Update PDB header parser to get REMARK350

flat35hd99 · Oct 30, 2021 · c4aae6f · c4aae6f
1 parent a82abec
commit c4aae6f
Showing 1 changed file with 43 additions and 0 deletions.
diff --git a/Bio/PDB/parse_pdb_header.py b/Bio/PDB/parse_pdb_header.py
@@ -194,6 +194,8 @@ def _parse_pdb_header_list(header):
         "source": {"1": {"misc": ""}},
         "has_missing_residues": False,
         "missing_residues": [],
+        "chain_ids_to_work_symmetry_operator": [],
+        "symmetry_operator": [],
     }
 
     pdbh_dict["structure_reference"] = _get_references(header)
@@ -318,6 +320,47 @@ def _parse_pdb_header_list(header):
                             pdbh_dict["astral"][remark_99_keyval[0]] = remark_99_keyval[
                                 1
                             ]
+            elif hh.startswith("REMARK 350"):
+                if "APPLY THE FOLLOWING TO CHAINS:" in tail:
+                    chain_id_start_number = 42
+                    chain_ids_str = hh[chain_id_start_number:]
+                    chain_ids = [id.strip() for id in chain_ids_str.split(sep=", ")]
+                    pdbh_dict["chain_ids_to_work_symmetry_operator"] = chain_ids
+                elif re.match("BIOMT\d", tail):
+                    tail_word_list = tail.split()
+                    the_order_of_matrix = int(tail_word_list[1]) # 1, 2, 3, ...
+                    # First matrix must unit matrix.
+                    # It must be ignored.
+                    if the_order_of_matrix == 1:
+                        continue
+                    else:
+                        the_order_of_row = int(tail_word_list[0][-1]) # 1, 2, or 3
+                        matrix_row = [float(tail_word_list[i]) for i in [2,3,4]]
+                        translation_value = float(tail_word_list[-1])
+
+                        if the_order_of_row == 1:
+                            matrix_dict = {
+                                "matrix": [
+                                    matrix_row,
+                                ],
+                                "shift": [translation_value]
+                            }
+                            pdbh_dict["symmetry_operator"].append(matrix_dict)
+                        else:
+                            # symmetric_operator = [
+                            #     {
+                            #         "matrix": [
+                            #             [x11, x12, x13],
+                            #             [x21, x22, x23],
+                            #             [x31, x32, x33],
+                            #         ],
+                            #         "shift": [x, y, z]
+                            #     },
+                            #     {...},
+                            #     {...},
+                            # ]
+                            pdbh_dict["symmetry_operator"][the_order_of_matrix - 2]["matrix"].append(matrix_row)
+                            pdbh_dict["symmetry_operator"][the_order_of_matrix - 2]["shift"].append(translation_value)
         else:
             # print(key)
             pass