Mac binaries

[jabaws.git] / website / archive / binaries / mac / src / globplot / biopython-1.50 / Bio / SeqUtils / IsoelectricPoint.py

diff --git a/website/archive/binaries/mac/src/globplot/biopython-1.50/Bio/SeqUtils/IsoelectricPoint.py b/website/archive/binaries/mac/src/globplot/biopython-1.50/Bio/SeqUtils/IsoelectricPoint.py
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+# Copyright Yair Benita Y.Benita@pharm.uu.nl
+# Biopython (http://biopython.org) license applies
+
+"""Calculate isoelectric points of polypeptides using methods of Bjellqvist.
+
+pK values and the methos are taken from:
+
+* Bjellqvist, B.,Hughes, G.J., Pasquali, Ch., Paquet, N., Ravier, F., Sanchez,
+J.-Ch., Frutiger, S. & Hochstrasser, D.F.
+The focusing positions of polypeptides in immobilized pH gradients can be predicted
+from their amino acid sequences. Electrophoresis 1993, 14, 1023-1031. 
+
+* Bjellqvist, B., Basse, B., Olsen, E. and Celis, J.E.
+Reference points for comparisons of two-dimensional maps of proteins from
+different human cell types defined in a pH scale where isoelectric points correlate
+with polypeptide compositions. Electrophoresis 1994, 15, 529-539.
+
+I designed the algorithm according to a note by David L. Tabb, available at:
+http://fields.scripps.edu/DTASelect/20010710-pI-Algorithm.pdf
+
+"""
+
+positive_pKs = { 'Nterm': 7.5, 'K': 10.0, 'R': 12.0, 'H':5.98 }
+negative_pKs = { 'Cterm': 3.55, 'D': 4.05, 'E': 4.45, 'C':9.0, 'Y':10.0 }
+pKcterminal= {'D':4.55, 'E':4.75}
+pKnterminal = {'A':7.59, 'M':7.0, 'S':6.93, 'P':8.36, 'T':6.82, 'V':7.44, 'E':7.7}
+charged_aas = ('K', 'R', 'H', 'D', 'E', 'C', 'Y')
+
+# access this module through ProtParam.ProteinAnalysis class.
+# first make a ProteinAnalysis object and then call its isoelectric_point method.
+class IsoelectricPoint:
+    def __init__(self, ProteinSequence, AminoAcidsContent):
+        self.sequence = ProteinSequence        
+        self.charged_aas_content = self._select_charged(AminoAcidsContent)
+
+    # This function creates a dictionary with the contents of each charged aa, 
+    # plus Cterm and Nterm.
+    def _select_charged(self, AminoAcidsContent):
+        charged = {}    
+        for aa in charged_aas:
+            charged[aa] = float(AminoAcidsContent[aa])
+        charged['Nterm'] = 1.0
+        charged['Cterm'] = 1.0
+        return charged
+
+       #This function calculates the total charge of the protein at a given pH.                
+    def _chargeR(self, pH, pos_pKs, neg_pKs):
+        PositiveCharge = 0.0
+        for aa, pK in pos_pKs.iteritems():         
+             CR = 10**(pK-pH)
+             partial_charge = CR/(CR+1.0)
+             PositiveCharge += self.charged_aas_content[aa] * partial_charge 
+
+        NegativeCharge = 0.0
+        for aa, pK in neg_pKs.iteritems():         
+             CR = 10**(pH-pK)
+             partial_charge = CR/(CR+1.0)
+             NegativeCharge += self.charged_aas_content[aa] * partial_charge 
+
+        return PositiveCharge - NegativeCharge       
+       
+       # This is the action function, it tries different pH until the charge of the protein is 0 (or close).
+    def pi(self):        
+        pos_pKs = dict(positive_pKs)
+        neg_pKs = dict(negative_pKs)
+        nterm = self.sequence[0]
+        cterm = self.sequence[-1]    
+        if nterm in pKnterminal.keys():
+            pos_pKs['Nterm'] = pKnterminal[nterm]
+        if cterm in pKcterminal.keys():
+            neg_pKs['Cterm'] = pKcterminal[cterm]
+
+        # Bracket between pH1 and pH2
+        pH = 7.0
+        Charge = self._chargeR(pH, pos_pKs, neg_pKs)
+        if Charge > 0.0:
+            pH1 = pH
+            Charge1 = Charge
+            while Charge1 > 0.0:
+                pH = pH1 + 1.0
+                Charge = self._chargeR(pH, pos_pKs, neg_pKs)
+                if Charge > 0.0:
+                    pH1 = pH
+                    Charge1 = Charge
+                else:
+                    pH2 = pH
+                    Charge2 = Charge
+                    break
+        else:
+            pH2 = pH
+            Charge2 = Charge
+            while Charge2 < 0.0:
+                pH = pH2 - 1.0
+                Charge = self._chargeR(pH, pos_pKs, neg_pKs)
+                if Charge < 0.0:
+                    pH2 = pH
+                    Charge2 = Charge
+                else:
+                    pH1 = pH
+                    Charge1 = Charge
+                    break
+
+        # Bisection
+        while pH2 - pH1 > 0.0001 and Charge!=0.0:
+            pH = (pH1 + pH2) / 2.0
+            Charge = self._chargeR(pH, pos_pKs, neg_pKs)
+            if Charge > 0.0:
+                pH1 = pH
+                Charge1 = Charge
+            else:
+                pH2 = pH
+                Charge2 = Charge
+
+        return pH