bugfix in pdb parser

pdb that failed to parse: 2J88
it had a missing CA and so was excluded from res/pdb_idx, but then failed during full atom pass.

inference/utils.py

@@ -539,17 +539,13 @@ def parse_pdb(filename, **kwargs):
 
 def parse_pdb_lines(lines, parse_hetatom=False, ignore_het_h=True):
     # indices of residues observed in the structure
-    res = [
-        (l[22:26], l[17:20])
-        for l in lines
-        if l[:4] == "ATOM" and l[12:16].strip() == "CA"
-    ]
+    res, pdb_idx = [],[]
+    for l in lines:
+      if l[:4] == "ATOM" and l[12:16].strip() == "CA":
+        res.append((l[22:26], l[17:20]))
+        # chain letter, res num
+        pdb_idx.append((l[21:22].strip(), int(l[22:26].strip())))
     seq = [util.aa2num[r[1]] if r[1] in util.aa2num.keys() else 20 for r in res]
-    pdb_idx = [
-        (l[21:22].strip(), int(l[22:26].strip()))
-        for l in lines
-        if l[:4] == "ATOM" and l[12:16].strip() == "CA"
-    ]  # chain letter, res num
 
     # 4 BB + up to 10 SC atoms
     xyz = np.full((len(res), 14, 3), np.nan, dtype=np.float32)
@@ -562,16 +558,17 @@ def parse_pdb_lines(lines, parse_hetatom=False, ignore_het_h=True):
             " " + l[12:16].strip().ljust(3),
             l[17:20],
         )
-        idx = pdb_idx.index((chain, resNo))
-        # for i_atm, tgtatm in enumerate(util.aa2long[util.aa2num[aa]]):
-        for i_atm, tgtatm in enumerate(
-            util.aa2long[util.aa2num[aa]][:14]
-        ):  # Nate's proposed change
-            if (
-                tgtatm is not None and tgtatm.strip() == atom.strip()
-            ):  # ignore whitespace
-                xyz[idx, i_atm, :] = [float(l[30:38]), float(l[38:46]), float(l[46:54])]
-                break
+        if (chain,resNo) in pdb_idx:
+          idx = pdb_idx.index((chain, resNo))
+          # for i_atm, tgtatm in enumerate(util.aa2long[util.aa2num[aa]]):
+          for i_atm, tgtatm in enumerate(
+              util.aa2long[util.aa2num[aa]][:14]
+          ):  # Nate's proposed change
+              if (
+                  tgtatm is not None and tgtatm.strip() == atom.strip()
+              ):  # ignore whitespace
+                  xyz[idx, i_atm, :] = [float(l[30:38]), float(l[38:46]), float(l[46:54])]
+                  break
 
     # save atom mask
     mask = np.logical_not(np.isnan(xyz[..., 0]))