Bugfix: bonds from Lewis structure were wrong.

HISTORY.rst

@@ -1,6 +1,10 @@
 =======
 History
 =======
+2023.7.24 -- Bugfix in Lewis structure with bond orders
+ * Major issue in getting the bonds from the Lewis structure where the atoms and bond
+ orders were mixed up.
+
 2023.6.5 -- Bugfix working around MOPAC problem
  * MOPAC is not consistent about putting end of file and end of program markers in the
  AUX file. This caused carashed in SEAMM, which this fixes until MOPAC can be

mopac_step/lewis_structure.py

@@ -444,6 +444,15 @@ def analyze(self, indent="", lines=[], n_calculations=None):
  if P["use bonds"]:
  ids = configuration.atoms.ids
  if same:
+ iatoms = [ids[i] for i in bonds["i"]]
+ jatoms = [ids[j] for j in bonds["j"]]
+ configuration.bonds.delete()
+ configuration.bonds.append(
+ i=iatoms, j=jatoms, bondorder=bonds["bondorder"]
+ )
+ text += "\nReplaced the bonds in the configuration with those from the "
+ text += "Lewis structure.\n"
+ else:
  iatoms = []
  jatoms = []
  bondorders = []
@@ -458,15 +467,6 @@ def analyze(self, indent="", lines=[], n_calculations=None):
  i=iatoms, j=jatoms, bondorder=bonds["bondorder"]
  )
  text += "\nReplaced the bonds in the configuration with those from the "
- text += "Lewis structure.\n"
- else:
- iatoms = [ids[i] for i in bonds["i"]]
- jatoms = [ids[j] for j in bonds["j"]]
- configuration.bonds.delete()
- configuration.bonds.append(
- i=iatoms, j=jatoms, bondorder=bonds["bondorder"]
- )
- text += "\nReplaced the bonds in the configuration with those from the "
  text += "simple connectivity structure.\n"
 
  # Put any requested results into variables or tables