Replace QUIET argument with PERMISSIVE=2.

Bio/PDB/PDBParser.py

@@ -23,7 +23,7 @@ class PDBParser:
     Parse a PDB file and return a Structure object.
     """
 
-    def __init__(self, PERMISSIVE=1, get_header=0, QUIET=0, structure_builder=None):
+    def __init__(self, PERMISSIVE=1, get_header=0, structure_builder=None):
         """
         The PDB parser call a number of standard methods in an aggregated
         StructureBuilder object. Normally this object is instanciated by the
@@ -35,11 +35,8 @@ def __init__(self, PERMISSIVE=1, get_header=0, QUIET=0, structure_builder=None):
         o PERMISSIVE - int, if this is 0 exceptions in constructing the
         SMCRA data structure are fatal. If 1 (DEFAULT), the exceptions are 
         caught, but some residues or atoms will be missing. THESE EXCEPTIONS 
-        ARE DUE TO PROBLEMS IN THE PDB FILE!.
-
-        o QUIET - int, if this is 1, warnings issued in constructing the SMCRA data
-        will be supressed. If 0 (DEFAULT), they will not. These warnings might be
-        indicative of problems in the PDB file!        
+        ARE DUE TO PROBLEMS IN THE PDB FILE!. If 2, these exceptions will be 
+        caught but supressed from the output.       
 
         o structure_builder - an optional user implemented StructureBuilder class. 
         """
@@ -51,7 +48,6 @@ def __init__(self, PERMISSIVE=1, get_header=0, QUIET=0, structure_builder=None):
         self.trailer=None
         self.line_counter=0
         self.PERMISSIVE=PERMISSIVE
-        self.QUIET=QUIET
 
     # Public methods
 
@@ -63,7 +59,7 @@ def get_structure(self, id, file):
         o file - name of the PDB file OR an open filehandle
         """
 
-        if self.QUIET:
+        if self.PERMISSIVE == 2:
             warning_list = warnings.filters[:]
             warnings.filterwarnings('ignore', category=PDBConstructionWarning)
 
@@ -82,7 +78,7 @@ def get_structure(self, id, file):
         if handle_close:
             file.close()
 
-        if self.QUIET:
+        if self.PERMISSIVE == 2:
             warnings.filters = warning_list
 
         return structure