private void recordUnidentifiableModifiedResidues(List<ModifiedCompound> modComps) {
Set<StructureGroup> identifiedComps = new HashSet<StructureGroup>();
for (ModifiedCompound mc : modComps) {
identifiedComps.addAll(mc.getGroups(true));
}
// TODO: use the ModifiedAminoAcid after Andreas add that.
for (Group group : residues) {
if (group.getType().equals(GroupType.HETATM)) {
StructureGroup strucGroup = StructureUtil.getStructureGroup(group, true);
if (!identifiedComps.contains(strucGroup)) {
unidentifiableModifiedResidues.add(strucGroup);
}
}
}
}
private void processCrosslink1(
Map<Component, Set<Group>> mapCompGroups,
List<ModifiedCompound> modComps,
ProteinModification mod,
List<Component> components) {
// modified residue
// TODO: is this the correct logic for CROSS_LINK_1?
Set<Group> modifiedResidues = mapCompGroups.get(components.get(0));
if (modifiedResidues != null) {
for (Group residue : modifiedResidues) {
StructureGroup strucGroup = StructureUtil.getStructureGroup(residue, true);
ModifiedCompound modRes = new ModifiedCompoundImpl(mod, strucGroup);
modComps.add(modRes);
}
}
}