Delete unneeded directory

[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
deleted file mode 100644 (file)
index d53ee46..0000000
--- a/website/archive/binaries/mac/src/globplot/biopython-1.50/Bio/SeqUtils/IsoelectricPoint.py
+++ /dev/null
@@ -1,114 +0,0 @@
-# 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