example of alali use with grover search

Examples/interactingwithgrover.py

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+from qiskit.aqua.algorithms import Grover
+from qiskit.aqua import QuantumInstance
+from qiskit import Aer
+from qiskit import BasicAer
+from qiskit import execute
+from qiskit import QuantumCircuit
+from qiskit import QuantumRegister
+from qiskit.visualization import plot_histogram
+from pytket.circuit import Circuit
+from pytket.qiskit import tk_to_qiskit
+import ALALI
+
+#In this example, we will be setting up Grover's search on top of ALALI for Guanine. 
+# The results of this algorithm could be used to determine the differences in polarity, diffusional response, electron hole
+# behavior, and more. Note: No particular use case is given here. Rather, this tutorial is to show you how simple it is to connect
+# ALALI to IBM Q libraries. Please read the wiki to see how to best understand results for real use cases.
+
+
+#First, we will go ahead and get a graph for glycine.
+
+def getAtomicGraph(moleculeInfo):
+    glycineRep = ALALI.molecule(moleculeInfo, 'smi')
+    ALALI.print_circuit(glycineRep.circuit)
+    print(glycineRep.graph.nodes(data=True))
+    return glycineRep.graph 
+
+#now, we will set up our oracle function. This sets up the qubits so that they have different qubit frequencies and wavelengths
+#that can be used to represent the different characteristic that Grover will search for. In this case, 
+#we are going to set up a function that sets up every qubit's gate frequency of the number of valance electrons in each element
+#to help set up grover to help qubits represent electronic weight differences between atoms.
+def construct_oracle(graph):
+    """Generate the initial, unrouted circuit with the Rz gates based on electrostatics, given a networkx graph
+
+    Parameters
+    ----------
+    mol_graph : networkx graph
+        Networkx graph with nodes:atoms and edges:bonds
+
+    Returns
+    -------
+    pytket Circuit
+        simple pytket circuit with a qubit for each atom
+
+    Notes
+    -----
+    The qubits are labelled with integers that match the integers found in
+    the inputted networkx graph node labels"""
+    # - generate list of edges along with list of inverted edges
+    # - combine the inverted edges with non-inverted ones
+
+    edges = list(graph.edges)
+    inv_edges = [(edge[1], edge[0]) for edge in edges]
+    combinededges = [val for pair in zip(edges, inv_edges) for val in pair]
+
+    # Create circuit and unpack each edge, applying it as a our new circuit
+    constraint_test_circuit = Circuit(graph.number_of_nodes())
+    for qubit in range(graph.number_of_nodes()):
+        constraint_test_circuit.H(qubit)
+
+    # Go through every node and add the Rz gate that tries to represent electronic differences between the different atoms
+    for index in range(0, graph.number_of_nodes()):
+        if (graph.nodes[index]['symbol'] == 'O'):
+            constraint_test_circuit.Rz(6*(3.14)/2, index)
+        if (graph.nodes[index]['symbol'] == 'H'):
+            constraint_test_circuit.Rz(1*(3.14)/2, index)
+        if (graph.nodes[index]['symbol'] == 'N'):
+            constraint_test_circuit.Rz(5*(3.14)/2, index)
+        if (graph.nodes[index]['symbol'] == 'C'):
+            constraint_test_circuit.Rz(4*(3.14)/2, index)
+
+    return constraint_test_circuit
+
+#Now, we will actually set up our Grover diffusion algorithm. We will be following the same steps as laid out by IBM Qiskit's tutorials. (https://qiskit.org/textbook/ch-algorithms/grover.html#3.-Example:-3-Qubits-)
+#The main difference between their guide and ours is that we expanded upon their 3 qubit setup to create cells of such activity across all qubits, as 9 (number of nodes here) is a multiple of 3. 
+#But, it would make sense to use the CX and 2 gate setup as shown for any multiple of two. 
+
+def runGrovers(oracle):
+    """Apply inversion about the average step of Grover's algorithm."""
+
+    qubits = oracle.qubits
+    nqubits = len(qubits)
+
+    for q in range(nqubits):
+        oracle.H(q)
+        oracle.X(q)
+
+      # Do controlled-Z
+    for q in range(nqubits-2):
+        oracle.H(q+2)
+        oracle.CCX(q,q+1,q+2)
+        oracle.H(q+2)
+
+    for q in range(nqubits):
+        oracle.X(q)
+        oracle.H(q)
+    ALALI.print_circuit(oracle)
+    return oracle
+
+
+glycineSmiles = 'C(C(=O)O)N'
+oracle = construct_oracle(getAtomicGraph(glycineSmiles))
+#need to convert the pytket created circuit into one that IBM can understand
+grover_circuit = tk_to_qiskit(runGrovers(oracle))
+#need to measure all results
+grover_circuit.measure_all()
+#Now, we can setup an actual device to try out our search algorithm, yay!
+backend = Aer.get_backend('qasm_simulator')
+shots = 1024
+results = execute(grover_circuit, backend=backend, shots=shots).result()
+answer = results.get_counts()
+plot_histogram(answer)
+
+#Okay, now you should see a pretty graph showing you your different qubit states and their respective probabilities. 
+#As you can see, this algorithm does show the species within the chemical system that have the most polarity. However, this could 
+#be further refined to best actually fit the respecive noises seen by each element involved.
+
+
+