| """Plotting engines for Figure 5B (MagNET-Zero vs DFT on the DFT8K benchmark). |
| |
| The notebook computes residuals / functional-group error tables via `dft8k_residuals` and calls the |
| drawing functions here; `show_dft8k_molecule` renders the inline-only RDKit structure callouts (not |
| saved to disk). |
| """ |
| import numpy as np |
| import matplotlib.pyplot as plt |
| import seaborn as sns |
|
|
|
|
| def plot_dft8k_residual_histogram(errors, save_path, color="#5D737E", bin_width=0.0025, xlim=0.23, |
| grey_box=0.1, x_tick=0.05, figsize=(8, 3)): |
| """Draw the DFT8K residual histogram for one nucleus and save it to save_path (or skip saving |
| if save_path is None).""" |
| |
| |
| sns.set_theme(context="paper", style="white") |
| fig, ax = plt.subplots(figsize=figsize) |
| edges = np.arange(-xlim, xlim + bin_width, bin_width) |
| sns.histplot(x=errors, bins=edges, stat="count", element="bars", ax=ax, |
| color=color, edgecolor=None, alpha=0.9, linewidth=0) |
| ax.set_xlim(-xlim, xlim) |
| ax.set_xlabel("Residual vs. DFT8K (ppm)", fontsize=13) |
| ax.set_ylabel("Counts", fontsize=13) |
| if grey_box is not None: |
| ax.axvspan(-grey_box, grey_box, alpha=0.05, facecolor="k", edgecolor="none", zorder=0) |
| for xv in (-grey_box, grey_box): |
| ax.axvline(xv, color="k", ls="--", lw=1.0, alpha=0.35, zorder=1) |
| if x_tick is not None: |
| ax.set_xticks(np.arange(-np.floor(xlim / x_tick) * x_tick, xlim + x_tick / 2, x_tick)) |
| sns.despine(ax=ax, top=True, right=True) |
| ax.spines["left"].set_linewidth(0.6); ax.spines["bottom"].set_linewidth(0.6) |
| ax.tick_params(axis="both", which="major", direction="out", length=1.5, width=0.6, labelsize=10) |
| ax.minorticks_off() |
| fig.tight_layout() |
| if save_path: |
| fig.savefig(save_path, dpi=200, bbox_inches="tight") |
| plt.show() |
|
|
|
|
| def plot_dft8k_functional_group_errors(group_errors, nucleus, save_path, figsize=(7, 3.5)): |
| """Bar chart of mean |residual| by functional group for one nucleus, saved to save_path.""" |
| |
| |
| names = list(group_errors.keys()) |
| values = [group_errors[n]["mean_abs_error"] for n in names] |
| counts = [group_errors[n]["n_molecules"] for n in names] |
| fig, ax = plt.subplots(figsize=figsize) |
| bars = ax.bar(names, values, color="#4C9B8F") |
| for bar, n in zip(bars, counts): |
| ax.text(bar.get_x() + bar.get_width() / 2, bar.get_height(), f"n={n:,}", |
| ha="center", va="bottom", fontsize=8) |
| lbl = "¹H" if nucleus == "H" else "¹³C" |
| ax.set_ylabel(f"mean |{lbl} residual| (ppm)") |
| ax.set_title(f"{lbl} error by functional group (whole DFT8K set)") |
| fig.autofmt_xdate(rotation=30) |
| fig.tight_layout() |
| if save_path: |
| fig.savefig(save_path, dpi=200, bbox_inches="tight") |
| plt.show() |
|
|
|
|
| def show_dft8k_molecule(smiles, size=(350, 300)): |
| """Display an RDKit structure drawing for the given SMILES inline; nothing is saved to disk.""" |
| from rdkit import Chem |
| from rdkit.Chem.Draw import rdMolDraw2D |
| from IPython.display import Image, display |
| mol = Chem.MolFromSmiles(smiles) |
| if mol is None: |
| raise ValueError(f"RDKit could not parse SMILES: {smiles!r}") |
| drawer = rdMolDraw2D.MolDraw2DCairo(*size) |
| drawer.drawOptions().addStereoAnnotation = False |
| rdMolDraw2D.PrepareAndDrawMolecule(drawer, mol) |
| drawer.FinishDrawing() |
| display(Image(drawer.GetDrawingText())) |
|
|
