/**
* Generates a simple MultipleAlignment: 3 structures with the same Atoms but incorreclty aligned
* (offset of 1 position) without gaps.
*
* @return MultipleAlignment simple MSTA
* @throws StructureException
*/
private MultipleAlignment simpleMSTA() throws StructureException {
// Generate three identical Atom arrays
List<Atom[]> atomArrays = new ArrayList<Atom[]>(52);
for (int i = 0; i < 3; i++) atomArrays.add(makeDummyCA(52));
// Generate the incorrect alignment (0-1-2,1-2-3,etc)
List<List<Integer>> alnRes = new ArrayList<List<Integer>>(3);
for (int str = 0; str < 3; str++) {
List<Integer> chain = new ArrayList<Integer>(50);
for (int res = 0; res < 50; res++) chain.add(res + str);
alnRes.add(chain);
}
// MultipleAlignment generation
MultipleAlignment msa = new MultipleAlignmentImpl();
msa.getEnsemble().setAtomArrays(atomArrays);
BlockSet bs = new BlockSetImpl(msa);
Block b = new BlockImpl(bs);
b.setAlignRes(alnRes);
// We want the identity transfromations to maintain the missalignment
Matrix4d ident = new Matrix4d();
ident.setIdentity();
msa.setTransformations(Arrays.asList(ident, ident, ident));
return msa;
}
/**
* Generates a simple MultipleAlignment: 3 structures with the same Atoms but incorreclty aligned
* with gaps.
*
* @return MultipleAlignment gapped MSTA
* @throws StructureException
*/
private MultipleAlignment gappedMSTA() throws StructureException {
// Generate three identical Atom arrays
List<Atom[]> atomArrays = new ArrayList<Atom[]>(30);
for (int i = 0; i < 3; i++) atomArrays.add(makeDummyCA(30));
// Generate alignment with nulls and some missalignments
List<List<Integer>> alnRes = new ArrayList<List<Integer>>(3);
List<Integer> chain1 = Arrays.asList(1, 2, 3, 5, 8, 10, 12, 15, 17, 19, 22, null, 24, 27);
List<Integer> chain2 = Arrays.asList(1, null, 3, 6, 9, 11, 12, 15, null, 18, 22, 24, 26, 28);
List<Integer> chain3 = Arrays.asList(1, 2, 4, 7, 9, 10, null, 15, null, 17, 22, 24, 26, 28);
alnRes.add(chain1);
alnRes.add(chain2);
alnRes.add(chain3);
// MultipleAlignment generation
MultipleAlignment msa = new MultipleAlignmentImpl();
msa.getEnsemble().setAtomArrays(atomArrays);
BlockSet bs = new BlockSetImpl(msa);
Block b = new BlockImpl(bs);
b.setAlignRes(alnRes);
// We want the identity transfromations to mantain the missalignments
Matrix4d ident = new Matrix4d();
ident.setIdentity();
msa.setTransformations(Arrays.asList(ident, ident, ident));
return msa;
}
/**
* Generates an identity MultipleAlignment: 3 structures with the same Atoms and perfectly
* aligned, so that TM-score = 1 and RMSD = 0.
*
* @return MultipleAlignment identity
* @throws StructureException
*/
private MultipleAlignment identityMSTA() throws StructureException {
// Generate the identical Atom arrays
List<Atom[]> atomArrays = new ArrayList<Atom[]>(20);
for (int i = 0; i < 3; i++) atomArrays.add(makeDummyCA(20));
// Generate the identity alignment (1-1-1,2-2-2,etc)
List<List<Integer>> alnRes = new ArrayList<List<Integer>>(3);
for (int str = 0; str < 3; str++) {
List<Integer> chain = new ArrayList<Integer>(20);
for (int res = 0; res < 20; res++) chain.add(res);
alnRes.add(chain);
}
// MultipleAlignment generation
MultipleAlignment msa = new MultipleAlignmentImpl();
msa.getEnsemble().setAtomArrays(atomArrays);
BlockSet bs = new BlockSetImpl(msa);
Block b = new BlockImpl(bs);
b.setAlignRes(alnRes);
// Superimpose the alignment (which should give the identity matrices)
ReferenceSuperimposer imposer = new ReferenceSuperimposer();
imposer.superimpose(msa);
return msa;
}