cycle through reactants,products properly for TSs for cov_dep

zadorlab · Jan 9, 2025 · 29592b8 · 29592b8
1 parent 06a5643
commit 29592b8
Showing 1 changed file with 14 additions and 14 deletions.
diff --git a/pynta/main.py b/pynta/main.py
@@ -699,22 +699,22 @@ def setup_active_learning_loop(self):
 
         for ts in self.transition_states.keys():
             info_path = os.path.join(self.pynta_run_directory,ts,"info.json")
-            with open(info_path) as f:
-                info = json.load(f)
-            mol = Molecule().from_adjacency_list(info["adjlist"])
+            reactants = Molecule().from_adjacency_list(info["reactants"])
+            products = Molecule().from_adjacency_list(info["products"])
             keep_binding_vdW_bonds=False 
             keep_vdW_surface_bonds=False
-            for bd in mol.get_all_edges():
-                if bd.order == 0:
-                    if bd.atom1.is_surface_site() or bd.atom2.is_surface_site():
-                        keep_binding_vdW_bonds = True
-                        m = mol.copy(deep=True)
-                        b = m.get_bond(m.atoms(mol.atoms.index(bd.atom1)),m.atoms[mol.atoms.index(bd.atom2)])
-                        m.remove_bond(b)
-                        out = m.split()
-                        if len(out) == 1: #vdW bond is not only thing connecting adsorbate to surface
-                            keep_vdW_surface_bonds = True
-
+            for mol in [reactants,products]:
+                for bd in mol.get_all_edges():
+                    if bd.order == 0:
+                        if bd.atom1.is_surface_site() or bd.atom2.is_surface_site():
+                            keep_binding_vdW_bonds = True
+                            m = mol.copy(deep=True)
+                            b = m.get_bond(m.atoms(mol.atoms.index(bd.atom1)),m.atoms[mol.atoms.index(bd.atom2)])
+                            m.remove_bond(b)
+                            out = m.split()
+                            if len(out) == 1: #vdW bond is not only thing connecting adsorbate to surface
+                                keep_vdW_surface_bonds = True
+
             atoms = read(admol_name_path_dict[ts])
             st,_,_ = generate_TS_2D(atoms, info_path,  self.metal, self.surface_type, self.sites, self.site_adjacency, self.nslab,
                      max_dist=np.inf, allowed_structure_site_structures=allowed_structure_site_structures,