feat(pygal): implement line-reaction-coordinate

plots/line-reaction-coordinate/implementations/pygal.py

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+""" pyplots.ai
+line-reaction-coordinate: Reaction Coordinate Energy Diagram
+Library: pygal 3.1.0 | Python 3.14.3
+Quality: 85/100 | Created: 2026-03-21
+"""
+
+import numpy as np
+import pygal
+from pygal.style import Style
+
+
+# Data - Single-step exothermic reaction
+reactant_energy = 50.0  # kJ/mol
+transition_energy = 120.0  # kJ/mol
+product_energy = 20.0  # kJ/mol
+activation_energy = transition_energy - reactant_energy  # Ea = 70 kJ/mol
+enthalpy_change = product_energy - reactant_energy  # ΔH = -30 kJ/mol
+
+# Generate smooth energy profile
+n_points = 300
+reaction_coord = np.linspace(0, 10, n_points)
+
+# Gaussian barrier centered at transition state
+sigma = 1.2
+peak_pos = 5.0
+base_curve = reactant_energy + (transition_energy - reactant_energy) * np.exp(
+    -0.5 * ((reaction_coord - peak_pos) / sigma) ** 2
+)
+
+# Vectorized Hermite smoothstep transition to product energy
+t_raw = np.clip((reaction_coord - 6.5) / 2.0, 0.0, 1.0)
+smooth_t = t_raw * t_raw * (3 - 2 * t_raw)
+base_curve = base_curve * (1 - smooth_t) + product_energy * smooth_t
+
+# Vectorized tail flattening
+base_curve = np.where(reaction_coord < 1.5, reactant_energy, base_curve)
+base_curve = np.where(reaction_coord > 8.5, product_energy, base_curve)
+
+# Smooth join regions with repeated convolution
+kernel = np.ones(17) / 17
+energy_curve = base_curve.copy()
+for _ in range(3):
+    padded = np.pad(energy_curve, 17, mode="edge")
+    energy_curve = np.convolve(padded, kernel, mode="same")[17:-17]
+
+curve_points = list(zip(reaction_coord.tolist(), energy_curve.tolist(), strict=True))
+
+# Colorblind-safe palette
+BLUE = "#306998"
+DARK_BLUE = "#1A4971"
+TEAL = "#2980B9"
+ORANGE = "#E67E22"
+GRAY = "#AAAAAA"
+
+# Style — y-guides at key energies serve as reference lines
+custom_style = Style(
+    background="white",
+    plot_background="#FAFBFC",
+    foreground="#2C3E50",
+    foreground_strong="#2C3E50",
+    foreground_subtle="#CCCCCC",
+    colors=(BLUE, GRAY, GRAY, TEAL, ORANGE, DARK_BLUE, BLUE, BLUE),
+    title_font_size=60,
+    label_font_size=40,
+    major_label_font_size=36,
+    legend_font_size=32,
+    value_font_size=28,
+    stroke_width=5,
+)
+
+# Chart
+chart = pygal.XY(
+    width=4800,
+    height=2700,
+    style=custom_style,
+    title="line-reaction-coordinate \u00b7 pygal \u00b7 pyplots.ai",
+    x_title="Reaction Coordinate",
+    y_title="Potential Energy (kJ/mol)",
+    show_legend=True,
+    legend_at_bottom=True,
+    legend_at_bottom_columns=5,
+    show_x_guides=False,
+    show_y_guides=True,
+    show_x_labels=False,
+    dots_size=0,
+    stroke=True,
+    margin=80,
+    margin_left=260,
+    margin_right=160,
+    margin_bottom=200,
+    margin_top=120,
+    range=(8, 140),
+    xrange=(-0.2, 10.2),
+    truncate_legend=-1,
+    tooltip_border_radius=8,
+)
+
+# Main energy curve
+chart.add("Energy Profile", curve_points, stroke_style={"width": 6}, show_dots=False, fill=False)
+
+# Horizontal reference lines at reactant and product energy levels
+chart.add(
+    None,
+    [(0.0, reactant_energy), (10.0, reactant_energy)],
+    stroke_style={"width": 3, "dasharray": "16, 8"},
+    show_dots=False,
+)
+chart.add(
+    None,
+    [(0.0, product_energy), (10.0, product_energy)],
+    stroke_style={"width": 3, "dasharray": "16, 8"},
+    show_dots=False,
+)
+
+# Ea vertical indicator at transition state peak (teal — colorblind-safe)
+ea_x = peak_pos
+chart.add(
+    f"Ea = {activation_energy:.0f} kJ/mol",
+    [{"value": (ea_x, reactant_energy), "node": {"r": 14}}, {"value": (ea_x, transition_energy), "node": {"r": 14}}],
+    stroke_style={"width": 5, "dasharray": "8, 5"},
+)
+
+# ΔH vertical indicator (orange — colorblind-safe)
+dh_x = 8.5
+chart.add(
+    f"\u0394H = {enthalpy_change:.0f} kJ/mol",
+    [{"value": (dh_x, reactant_energy), "node": {"r": 14}}, {"value": (dh_x, product_energy), "node": {"r": 14}}],
+    stroke_style={"width": 5, "dasharray": "8, 5"},
+)
+
+# Transition state marker (larger, dark blue)
+chart.add(
+    "Transition State (\u2021)",
+    [{"value": (peak_pos, transition_energy), "node": {"r": 22}}],
+    stroke_style={"width": 0},
+    dots_size=22,
+)
+
+# Reactant marker
+chart.add(
+    f"Reactants ({reactant_energy:.0f} kJ/mol)",
+    [{"value": (1.0, reactant_energy), "node": {"r": 16}}],
+    stroke_style={"width": 0},
+    dots_size=16,
+)
+
+# Product marker
+chart.add(
+    f"Products ({product_energy:.0f} kJ/mol)",
+    [{"value": (9.5, product_energy), "node": {"r": 16}}],
+    stroke_style={"width": 0},
+    dots_size=16,
+)
+
+# Custom y-axis labels at chemically meaningful values
+chart.y_labels = [
+    {"label": f"{product_energy:.0f}", "value": product_energy},
+    {"label": f"{reactant_energy:.0f}", "value": reactant_energy},
+    {"label": "80", "value": 80},
+    {"label": "100", "value": 100},
+    {"label": f"{transition_energy:.0f}", "value": transition_energy},
+]
+
+# Save
+chart.render_to_file("plot.html")
+chart.render_to_png("plot.png")