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);
}
}
}
}
/**
* 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);
}
}
}
}
/** 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;
}
/**
* @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));
}
}