/**
* identify additional groups that are not directly attached to amino acids.
*
* @param mc {@link ModifiedCompound}.
* @param chain a {@link Chain}.
* @return a list of added groups.
*/
private void identifyAdditionalAttachments(
ModifiedCompound mc, List<Group> ligands, Map<String, Chain> mapChainIdChain) {
if (ligands.isEmpty()) {
return;
}
// TODO: should the additional groups only be allowed to the identified
// ligands or both amino acids and ligands? Currently only on ligands
// ligands to amino acid bonds for same modification of unknown category
// will be combined in mergeModComps()
// TODO: how about chain-chain links?
List<Group> identifiedGroups = new ArrayList<Group>();
for (StructureGroup num : mc.getGroups(false)) {
Group group;
try {
// String numIns = "" + num.getResidueNumber();
// if (num.getInsCode() != null) {
// numIns += num.getInsCode();
// }
ResidueNumber resNum = new ResidueNumber();
resNum.setChainId(num.getChainId());
resNum.setSeqNum(num.getResidueNumber());
resNum.setInsCode(num.getInsCode());
// group = chain.getGroupByPDB(numIns);
group = mapChainIdChain.get(num.getChainId()).getGroupByPDB(resNum);
} catch (StructureException e) {
logger.error("Exception: ", e);
// should not happen
continue;
}
identifiedGroups.add(group);
}
int start = 0;
int n = identifiedGroups.size();
while (n > start) {
for (Group group1 : ligands) {
for (int i = start; i < n; i++) {
Group group2 = identifiedGroups.get(i);
if (!identifiedGroups.contains(group1)) {
List<Atom[]> linkedAtoms =
StructureUtil.findAtomLinkages(group1, group2, false, bondLengthTolerance);
if (!linkedAtoms.isEmpty()) {
for (Atom[] atoms : linkedAtoms) {
mc.addAtomLinkage(
StructureUtil.getStructureAtomLinkage(atoms[0], false, atoms[1], false));
}
identifiedGroups.add(group1);
break;
}
}
}
}
start = n;
n = identifiedGroups.size();
}
}
/**
* Record unidentifiable atom linkages in a chain. Only linkages between two residues or one
* residue and one ligand will be recorded.
*/
private void recordUnidentifiableAtomLinkages(
List<ModifiedCompound> modComps, List<Group> ligands) {
// first put identified linkages in a map for fast query
Set<StructureAtomLinkage> identifiedLinkages = new HashSet<StructureAtomLinkage>();
for (ModifiedCompound mc : modComps) {
identifiedLinkages.addAll(mc.getAtomLinkages());
}
// record
// cross link
int nRes = residues.size();
for (int i = 0; i < nRes - 1; i++) {
Group group1 = residues.get(i);
for (int j = i + 1; j < nRes; j++) {
Group group2 = residues.get(j);
List<Atom[]> linkages =
StructureUtil.findAtomLinkages(group1, group2, true, bondLengthTolerance);
for (Atom[] atoms : linkages) {
StructureAtomLinkage link =
StructureUtil.getStructureAtomLinkage(atoms[0], true, atoms[1], true);
unidentifiableAtomLinkages.add(link);
}
}
}
// attachment
int nLig = ligands.size();
for (int i = 0; i < nRes; i++) {
Group group1 = residues.get(i);
for (int j = 0; j < nLig; j++) {
Group group2 = ligands.get(j);
if (group1.equals(group2)) { // overlap between residues and ligands
continue;
}
List<Atom[]> linkages =
StructureUtil.findAtomLinkages(group1, group2, false, bondLengthTolerance);
for (Atom[] atoms : linkages) {
StructureAtomLinkage link =
StructureUtil.getStructureAtomLinkage(atoms[0], true, atoms[1], false);
unidentifiableAtomLinkages.add(link);
}
}
}
}