Add function to check that a file is a PDB

doc/modules/frontend.rst

@@ -37,6 +37,8 @@ The :mod:`saliweb.frontend` Python module
 
 .. autofunction:: check_modeller_key
 
+.. autofunction:: check_pdb
+
 .. autofunction:: pdb_code_exists
 
 .. autofunction:: get_pdb_code

python/saliweb/frontend/__init__.py

@@ -472,6 +472,28 @@ def check_email(email, required=False):
             "Please provide a valid return email address")
 
 
+def check_pdb(filename, show_filename=None):
+    """Check that a PDB file really looks like a PDB file.
+       If it does not, raise an :exc:`InputValidationError` exception.
+
+       :param str filename: The PDB file to check.
+       :param str show_filename: If provided, include this filename in any
+              error message to identify the PDB file (useful for services
+              that allow upload of multiple PDB files).
+    """
+    if show_filename:
+        pdb_file = "PDB file %s" % show_filename
+    else:
+        pdb_file = "PDB file"
+    # Use latin1 to avoid decode errors with 8-bit characters
+    with open(filename, encoding='latin1') as fh:
+        for line in fh:
+            if line.startswith('ATOM  ') or line.startswith('HETATM'):
+                return
+    raise InputValidationError("%s contains no ATOM or HETATM records!"
+                               % pdb_file)
+
+
 def check_modeller_key(modkey):
     """Check a provided MODELLER key.
        If the key is empty or invalid, raise an

test/pyfrontend/test_frontend.py

@@ -174,6 +174,27 @@ def test_check_email_optional(self):
                           tf, 'garbage')
         tf("test@test.com")
 
+    def test_check_pdb(self):
+        """Test check_pdb"""
+        with util.temporary_directory() as tmpdir:
+            good_pdb = os.path.join(tmpdir, 'good.pdb')
+            with open(good_pdb, 'w') as fh:
+                fh.write("REMARK  6  TEST REMARK\n")
+                fh.write(
+                    "ATOM      1  N   ALA C   1      27.932  14.488   4.257  "
+                    "1.00 23.91           N\n")
+            bad_pdb = os.path.join(tmpdir, 'bad.pdb')
+            with open(bad_pdb, 'w') as fh:
+                fh.write("not a pdb\n")
+
+            saliweb.frontend.check_pdb(good_pdb)
+            saliweb.frontend.check_pdb(good_pdb, show_filename='good.pdb')
+            self.assertRaises(saliweb.frontend.InputValidationError,
+                              saliweb.frontend.check_pdb, bad_pdb)
+            self.assertRaises(saliweb.frontend.InputValidationError,
+                              saliweb.frontend.check_pdb, bad_pdb,
+                              show_filename='bad.pdb')
+
     def test_check_modeller_key(self):
         """Test check_modeller_key function"""
         class MockApp(object):