use site_index for get_populated_sites

autoadsorbate/Smile.py

@@ -77,6 +77,7 @@ def conformers_from_smile(
         conf = mol.GetConformer(conf_id)
         positions = conf.GetPositions()
         atoms = Atoms(symbols, positions=positions)
+        atoms.info["smiles"] = smiles
         conformer_trj.append(atoms)
 
     print(f'User requested {to_initialize = } conformers.')

autoadsorbate/Surf.py

@@ -1608,7 +1608,7 @@ def drop_fragment_to_z_zero(atoms: Atoms) -> None:
     atoms.positions -= np.array([0, 0, min_z])
 
 
-def conformer_to_site(atoms, site, conformer, mode="optimize", overlap_thr=0):
+def conformer_to_site(atoms, site, conformer, mode="optimize", overlap_thr=0, use_swirl=True):
     """
     Aligns and attaches a conformer to a specified site on a slab of atoms, optimizing the orientation to minimize overlap.
 
@@ -1618,6 +1618,9 @@ def conformer_to_site(atoms, site, conformer, mode="optimize", overlap_thr=0):
     conformer (object): An object containing the conformer to be attached.
     mode (str): The mode of operation. Currently, only 'optimize' is supported. Default is 'optimize'.
     overlap_thr (float): The overlap threshold. Default is 0.0.
+    use_swirl (bool): Whether to optimize marked fragments with swirl_fragment
+        for Cl-marked monodentates and swing_fragment for S1S-marked
+        bidentates. Default is True.
 
     Returns:
     object: The combined atoms object with the conformer attached and optimized.
@@ -1660,25 +1663,33 @@ def conformer_to_site(atoms, site, conformer, mode="optimize", overlap_thr=0):
     # out_atoms.info['site_info'] = site
 
     if conformer.info["smiles"][:3] == "S1S":
-        out_atoms = swing_fragment(
-            atoms=out_atoms,
-            fragment_index=n_f,
-            site=site,
-            resolution=10,
-            mode=mode,
-            span_angle=50,
-            overlap_thr=overlap_thr,
-        )
+        if use_swirl:
+            out_atoms = swing_fragment(
+                atoms=out_atoms,
+                fragment_index=n_f,
+                site=site,
+                resolution=10,
+                mode=mode,
+                span_angle=50,
+                overlap_thr=overlap_thr,
+            )
+        else:
+            out_atoms.info["mdf"] = minimum_fragment_distance(out_atoms)
+            out_atoms = [out_atoms]
 
     if conformer.info["smiles"][:2] == "Cl":
-        out_atoms = swirl_fragment(
-            atoms=out_atoms,
-            fragment_index=n_f,
-            site=site,
-            resolution=10,
-            mode="optimize",
-            overlap_thr=0.0,
-        )
+        if use_swirl:
+            out_atoms = swirl_fragment(
+                atoms=out_atoms,
+                fragment_index=n_f,
+                site=site,
+                resolution=10,
+                mode="optimize",
+                overlap_thr=0.0,
+            )
+        else:
+            out_atoms.info["mdf"] = minimum_fragment_distance(out_atoms)
+            out_atoms = [out_atoms]
 
     return out_atoms
 

autoadsorbate/autoadsorbate.py

@@ -626,19 +626,23 @@ def get_populated_sites(
         overlap_thr=1.5,
         verbose=False,
         parallel=None,
+        use_swirl=True,
     ):
         """
         Populates the specified sites with the given fragment, optimizing the orientation to minimize overlap.
 
         Parameters:
         fragment (object): An object containing the fragment to be attached.
-        site_index (str or int): The index of the site to be populated. Default is 'all'.
+        site_index (str or int or list[int]): The index of the site to be populated. Default is 'all'.
         sample_rotation (bool): Whether to sample different rotations of the fragment. Default is True.
         mode (str): The mode of operation. Can be 'heuristic' or 'all'. Default is 'heuristic'.
         conformers_per_site_cap (int or None): The maximum number of conformers per site. Default None mean the maximum number of conformers.
         overlap_thr (float): The overlap threshold. Default is 1.5.
         verbose (bool): Whether to print detailed information during execution. Default is False.
         parallel (int): If value >0, parallelize the configuration on the number of CPU specified. Default None
+        use_swirl (bool): Whether to optimize marked fragments with swirl_fragment
+            for Cl-marked monodentates and swing_fragment for S1S-marked
+            bidentates. Default is True.
 
         Returns:
         list: A list containing the optimized atoms objects for each site.
@@ -649,6 +653,11 @@ def get_populated_sites(
 
         all_sites = {}
         site_df = self.site_df
+
+        if isinstance(site_index, int):
+            site_df = site_df.loc[[site_index]]
+        elif isinstance(site_index, list):
+            site_df = site_df.loc[site_index]
 
         if mode.lower() == "all":
             sites = [site_df.loc[i].to_dict() for i in site_df.index.values]
@@ -686,7 +695,10 @@ def get_populated_sites(
                     ca.rotate(a, "z")
                     conformers.append(ca)
         else:
-            conformers = [c.copy() for c in fragment.conformers]
+            conformers = [
+                fragment.get_conformer(i)
+                for i, _ in enumerate(fragment.conformers)
+            ]
 
         out_trj = []
 
@@ -702,13 +714,13 @@ def get_populated_sites(
 
             if parallel != None:
 
-                c_trj.extend(Parallel(n_jobs=parallel)(delayed(conformer_to_site)(self.atoms, site, conformer, mode="optimize", overlap_thr=0) for conformer in conformers))
+                c_trj.extend(Parallel(n_jobs=parallel)(delayed(conformer_to_site)(self.atoms, site, conformer, mode="optimize", overlap_thr=0, use_swirl=use_swirl) for conformer in conformers))
                 c_trj = [x[0] for x in c_trj]
 
             else:
                 for conformer in conformers:
                     c_trj += conformer_to_site(
-                        self.atoms, site, conformer, mode="optimize", overlap_thr=0
+                        self.atoms, site, conformer, mode="optimize", overlap_thr=0, use_swirl=use_swirl
                     )  # the zero is intentional
 
             if conformers_per_site_cap == None: