Fixes for plots, handling some failed calculations.

first_paper_example/generation.py

@@ -23,6 +23,15 @@
 )
 
 
+def failed_cage(
+    name: str,
+    database: cgexplore.utilities.AtomliteDatabase,
+) -> None:
+    """Save failed cage."""
+    res_dict = {"optimised": False}
+    database.add_properties(key=name, property_dict=res_dict)
+
+
 def optimise_cage(
     molecule: stk.Molecule,
     name: str,
@@ -307,28 +316,34 @@ def build_populations(
                 ),
             )
 
-            conformer = optimise_cage(
-                molecule=cage,
-                name=name,
-                output_dir=calculation_output,
-                forcefield=forcefield,
-                platform=platform,
-                database=database,
-            )
-            if conformer is not None:
-                conformer.molecule.write(
-                    str(struct_output / f"{name}_optc.mol")
+            try:
+                conformer = optimise_cage(
+                    molecule=cage,
+                    name=name,
+                    output_dir=calculation_output,
+                    forcefield=forcefield,
+                    platform=platform,
+                    database=database,
                 )
-            count += 1
+                if conformer is not None:
+                    conformer.molecule.write(
+                        str(struct_output / f"{name}_optc.mol")
+                    )
+                count += 1
 
-            analyse_cage(
-                conformer=conformer,
-                name=name,
-                output_dir=calculation_output,
-                forcefield=forcefield,
-                node_element=node_element,
-                ligand_element=ligand_element,
-                database=database,
-            )
+                analyse_cage(
+                    conformer=conformer,
+                    name=name,
+                    output_dir=calculation_output,
+                    forcefield=forcefield,
+                    node_element=node_element,
+                    ligand_element=ligand_element,
+                    database=database,
+                )
+            except openmm.OpenMMException:
+                failed_cage(
+                    name=name,
+                    database=database,
+                )
 
         logging.info("%s %s cages built.", count, population)

first_paper_example/plot_cages.py

@@ -742,22 +742,22 @@ def si_shape_fig(
     plt.close()
 
 
-def add_energy_to_ax(ax: mpl.Axes, energy: float) -> None:
+def add_energy_to_ax(ax: mpl.axes, energy: float) -> None:
     """Add energy to ax."""
     colorcode = "#345995" if energy <= isomer_energy() else "#CA1551"
 
     ax.set_title(round(energy, 1), fontsize=16, color=colorcode)
 
 
-def add_text_to_ax(ax: mpl.Axes, text: str) -> None:
+def add_text_to_ax(ax: mpl.axes, text: str) -> None:
     """Add text to ax."""
     x = 0.05
     y = 0.25
     ax.text(x=x, y=y, s=text, fontsize=16, transform=ax.transAxes)
 
 
 def add_structure_to_ax(
-    ax: mpl.Axes,
+    ax: mpl.axes,
     struct_name: str,
     struct_output: pathlib.Path,
     struct_figure_output: pathlib.Path,
@@ -994,8 +994,11 @@ def check_odd_outcomes(
             cdata = ton_data[ton_data["cage_name"] == cage_name]
             pair_name = get_paired_cage_name(cage_name)
             pdata = tdata[tdata["cage_name"] == pair_name]
-            ton_energy = float(cdata["energy_per_bb"].iloc[0])
-            toff_energy = float(pdata["energy_per_bb"].iloc[0])
+            try:
+                ton_energy = float(cdata["energy_per_bb"].iloc[0])
+                toff_energy = float(pdata["energy_per_bb"].iloc[0])
+            except IndexError:
+                continue
 
             # Ignore rounding errors in near zero cases.
             if ton_energy < 1e-1:  # noqa: PLR2004

first_paper_example/plot_distributions.py

@@ -835,11 +835,13 @@ def plot_topology_pore_flex(data, figure_output: pathlib.Path) -> None:
             cdata = ton_data[ton_data["cage_name"] == cage_name]
             pair_name = get_paired_cage_name(cage_name)
             pdata = tdata[tdata["cage_name"] == pair_name]
-
-            ton_energy = float(cdata["energy_per_bb"].iloc[0])
-            toff_energy = float(pdata["energy_per_bb"].iloc[0])
-            ton_pore = float(cdata["pore"].iloc[0])
-            toff_pore = float(pdata["pore"].iloc[0])
+            try:
+                ton_energy = float(cdata["energy_per_bb"].iloc[0])
+                toff_energy = float(pdata["energy_per_bb"].iloc[0])
+                ton_pore = float(cdata["pore"].iloc[0])
+                toff_pore = float(pdata["pore"].iloc[0])
+            except IndexError:
+                continue
             rel_difference = (ton_pore - toff_pore) / toff_pore
 
             differences.append(rel_difference)

first_paper_example/plot_maps.py

@@ -816,7 +816,7 @@ def pd_3p64p8_figure_bite_angle(
     """Make a plot."""
     logging.info("running pd_3p64p8_figure_bite_angle")
 
-    color_map = ("3P6", "4P8")
+    color_map = {"3P6": "tab:orange", "4P8": "tab:green"}
 
     fig, ax = plt.subplots(figsize=(8, 2.5))
     trim = all_data[all_data["vdws"] == "von"]
@@ -832,13 +832,13 @@ def pd_3p64p8_figure_bite_angle(
             ey = float(tdata["energy_per_bb"].iloc[0])
             tstr_points[tstr].append((ba, ey))
 
-    next(ax._get_lines.prop_cycler)["color"]  # noqa: SLF001
     for tstr in color_map:
         ax.plot(
             [i[0] for i in tstr_points[tstr]],
             [i[1] for i in tstr_points[tstr]],
             alpha=1.0,
             # edgecolor="k",
+            markerfacecolor=color_map[tstr],
             lw=3,
             marker="o",
             markeredgecolor="k",

first_paper_example/plot_parities.py

@@ -48,9 +48,12 @@ def parity_1(all_data: pd.DataFrame, figure_output: pathlib.Path) -> None:
             cage_name = str(row["cage_name"])
             pair_name = get_paired_cage_name(cage_name)
             d2_row = tdata[tdata["cage_name"] == pair_name]
-            d2_energy = float(d2_row["energy_per_bb"].iloc[0])
+            try:
+                d2_energy = float(d2_row["energy_per_bb"].iloc[0])
 
-            diffdata.append(d1_energy - d2_energy)
+                diffdata.append(d1_energy - d2_energy)
+            except IndexError:
+                pass
 
         xpos = tcpos[tstr]