Add IPC2 to RPG and make it the default one

rpg/RapidPeptidesGenerator.py

@@ -272,9 +272,9 @@ def main():
                         "error(s) (--quiet enable, overwrite -v). If output "
                         "filename already exists, output file will be "
                         "overwritten.")
-    parser.add_argument("-p", "--pka", metavar="", choices=['ipc', 'stryer'],
-                        default="ipc", help="Define pKa values. Either 'ipc' "
-                        "or 'stryer' (default: ipc)")
+    parser.add_argument("-p", "--pka", metavar="", choices=['ipc2', 'stryer', 'ipc'],
+                        default="ipc2", help="Define pKa values. Either 'ipc2' "
+                        "'stryer' or 'ipc' (deprecated) (default: ipc2)")
     group_output = parser.add_mutually_exclusive_group()
     group_output.add_argument("-o", "--outputfile", type=str, metavar="",
                               default="", help="Optional result file "
@@ -306,9 +306,11 @@ def main():
         args.miscleavage = []  # No miscleavage on concurrent, infinite time
 
     # --pka option
-    aa_pka = core.AA_PKA_IPC
+    aa_pka = core.AA_PKA_IPC_2
     if args.pka == "stryer":
         aa_pka = core.AA_PKA_S
+    elif args.pka == "ipc":
+        aa_pka = core.AA_PKA_IPC
 
     # --list option
     if args.list:

rpg/core.py

@@ -86,6 +86,17 @@ AA_PKA_IPC = {"Nterm" : 9.564,
               "Y" : 10.071,
               "Cterm" : 2.383}
 """pKa of important amino acid to compute pI (from IPC_peptide. See http://isoelectric.org/theory.html for details)."""
+# IPC_peptide2
+AA_PKA_IPC_2 = {"Nterm" : 7.947,
+              "C" : 9.454,
+              "D" : 3.969,
+              "E" : 4.507,
+              "H" : 6.439,
+              "K" : 8.165,
+              "R" : 11.493,
+              "Y" : 9.153,
+              "Cterm" : 2.977}
+"""pKa of important amino acid to compute pI (from IPC_peptide2. See http://www.ipc2-isoelectric-point.org/ for details)."""
 
 def handle_errors(message="", err=1, error_type=""):
     """Custom handling of errors and warnings.

rpg/sequence.py

@@ -68,9 +68,11 @@ class Peptide:
 
     # self representation for print
     def __repr__(self):
-        pka = "IPC"
+        pka = "IPC2"
         if self.aa_pka == core.AA_PKA_S:
             pka = "Stryer"
+        elif self.aa_pka == core.AA_PKA_IPC:
+            pka = "IPC"
         return "Original header: " + self.header + "\nNo. peptide: " + \
             str(self.nb_peptide) + "\nEnzyme: " + self.enzyme_name + \
             "\nCleav. pos: " + str(self.position) + "\nPep. size: " + \