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Sourcecode: python-biopython version File versions

test_ProtParam.py

from Bio.SeqUtils import ProtParam, ProtParamData

def PrintDictionary(MyDict):
      for i in MyDict.keys():
            print "%s\t%.2f" %(i, MyDict[i])
      print ""

X = ProtParam.ProteinAnalysis("MAEGEITTFTALTEKFNLPPGNYKKPKLLYCSNGGHFLRILPDGTVDGTRDRSDQHIQLQLSAESVGEVYIKSTETGQYLAMDTSGLLYGSQTPSEECLFLERLEENHYNTYTSKKHAEKNWFVGLKKNGSCKRGPRTHYGQKAILFLPLPV")
print "Amino acid\tCount\n",
PrintDictionary(X.count_amino_acids())
print "Amino acid\tFraction\n",
PrintDictionary(X.get_amino_acids_percent())
print "Molecular weight of test protein:", X.molecular_weight()
print "Aromaticity of test protein: %.2f" % X.aromaticity()
print "Instability index of test protein: %.2f" % X.instability_index()
print "length of flexibility list:", len(X.flexibility())
print "The isoelectric point of the test protein is: %.2f" % X.isoelectric_point()
Helix, Turn, Sheet = X.secondary_structure_fraction()
print "Fraction of amino acids in Helix: %.2f" % Helix
print "Fraction of amino acids in Turn: %.2f" % Turn
print "Fraction of amino acids in Sheet: %.2f" % Sheet
print "\nKyte and Doolittle protein scale:"
for i in X.protein_scale(ProtParamData.kd, 9, 0.4):
      print "%.3f" %i
print "\nGRAVY:"
print X.gravy()

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