/**
* Record unidentifiable atom linkages in a chain. Only linkages between two residues or one
* residue and one ligand will be recorded.
*/
private void recordUnidentifiableAtomLinkages(
List<ModifiedCompound> modComps, List<Group> ligands) {
// first put identified linkages in a map for fast query
Set<StructureAtomLinkage> identifiedLinkages = new HashSet<StructureAtomLinkage>();
for (ModifiedCompound mc : modComps) {
identifiedLinkages.addAll(mc.getAtomLinkages());
}
// record
// cross link
int nRes = residues.size();
for (int i = 0; i < nRes - 1; i++) {
Group group1 = residues.get(i);
for (int j = i + 1; j < nRes; j++) {
Group group2 = residues.get(j);
List<Atom[]> linkages =
StructureUtil.findAtomLinkages(group1, group2, true, bondLengthTolerance);
for (Atom[] atoms : linkages) {
StructureAtomLinkage link =
StructureUtil.getStructureAtomLinkage(atoms[0], true, atoms[1], true);
unidentifiableAtomLinkages.add(link);
}
}
}
// attachment
int nLig = ligands.size();
for (int i = 0; i < nRes; i++) {
Group group1 = residues.get(i);
for (int j = 0; j < nLig; j++) {
Group group2 = ligands.get(j);
if (group1.equals(group2)) { // overlap between residues and ligands
continue;
}
List<Atom[]> linkages =
StructureUtil.findAtomLinkages(group1, group2, false, bondLengthTolerance);
for (Atom[] atoms : linkages) {
StructureAtomLinkage link =
StructureUtil.getStructureAtomLinkage(atoms[0], true, atoms[1], false);
unidentifiableAtomLinkages.add(link);
}
}
}
}
/** Merge identified modified compounds if linked. */
private void mergeModComps(List<ModifiedCompound> modComps) {
TreeSet<Integer> remove = new TreeSet<Integer>();
int n = modComps.size();
for (int icurr = 1; icurr < n; icurr++) {
ModifiedCompound curr = modComps.get(icurr);
String id = curr.getModification().getId();
if (ProteinModificationRegistry.getById(id).getCategory() != ModificationCategory.UNDEFINED)
continue;
// find linked compounds that before curr
// List<Integer> merging = new ArrayList<Integer>();
int ipre = 0;
for (; ipre < icurr; ipre++) {
if (remove.contains(ipre)) continue;
ModifiedCompound pre = modComps.get(ipre);
if (!Collections.disjoint(pre.getGroups(false), curr.getGroups(false))) {
break;
}
}
if (ipre < icurr) {
ModifiedCompound mcKeep = modComps.get(ipre);
// merge modifications of the same type
if (mcKeep.getModification().getId().equals(id)) {
// merging the current one to the previous one
mcKeep.addAtomLinkages(curr.getAtomLinkages());
remove.add(icurr);
}
}
}
Iterator<Integer> it = remove.descendingIterator();
while (it.hasNext()) {
modComps.remove(it.next().intValue());
}
}