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uibcdf · May 2, 2024 · 21cb8d2 · 21cb8d2
1 parent d5b599e
commit 21cb8d2
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Showing 3 changed files with 53 additions and 1,023 deletions.
diff --git a/molsysmt/build/add_missing_bonds.py b/molsysmt/build/add_missing_bonds.py
@@ -5,8 +5,7 @@
 @digest()
 def add_missing_bonds(molecular_system, threshold='2 angstroms', selection='all',
                       structure_indices=0, syntax='MolSysMT', engine='MolSysMT',
-                      with_templates=True, with_distances=True, in_place=True,
-                      skip_digestion=False):
+                      in_place=True, skip_digestion=False):
     """
     To be written soon...
     """
@@ -18,7 +17,6 @@ def add_missing_bonds(molecular_system, threshold='2 angstroms', selection='all'
 
         bonds = get_missing_bonds(molecular_system, threshold=threshold, selection=selection,
                                  structure_indices=structure_indices, syntax=syntax,
-                                 with_templates=with_templates, with_distances=with_distances,
                                  skip_digestion=True)
 
         return add_bonds(molecular_system, bonds, in_place=in_place, skip_digestion=True)

diff --git a/molsysmt/build/get_missing_bonds.py b/molsysmt/build/get_missing_bonds.py
@@ -44,6 +44,8 @@ def get_missing_bonds(molecular_system, threshold='2 angstroms', selection='all'
         from molsysmt.element.group.small_molecule import get_bonded_atom_pairs as _bonds_in_small_molecule
         from molsysmt.element.group.terminal_capping import is_n_terminal_capping, is_c_terminal_capping
 
+        old_bonds = get(molecular_system, bonded_atom_pairs=True)
+
         aux_lists = get(molecular_system, element='group', selection=selection, group_name=True,
                         group_type=True, atom_index=True, atom_name=True,
                         skip_digestion=True)
@@ -149,6 +151,15 @@ def get_missing_bonds(molecular_system, threshold='2 angstroms', selection='all'
                     tmp_bonds += bond
             bonds = tmp_bonds
 
+
+        if old_bonds:
+
+            tmp_bonds = []
+            for ii in bonds:
+                if ii not in old_bonds:
+                    tmp_bonds.append(ii)
+            bonds = tmp_bonds
+
     elif engine=="pytraj":
 
         from molsysmt.basic import convert, get
@@ -182,8 +193,8 @@ def get_missing_bonds(molecular_system, threshold='2 angstroms', selection='all'
 
         raise NotImplementedMethodError
 
-    #if sorted:
-    #    bonds = _sorted(bonds)
+    if sorted:
+        bonds = _sorted(bonds)
 
     return bonds