def test5loadResidues(self):
mmult = MMULT("../../alignmentFiles/mmult.list-FINAL.aln")
mmult.load()
mmult.loadResidues()
residues = mmult.pdbResiduesOrder
for (pdbFileName, number) in residues.items():
print("%s - %d \n" %(pdbFileName, number))
def test1Load(self):
mmult = MMULT("../../alignmentFiles/mmult.list-FINAL.aln")
mmult.load()
keys = mmult.alignments.keys()
keys.sort()
for key in keys:
print("%s %s \n" % (key, mmult.alignments[key]))
mmult.serialize("../../alignmentFiles/mmult.list-FINAL.alnF")
def test7percentageFileName(self):
mmult = MMULT("../../alignmentFiles/mmult.list-FINAL.aln")
percentageFileName = "../../alignmentFiles/percentage.aux"
mmult.load()
mmult.loadResidues()
mmult.computePercentageOfAlignment()
mmult.serializePercentageOfAlignment(percentageFileName)
def test6getResidueNumber(self):
mmult = MMULT("../../alignmentFiles/mmult.aux")
mmult.load()
pdbFileName = "1a0hA02.pdb"
pdbFileName2 = "1avgL00.pdb"
pdbFileName3 = "1bbrJ00.pdb"
assert 0 == mmult.getPositionInPDB(pdbFileName, 0)
assert -1 == mmult.getPositionInPDB(pdbFileName, 1)
assert 1 == mmult.getPositionInPDB(pdbFileName, 2)
assert 2 == mmult.getPositionInPDB(pdbFileName, 3)
assert 3 == mmult.getPositionInPDB(pdbFileName, 4)
assert -1 == mmult.getPositionInPDB(pdbFileName2, 0)
assert -1 == mmult.getPositionInPDB(pdbFileName2, 1)
assert 0 == mmult.getPositionInPDB(pdbFileName2, 2)
assert 1 == mmult.getPositionInPDB(pdbFileName2, 3)
assert 2 == mmult.getPositionInPDB(pdbFileName2, 4)
assert -1 == mmult.getPositionInPDB(pdbFileName3, 0)
assert -1 == mmult.getPositionInPDB(pdbFileName3, 1)
assert 0 == mmult.getPositionInPDB(pdbFileName2, 2)
assert 1 == mmult.getPositionInPDB(pdbFileName2, 3)
assert 2 == mmult.getPositionInPDB(pdbFileName2, 4)
assert -1 == mmult.getPositionInPDB(pdbFileName3, 5)
assert 3 == mmult.getPositionInPDB(pdbFileName3, 6)
mmult = MMULT("../../alignmentFiles/mmult.list-FINAL.aln")
mmult.load()
assert 69 == mmult.getPositionInPDB(pdbFileName, 69)
assert -1 == mmult.getPositionInPDB(pdbFileName2, 69)
assert 34 == mmult.getPositionInPDB(pdbFileName3, 68)
def test4findFirstAlignedResidue(self):
mmult = MMULT("../../alignmentFiles/mmult.list-FINAL.aln")
mmult.load()
assert mmult.findFirstAlignedResidue("1a0hA02.pdb") == 0
assert mmult.findFirstAlignedResidue("1avgL00.pdb") == 29
def test2computePercentageOfAlignment(self):
mmult = MMULT("../../alignmentFiles/mmult.list-FINAL.aln")
mmult.load()
mmult.computePercentageOfAlignment()
for residue in mmult.residues.items():
print ("[%d] = %f\n" % (residue[0], residue[1]))
