/** * 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); } }