More graceful handling of non-critical errors in PDB headers.

Fixes #170
Electrostatics · Dec 27, 2020 · 8c810ca · 8c810ca
1 parent 34458b6
commit 8c810ca
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Showing 2 changed files with 12 additions and 7 deletions.
diff --git a/docs/releases.rst b/docs/releases.rst
@@ -11,6 +11,8 @@ Changes
 
 * Improved documentation of constants in modules.
 
+* Improved handling of improperly formatted PDB records that are not ``HETATM`` or ``ATOM``.
+
 ******************
 3.1.0 (2020-12-22)
 ******************

diff --git a/pdb2pqr/pdb.py b/pdb2pqr/pdb.py
@@ -2578,13 +2578,16 @@ def read_pdb(file_):
                 klass = LINE_PARSERS[record]
                 obj = klass(line)
                 pdblist.append(obj)
-        except KeyError as details:
-            errlist.append(record)
-            _LOGGER.error(f"Error parsing line: {details}")
-            _LOGGER.error(f"<{line.strip()}>")
-            _LOGGER.error(
-                f"Truncating remaining errors for record type:{record}"
-            )
+        except (KeyError, ValueError) as details:
+            if record not in ["HETATM", "ATOM"]:
+                errlist.append(record)
+                _LOGGER.error(f"Error parsing line: {details}")
+                _LOGGER.error(f"<{line.strip()}>")
+                _LOGGER.error(
+                    f"Truncating remaining errors for record type:{record}"
+                )
+            else:
+                raise details
         except IndexError as details:
             if record in ["ATOM", "HETATM"]:
                 try: