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 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 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]))