/**
* Note: if you change this unit test, also change the cook book:
* http://www.biojava.org/wiki/BioJava:CookBook3:SupportedProtMod
*/
public void testGetBy() {
ProteinModification mod;
Set<ProteinModification> mods;
mod = ProteinModificationRegistry.getById("0001");
assertNotNull(mod);
// a set of protein modifications by RESID ID
mods = ProteinModificationRegistry.getByResidId("AA0151");
assertNotNull(mods);
// a set of protein modifications by PSI-MOD ID
mods = ProteinModificationRegistry.getByPsimodId("MOD:00305");
assertNotNull(mods);
// a set of protein modifications by PDBCC ID
mods = ProteinModificationRegistry.getByPdbccId("SEP");
assertNotNull(mods);
// a set of protein modifications by category
mods = ProteinModificationRegistry.getByCategory(ModificationCategory.ATTACHMENT);
assertNotNull(mods);
// a set of protein modifications by occurrence type
mods = ProteinModificationRegistry.getByOccurrenceType(ModificationOccurrenceType.NATURAL);
assertNotNull(mods);
// a set of protein modifications by a keyword
mods = ProteinModificationRegistry.getByKeyword("phosphoprotein");
assertNotNull(mods);
// a set of protein modifications by involved components.
mods = ProteinModificationRegistry.getByComponent(Component.of("FAD"));
assertNotNull(mods);
}
/**
* Test the initialization registry of common protein modifications. Note: if you change this unit
* test, also change the cook book: http://www.biojava.org/wiki/BioJava:CookBook3:SupportedProtMod
*/
public void testRegisterCommonModification() {
Set<ProteinModification> mods = ProteinModificationRegistry.allModifications();
assertTrue(mods != null && !mods.isEmpty());
// logger.info("There are totally "+mods.size()
// +" protein modifications registered.");
//
// printModifications(mods);
}
/**
* Note: if you change this unit test, also change the cook book:
* http://www.biojava.org/wiki/BioJava:CookBook3:AddProtMod
*/
public void testRegisterModification() {
// define the involved components, in this case two cystines (CYS)
List<Component> components = new ArrayList<Component>(2);
components.add(Component.of("CYS"));
components.add(Component.of("CYS"));
// define the atom linkages between the components, in this case the SG atoms on both CYS groups
ModificationLinkage linkage = new ModificationLinkage(components, 0, "SG", 1, "SG");
// define the modification condition, i.e. what components are involved and what atoms are
// linked between them
ModificationCondition condition =
new ModificationConditionImpl(components, Collections.singletonList(linkage));
// build a modification
ProteinModification mod =
new ProteinModificationImpl.Builder(
"0018_test",
ModificationCategory.CROSS_LINK_2,
ModificationOccurrenceType.NATURAL,
condition)
.setDescription(
"A protein modification that effectively cross-links two L-cysteine residues to form L-cystine.")
.setFormula("C 6 H 8 N 2 O 2 S 2")
.setResidId("AA0025")
.setResidName("L-cystine")
.setPsimodId("MOD:00034")
.setPsimodName("L-cystine (cross-link)")
.setSystematicName("(R,R)-3,3'-disulfane-1,2-diylbis(2-aminopropanoic acid)")
.addKeyword("disulfide bond")
.addKeyword("redox-active center")
.build();
// register the modification
ProteinModificationRegistry.register(mod);
assertNotNull(ProteinModificationRegistry.getById("0018_test"));
}
/** 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());
}
}
/**
* 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());
}
