add write tests

prody/tests/datafiles/__init__.py

@@ -282,6 +282,16 @@
         'anisousA': array([[1.3327, 0.8826, 0.7048, 0.0444, 0.3365, 0.1618]]),
         'anisousB': array([[1.3306, 0.8825, 0.7058, 0.0438, 0.338 , 0.1608]])
     },
+    '6flr_sel': {
+        'pdb': '6flr',
+        'file': 'pdb6flr_B234.pdb',
+        'atoms': 1,
+        'ca_atoms': 1,
+        'models': 2,
+        'biomols': 1,
+        'anisousA': array([[1.3327, 0.8826, 0.7048, 0.0444, 0.3365, 0.1618]]),
+        'anisousB': array([[1.3306, 0.8825, 0.7058, 0.0438, 0.338 , 0.1608]])
+    },
     'gromacs': {
         'pdb': '6fpj',
         'file': 'pdb6fpj_Bb_fixed_solv_ions.pdb',

prody/tests/datafiles/pdb6flr_B234.pdb

@@ -0,0 +1,11 @@
+REMARK Selection 'resname HIS and...234 and name CA'
+HELIX   21 AC3 HIS B  234  HIS B  234  1                                   1    
+MODEL        1
+ATOM      1  CA AHIS B 234      14.092 -10.803  78.631  0.50 76.86           C  
+ANISOU    1  CA AHIS B 234    13327   8826   7048    444   3365   1618       C  
+ENDMDL                                                                          
+MODEL        2
+ATOM      1  CA  HIS B 234      13.993 -10.729  78.621  0.50 76.86           C  
+ANISOU    1  CA  HIS B 234    13306   8825   7058    438   3380   1608       C  
+ENDMDL                                                                          
+END                                                                             

prody/tests/proteins/test_pdbfile.py

@@ -270,6 +270,10 @@ def setUp(self):
         self.hex_ter = parsePDB(DATA_FILES['hex_ter']['path'])
         self.h36_ter = parsePDB(DATA_FILES['h36_ter']['path'])
 
+        self.altlocs = DATA_FILES['6flr']
+        self.altloc_full = parsePDB(self.altlocs, altloc=None)
+        self.altloc_sel = parsePDB(DATA_FILES['6flr_sel'])
+
     msg = 'user does not have write access to temp dir {0:s}'.format(TEMPDIR)
 
     @dec.slow
@@ -421,7 +425,30 @@ def testWritingHybrid36Ter(self):
 
         serial_A0000_line = lines[100000]
         self.assertEqual(serial_A0000_line[6:11], 'A0000',
-            'writePDB failed to write correct h36 serial') 
+            'writePDB failed to write correct h36 serial')
+
+    def testWritingHexTer(self):
+        """Test if output from writing hexadecimal with TER lines is as expected."""
+
+        hisB234 = self.altloc_full.select('resname HIS and chain B and resnum 234 and name CA')
+        out = writePDB(self.tmp, hisB234)
+
+        fi = open(out, 'r')
+        lines1 = fi.readlines()
+        fi.close()
+
+        fi = open(self.altloc_sel, 'r')
+        lines2 = fi.readlines()
+        fi.close()
+
+        self.assertEqual(len(lines1), len(lines2),
+            'writePDB failed to write enough lines for 6flr selection with altloc None (11)')
+
+        self.assertEqual(lines1[4], lines2[4],
+            'writePDB failed to write correct ANISOU line 4 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')
 
     @dec.slow
     def tearDown(self):