/**
* Read protein modifications from XML file and register them.
*
* @param isXml {@link InputStream} of the XML file.
* @throws IOException if failed to read the XML file.
* @throws ParserConfigurationException if parse errors occur.
* @throws SAXException the {@link DocumentBuilder} cannot be created.
*/
public static void registerProteinModificationFromXml(InputStream isXml)
throws IOException, ParserConfigurationException, SAXException {
if (isXml == null) {
throw new IllegalArgumentException("Null argument.");
}
DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
DocumentBuilder builder = factory.newDocumentBuilder();
Document doc = builder.parse(isXml);
NodeList modNodes = doc.getElementsByTagName("Entry");
int modSize = modNodes.getLength();
List<Node> nodes;
for (int iMod = 0; iMod < modSize; iMod++) {
Node modNode = modNodes.item(iMod);
Map<String, List<Node>> infoNodes = getChildNodes(modNode);
// ID
nodes = infoNodes.get("Id");
if (nodes == null || nodes.size() != 1) {
throw new RuntimeException("Each modification must have exact " + "one <Id> field.");
}
String id = nodes.get(0).getTextContent();
// modification category
nodes = infoNodes.get("Category");
if (nodes == null || nodes.size() != 1) {
throw new RuntimeException(
"Each modification must have exact "
+ "one <Category> field. See Modification "
+ id
+ ".");
}
ModificationCategory cat = ModificationCategory.getByLabel(nodes.get(0).getTextContent());
if (cat == null) {
throw new RuntimeException(
nodes.get(0).getTextContent()
+ " is not defined as an modification category."
+ " See Modification "
+ id
+ ".");
}
// occurrence type
nodes = infoNodes.get("Occurrence");
if (nodes == null || nodes.size() != 1) {
throw new RuntimeException(
"Each modification must have exact "
+ "one <Occurrence> field. See Modification "
+ id
+ ".");
}
ModificationOccurrenceType occType =
ModificationOccurrenceType.getByLabel(nodes.get(0).getTextContent());
if (occType == null) {
throw new RuntimeException(
nodes.get(0).getTextContent()
+ " is not defined as an modification occurence type."
+ " See Modification "
+ id
+ ".");
}
// condition
ModificationCondition condition = null;
{
nodes = infoNodes.get("Condition");
if (nodes == null || nodes.size() != 1) {
throw new RuntimeException(
"Each modification must have exact "
+ "one <Condition> field. See Modification "
+ id
+ ".");
}
Node compsNode = nodes.get(0);
// keep track of the labels of component indices
Map<String, Integer> mapLabelComp = new HashMap<String, Integer>();
Map<String, List<Node>> compInfoNodes = getChildNodes(compsNode);
// components
List<Node> compNodes = compInfoNodes.get("Component");
int sizeComp = compNodes.size();
List<Component> comps = new ArrayList<Component>(sizeComp);
for (int iComp = 0; iComp < sizeComp; iComp++) {
Node compNode = compNodes.get(iComp);
// comp label
NamedNodeMap compNodeAttrs = compNode.getAttributes();
Node labelNode = compNodeAttrs.getNamedItem("component");
if (labelNode == null) {
throw new RuntimeException(
"Each component must have a label." + " See Modification " + id + ".");
}
String label = labelNode.getTextContent();
if (mapLabelComp.containsKey(label)) {
throw new RuntimeException(
"Each component must have a unique label." + " See Modification " + id + ".");
}
// comp PDBCC ID
Set<String> compIds = new HashSet<String>();
List<Node> compIdNodes = getChildNodes(compNode).get("Id");
if (compIdNodes != null) {
for (Node compIdNode : compIdNodes) {
NamedNodeMap compIdNodeAttr = compIdNode.getAttributes();
Node compIdSource = compIdNodeAttr.getNamedItem("source");
if (compIdSource != null && compIdSource.getTextContent().equals("PDBCC")) {
String strComps = compIdNode.getTextContent();
if (strComps.isEmpty()) {
throw new RuntimeException("Empty component." + " See Modification " + id + ".");
}
compIds.addAll(Arrays.asList(strComps.split(",")));
}
}
}
if (compIds.isEmpty()) {
throw new RuntimeException(
"Each component must have a PDBCC ID." + " See Modification " + id + ".");
}
// terminal
boolean nTerminal = false;
boolean cTerminal = false;
List<Node> compTermNode = getChildNodes(compNode).get("Terminal");
if (compTermNode != null) {
if (compTermNode.size() != 1) {
throw new RuntimeException(
"Only one <Terminal> condition is allowed for "
+ "each component. See Modification "
+ id
+ ".");
}
String nc = compTermNode.get(0).getTextContent();
if (nc.equals("N")) {
nTerminal = true;
} else if (nc.equals("C")) {
cTerminal = true;
} else {
throw new RuntimeException(
"Only N or C is allowed for <Terminal>." + " See Modification " + id + ".");
}
}
// register
Component comp = Component.of(compIds, nTerminal, cTerminal);
comps.add(comp);
mapLabelComp.put(label, comps.size() - 1);
}
// bonds
List<Node> bondNodes = compInfoNodes.get("Bond");
List<ModificationLinkage> linkages = null;
if (bondNodes != null) {
int sizeBonds = bondNodes.size();
linkages = new ArrayList<ModificationLinkage>(sizeBonds);
for (int iBond = 0; iBond < sizeBonds; iBond++) {
Node bondNode = bondNodes.get(iBond);
Map<String, List<Node>> bondChildNodes = getChildNodes(bondNode);
if (bondChildNodes == null) {
throw new RuntimeException(
"Each bond must contain two atoms" + " See Modification " + id + ".");
}
List<Node> atomNodes = bondChildNodes.get("Atom");
if (atomNodes == null || atomNodes.size() != 2) {
throw new RuntimeException(
"Each bond must contain two atoms" + " See Modification " + id + ".");
}
// atom 1
NamedNodeMap atomNodeAttrs = atomNodes.get(0).getAttributes();
Node compNode = atomNodeAttrs.getNamedItem("component");
if (compNode == null) {
throw new RuntimeException(
"Each atom must on a component." + " See Modification " + id + ".");
}
String labelComp1 = compNode.getTextContent();
int iComp1 = mapLabelComp.get(labelComp1);
Node labelNode = atomNodeAttrs.getNamedItem("atom");
String labelAtom1 = labelNode == null ? null : labelNode.getTextContent();
String atom1 = atomNodes.get(0).getTextContent();
if (atom1.isEmpty()) {
throw new RuntimeException(
"Each atom must have a name. Please use wildcard * if unknown."
+ " See Modification "
+ id
+ ".");
}
List<String> potentialAtoms1 = Arrays.asList(atom1.split(","));
// atom 2
atomNodeAttrs = atomNodes.get(1).getAttributes();
compNode = atomNodeAttrs.getNamedItem("component");
if (compNode == null) {
throw new RuntimeException(
"Each atom must on a component." + " See Modification " + id + ".");
}
String labelComp2 = compNode.getTextContent();
int iComp2 = mapLabelComp.get(labelComp2);
labelNode = atomNodeAttrs.getNamedItem("atom");
String labelAtom2 = labelNode == null ? null : labelNode.getTextContent();
String atom2 = atomNodes.get(1).getTextContent();
if (atom2.isEmpty()) {
throw new RuntimeException(
"Each atom must have a name. Please use wildcard * if unknown."
+ " See Modification "
+ id
+ ".");
}
List<String> potentialAtoms2 = Arrays.asList(atom2.split(","));
// add linkage
ModificationLinkage linkage =
new ModificationLinkage(
comps,
iComp1,
potentialAtoms1,
labelAtom1,
iComp2,
potentialAtoms2,
labelAtom2);
linkages.add(linkage);
}
}
condition = new ModificationConditionImpl(comps, linkages);
} // end of condition
ProteinModificationImpl.Builder modBuilder =
new ProteinModificationImpl.Builder(id, cat, occType, condition);
// description
nodes = infoNodes.get("Description");
if (nodes != null && !nodes.isEmpty()) {
modBuilder.setDescription(nodes.get(0).getTextContent());
}
// cross references
nodes = infoNodes.get("CrossReference");
if (nodes != null) {
for (Node node : nodes) {
Map<String, List<Node>> xrefInfoNodes = getChildNodes(node);
// source
List<Node> xrefNode = xrefInfoNodes.get("Source");
if (xrefNode == null || xrefNode.size() != 1) {
throw new RuntimeException(
"Error in XML file: "
+ "a cross reference must contain exactly one <Source> field."
+ " See Modification "
+ id
+ ".");
}
String xrefDb = xrefNode.get(0).getTextContent();
// id
xrefNode = xrefInfoNodes.get("Id");
if (xrefNode == null || xrefNode.size() != 1) {
throw new RuntimeException(
"Error in XML file: "
+ "a cross reference must contain exactly one <Id> field."
+ " See Modification "
+ id
+ ".");
}
String xrefId = xrefNode.get(0).getTextContent();
// name
String xrefName = null;
xrefNode = xrefInfoNodes.get("Name");
if (xrefNode != null && !xrefNode.isEmpty()) {
xrefName = xrefNode.get(0).getTextContent();
}
if (xrefDb.equals("PDBCC")) {
modBuilder.setPdbccId(xrefId).setPdbccName(xrefName);
} else if (xrefDb.equals("RESID")) {
modBuilder.setResidId(xrefId).setResidName(xrefName);
} else if (xrefDb.equals("PSI-MOD")) {
modBuilder.setPsimodId(xrefId).setPsimodName(xrefName);
}
}
} // end of cross references
// formula
nodes = infoNodes.get("Formula");
if (nodes != null && !nodes.isEmpty()) {
modBuilder.setFormula(nodes.get(0).getTextContent());
}
// keywords
nodes = infoNodes.get("Keyword");
if (nodes != null && !nodes.isEmpty()) {
for (Node node : nodes) {
modBuilder.addKeyword(node.getTextContent());
}
}
ProteinModificationRegistry.register(modBuilder.build());
}
}
/**
* @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));
}
}
