Merge pull request #1734 from jamesmkrieger/prody-master

fix secstr writing
prody · Aug 11, 2023 · f38e591 · f38e591
2 parents 7cb59a9 + d51db04
commit f38e591
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Showing 2 changed files with 25 additions and 14 deletions.
diff --git a/prody/proteins/pdbfile.py b/prody/proteins/pdbfile.py
@@ -1057,13 +1057,13 @@ def _evalAltlocs(atomgroup, altloc, chainids, resnums, resnames, atomnames):
 #             '                               %5d\n')
 
 HELIXLINE = ('HELIX  {serNum:3d} {helixID:>3s} '
-             '{initResName:<3s}{initChainID:2s} {initSeqNum:4d}{initICode:1s} '
-             '{endResName:<3s}{endChainID:2s} {endSeqNum:4d}{endICode:1s}'
-             '{helixClass:2d}                               {length:5d}\n')
+             '{initResName:<3s}{initChainID:>2s} {initSeqNum:4d}{initICode:1s} '
+             '{endResName:<3s}{endChainID:>2s} {endSeqNum:4d}{endICode:1s}'
+             '{helixClass:2d}                               {length:5d}    \n')
 
 SHEETLINE = ('SHEET  {strand:3d} {sheetID:>3s}{numStrands:2d} '
-             '{initResName:3s}{initChainID:2s}{initSeqNum:4d}{initICode:1s} '
-             '{endResName:3s}{endChainID:2s}{endSeqNum:4d}{endICode:1s}{sense:2d} \n')
+             '{initResName:3s}{initChainID:>2s}{initSeqNum:4d}{initICode:1s} '
+             '{endResName:3s}{endChainID:>2s}{endSeqNum:4d}{endICode:1s}{sense:2d} \n')
 
 PDBLINE_LT100K = ('%-6s%5d %-4s%1s%-3s%2s%4d%1s   '
                   '%8.3f%8.3f%8.3f%6.2f%6.2f      '

diff --git a/prody/tests/proteins/test_pdbfile.py b/prody/tests/proteins/test_pdbfile.py
@@ -209,6 +209,8 @@ def setUp(self):
         self.ag = parsePDB(self.pdb['path'])
         self.tmp = os.path.join(TEMPDIR, 'test.pdb')
 
+        self.ubi = parsePDB(DATA_FILES['1ubi']['path'], secondary=True)
+
         self.hex = parsePDB(DATA_FILES['hex']['path'])
         self.h36 = parsePDB(DATA_FILES['h36']['path'])
 
@@ -279,11 +281,20 @@ def testWritingHybrid36(self):
 
         serial_99999_line = lines[99999]
         self.assertEqual(serial_99999_line[6:11], '99999',
-            'writePDB failed to write correct pre-h36 serial')        
+            'writePDB failed to write correct pre-h36 serial')
 
         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')
+
+    @dec.slow
+    @unittest.skipUnless(os.access(TEMPDIR, os.W_OK), msg)
+    def testWritingSecstrs(self):
+        """Test if output from writing secstrs is as expected."""
+
+        out = writePDB(self.tmp, self.ubi)
+        ubi_new = parsePDB(out, secondary=True)
+        self.assertListEqual(list(self.ubi.getSecstrs()), list(ubi_new.getSecstrs()))
 
     @dec.slow
     @unittest.skipUnless(os.access(TEMPDIR, os.W_OK), msg)
@@ -299,13 +310,6 @@ def testModelArgument(self):
             assert_equal(out.getCoords(), self.ag.getCoordsets(i),
                  'failed to write model {0} coordinates correctly'.format(i+1))
 
-    @dec.slow
-    def tearDown(self):
-        """Remove test file."""
-
-        if os.path.isfile(self.tmp):
-            os.remove(self.tmp)
-
     @dec.slow
     @unittest.skipUnless(os.access(TEMPDIR, os.W_OK), msg)
     def testWritingHexTer(self):
@@ -366,6 +370,13 @@ def testWritingHybrid36Ter(self):
         self.assertEqual(serial_A0000_line[6:11], 'A0000',
             'writePDB failed to write correct h36 serial') 
 
+    @dec.slow
+    def tearDown(self):
+        """Remove test file."""
+
+        if os.path.isfile(self.tmp):
+            os.remove(self.tmp)
+
 
 class TestParsePDBHeaderAndAllModels(unittest.TestCase):