Add resolution saving

atomium/files/pdb2pdbdict.py

@@ -16,6 +16,7 @@ def pdb_to_pdb_dict(pdb):
     pdb_dict["deposition_date"] = pdb._deposition_date
     pdb_dict["code"] = pdb._code
     pdb_dict["title"] = pdb._title
+    pdb_dict["resolution"] = pdb._resolution
     return pdb_dict
 
 
@@ -38,7 +39,7 @@ def structure_to_pdb_dict(structure):
     connections = structure_to_connections(structure)
     return {
      "models": [model], "connections": connections,
-     "deposition_date": None, "code": None, "title": None
+     "deposition_date": None, "code": None, "title": None, "resolution": None
     }
 
 

atomium/files/pdbdict2pdbstring.py

@@ -41,6 +41,14 @@ def pack_header(lines, pdb_dict):
          chunk
         ).ljust(80) for number, chunk in enumerate(title_chunks, start=1)]
         lines += title_records
+    if pdb_dict["resolution"] is not None:
+        lines.append("REMARK   2".ljust(80))
+        if pdb_dict["resolution"] == 0:
+            lines.append("REMARK   2 RESOLUTION. NOT APPLICABLE.".ljust(80))
+        else:
+            lines.append("REMARK   2 RESOLUTION.    {:.2f} ANGSTROMS.".format(
+             pdb_dict["resolution"]
+            ).ljust(80))
 
 
 def pack_structure(lines, pdb_dict):

atomium/files/pdbstring2pdbdict.py

@@ -38,7 +38,7 @@ def extract_header(pdb_dict, lines):
         if int(remark[7:10]) == 2 and remark[10:].strip():
             try:
                 pdb_dict["resolution"] = float(remark[10:].strip().split()[1])
-            except ValueError: pdb_dict["resolution"] = None
+            except ValueError: pdb_dict["resolution"] = 0
             break
     else:
         pdb_dict["resolution"] = None

tests/integration/files/1cbn_output.pdb

@@ -1,6 +1,7 @@
 HEADER                                            11-OCT-91   1CBN
 TITLE     ATOMIC RESOLUTION (0.83 ANGSTROMS) CRYSTAL STRUCTURE OF THE HYDROPHOBI
 TITLE    2 C PROTEIN CRAMBIN AT 130 K
+REMARK   2
 REMARK   2 RESOLUTION.    0.83 ANGSTROMS.
 ATOM      1  N   THR A   1      16.864  14.059   3.442  1.00  6.22           N
 ATOM      3  CA  THR A   1      16.868  12.814   4.233  1.00  4.45           C

tests/integration/files/1lol_output.pdb

@@ -1,6 +1,7 @@
 HEADER                                            06-MAY-02   1LOL
 TITLE     CRYSTAL STRUCTURE OF OROTIDINE MONOPHOSPHATE DECARBOXYLASE COMPLEX WIT
 TITLE    2 H XMP
+REMARK   2
 REMARK   2 RESOLUTION.    1.90 ANGSTROMS.
 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

tests/integration/files/5xme_output.pdb

@@ -1,5 +1,6 @@
 HEADER                                            15-MAY-17   5XME
 TITLE     SOLUTION STRUCTURE OF C-TERMINAL DOMAIN OF TRADD
+REMARK   2
 REMARK   2 RESOLUTION. NOT APPLICABLE.
 MODEL        1
 ATOM      1  N   ALA A 199      33.969  -8.430  -0.271  1.00                 N

tests/integration/test_pdb.py

@@ -123,7 +123,7 @@ def test_can_read_pdb(self):
 
     def test_can_read_multi_model_pdbs(self):
         pdb = atomium.pdb_from_file("tests/integration/files/5xme.pdb")
-        self.assertEqual(pdb.resolution(), None)
+        self.assertEqual(pdb.resolution(), 0)
 
         models = pdb.models()
         self.assertEqual(len(models), 10)

tests/unit/files_tests/test_pdb_dict_to_pdb_string.py

@@ -24,7 +24,7 @@ class HeaderPackingTests(TestCase):
     def setUp(self):
         self.pdb_dict = {
          "deposition_date": datetime(1990, 9, 1).date(),
-         "code": "1XYZ", "title": "ABC" * 40
+         "code": "1XYZ", "title": "ABC" * 40, "resolution": 1.9
         }
         self.lines = []
 
@@ -34,12 +34,15 @@ def test_can_pack_full_header(self):
         self.assertEqual(self.lines, [
          "HEADER" + " " * 44 + "01-SEP-90   1XYZ" + " " * 14,
          "TITLE     " + "ABC" * 23 + "A",
-         "TITLE    2 " + "BC" + "ABC" * 16 + " " * 19
+         "TITLE    2 " + "BC" + "ABC" * 16 + " " * 19,
+         "REMARK   2" + " " * 70,
+         "REMARK   2 RESOLUTION.    1.90 ANGSTROMS.".ljust(80)
         ])
 
 
     def test_can_pack_deposition_date(self):
         self.pdb_dict["code"], self.pdb_dict["title"] = None, None
+        self.pdb_dict["resolution"] = None
         pack_header(self.lines, self.pdb_dict)
         self.assertEqual(self.lines, [
          "HEADER" + " " * 44 + "01-SEP-90       " + " " * 14,
@@ -48,6 +51,7 @@ def test_can_pack_deposition_date(self):
 
     def test_can_pack_code(self):
         self.pdb_dict["deposition_date"], self.pdb_dict["title"] = None, None
+        self.pdb_dict["resolution"] = None
         pack_header(self.lines, self.pdb_dict)
         self.assertEqual(self.lines, [
          "HEADER" + " " * 44 + "            1XYZ" + " " * 14,
@@ -56,13 +60,31 @@ def test_can_pack_code(self):
 
     def test_can_pack_title(self):
         self.pdb_dict["deposition_date"], self.pdb_dict["code"] = None, None
+        self.pdb_dict["resolution"] = None
         pack_header(self.lines, self.pdb_dict)
         self.assertEqual(self.lines, [
          "TITLE     " + "ABC" * 23 + "A",
          "TITLE    2 " + "BC" + "ABC" * 16 + " " * 19
         ])
 
 
+    def test_can_pack_resolution(self):
+        self.pdb_dict["deposition_date"], self.pdb_dict["title"] = None, None
+        self.pdb_dict["code"] = None
+        pack_header(self.lines, self.pdb_dict)
+        self.assertEqual(self.lines[0], "REMARK   2" + " " * 70)
+        self.assertEqual(self.lines[1],  "REMARK   2 RESOLUTION.    1.90 ANGSTROMS.".ljust(80))
+
+
+    def test_can_pack_zero_resolution(self):
+        self.pdb_dict["deposition_date"], self.pdb_dict["title"] = None, None
+        self.pdb_dict["code"] = None
+        self.pdb_dict["resolution"] = 0
+        pack_header(self.lines, self.pdb_dict)
+        self.assertEqual(self.lines[0], "REMARK   2" + " " * 70)
+        self.assertEqual(self.lines[1],  "REMARK   2 RESOLUTION. NOT APPLICABLE.".ljust(80))
+
+
 
 class StructurePackingTests(TestCase):
 

tests/unit/files_tests/test_pdb_string_to_pdb_dict.py

@@ -103,7 +103,7 @@ def test_empty_remark_extraction(self, mock_lines, mock_line):
         extract_header(self.pdb_dict, self.lines)
         mock_lines.assert_any_call("TITLE", self.lines)
         mock_lines.assert_any_call("REMARK", self.lines)
-        self.assertEqual(self.pdb_dict["resolution"], None)
+        self.assertEqual(self.pdb_dict["resolution"], 0)
 
 
     @patch("atomium.files.pdbstring2pdbdict.get_line")

tests/unit/files_tests/test_pdb_to_pdb_dict.py

@@ -10,12 +10,13 @@ def test_can_convert_pdb_to_pdb_dict_one_model(self, mock_dict):
         pdb._deposition_date = "D"
         pdb._code = "C"
         pdb._title = "T"
+        pdb._resolution = 1.5
         pdb._models = ["model1"]
         mock_dict.return_value = {"models": ["m1"], "connections": ["c1", "c2"]}
         pdb_dict = pdb_to_pdb_dict(pdb)
         mock_dict.assert_called_with("model1")
         self.assertEqual(pdb_dict, {
-         "deposition_date": "D", "code": "C", "title": "T",
+         "deposition_date": "D", "code": "C", "title": "T", "resolution": 1.5,
          "models": ["m1"], "connections": ["c1", "c2"]
         })
 
@@ -26,6 +27,7 @@ def test_can_convert_pdb_to_pdb_dict_two_models(self, mock_dict):
         pdb._deposition_date = "D"
         pdb._code = "C"
         pdb._title = "T"
+        pdb._resolution = 1.5
         pdb._models = ["model1", "model2"]
         mock_dict.side_effect = [
          {"models": ["m1"], "connections": ["c1", "c2"]},
@@ -35,7 +37,7 @@ def test_can_convert_pdb_to_pdb_dict_two_models(self, mock_dict):
         mock_dict.assert_any_call("model1")
         mock_dict.assert_any_call("model2")
         self.assertEqual(pdb_dict, {
-         "deposition_date": "D", "code": "C", "title": "T",
+         "deposition_date": "D", "code": "C", "title": "T", "resolution": 1.5,
          "models": ["m1", "m2"], "connections": ["c1", "c2"]
         })
 
@@ -69,6 +71,7 @@ def test_can_convert_model_to_pdb_dict(self, mock_con, mock_res, mock_chain, moc
          "deposition_date": None,
          "code": None,
          "title": None,
+         "resolution": None,
          "models": [{
           "chains": ["chain1", "chain2"],
           "molecules": ["mol1", "mol2"]