Remove cycle closure stuff since that's in different PR

cinnabar/femap.py

@@ -492,69 +492,3 @@ def draw_graph(self, title: str = "", filename: Union[str, None] = None):
         else:
             plt.savefig(filename, bbox_inches="tight")
 
-    def get_cycle_closure(self):
-        """Calculate the sum of DDG along all ligand cycles as a measure of convergence."""
-        network = self.to_legacy_graph()
-        y = [x[2]["calc_DDG"] for x in network.edges(data=True)]
-
-        # Find all ligand cycles
-        cycles = sorted(nx.simple_cycles(network.to_undirected()))
-        edges = network.edges
-
-        # Loop over cycles, calculate sum of DG along cycle
-        dict = {}
-        for cycle in cycles:
-
-            # Store DDG values along the cycle
-            sum_ddgs = 0
-            for inx, ligand in enumerate(cycle):
-                if inx < len(cycle) - 1:
-                    ligA = ligand
-                    ligB = cycle[inx + 1]
-                # Last ligand is connected to first ligand
-                else:
-                    ligA = ligand
-                    ligB = cycle[0]
-                # depending on the direction the edge was calculated,
-                # the sign of the DDG has to change
-                if (ligA, ligB) in list(edges):
-                    ddg = y[list(edges).index((ligA, ligB))]
-                elif (ligB, ligA) in edges:
-                    ddg = -y[list(edges).index((ligB, ligA))]
-                # sum up DDGs along cycle
-                sum_ddgs += ddg
-
-            # divide by sqrt of number of ligands in the cycle
-            # to get cycle closure error PER EDGE
-            cc = abs(sum_ddgs / math.sqrt(len(cycle)))
-            # Store cycle and cycle closure in dict
-            dict[','.join(cycle)] = round(cc, 2)
-
-        # Sort cycle closure from high to low
-        sorted_list = sorted(dict.items(), key=lambda x: x[1], reverse=True)
-
-        return sorted_list
-
-    def store_cycle_closure_to_csv(self, file='cycle_closure.csv'):
-        """Save cycle closure, sorted from highest cycle closure to lowest
-        in a csv file."""
-        sorted_list = get_cycle_closure(self)
-
-        # CSV file to store results
-        f = open(file, 'w')
-        writer = csv.writer(f, lineterminator='\n')
-        header = '# ligands in cycle, sum(DDGs) / ' \
-                 'sqrt(number of ligands in cycle)\n'
-        f.write(header)
-        writer.writerows(sorted_list)
-        f.close()
-
-        return
-
-    def plot_hist_cycle_closure(self, file='cycle_closure_hist.png'):
-
-        sorted_list = get_cycle_closure(self)
-
-        plt.hist([s[1] for s in sorted_list])
-        plt.xlabel('Cycle closure in kcal/mol')
-        plt.savefig(file, bbox_inches="tight")