use box from pdb in correct fashion

marrink-lab · Aug 25, 2023 · 8932b99 · 8932b99
1 parent e3dff3f
commit 8932b99
Showing 1 changed file with 2 additions and 4 deletions.
diff --git a/polyply/src/topology.py b/polyply/src/topology.py
@@ -40,16 +40,14 @@
 def _coord_parser(path, extension):
     reader = COORD_PARSERS[extension]
     molecules = reader(path, exclude=())
-    box = None
     if extension == "pdb":
-        if hasattr(reader, "cryst"):
-            box = np.array([reader.cryst[item] for item in ['a', 'b', 'c', 'alpha', 'beta', 'gamma']])
         molecule = molecules[0]
         for new_mol in molecules[1:]:
             molecule.merge_molecule(new_mol)
     else:
         molecule = molecules
-        box = molecule.box
+
+    box = molecule.box
     positions = np.array(list(nx.get_node_attributes(molecule, "position").values()))
     return positions, box