Topology update calls

topology/core/site.py

@@ -29,6 +29,18 @@ def __init__(self,
         self._connections = list()
 
     def add_connection(self, other_site):
+        """ Add a connection between sites
+
+        Parameters
+        ---------
+        other_site : top.Site
+
+        Notes
+        -----
+        This function WILL NOT include ConnectionType information.
+        If ConnectionType information needs to be passed,
+        call top.add_connection
+        """
         self._connections.append(other_site)
 
     @property

topology/core/topology.py

@@ -19,6 +19,12 @@ def __init__(self, name="Topology", box=None):
         self._site_list = list()
         self._connection_list = list()
 
+        self._atom_types = list()
+        self._connection_types = list()
+
+        self._atom_type_functionals = list()
+        self._connection_type_functionals = list()
+
     def add_site(self, site):
         self._site_list.append(site)
 
@@ -42,6 +48,22 @@ def box(self, box):
     def n_sites(self):
         return len(self._site_list)
 
+    @property
+    def atom_types(self):
+        return self._atom_types
+
+    @property
+    def connection_types(self):
+        return self._connection_types
+
+    @property
+    def atom_type_functionals(self):
+        return [atype.nb_function for atype in self.atom_types]
+
+    @property
+    def connection_type_functionals(self):
+        return [ctype.potential_function for ctype in self.connection_types]
+
     def positions(self):
         xyz = np.empty(shape=(self.n_sites, 3)) * u.nm
         for i, site in enumerate(self.site_list):
@@ -63,13 +85,36 @@ def n_connections(self):
     def add_connection(self, connection):
         self._connection_list.append(connection)
 
+    def update_top(self):
+        """ Update the entire topology's unique types
+
+        Notes
+        -----
+        Will update: atom_types, connnection_types
+        """
+        self.update_atom_types()
+        self.update_connection_list()
+        self.update_connection_types()
+
+    def update_atom_types(self):
+        self._atom_types = []
+        for site in self.site_list:
+            if site.atom_type not in self._atom_types:
+                self._atom_types.append(site.atom_type)
+
     def update_connection_list(self):
         for site in self.site_list:
             for neighbor in site.connections:
                 temp_connection = Connection(site, neighbor, update=False)
                 if temp_connection not in self.connection_list:
                     self.add_connection(Connection(site, neighbor, update=True))
 
+    def update_connection_types(self):
+        self._connection_types = []
+        for connection in self.connection_list:
+            if connection.connection_type not in self._connection_types:
+                self._connection_types.append(connection.connection_type)
+
     def __repr__(self):
         descr = list('<')
         descr.append(self.name + ' ')

topology/tests/test_topology.py

@@ -4,7 +4,9 @@
 
 from topology.core.topology import Topology
 from topology.core.site import Site
+from topology.core.atom_type import AtomType
 from topology.core.connection import Connection
+from topology.core.connection_type import ConnectionType
 from topology.core.box import Box
 from topology.tests.base_test import BaseTest
 from topology.testing.utils import allclose
@@ -56,3 +58,67 @@ def test_positions_dtype(self):
         assert top.positions().dtype == float
         assert top.positions().units == u.nm
         assert isinstance(top.positions(), u.unyt_array)
+
+    def test_top_update(self):
+        top = Topology()
+        top.update_top()
+        assert top.n_sites == 0
+        assert len(top.atom_types) == 0
+        assert len(top.atom_type_functionals) == 0
+        assert top.n_connections == 0
+        assert len(top.connection_types) == 0
+        assert len(top.connection_type_functionals) == 0
+
+        atomtype = AtomType()
+        site1 = Site(name='site1', atom_type=atomtype)
+        top.add_site(site1)
+        site2 = Site(name='site2', atom_type=atomtype)
+        top.add_site(site2)
+        assert top.n_sites == 2
+        assert len(top.atom_types) == 0
+        assert len(top.atom_type_functionals) == 0
+        assert top.n_connections == 0
+        assert len(top.connection_types) == 0
+        assert len(top.connection_type_functionals) == 0
+        top.update_atom_types()
+        assert top.n_sites == 2
+        assert len(top.atom_types) == 1
+        assert len(top.atom_type_functionals) == 1
+        assert top.n_connections == 0
+        assert len(top.connection_types) == 0
+        assert len(top.connection_type_functionals) == 0
+
+
+        ctype = ConnectionType()
+        connection_12 = Connection(site1=site1, site2=site2, 
+                connection_type=ctype)
+        top.add_connection(connection_12)
+        assert top.n_sites == 2
+        assert len(top.atom_types) == 1
+        assert len(top.atom_type_functionals) == 1
+        assert top.n_connections == 1
+        assert len(top.connection_types) == 0
+        assert len(top.connection_type_functionals) == 0
+        top.update_connection_types()
+        assert top.n_sites == 2
+        assert len(top.atom_types) == 1
+        assert len(top.atom_type_functionals) == 1
+        assert top.n_connections == 1
+        assert len(top.connection_types) == 1
+        assert len(top.connection_type_functionals) == 1
+
+        site1.atom_type = AtomType(nb_function='sigma*epsilon')
+        assert top.n_sites == 2
+        assert len(top.atom_types) == 1
+        assert len(top.atom_type_functionals) == 1
+        assert top.n_connections == 1
+        assert len(top.connection_types) == 1
+        assert len(top.connection_type_functionals) == 1
+        top.update_atom_types()
+        assert top.n_sites == 2
+        assert len(top.atom_types) == 2
+        assert len(top.atom_type_functionals) == 2
+        assert top.n_connections == 1
+        assert len(top.connection_types) == 1
+        assert len(top.connection_type_functionals) == 1
+