/** 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; }