/**
* Identify a set of modifications in a a list of chains.
*
* @param chains query {@link Chain}s.
* @param potentialModifications query {@link ProteinModification}s.
*/
public void identify(
final List<Chain> chains, final Set<ProteinModification> potentialModifications) {
if (chains == null) {
throw new IllegalArgumentException("Null structure.");
}
if (potentialModifications == null) {
throw new IllegalArgumentException("Null potentialModifications.");
}
reset();
if (potentialModifications.isEmpty()) {
return;
}
Map<String, Chain> mapChainIdChain = new HashMap<String, Chain>(chains.size());
residues = new ArrayList<Group>();
List<Group> ligands = new ArrayList<Group>();
Map<Component, Set<Group>> mapCompGroups = new HashMap<Component, Set<Group>>();
for (Chain chain : chains) {
mapChainIdChain.put(chain.getChainID(), chain);
List<Group> ress = StructureUtil.getAminoAcids(chain);
// List<Group> ligs = chain.getAtomLigands();
List<Group> ligs = StructureTools.filterLigands(chain.getAtomGroups());
residues.addAll(ress);
residues.removeAll(ligs);
ligands.addAll(ligs);
addModificationGroups(potentialModifications, ress, ligs, mapCompGroups);
}
if (residues.isEmpty()) {
String pdbId = "?";
if (chains.size() > 0) {
Structure struc = chains.get(0).getParent();
if (struc != null) pdbId = struc.getPDBCode();
}
logger.warn(
"No amino acids found for {}. Either you did not parse the PDB file with alignSEQRES records, or this record does not contain any amino acids.",
pdbId);
}
List<ModifiedCompound> modComps = new ArrayList<ModifiedCompound>();
for (ProteinModification mod : potentialModifications) {
ModificationCondition condition = mod.getCondition();
List<Component> components = condition.getComponents();
if (!mapCompGroups.keySet().containsAll(components)) {
// not all components exist for this mod.
continue;
}
int sizeComps = components.size();
if (sizeComps == 1) {
processCrosslink1(mapCompGroups, modComps, mod, components);
} else {
processMultiCrosslink(mapCompGroups, modComps, mod, condition);
}
}
if (recordAdditionalAttachments) {
// identify additional groups that are not directly attached to amino acids.
for (ModifiedCompound mc : modComps) {
identifyAdditionalAttachments(mc, ligands, mapChainIdChain);
}
}
mergeModComps(modComps);
identifiedModifiedCompounds.addAll(modComps);
// record unidentifiable linkage
if (recordUnidentifiableModifiedCompounds) {
recordUnidentifiableAtomLinkages(modComps, ligands);
recordUnidentifiableModifiedResidues(modComps);
}
}
