Merge pull request #8 from Electrostatics/nathan/edge

Improve parsing of PDB edge cases

docs/changelog.rst

@@ -4,6 +4,11 @@
 Change log
 ==========
 
+1.1.0
+=====
+
+* Added additional test cases covering OBSLTE (3WXV), SPRSDE (6KS0) and fixed associated bugs.
+
 1.0.0
 =====
 

old_pdb/annotation.py

@@ -461,7 +461,7 @@ def __str__(self):
             else:
                 string = "OBSLTE    "
             string += (
-                f" {date_format(self.replace_date):9} {self.id_code}       "
+                f" {date_format(self.replace_date):9} {self.id_code}     "
             )
             for code in chunk:
                 if code is not None:
@@ -972,7 +972,7 @@ def parse_line(self, line):
 
     def __str__(self):
         strings = []
-        for ichunk, chunk in grouper(self.id_codes, 14):
+        for ichunk, chunk in enumerate(grouper(self.id_codes, 14)):
             string = ""
             continuation = ichunk + 1
             if continuation > 1:
@@ -1054,7 +1054,7 @@ def parse_line(self, line):
 
     def __str__(self):
         strings = []
-        for ichunk, chunk in grouper(self.super_id_codes, 8):
+        for ichunk, chunk in enumerate(grouper(self.super_id_codes, 8)):
             continuation = ichunk + 1
             if continuation > 1:
                 string = f"SPRSDE  {continuation:>2}                    "

setup.py

@@ -4,7 +4,7 @@
 
 setuptools.setup(
     name="old_pdb",
-    version="1.0.0",
+    version="1.1.0",
     description=(
         "This code reads and writes the old Protein Data Bank format."
     ),