Fix bug skipping ccd bonds when constructing molsys

src/chilife/MolSys.py

@@ -1002,7 +1002,9 @@ def __init__(
 
         # Atoms creation is required to be last
         self.atoms = AtomSelection(self, self.mask, self._bond_mask)
-        self.topology = Topology(self, bonds, bond_types) if bonds is not None else None
+        self.topology = (
+            Topology(self, self._bonds, self._bond_types) if bonds is not None else None
+        )
 
     @classmethod
     def from_pdb(cls, file_name, sort_atoms=False, **kwargs):

src/chilife/__init__.py

@@ -1,9 +1,24 @@
 import logging
+
 logging.getLogger("MDAnalysis").setLevel(logging.ERROR)
 
-from .chilife import (distance_distribution, confidence_interval, create_library, create_dlibrary, add_rotlib_dir,
-                      remove_rotlib_dir, add_library, remove_library, add_dihedral_def, add_to_defaults,
-                      remove_from_defaults, list_available_rotlibs, rotlib_info, repack, add_to_toml)
+from .chilife import (
+    distance_distribution,
+    confidence_interval,
+    create_library,
+    create_dlibrary,
+    add_rotlib_dir,
+    remove_rotlib_dir,
+    add_library,
+    remove_library,
+    add_dihedral_def,
+    add_to_defaults,
+    remove_from_defaults,
+    list_available_rotlibs,
+    rotlib_info,
+    repack,
+    add_to_toml,
+)
 from .globals import *
 from .io import *
 from .alignment_methods import parse_backbone, global_mx, local_mx
@@ -29,4 +44,4 @@
 # SpinLabel = SpinLabel.SpinLabel
 # dSpinLabel = dSpinLabel.dSpinLabel
 
-__version__ = '1.2.0'
+__version__ = "1.2.1"