Debugging

lcmd-epfl · May 2, 2024 · 0a6298c · 0a6298c
1 parent c568bb0
commit 0a6298c
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Showing 2 changed files with 4 additions and 3 deletions.
diff --git a/cell2mol/c2m_driver.py b/cell2mol/c2m_driver.py
@@ -90,7 +90,7 @@
     # Loads the reference molecules and checks_missing_H
     # TODO : reconstruct the unit cell without using reference molecules
     # TODO : reconstruct the unit cell using (only reconstruction of) reference molecules and Space group
-    newcell.get_reference_molecules(ref_labels, ref_fracs, cov_factor=1.4, debug=debug) 
+    newcell.get_reference_molecules(ref_labels, ref_fracs, debug=debug) 
     ref_pos = frac2cart_fromparam(ref_fracs, cellparam)
     writexyz(current_dir, "Ref_All_{}.xyz".format(name), ref_labels, ref_pos)
     if not newcell.has_isolated_H:  newcell.check_missing_H(debug=debug)                                     

diff --git a/cell2mol/missingH.py b/cell2mol/missingH.py
@@ -129,7 +129,7 @@ def check_missingH(refmoleclist: list, debug: int=0):
                         if ismissingH:
                             if debug >= 2: print("")
                             if debug >= 2: print(f"WARNING in Missing H function for: {ref.type}, {idx}, {ref.labels}")
-                            if debug >= 2: print(f"C Atom {kdx} has missing H atoms")
+                            if debug >= 2: print(f"C Atom {kdx} {a.get_parent_index('molecule')} has missing H atoms")
                             if debug >= 2: print(report)
                             Missing_H_in_C = True
         else:
@@ -147,11 +147,12 @@ def check_missingH(refmoleclist: list, debug: int=0):
                             print("Adjacency",a.adjacency)
                             for adj in a.adjacency:
                                 bonded_atom_coord.append(lig.get_parent("molecule").coord[adj])
+
                             ismissingH, report = get_missingH_from_adjacency(a.atnum, a.coord, bonded_atom_coord)
                             if ismissingH:
                                 if debug >= 2: print("")
                                 if debug >= 2: print(f"WARNING in Missing H function for: {ref.type}, {idx}, {jdx}, {lig.labels}")
-                                if debug >= 2: print(f"C Atom {kdx} has missing H atoms")
+                                if debug >= 2: print(f"C Atom {kdx} {a.get_parent_index('molecule')} has missing H atoms")
                                 if debug >= 2: print(report)
                                 Missing_H_in_C = True