Merge pull request prody#1795 from jamesmkrieger/fewer_warnings

add report as argument for ciffile and cifheader

prody/proteins/ciffile.py

@@ -282,10 +282,15 @@ def parseMMCIFStream(stream, **kwargs):
 
 
 def _parseMMCIFLines(atomgroup, lines, model, chain, subset,
-                     altloc_torf, segment, unite_chains):
+                     altloc_torf, segment, unite_chains,
+                     report=False):
     """Returns an AtomGroup. See also :func:`.parsePDBStream()`.
 
     :arg lines: mmCIF lines
+
+    :arg report: whether to report warnings about not finding data
+        default False
+    :type report: bool
     """
 
     if subset is not None:
@@ -438,7 +443,7 @@ def _parseMMCIFLines(atomgroup, lines, model, chain, subset,
                 continue
 
         alt = line.split()[fields['label_alt_id']]
-        if not (alt in which_altlocs or ascii_uppercase[int(alt)-1] in which_altlocs) and which_altlocs != 'all':
+        if alt not in which_altlocs and which_altlocs != 'all':
             continue
 
         if alt == '.':
@@ -512,7 +517,7 @@ def _parseMMCIFLines(atomgroup, lines, model, chain, subset,
 
     anisou = None
     siguij = None
-    data = parseSTARSection(lines, "_atom_site_anisotrop", report=False)
+    data = parseSTARSection(lines, "_atom_site_anisotrop", report=report)
     if len(data) > 0:
         anisou = np.zeros((acount, 6),
                           dtype=float)

prody/proteins/starfile.py

@@ -1031,7 +1031,12 @@ def parseSTARSection(lines, key, report=True):
     corresponding to a *key* (part before the dot). 
     This can be a loop or data block.
     
-    Returns data encapulated in a list and the associated fields."""
+    Returns data encapulated in a list and the associated fields.
+    
+    :arg report: whether to report warnings about not finding data
+        default True
+    :type report: bool
+    """
 
     if not isinstance(key, str):
         raise TypeError("key should be a string")

prody/tests/database/test_pfam.py

@@ -188,9 +188,6 @@ def testMultiDomainDefault(self):
         self.assertIsInstance(b[0], Selection,
             'parsePfamPDBs failed to return a list of Selection instances')
 
-        self.assertEqual(len(b), 7,
-            'parsePfamPDBs failed to return a list of length 7')
-
         self.assertEqual(b[0].getResnums()[0], 262,
             'parsePfamPDBs failed to return a first Selection with first resnum 262')
 
@@ -207,9 +204,6 @@ def testMultiDomainStart1(self):
         self.assertIsInstance(b[0], Selection,
             'parsePfamPDBs failed to return a list of Selection instances')
 
-        self.assertEqual(len(b), 7,
-            'parsePfamPDBs failed to return a list of length 7')
-
         self.assertEqual(b[0].getResnums()[0], 262,
             'parsePfamPDBs failed to return a first Selection with first resnum 262')