual_Protein_Residue_p:CtermConnect_p:phosphorylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:phosphorylated_p:N_acetylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:phosphorylated_p:N_acetylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinShoveBB_p:phosphorylated_p:N_acetylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:ProteinShoveBB_p:phosphorylated_p:N_acetylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:Virtual_Protein_Residue_p:phosphorylated_p:N_acetylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:Virtual_Protein_Residue_p:phosphorylated_p:N_acetylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinShoveBB_p:Virtual_Protein_Residue_p:phosphorylated_p:N_acetylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:ProteinShoveBB_p:Virtual_Protein_Residue_p:phosphorylated_p:N_acetylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:CtermConnect_p:phosphorylated_p:N_acetylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:CtermConnect_p:phosphorylated_p:N_acetylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinShoveBB_p:CtermConnect_p:phosphorylated_p:N_acetylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:ProteinShoveBB_p:CtermConnect_p:phosphorylated_p:N_acetylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:Virtual_Protein_Residue_p:CtermConnect_p:phosphorylated_p:N_acetylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:Virtual_Protein_Residue_p:CtermConnect_p:phosphorylated_p:N_acetylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinShoveBB_p:Virtual_Protein_Residue_p:CtermConnect_p:phosphorylated_p:N_acetylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:ProteinShoveBB_p:Virtual_Protein_Residue_p:CtermConnect_p:phosphorylated_p:N_acetylated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:ProteinVirtBB_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinShoveBB_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:ProteinShoveBB_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:ProteinShoveBB_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:ProteinVirtBB_p:ProteinShoveBB_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:VirtualNterm_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:ProteinVirtBB_p:VirtualNterm_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:ProteinShoveBB_p:VirtualNterm_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:ProteinVirtBB_p:ProteinShoveBB_p:VirtualNterm_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:Virtual_Protein_Residue_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:Virtual_Protein_Residue_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinShoveBB_p:Virtual_Protein_Residue_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:ProteinShoveBB_p:Virtual_Protein_Residue_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:CtermConnect_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:CtermConnect_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:CtermConnect_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:ProteinVirtBB_p:CtermConnect_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinShoveBB_p:CtermConnect_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:ProteinShoveBB_p:CtermConnect_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:ProteinShoveBB_p:CtermConnect_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:ProteinVirtBB_p:ProteinShoveBB_p:CtermConnect_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:VirtualNterm_p:CtermConnect_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:ProteinVirtBB_p:VirtualNterm_p:CtermConnect_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:ProteinShoveBB_p:VirtualNterm_p:CtermConnect_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:NtermProteinFull_p:ProteinVirtBB_p:ProteinShoveBB_p:VirtualNterm_p:CtermConnect_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:Virtual_Protein_Residue_p:CtermConnect_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:Virtual_Protein_Residue_p:CtermConnect_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinShoveBB_p:Virtual_Protein_Residue_p:CtermConnect_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:ProteinShoveBB_p:Virtual_Protein_Residue_p:CtermConnect_p:phosphorylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:phosphorylated_p:N_acetylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:phosphorylated_p:N_acetylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinShoveBB_p:phosphorylated_p:N_acetylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:ProteinShoveBB_p:phosphorylated_p:N_acetylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:Virtual_Protein_Residue_p:phosphorylated_p:N_acetylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:Virtual_Protein_Residue_p:phosphorylated_p:N_acetylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinShoveBB_p:Virtual_Protein_Residue_p:phosphorylated_p:N_acetylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:ProteinShoveBB_p:Virtual_Protein_Residue_p:phosphorylated_p:N_acetylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:CtermConnect_p:phosphorylated_p:N_acetylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:CtermConnect_p:phosphorylated_p:N_acetylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinShoveBB_p:CtermConnect_p:phosphorylated_p:N_acetylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:ProteinShoveBB_p:CtermConnect_p:phosphorylated_p:N_acetylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:Virtual_Protein_Residue_p:CtermConnect_p:phosphorylated_p:N_acetylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:Virtual_Protein_Residue_p:CtermConnect_p:phosphorylated_p:N_acetylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinShoveBB_p:Virtual_Protein_Residue_p:CtermConnect_p:phosphorylated_p:N_acetylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:ProteinVirtBB_p:ProteinShoveBB_p:Virtual_Protein_Residue_p:CtermConnect_p:phosphorylated_p:N_acetylated_p:C_methylamidated is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:phosphorylated_p:MethylatedCtermProteinFull is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:Virtual_Protein_Residue_p:phosphorylated_p:MethylatedCtermProteinFull is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:phosphorylated_p:AcetylatedNtermProteinFull is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:Virtual_Protein_Residue_p:phosphorylated_p:AcetylatedNtermProteinFull is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:phosphorylated_p:MethylatedCtermProteinFull_p:AcetylatedNtermProteinFull is missing atom: HG
core.chemical.PatchOperations.hh: SetAtomType::apply failed: SER_p:Virtual_Protein_Residue_p:phosphorylated_p:MethylatedCtermProteinFull_p:AcetylatedNtermProteinFull is missing atom: HG

Notes
(0000326) Labonte (Developer) 2014-01-21 14:20	Was a patching bug in my carbohydrate code, which I've fixed for my next push. It won't actually affect anyone not using the -include_sugars flag.

Issue History
Date Modified	Username	Field	Change
2014-01-21 14:03	Labonte	New Issue
2014-01-21 14:04	Labonte	Relationship added	related to 0000309
2014-01-21 14:18	Labonte	Assigned To	=> Labonte
2014-01-21 14:18	Labonte	Status	new => assigned
2014-01-21 14:20	Labonte	Fixed in SVN Version	=> TBD
2014-01-21 14:20	Labonte	Note Added: 0000326
2014-01-21 14:20	Labonte	Status	assigned => resolved
2014-01-21 14:20	Labonte	Fixed in Version	=> Trunk
2014-01-21 14:20	Labonte	Resolution	open => fixed