Merge pull request #1808 from jamesmkrieger/pdb_fixes

Several fixes related to fetching and writing pdb files

prody/atomic/pointer.py

@@ -273,6 +273,15 @@ def _getSubset(self, label):
                             .intersection(set(self._getIndices()))), int)
         subset.sort()
         return subset
+
+    def getAnisous(self):
+        """Returns a copy of anisotropic temperature factors from the active coordinate set."""
+
+        if self._ag._anisous is not None:
+            # Since this is not slicing, a view is not returned
+            return self._ag._anisous[self.getACSIndex(), self._indices]
+
+    _getAnisous = getAnisous
 
     def _iterBonds(self):
         """Yield pairs of indices for bonded atoms that are within the pointer.

prody/proteins/localpdb.py

@@ -216,7 +216,7 @@ def fetchPDB(*pdb, **kwargs):
 
     folder = kwargs.get('folder', '.')
     compressed = kwargs.get('compressed')
-    format_ = kwargs.get('format')
+    format_ = kwargs.get('format', 'pdb')
 
     # check *folder* specified by the user, usually pwd ('.')
     filedict = findPDBFiles(folder, compressed=compressed, 

prody/tests/datafiles/6zu5_sel_SE0_SF0_10-20.pdb

@@ -0,0 +1,24 @@
+REMARK Selection 'name CA and seg...resnum 10 to 20'
+ATOM      1  CA  LYS Z  10     241.064 218.683 115.080  1.00 76.19       SE0 C  
+ATOM      2  CA  ARG Z  11     241.395 216.353 112.126  1.00 78.29       SE0 C  
+ATOM      3  CA  LEU Z  12     238.042 214.694 112.724  1.00 77.55       SE0 C  
+ATOM      4  CA  ASN Z  13     236.407 218.088 113.221  1.00 75.95       SE0 C  
+ATOM      5  CA  ALA Z  14     237.705 219.231 109.829  1.00 74.73       SE0 C  
+ATOM      6  CA  PRO Z  15     235.172 219.530 106.991  1.00 73.66       SE0 C  
+ATOM      7  CA  SER Z  16     234.780 216.288 105.093  1.00 75.83       SE0 C  
+ATOM      8  CA  SER Z  17     234.971 218.169 101.797  1.00 76.09       SE0 C  
+ATOM      9  CA  TRP Z  18     238.691 218.624 102.453  1.00 75.23       SE0 C  
+ATOM     10  CA  GLN Z  19     239.073 214.811 102.251  1.00 80.09       SE0 C  
+ATOM     11  CA  LEU Z  20     241.546 214.456 105.094  1.00 80.45       SE0 C  
+ATOM     12  CA  LEU B  10     168.714  96.728 179.585  1.00 83.97       SF0 C  
+ATOM     13  CA  LEU B  11     169.608  98.301 182.936  1.00 85.19       SF0 C  
+ATOM     14  CA  LEU B  12     172.320 100.641 184.178  1.00 84.57       SF0 C  
+ATOM     15  CA  PHE B  13     174.993  98.778 186.200  1.00 83.57       SF0 C  
+ATOM     16  CA  ASP B  14     172.684  95.721 185.895  1.00 86.57       SF0 C  
+ATOM     17  CA  LYS B  15     170.596  97.232 188.710  1.00 85.32       SF0 C  
+ATOM     18  CA  TYR B  16     168.849 100.479 187.837  1.00 85.19       SF0 C  
+ATOM     19  CA  SER B  17     166.316 100.980 185.057  1.00 87.78       SF0 C  
+ATOM     20  CA  ARG B  18     166.755 104.070 182.910  1.00 88.01       SF0 C  
+ATOM     21  CA  ASP B  19     163.206 103.794 181.561  1.00 90.86       SF0 C  
+ATOM     22  CA  GLU B  20     161.410 104.550 184.827  1.00 90.52       SF0 C  
+END                                                                             

prody/tests/datafiles/__init__.py

@@ -245,6 +245,16 @@
         'atoms': 165175,
         'segment_SX0_atoms': 1089,
     },
+    '6zu5_sel': {
+        'pdb': '6zu5',
+        'file': '6zu5_sel_SE0_SF0_10-20.pdb',
+        'atoms': 22,
+        'segment_SF0_atoms': 11,
+        'chid_order': ['Z', 'Z', 'Z', 'Z', 'Z', 'Z', 'Z', 'Z', 'Z', 'Z', 'Z',
+                       'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B'],
+        'sorted_order': ['B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B', 'B',
+                         'Z', 'Z', 'Z', 'Z', 'Z', 'Z', 'Z', 'Z', 'Z', 'Z', 'Z']
+    },
     '3hsy': {
         'pdb': '3hsy',
         'file': 'pdb3hsy.pdb',

prody/tests/proteins/test_pdbfile.py

@@ -277,9 +277,13 @@ def setUp(self):
         self.h36_ter = parsePDB(DATA_FILES['h36_ter']['path'])
 
         self.altlocs = DATA_FILES['6flr']
-        self.altloc_full = parsePDB(self.altlocs['path'], altloc=None)
+        self.altloc_full = parsePDB(self.altlocs['path'], altloc=None,
+                                    secondary=False)
         self.altloc_sel = DATA_FILES['6flr_sel']['path']
 
+        self.sort_sel = DATA_FILES['6zu5_sel']
+        self.sort_sel_ag = parsePDB(self.sort_sel['path'])
+
     msg = 'user does not have write access to temp dir {0:s}'.format(TEMPDIR)
 
     @dec.slow
@@ -447,11 +451,11 @@ def testWritingAltlocModels(self):
         lines2 = fi.readlines()
         fi.close()
 
-        self.assertEqual(lines1[4], lines2[4],
-            'writePDB failed to write correct ANISOU line 4 for 6flr selection with altloc None')
+        self.assertEqual(lines1[3], lines2[3],
+            'writePDB failed to write correct ANISOU line 3 for 6flr selection with altloc None')
 
-        self.assertEqual(lines1[8], lines2[8],
-            'writePDB failed to write correct ANISOU line 8 for 6flr selection with altloc None')
+        self.assertEqual(lines1[7], lines2[7],
+            'writePDB failed to write correct ANISOU line 7 for 6flr selection with altloc None')
 
     def testWriteEnsembleToPDB(self):
         """Test that writePDB can handle ensembles."""
@@ -463,6 +467,16 @@ def testWriteEnsembleToPDB(self):
         assert_equal(out.getCoords(), self.ag.getCoordsets(0),
                 'failed to write ensemble model 1 coordinates correctly')
 
+    @dec.slow
+    @unittest.skipUnless(os.access(TEMPDIR, os.W_OK), msg)
+    def testWritingAtomMap(self):
+        """Test if output from writing a sorted AtomMap works and is as expected."""
+
+        sorted_sel = sortAtoms(self.sort_sel_ag, 'chain')
+        out = writePDB(self.tmp, sorted_sel)
+        new = parsePDB(out)
+        self.assertListEqual(list(new.getChids()), self.sort_sel['sorted_order'])
+
     @dec.slow
     def tearDown(self):
         """Remove test file."""