Fix bug in parsing pdb files

brennanaba · Aug 11, 2021 · 929dc05 · 929dc05
1 parent ce6bf9b
commit 929dc05
Showing 1 changed file with 5 additions and 1 deletion.
diff --git a/ABlooper/ABlooper.py b/ABlooper/ABlooper.py
@@ -73,7 +73,11 @@ def __extract_BB_coords(self):
                     i += 1
                 if cut[2] in self.__atoms:
                     j = self.__atoms.index(cut[2])
-                    coors[i, j] = np.float_(cut[6:9])
+                    # Using split for corrds doesn't always work. Following Biopython approach:
+                    x = float(line[30:38])
+                    y = float(line[38:46])
+                    z = float(line[46:54])
+                    coors[i, j] = np.array([x,y,z])
 
             # If missed CB (GLY) then add CA instead
             coors[:, 3] = np.where(np.all(coors[:, 3] != coors[:, 3], axis=-1, keepdims=True), coors[:, 0], coors[:, 3])