Merge branch 'main' into update_port_access_labels

mbuild/compound.py

@@ -1331,7 +1331,7 @@ def is_independent(self):
         if not self.parent:
             # This is the very top level, and hence have to be independent
             return True
-        elif not list(self.root.bonds()):
+        elif not self.root.bond_graph:
             # If there is no bond in the top level, then everything is independent
             return True
         else:
@@ -1679,6 +1679,52 @@ def _visualize_nglview(self, show_ports=False, color_scheme={}):
         overwrite_nglview_default(widget)
         return widget
 
+    def flatten(self, inplace=True):
+        """Flatten the hierarchical structure of the Compound.
+
+        Modify the mBuild Compound to become a Compound where there is
+        a single container (self) that contains all the particles.
+
+        Parameter
+        ---------
+        inplace : bool, optional, default=True
+            Option to perform the flatten operation inplace or return a copy
+
+        Return
+        ------
+        self : mb.Compound or None
+            return a flatten Compound if inplace is False.
+        """
+        ports_list = list(self.all_ports())
+        children_list = list(self.children)
+        particle_list = list(self.particles())
+        bond_graph = self.root.bond_graph
+
+        # Make a list of bond that involved the particles of this compound.
+        # This include bonds made exist between this compound and other
+        # component of the system
+        new_bonds = list()
+        for particle in particle_list:
+            for neighbor in bond_graph._adj.get(particle, []):
+                new_bonds.append((particle, neighbor))
+
+        # Remove all the children
+        if inplace:
+            for child in children_list:
+                # Need to handle the case when child is a port
+                self.remove(child)
+
+            # Re-add the particles and bonds
+            self.add(particle_list)
+            self.add(ports_list)
+
+            for bond in new_bonds:
+                self.add_bond(bond)
+        else:
+            comp = clone(self)
+            comp.flatten(inplace=True)
+            return comp
+
     def update_coordinates(self, filename, update_port_locations=True):
         """Update the coordinates of this Compound from a file.
 

mbuild/tests/test_compound.py

@@ -692,6 +692,41 @@ def test_particle_in_particle(self):
         assert len(list(parent.ancestors())) == 0
         assert next(parent.particles_by_name("A")) == part
 
+    def test_flatten_eth(self, ethane):
+        # Before flattening
+        assert len(ethane.children) == 2
+        assert ethane.n_particles == 8
+        assert ethane.n_bonds == 7
+
+        # Flatten with inplace = False
+        copy = ethane.flatten(inplace=False)
+        assert ethane.n_particles == copy.n_particles == len(copy.children)
+        assert ethane.n_bonds == copy.n_bonds
+
+        # After flattening
+        ethane.flatten()
+        assert len(ethane.children) == ethane.n_particles == 8
+        assert ethane.n_bonds == 7
+
+    def test_flatten_box_of_eth(self, ethane):
+        box_of_eth = mb.fill_box(compound=ethane, n_compounds=2, box=[1, 1, 1])
+        # Before flattening
+        assert len(box_of_eth.children) == 2
+        assert box_of_eth.n_bonds == 7 * 2
+        assert box_of_eth.n_particles == 8 * 2
+
+        # After flattening
+        box_of_eth.flatten()
+        assert len(box_of_eth.children) == box_of_eth.n_particles == 8 * 2
+        assert box_of_eth.n_bonds == 7 * 2
+
+    def test_flatten_with_port(self, ethane):
+        ethane.remove(ethane[2])
+        original_ports = ethane.all_ports()
+        ethane.flatten()
+        assert len(ethane.all_ports()) == len(original_ports)
+        assert ethane.all_ports()[0] == original_ports[0]
+
     @pytest.mark.skipif(
         not has_openbabel, reason="Open Babel package not installed"
     )