mgltools-molkit (1.5.6~rc3~cvs.20120206-1) fix_string_exceptions.patch

Summary

 MolKit/pdb2pqr/pdb2pka/NEWligand_topology.py |    2 +-
 MolKit/pdb2pqr/pdb2pka/inputgen_pKa.py       |    8 +++++---
 MolKit/pdb2pqr/pdb2pka/ligand_topology.py    |    2 +-
 MolKit/pdb2pqr/pdb2pka/ligandclean/ligff.py  |    2 +-
 MolKit/pdb2pqr/pdb2pka/pka.py                |    6 +++---
 5 files changed, 11 insertions(+), 9 deletions(-)

    
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Patch contents

Description: use 'raise exception()' instead of simple 'raise'
Author: Piotr O┼╝arowski <piotr@debian.org>
Last-Update: 2010-06-30
Index: mgltools-molkit-1.5.4.cvs.20090603/MolKit/pdb2pqr/pdb2pka/NEWligand_topology.py
===================================================================
--- mgltools-molkit-1.5.4.cvs.20090603.orig/MolKit/pdb2pqr/pdb2pka/NEWligand_topology.py
+++ mgltools-molkit-1.5.4.cvs.20090603/MolKit/pdb2pqr/pdb2pka/NEWligand_topology.py
@@ -405,7 +405,7 @@ class get_ligand_topology:
                 self.biglist.append(real_list)
             return 
         else:
-            raise 'this should not happen'
+            raise Exception('this should not happen')
 
     #
     # -----
Index: mgltools-molkit-1.5.4.cvs.20090603/MolKit/pdb2pqr/pdb2pka/inputgen_pKa.py
===================================================================
--- mgltools-molkit-1.5.4.cvs.20090603.orig/MolKit/pdb2pqr/pdb2pka/inputgen_pKa.py
+++ mgltools-molkit-1.5.4.cvs.20090603/MolKit/pdb2pqr/pdb2pka/inputgen_pKa.py
@@ -136,7 +136,9 @@ class inputGen:
             #
             # Not a known type
             #
-            raise 'unknown type',type
+            # TODO: Exception() is used here instead of TypeError for backwards compatibility, fix it once sure that no TypeError is fine
+            #raise TypeError('unknown type',type)
+            raise Exception('unknown type',type)
         return
         
     def getText_sub(self):
@@ -165,7 +167,7 @@ class inputGen:
             text += "    nlev 4\n"
             
         else:
-            raise 'unknown method'
+            raise Exception('unknown method')
         #
         text += "    mol 1\n"                            
         text += "    lpbe\n"                             
@@ -214,7 +216,7 @@ class inputGen:
         #
         # Eh?
         #
-        raise 'type not set'
+        raise Exception('type not set')
 
     #
     # ------
Index: mgltools-molkit-1.5.4.cvs.20090603/MolKit/pdb2pqr/pdb2pka/ligand_topology.py
===================================================================
--- mgltools-molkit-1.5.4.cvs.20090603.orig/MolKit/pdb2pqr/pdb2pka/ligand_topology.py
+++ mgltools-molkit-1.5.4.cvs.20090603/MolKit/pdb2pqr/pdb2pka/ligand_topology.py
@@ -399,7 +399,7 @@ class get_ligand_topology:
                 self.biglist.append(real_list)
             return 
         else:
-            raise 'this should not happen'
+            raise Exception('this should not happen')
 
     #
     # -----
Index: mgltools-molkit-1.5.4.cvs.20090603/MolKit/pdb2pqr/pdb2pka/ligandclean/ligff.py
===================================================================
--- mgltools-molkit-1.5.4.cvs.20090603.orig/MolKit/pdb2pqr/pdb2pka/ligandclean/ligff.py
+++ mgltools-molkit-1.5.4.cvs.20090603/MolKit/pdb2pqr/pdb2pka/ligandclean/ligff.py
@@ -354,7 +354,7 @@ class ligand_charge_handler(MOL2MOLECULE
             if BondiiRadiiDict.has_key(ele):
                 radius = BondiiRadiiDict[ele]
             else:
-                raise 'radius not known for',ele
+                raise Exception('radius not known for',ele)
             #
             # Store the radii and charges
             #
Index: mgltools-molkit-1.5.4.cvs.20090603/MolKit/pdb2pqr/pdb2pka/pka.py
===================================================================
--- mgltools-molkit-1.5.4.cvs.20090603.orig/MolKit/pdb2pqr/pdb2pka/pka.py
+++ mgltools-molkit-1.5.4.cvs.20090603/MolKit/pdb2pqr/pdb2pka/pka.py
@@ -867,7 +867,7 @@ class pKaRoutines:
         if abs(totphi)<0.01 or abs(totcrg)<0.01:
             print 'total abs phi',totphi
             print 'total abs crg',totcrg
-            raise 'Something is rotten'
+            raise Exception('Something is rotten')
         print
         print
         return energy
@@ -1071,7 +1071,7 @@ class pKaRoutines:
         #
         if get_neutral_state:
             if not neutral_state:
-                raise "no neutral state for",residue.resSeq
+                raise Exception("no neutral state for",residue.resSeq)
             return neutral_state
         #
         # Make sure that the charges add up to integers by adding extra atoms
@@ -1129,7 +1129,7 @@ class pKaRoutines:
             if added is None and sum>0.001:
                 print sum
                 print atomnames
-                raise 'Could not find integer charge state'
+                raise Exception('Could not find integer charge state')
         return atomnames
 
     #