Fix bugs with segnames

Writing out was buggy (wrong n to snprintf).  Modify test to evaluate
segnames with obabel and only test bindings if they are present.

src/formats/pdbformat.cpp

@@ -689,7 +689,7 @@ namespace OpenBabel
             snprintf(type_name,5,"%s",(char*)res->GetAtomID(atom).c_str());
             the_chain = res->GetChain();
 
-            snprintf(segname,4,"%s", (char*)res->GetSegName().c_str());
+            snprintf(segname,5,"%s", (char*)res->GetSegName().c_str());
 
             //two char. elements are on position 13 and 14 one char. start at 14
             if (strlen(OBElements::GetSymbol(atom->GetAtomicNum())) == 1)

test/testpdbformat.py

@@ -25,25 +25,47 @@ class TestPDBFormat(BaseTest):
 
     def testSegname(self):
       """Test that different segments are put in different residues"""
-      mol = pybel.readstring('pdb','''ATOM    102  N   CYS A  16      59.916  27.715  54.719  1.00 30.93         A N
-ATOM    104  C   CYS A  16      61.349  29.663  54.116  1.00 31.27         A C
-ATOM    105  O   CYS A  16      62.398  30.296  54.175  1.00 31.42         A O
-ATOM    106  CB  CYS A  16      62.233  27.349  54.045  1.00 30.95         A C
-ATOM    107  SG  CYS A  16      62.584  25.823  54.921  1.00 31.06         A S
+      self.pdbin = '''ATOM    102  N   CYS A  16      59.916  27.715  54.719  1.00 30.93      AAAA N
+ATOM    104  C   CYS A  16      61.349  29.663  54.116  1.00 31.27      AAAA C
+ATOM    105  O   CYS A  16      62.398  30.296  54.175  1.00 31.42      AAAA O
+ATOM    106  CB  CYS A  16      62.233  27.349  54.045  1.00 30.95      AAAA C
+ATOM    107  SG  CYS A  16      62.584  25.823  54.921  1.00 31.06      AAAA S
 ATOM   2492  N   CYS A  16      46.752  17.445  54.719  1.00 30.93         B N
 ATOM   2493  CA  CYS A  16      45.412  16.879  54.750  1.00 31.03         B C
 ATOM   2494  C   CYS A  16      45.319  15.497  54.116  1.00 31.27         B C
 ATOM   2495  O   CYS A  16      44.270  14.864  54.175  1.00 31.42         B O
 ATOM   2496  CB  CYS A  16      44.435  17.811  54.045  1.00 30.95         B C
 ATOM   2497  SG  CYS A  16      44.084  19.337  54.921  1.00 31.06         B S
-''')
-      self.assertTrue(len(mol.residues) == 2)
-      cnts = {'A':0,'B':0}
-      for a in mol.atoms:
-          r = a.OBAtom.GetResidue()
-          cnts[r.GetSegName().strip()] += 1
-      self.assertEqual(cnts['A'],5)
-      self.assertEqual(cnts['B'],6)
+'''
+      self.pdbout = '''ATOM      1  N   CYS A  16      59.916  27.715  54.719  1.00  0.00      AAAA N  
+ATOM      2  C   CYS A  16      61.349  29.663  54.116  1.00  0.00      AAAA C  
+ATOM      3  O   CYS A  16      62.398  30.296  54.175  1.00  0.00      AAAA O  
+ATOM      4  CB  CYS A  16      62.233  27.349  54.045  1.00  0.00      AAAA C  
+ATOM      5  SG  CYS A  16      62.584  25.823  54.921  1.00  0.00      AAAA S  
+ATOM      6  N   CYS A  16      46.752  17.445  54.719  1.00  0.00         B N  
+ATOM      7  CA  CYS A  16      45.412  16.879  54.750  1.00  0.00         B C  
+ATOM      8  C   CYS A  16      45.319  15.497  54.116  1.00  0.00         B C  
+ATOM      9  O   CYS A  16      44.270  14.864  54.175  1.00  0.00         B O  
+ATOM     10  CB  CYS A  16      44.435  17.811  54.045  1.00  0.00         B C  
+ATOM     11  SG  CYS A  16      44.084  19.337  54.921  1.00  0.00         B S  '''
+
+      output, error = run_exec(self.pdbin,
+                                     "obabel -ipdb -opdb")
+
+      #pull out only atoms
+      outatoms = '\n'.join([line for line in output.split('\n') if line.startswith('ATOM')])
+      self.assertEqual(outatoms, self.pdbout)
+
+      #skip if bindings not present
+      if pybel:
+        mol = pybel.readstring('pdb',self.pdbin)
+        self.assertTrue(len(mol.residues) == 2)
+        cnts = {'AAAA':0,'B':0}
+        for a in mol.atoms:
+            r = a.OBAtom.GetResidue()
+            cnts[r.GetSegName().strip()] += 1
+        self.assertEqual(cnts['AAAA'],5)
+        self.assertEqual(cnts['B'],6)
 
     def testInsertionCodes(self):
         """