/** 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());
}
}
/**
* 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());
}
}
/**
* Identify all registered modifications in chains.
*
* @param chains query {@link Chain}s.
*/
public void identify(final List<Chain> chains) {
identify(chains, ProteinModificationRegistry.allModifications());
}
/**
* Identify all registered modifications in a structure.
*
* @param structure
*/
public void identify(final Structure structure) {
identify(structure, ProteinModificationRegistry.allModifications());
}