Merge pull request #158 from ihmwg/rebranding

Rebrand PDB-Dev to PDB-IHM, add support for BMRbig database

docs/introduction.rst

@@ -23,7 +23,7 @@ that is compliant with the
 `IHMCIF extension <https://github.com/ihmwg/IHMCIF>`_
 to the `PDBx/mmCIF dictionary <https://mmcif.wwpdb.org/>`_,
 suitable for deposition in the
-`PDB-Dev repository <https://pdb-dev.wwpdb.org/>`_. The files are best viewed
+`PDB-IHM repository <https://pdb-ihm.org/>`_. The files are best viewed
 in a viewer that supports IHMCIF, such as
 `UCSF ChimeraX <https://www.cgl.ucsf.edu/chimerax/>`_, although they may be
 partially viewable in regular PDBx mmCIF viewers (likely only the atomic

examples/validate_pdb_dev.py → examples/validate_pdb_ihm.py

@@ -1,5 +1,5 @@
 # This example demonstrates the use of the Python IHM library's validator.
-# A structure is downloaded from the PDB-Dev database and checked against
+# A structure is downloaded from the PDB-IHM database and checked against
 # the PDBx and IHM dictionaries for compliance. This validator can be used
 # to perform basic integrity checking against any mmCIF dictionary; for an
 # example of using it to validate homology models against the ModelCIF
@@ -36,9 +36,9 @@
 # Validate a structure against PDBx+IHM.
 # A correct structure here should result in no output; an invalid structure
 # will result in a ValidatorError Python exception.
-# Here, a structure from PDB-Dev (which should be valid) is used.
-acc = 'PDBDEV_00000001'
-cif = urllib2.urlopen('https://pdb-dev.wwpdb.org/cif/%s.cif' % acc).read()
+# Here, a structure from PDB-IHM (which should be valid) is used.
+acc = '8zz1'
+cif = urllib2.urlopen('https://pdb-ihm.org/cif/%s.cif' % acc).read()
 
 # The encoding for mmCIF files isn't strictly defined, so first try UTF-8
 # and if that fails, strip out any non-ASCII characters. This ensures that

ihm/__init__.py

@@ -75,7 +75,7 @@ class System(object):
        :param str model_details: Detailed description of the system, like an
                                  abstract.
        :param databases: If this system is part of one or more official
-              databases (e.g. PDB, PDB-Dev, SwissModel), details of
+              databases (e.g. PDB, SwissModel), details of
               the database identifiers.
        :type databases: sequence of :class:`Database`
     """
@@ -690,7 +690,7 @@ class Database(object):
     """Information about a System that is part of an official database.
 
        If a :class:`System` is part of one or more official databases
-       (e.g. PDB, PDB-Dev, SwissModel), this class contains details of the
+       (e.g. PDB, SwissModel), this class contains details of the
        database identifiers. It should be passed to the :class:`System`
        constructor.
 

ihm/location.py

@@ -100,6 +100,10 @@ class PDBLocation(DatabaseLocation):
 
 class PDBDevLocation(DatabaseLocation):
     """Something stored in the PDB-Dev database.
+       This should only be used for legacy entries. All former PDB-Dev entries
+       (now PDB-IHM) should now have PDB identifiers; use :class:`PDBLocation`
+       instead.
+
        See :class:`DatabaseLocation` for a description of the parameters
        and :class:`Location` for discussion of the usage of these objects."""
     db_name = 'PDB-Dev'
@@ -189,6 +193,13 @@ class ProteomeXchangeLocation(DatabaseLocation):
     db_name = 'ProteomeXchange'
 
 
+class BMRbigLocation(DatabaseLocation):
+    """Something stored in the BMRbig database.
+       See :class:`DatabaseLocation` for a description of the parameters
+       and :class:`Location` for discussion of the usage of these objects."""
+    db_name = 'BMRbig'
+
+
 class FileLocation(Location):
     """Base class for an individual file or directory stored externally.
 

ihm/model.py

@@ -459,7 +459,7 @@ def _write_frame(self, x, y, z):
                 b'Produced by python-ihm, https://github.com/ihmwg/python-ihm',
                 b'This file is designed to be used in combination with an '
                 b'mmCIF file',
-                b'See PDB-Dev at https://pdb-dev.wwpdb.org/ for more details']
+                b'See PDB-IHM at https://pdb-ihm.org/ for more details']
             self._write_header(self.ncoord, remarks)
         else:
             if len(x) != self.ncoord:

test/test_examples.py

@@ -24,11 +24,11 @@ class Tests(unittest.TestCase):
     @unittest.skipIf('APPVEYOR' in os.environ,
                      "AppVeyor environments have old SSL certs")
     @unittest.skipIf('GITHUB_ACTIONS' in os.environ,
-                     "Example is slow and fails when PDB-Dev is down")
+                     "Example is slow and fails when PDB-IHM is down")
     def test_validator_example(self):
         """Test validator example"""
         subprocess.check_call([sys.executable,
-                               get_example_path("validate_pdb_dev.py")])
+                               get_example_path("validate_pdb_ihm.py")])
 
     def test_simple_docking_example(self):
         """Test simple-docking example"""

test/test_location.py

@@ -123,6 +123,15 @@ def test_proteome_xchange_location(self):
         self.assertEqual(d.version, 1)
         self.assertEqual(d.details, 'foo')
 
+    def test_bmr_big_location(self):
+        """Test BMRbigLocation class"""
+        d = ihm.location.BMRbigLocation(
+            'abc', version=1, details='foo')
+        self.assertEqual(d.db_name, 'BMRbig')
+        self.assertEqual(d.access_code, 'abc')
+        self.assertEqual(d.version, 1)
+        self.assertEqual(d.details, 'foo')
+
     def test_empiar_location(self):
         """Test EMPIARLocation class"""
         d = ihm.location.EMPIARLocation('abc', version=1, details='foo')