private Set<Component> unionComponentSet(Set<Component> set1, Set<Component> set2) { if (set1 == null && set2 == null) return Collections.emptySet(); if (set1 == null) return set2; if (set2 == null) return set1; Set<Component> set = new HashSet<Component>(set1.size() + set2.size()); set.addAll(set1); set.addAll(set2); return set; }
/** 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()); } }
/** Always returns the empty set */ @Override public Set<java.util.Map.Entry<K, K>> entrySet() { return Collections.emptySet(); }
/** * @param modifications a set of {@link ProteinModification}s. * @param residues * @param ligands * @param saveTo save result to * @return map from component to list of corresponding residues in the chain. */ private void addModificationGroups( final Set<ProteinModification> modifications, final List<Group> residues, final List<Group> ligands, final Map<Component, Set<Group>> saveTo) { if (residues == null || ligands == null || modifications == null) { throw new IllegalArgumentException("Null argument(s)."); } Map<Component, Set<Component>> mapSingleMultiComps = new HashMap<Component, Set<Component>>(); for (ProteinModification mod : modifications) { ModificationCondition condition = mod.getCondition(); for (Component comp : condition.getComponents()) { for (String pdbccId : comp.getPdbccIds()) { Component single = Component.of(Collections.singleton(pdbccId), comp.isNTerminal(), comp.isCTerminal()); Set<Component> mult = mapSingleMultiComps.get(single); if (mult == null) { mult = new HashSet<Component>(); mapSingleMultiComps.put(single, mult); } mult.add(comp); } } } { // ligands Set<Component> ligandsWildCard = mapSingleMultiComps.get(Component.of("*")); for (Group group : ligands) { String pdbccId = group.getPDBName().trim(); Set<Component> comps = mapSingleMultiComps.get(Component.of(pdbccId)); for (Component comp : unionComponentSet(ligandsWildCard, comps)) { Set<Group> gs = saveTo.get(comp); if (gs == null) { gs = new LinkedHashSet<Group>(); saveTo.put(comp, gs); } gs.add(group); } } } { // residues if (residues.isEmpty()) { return; } Set<Component> residuesWildCard = mapSingleMultiComps.get(Component.of("*")); // for all residues for (Group group : residues) { String pdbccId = group.getPDBName().trim(); Set<Component> comps = mapSingleMultiComps.get(Component.of(pdbccId)); for (Component comp : unionComponentSet(residuesWildCard, comps)) { Set<Group> gs = saveTo.get(comp); if (gs == null) { gs = new LinkedHashSet<Group>(); saveTo.put(comp, gs); } gs.add(group); } } // for N-terminal int nRes = residues.size(); int iRes = 0; Group res; do { // for all ligands on N terminal and the first residue res = residues.get(iRes++); Set<Component> nTermWildCard = mapSingleMultiComps.get(Component.of("*", true, false)); Set<Component> comps = mapSingleMultiComps.get(Component.of(res.getPDBName(), true, false)); for (Component comp : unionComponentSet(nTermWildCard, comps)) { Set<Group> gs = saveTo.get(comp); if (gs == null) { gs = new LinkedHashSet<Group>(); saveTo.put(comp, gs); } gs.add(res); } } while (iRes < nRes && ligands.contains(res)); // for C-terminal iRes = residues.size() - 1; do { // for all ligands on C terminal and the last residue res = residues.get(iRes--); Set<Component> cTermWildCard = mapSingleMultiComps.get(Component.of("*", false, true)); Set<Component> comps = mapSingleMultiComps.get(Component.of(res.getPDBName(), false, true)); for (Component comp : unionComponentSet(cTermWildCard, comps)) { Set<Group> gs = saveTo.get(comp); if (gs == null) { gs = new LinkedHashSet<Group>(); saveTo.put(comp, gs); } gs.add(res); } } while (iRes >= 0 && ligands.contains(res)); } }
/** * Identify a set of modifications in a a chains. * * @param chain query {@link Chain}. * @param potentialModifications query {@link ProteinModification}s. */ public void identify(final Chain chain, final Set<ProteinModification> potentialModifications) { identify(Collections.singletonList(chain), potentialModifications); }
/** * Identify all registered modifications in a chain. * * @param chain query {@link Chain}. */ public void identify(final Chain chain) { identify(Collections.singletonList(chain)); }