/**
* @param linkages
* @param atomLinkages
* @return true if atomLinkages satisfy the condition; false, otherwise.
*/
private boolean matchLinkages(List<ModificationLinkage> linkages, List<Atom[]> atomLinkages) {
int nLink = linkages.size();
if (nLink != atomLinkages.size()) {
return false;
}
for (int i = 0; i < nLink - 1; i++) {
ModificationLinkage link1 = linkages.get(i);
Atom[] atoms1 = atomLinkages.get(i);
for (int j = i + 1; j < nLink; j++) {
ModificationLinkage link2 = linkages.get(j);
Atom[] atoms2 = atomLinkages.get(j);
// check components
if (((link1.getIndexOfComponent1() == link2.getIndexOfComponent1())
!= (atoms1[0].getGroup().equals(atoms2[0].getGroup())))
|| ((link1.getIndexOfComponent1() == link2.getIndexOfComponent2())
!= (atoms1[0].getGroup().equals(atoms2[1].getGroup())))
|| ((link1.getIndexOfComponent2() == link2.getIndexOfComponent1())
!= (atoms1[1].getGroup().equals(atoms2[0].getGroup())))
|| ((link1.getIndexOfComponent2() == link2.getIndexOfComponent2())
!= (atoms1[1].getGroup().equals(atoms2[1].getGroup())))) {
return false;
}
// check atoms
String label11 = link1.getLabelOfAtomOnComponent1();
String label12 = link1.getLabelOfAtomOnComponent2();
String label21 = link2.getLabelOfAtomOnComponent1();
String label22 = link2.getLabelOfAtomOnComponent2();
if ((label11 != null && label21 != null && label11.equals(label21))
!= (atoms1[0].equals(atoms2[0]))
|| (label11 != null && label22 != null && label11.equals(label22))
!= (atoms1[0].equals(atoms2[1]))
|| (label12 != null && label21 != null && label12.equals(label21))
!= (atoms1[1].equals(atoms2[0]))
|| (label12 != null && label22 != null && label12.equals(label22))
!= (atoms1[1].equals(atoms2[1]))) {
return false;
}
}
}
return true;
}
/** Get matched atoms for all linkages. */
private List<List<Atom[]>> getMatchedAtomsOfLinkages(
ModificationCondition condition, Map<Component, Set<Group>> mapCompGroups) {
List<ModificationLinkage> linkages = condition.getLinkages();
int nLink = linkages.size();
List<List<Atom[]>> matchedAtomsOfLinkages = new ArrayList<List<Atom[]>>(nLink);
for (int iLink = 0; iLink < nLink; iLink++) {
ModificationLinkage linkage = linkages.get(iLink);
Component comp1 = linkage.getComponent1();
Component comp2 = linkage.getComponent2();
// boolean isAA1 = comp1.;
// boolean isAA2 = comp2.getType()==true;
Set<Group> groups1 = mapCompGroups.get(comp1);
Set<Group> groups2 = mapCompGroups.get(comp2);
List<Atom[]> list = new ArrayList<Atom[]>();
List<String> potentialNamesOfAtomOnGroup1 = linkage.getPDBNameOfPotentialAtomsOnComponent1();
for (String name : potentialNamesOfAtomOnGroup1) {
if (name.equals("*")) {
// wildcard
potentialNamesOfAtomOnGroup1 = null; // search all atoms
break;
}
}
List<String> potentialNamesOfAtomOnGroup2 = linkage.getPDBNameOfPotentialAtomsOnComponent2();
for (String name : potentialNamesOfAtomOnGroup2) {
if (name.equals("*")) {
// wildcard
potentialNamesOfAtomOnGroup2 = null; // search all atoms
break;
}
}
for (Group g1 : groups1) {
for (Group g2 : groups2) {
if (g1.equals(g2)) {
continue;
}
// only for wildcard match of two residues
boolean ignoreNCLinkage =
potentialNamesOfAtomOnGroup1 == null
&& potentialNamesOfAtomOnGroup2 == null
&& residues.contains(g1)
&& residues.contains(g2);
Atom[] atoms =
StructureUtil.findNearestAtomLinkage(
g1,
g2,
potentialNamesOfAtomOnGroup1,
potentialNamesOfAtomOnGroup2,
ignoreNCLinkage,
bondLengthTolerance);
if (atoms != null) {
list.add(atoms);
}
}
}
if (list.isEmpty()) {
// broken linkage
break;
}
matchedAtomsOfLinkages.add(list);
}
return matchedAtomsOfLinkages;
}