testing of topology in graph

Pipfile

@@ -6,11 +6,5 @@ name = "pypi"
 [packages]
 mdstudio = {path = "../../mdstudio/", editable = true}
 local = {path = "./", editable = true}
-
-mdstudio = {path = "../../mdstudio/", editable = true}
-local = {path = "./", editable = true}
-cerise_client = ">=0.2.4"
-numpy = "*"
-pyparsing = "*"
-panedr = ">=0.2"
-retrying = ">=1.3.3"
+lie_graph = "*"
+numpy = "*"

setup.py

@@ -39,7 +39,7 @@
     packages=find_packages(),
     package_data={'lie_topology': ['data/*']},
     py_modules=[distribution_name],
-    install_requires=['mdstudio', 'numpy'],
+    install_requires=['mdstudio', 'numpy','lie_graph'],
     include_package_data=False,
     zip_safe=True,
     classifiers=[

tests/__main__.py

@@ -0,0 +1,83 @@
+from lie_graph import GraphAxis
+from enum import Enum
+
+class NodeType(Enum):
+    Atom     = 1
+    Molecule = 2
+    Group    = 3
+    Angle    = 4
+    Dihedral = 5
+
+class EdgeType(Enum):
+    Bond     = 1
+    Angle    = 2
+    Dihedral = 3
+
+if __name__ == '__main__':
+
+    print('running debug version of lie_topology')
+    system = GraphAxis()
+
+    # testing a molecule graph setup
+    system = GraphAxis()
+    system.add_node(type=NodeType.Atom, name='H1', atom_number='0', element='H')
+    system.add_node(type=NodeType.Atom, name='H2', atom_number='1', element='H')
+    system.add_node(type=NodeType.Atom, name='C1', atom_number='2', element='C')
+    system.add_node(type=NodeType.Atom, name='H3', atom_number='3', element='H')
+    system.add_node(type=NodeType.Atom, name='C2', atom_number='4', element='C')
+    system.add_node(type=NodeType.Atom, name='H4', atom_number='5', element='H')
+    system.add_node(type=NodeType.Atom, name='H5', atom_number='6', element='H')
+    system.add_node(type=NodeType.Atom, name='C3', atom_number='7', element='C')
+    system.add_node(type=NodeType.Atom, name='H6', atom_number='8', element='H')
+    system.add_node(type=NodeType.Atom, name='H7', atom_number='9', element='H')
+    system.add_node(type=NodeType.Atom, name='H8', atom_number='10', element='H')
+
+    system.add_node(type=NodeType.Molecule, name='Propane')
+
+    angle_1_nid = system.add_node(type=NodeType.Angle)
+
+    print(system)
+    print(system.query_nodes(query={'element':'H'}))
+    print(system.query_nodes(query={'name':'H8'}))
+    print(system.query_nodes(query={'type':NodeType.Atom}))
+    print(system.query_nodes(query={'type':NodeType.Molecule}))
+
+    system.add_edge(system.query_nodes(query={'name':'H1'}).nid, 
+                    system.query_nodes(query={'name':'C1'}).nid,
+                    type=EdgeType.Bond)
+    system.add_edge(system.query_nodes(query={'name':'H2'}).nid, 
+                    system.query_nodes(query={'name':'C1'}).nid,
+                    type=EdgeType.Bond)
+    system.add_edge(system.query_nodes(query={'name':'C1'}).nid, 
+                    system.query_nodes(query={'name':'H3'}).nid,
+                    type=EdgeType.Bond)
+    system.add_edge(system.query_nodes(query={'name':'C1'}).nid, 
+                    system.query_nodes(query={'name':'C2'}).nid,
+                    type=EdgeType.Bond)
+    system.add_edge(system.query_nodes(query={'name':'C2'}).nid, 
+                    system.query_nodes(query={'name':'H4'}).nid,
+                    type=EdgeType.Bond)
+    system.add_edge(system.query_nodes(query={'name':'C2'}).nid, 
+                    system.query_nodes(query={'name':'H5'}).nid,
+                    type=EdgeType.Bond)
+    system.add_edge(system.query_nodes(query={'name':'C2'}).nid, 
+                    system.query_nodes(query={'name':'C3'}).nid,
+                    type=EdgeType.Bond)
+    system.add_edge(system.query_nodes(query={'name':'C3'}).nid, 
+                    system.query_nodes(query={'name':'H6'}).nid,
+                    type=EdgeType.Bond)
+    system.add_edge(system.query_nodes(query={'name':'C3'}).nid, 
+                    system.query_nodes(query={'name':'H7'}).nid,
+                    type=EdgeType.Bond)
+    system.add_edge(system.query_nodes(query={'name':'C3'}).nid, 
+                    system.query_nodes(query={'name':'H8'}).nid,
+                    type=EdgeType.Bond)
+
+    system.add_edge(angle_1_nid, system.query_nodes(query={'name':'H1'}).nid, type=EdgeType.Angle)
+    system.add_edge(angle_1_nid, system.query_nodes(query={'name':'C1'}).nid, type=EdgeType.Angle)
+    system.add_edge(angle_1_nid, system.query_nodes(query={'name':'H3'}).nid, type=EdgeType.Angle)
+
+    #system.add_node(type=Type.Molecule, node=system )
+    print ( "___TEST_EDGES__" )
+    print(system)
+    print(system.query_edges(query={'type':EdgeType.Angle}))