Add saving of rfactor in PDBs

atomium/files/pdb2pdbdict.py

@@ -17,6 +17,7 @@ def pdb_to_pdb_dict(pdb):
     pdb_dict["code"] = pdb._code
     pdb_dict["title"] = pdb._title
     pdb_dict["resolution"] = pdb._resolution
+    pdb_dict["rfactor"] = pdb._rfactor
     pdb_dict["organism"] = pdb._organism
     pdb_dict["expression_system"] = pdb._expression_system
     pdb_dict["technique"] = pdb._technique
@@ -45,7 +46,7 @@ def structure_to_pdb_dict(structure):
      "models": [model], "connections": connections,
      "deposition_date": None, "code": None, "title": None, "resolution": None,
      "organism": None, "expression_system": None, "technique": None,
-     "classification": None
+     "classification": None, "rfactor": None
     }
 
 

atomium/files/pdbdict2pdbstring.py

@@ -28,6 +28,7 @@ def pack_annotation(lines, pdb_dict):
     pack_source(lines, pdb_dict)
     pack_technique(lines, pdb_dict)
     pack_resolution(lines, pdb_dict)
+    pack_rfactor(lines, pdb_dict)
 
 
 def pack_header(lines, pdb_dict):
@@ -82,6 +83,19 @@ def pack_resolution(lines, pdb_dict):
             ).ljust(80))
 
 
+def pack_rfactor(lines, pdb_dict):
+    """Adds REMARK records to a list of lines for rfactor.
+
+    :param list lines: The record lines to add to.
+    :param dict pdb_dict: The data dictionary to pack."""
+
+    if pdb_dict["rfactor"] is not None:
+        lines.append("REMARK   3".ljust(80))
+        lines.append("REMARK   3   R VALUE            (WORKING SET) : {}".format(
+         pdb_dict["rfactor"]
+        ).ljust(80))
+
+
 def pack_source(lines, pdb_dict):
     """Adds SOURCE records to a list of lines for source organism and
     expression system.

tests/integration/files/1lol_output.pdb

@@ -6,6 +6,8 @@ SOURCE   2 EXPRESSION_SYSTEM: COOL NEW ORGANISM;
 EXPDTA    MEME DIFFRACTION
 REMARK   2
 REMARK   2 RESOLUTION.    1.90 ANGSTROMS.
+REMARK   3
+REMARK   3   R VALUE            (WORKING SET) : 0.193
 ATOM      1  N   VAL A  11       3.696  33.898  63.219  1.00  21.5           N
 ATOM      2  CA  VAL A  11       3.198  33.218  61.983  1.00 19.76           C
 ATOM      3  C   VAL A  11       3.914  31.863  61.818  1.00 19.29           C

tests/unit/files_tests/test_pdb_dict_to_pdb_string.py

@@ -9,7 +9,7 @@ def setUp(self):
         self.pdb_dict = {
          "deposition_date": datetime(1990, 9, 1).date(),
          "code": "1XYZ", "title": "ABC" * 40, "resolution": 1.9,
-         "technique": "TECH", "classification": "CLASS",
+         "technique": "TECH", "classification": "CLASS", "rfactor": 3.4,
          "organism": "HOMO SAPIENS", "expression_system": "MUS MUSCULUS"
         }
         self.lines = []
@@ -37,13 +37,15 @@ class AnnotationPackingTests(PdbStringCreationTest):
     @patch("atomium.files.pdbdict2pdbstring.pack_header")
     @patch("atomium.files.pdbdict2pdbstring.pack_title")
     @patch("atomium.files.pdbdict2pdbstring.pack_resolution")
+    @patch("atomium.files.pdbdict2pdbstring.pack_rfactor")
     @patch("atomium.files.pdbdict2pdbstring.pack_source")
     @patch("atomium.files.pdbdict2pdbstring.pack_technique")
-    def test_can_pack_annotation(self, mock_tech, mock_source, mock_res, mock_title, mock_head):
+    def test_can_pack_annotation(self, mock_tech, mock_source, mock_rfac, mock_res, mock_title, mock_head):
         pack_annotation(self.lines, self.pdb_dict)
         mock_head.assert_called_with(self.lines, self.pdb_dict)
         mock_title.assert_called_with(self.lines, self.pdb_dict)
         mock_res.assert_called_with(self.lines, self.pdb_dict)
+        mock_rfac.assert_called_with(self.lines, self.pdb_dict)
         mock_source.assert_called_with(self.lines, self.pdb_dict)
         mock_tech.assert_called_with(self.lines, self.pdb_dict)
 
@@ -120,6 +122,23 @@ def test_can_pack_zero_resolution(self):
 
 
 
+class RfactorPackingTests(PdbStringCreationTest):
+
+    def test_can_pack_resolution(self):
+        pack_rfactor(self.lines, self.pdb_dict)
+        self.assertEqual(self.lines[0], "REMARK   3" + " " * 70)
+        self.assertEqual(
+         self.lines[1],  "REMARK   3   R VALUE            (WORKING SET) : 3.4".ljust(80)
+        )
+
+
+    def test_can_pack_no_rfactor(self):
+        self.pdb_dict["resolution"] = None
+        pack_resolution(self.lines, self.pdb_dict)
+        self.assertEqual(self.lines, [])
+
+
+
 class SourcePackingTests(PdbStringCreationTest):
 
     def test_can_pack_source(self):
@@ -150,7 +169,7 @@ def test_can_pack_nothing(self):
         self.pdb_dict["technique"] = None
         pack_technique(self.lines, self.pdb_dict)
         self.assertEqual(self.lines, [])
-        
+
 
 
 class StructurePackingTests(TestCase):

tests/unit/files_tests/test_pdb_to_pdb_dict.py

@@ -11,6 +11,7 @@ def test_can_convert_pdb_to_pdb_dict_one_model(self, mock_dict):
         pdb._code = "C"
         pdb._title = "T"
         pdb._resolution = 1.5
+        pdb._rfactor = 1.8
         pdb._organism = "O"
         pdb._expression_system = "E"
         pdb._technique = "T"
@@ -22,7 +23,7 @@ def test_can_convert_pdb_to_pdb_dict_one_model(self, mock_dict):
         self.assertEqual(pdb_dict, {
          "deposition_date": "D", "code": "C", "title": "T", "resolution": 1.5,
          "organism": "O", "expression_system": "E", "technique": "T",
-         "classification": "CLASS",
+         "classification": "CLASS", "rfactor": 1.8,
          "models": ["m1"], "connections": ["c1", "c2"]
         })
 
@@ -34,6 +35,7 @@ def test_can_convert_pdb_to_pdb_dict_two_models(self, mock_dict):
         pdb._code = "C"
         pdb._title = "T"
         pdb._resolution = 1.5
+        pdb._rfactor = 1.8
         pdb._organism = "O"
         pdb._expression_system = "E"
         pdb._technique = "T"
@@ -49,7 +51,7 @@ def test_can_convert_pdb_to_pdb_dict_two_models(self, mock_dict):
         self.assertEqual(pdb_dict, {
          "deposition_date": "D", "code": "C", "title": "T", "resolution": 1.5,
          "organism": "O", "expression_system": "E", "technique": "T",
-         "classification": "CLASS",
+         "classification": "CLASS", "rfactor": 1.8,
          "models": ["m1", "m2"], "connections": ["c1", "c2"]
         })
 
@@ -84,6 +86,7 @@ def test_can_convert_model_to_pdb_dict(self, mock_con, mock_res, mock_chain, moc
          "code": None,
          "title": None,
          "resolution": None,
+         "rfactor": None,
          "organism": None,
          "expression_system": None,
          "technique": None,