/**
* Assembly the matched linkages.
*
* @param matchedAtomsOfLinkages
* @param mod
* @param condition
* @param ret ModifiedCompound will be stored here.
*/
private void assembleLinkages(
List<List<Atom[]>> matchedAtomsOfLinkages,
ProteinModification mod,
List<ModifiedCompound> ret) {
ModificationCondition condition = mod.getCondition();
List<ModificationLinkage> modLinks = condition.getLinkages();
int nLink = matchedAtomsOfLinkages.size();
int[] indices = new int[nLink];
Set<ModifiedCompound> identifiedCompounds = new HashSet<ModifiedCompound>();
while (indices[0] < matchedAtomsOfLinkages.get(0).size()) {
List<Atom[]> atomLinkages = new ArrayList<Atom[]>(nLink);
for (int iLink = 0; iLink < nLink; iLink++) {
Atom[] atoms = matchedAtomsOfLinkages.get(iLink).get(indices[iLink]);
atomLinkages.add(atoms);
}
if (matchLinkages(modLinks, atomLinkages)) {
// matched
int n = atomLinkages.size();
List<StructureAtomLinkage> linkages = new ArrayList<StructureAtomLinkage>(n);
for (int i = 0; i < n; i++) {
Atom[] linkage = atomLinkages.get(i);
StructureAtomLinkage link =
StructureUtil.getStructureAtomLinkage(
linkage[0], residues.contains(linkage[0].getGroup()),
linkage[1], residues.contains(linkage[1].getGroup()));
linkages.add(link);
}
ModifiedCompound mc = new ModifiedCompoundImpl(mod, linkages);
if (!identifiedCompounds.contains(mc)) {
ret.add(mc);
identifiedCompounds.add(mc);
}
}
// indices++ (e.g. [0,0,1]=>[0,0,2]=>[1,2,0])
int i = nLink - 1;
while (i >= 0) {
if (i == 0 || indices[i] < matchedAtomsOfLinkages.get(i).size() - 1) {
indices[i]++;
break;
} else {
indices[i] = 0;
i--;
}
}
}
}
private void processMultiCrosslink(
Map<Component, Set<Group>> mapCompGroups,
List<ModifiedCompound> modComps,
ProteinModification mod,
ModificationCondition condition) {
// for multiple components
// find linkages first
List<List<Atom[]>> matchedAtomsOfLinkages = getMatchedAtomsOfLinkages(condition, mapCompGroups);
if (matchedAtomsOfLinkages.size() != condition.getLinkages().size()) {
return;
}
assembleLinkages(matchedAtomsOfLinkages, mod, modComps);
}
/** Get matched atoms for all linkages. */
private List<List<Atom[]>> getMatchedAtomsOfLinkages(
ModificationCondition condition, Map<Component, Set<Group>> mapCompGroups) {
List<ModificationLinkage> linkages = condition.getLinkages();
int nLink = linkages.size();
List<List<Atom[]>> matchedAtomsOfLinkages = new ArrayList<List<Atom[]>>(nLink);
for (int iLink = 0; iLink < nLink; iLink++) {
ModificationLinkage linkage = linkages.get(iLink);
Component comp1 = linkage.getComponent1();
Component comp2 = linkage.getComponent2();
// boolean isAA1 = comp1.;
// boolean isAA2 = comp2.getType()==true;
Set<Group> groups1 = mapCompGroups.get(comp1);
Set<Group> groups2 = mapCompGroups.get(comp2);
List<Atom[]> list = new ArrayList<Atom[]>();
List<String> potentialNamesOfAtomOnGroup1 = linkage.getPDBNameOfPotentialAtomsOnComponent1();
for (String name : potentialNamesOfAtomOnGroup1) {
if (name.equals("*")) {
// wildcard
potentialNamesOfAtomOnGroup1 = null; // search all atoms
break;
}
}
List<String> potentialNamesOfAtomOnGroup2 = linkage.getPDBNameOfPotentialAtomsOnComponent2();
for (String name : potentialNamesOfAtomOnGroup2) {
if (name.equals("*")) {
// wildcard
potentialNamesOfAtomOnGroup2 = null; // search all atoms
break;
}
}
for (Group g1 : groups1) {
for (Group g2 : groups2) {
if (g1.equals(g2)) {
continue;
}
// only for wildcard match of two residues
boolean ignoreNCLinkage =
potentialNamesOfAtomOnGroup1 == null
&& potentialNamesOfAtomOnGroup2 == null
&& residues.contains(g1)
&& residues.contains(g2);
Atom[] atoms =
StructureUtil.findNearestAtomLinkage(
g1,
g2,
potentialNamesOfAtomOnGroup1,
potentialNamesOfAtomOnGroup2,
ignoreNCLinkage,
bondLengthTolerance);
if (atoms != null) {
list.add(atoms);
}
}
}
if (list.isEmpty()) {
// broken linkage
break;
}
matchedAtomsOfLinkages.add(list);
}
return matchedAtomsOfLinkages;
}