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feat(matplotlib): implement line-reaction-coordinate (#5155)
## Implementation: `line-reaction-coordinate` - matplotlib Implements the **matplotlib** version of `line-reaction-coordinate`. **File:** `plots/line-reaction-coordinate/implementations/matplotlib.py` **Parent Issue:** #4409 --- :robot: *[impl-generate workflow](https://github.com/MarkusNeusinger/pyplots/actions/runs/23388404489)* --------- Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
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‎plots/line-reaction-coordinate/implementations/matplotlib.py‎

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""" pyplots.ai
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line-reaction-coordinate: Reaction Coordinate Energy Diagram
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Library: matplotlib 3.10.8 | Python 3.14.3
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Quality: 91/100 | Created: 2026-03-21
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"""
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import matplotlib.pyplot as plt
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import numpy as np
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from matplotlib.patches import FancyArrowPatch
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# Data
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reactant_energy = 50.0
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transition_energy = 120.0
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product_energy = 20.0
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peak_pos = 0.45
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reaction_coord = np.linspace(0, 1, 500)
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sigma = 0.13
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baseline = reactant_energy + (product_energy - reactant_energy) * (3 * reaction_coord**2 - 2 * reaction_coord**3)
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gaussian_bump = (transition_energy - (reactant_energy + product_energy) / 2) * np.exp(
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-((reaction_coord - peak_pos) ** 2) / (2 * sigma**2)
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)
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energy = baseline + gaussian_bump
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peak_idx = np.argmax(energy)
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actual_peak = energy[peak_idx]
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peak_x = reaction_coord[peak_idx]
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# Plot
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fig, ax = plt.subplots(figsize=(16, 9))
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ax.plot(reaction_coord, energy, color="#306998", linewidth=3.5, zorder=3)
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# Dashed reference lines at reactant and product energy levels
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ax.hlines(reactant_energy, -0.05, 0.20, colors="#999999", linestyles="--", linewidth=1.5, alpha=0.5)
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ax.hlines(reactant_energy, 0.82, 1.12, colors="#999999", linestyles="--", linewidth=1.5, alpha=0.5)
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ax.hlines(product_energy, 0.78, 1.12, colors="#999999", linestyles="--", linewidth=1.5, alpha=0.5)
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# Transition state marker
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ax.scatter([peak_x], [actual_peak], s=140, color="#C84B31", zorder=4, edgecolors="white", linewidth=1.5)
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# Labels
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ax.text(
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0.02, reactant_energy + 4, "Reactants\n(50 kJ/mol)", fontsize=16, fontweight="medium", color="#333333", va="bottom"
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)
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ax.text(0.78, product_energy - 4, "Products\n(20 kJ/mol)", fontsize=16, fontweight="medium", color="#333333", va="top")
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ax.text(
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peak_x,
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actual_peak + 5,
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"Transition State",
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fontsize=16,
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fontweight="medium",
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color="#C84B31",
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va="bottom",
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ha="center",
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)
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# Activation energy arrow (Ea)
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ea_x = 0.14
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arrow_ea = FancyArrowPatch(
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(ea_x, reactant_energy),
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(ea_x, actual_peak),
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arrowstyle="<->",
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mutation_scale=18,
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linewidth=2,
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color="#E07A2F",
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zorder=5,
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)
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ax.add_patch(arrow_ea)
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ea_value = actual_peak - reactant_energy
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ax.text(
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ea_x + 0.03,
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(reactant_energy + actual_peak) / 2,
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f"$E_a$ = {ea_value:.0f} kJ/mol",
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fontsize=16,
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fontweight="bold",
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color="#E07A2F",
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ha="left",
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va="center",
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bbox={"boxstyle": "round,pad=0.3", "facecolor": "white", "edgecolor": "none", "alpha": 0.9},
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)
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# Enthalpy change arrow (ΔH)
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dh_x = 1.05
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arrow_dh = FancyArrowPatch(
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(dh_x, reactant_energy),
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(dh_x, product_energy),
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arrowstyle="<->",
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mutation_scale=18,
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linewidth=2,
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color="#2D8659",
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zorder=5,
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)
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ax.add_patch(arrow_dh)
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dh_value = product_energy - reactant_energy
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ax.text(
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dh_x + 0.02,
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(reactant_energy + product_energy) / 2,
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f"$\\Delta H$ = {dh_value:.0f} kJ/mol",
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fontsize=16,
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fontweight="bold",
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color="#2D8659",
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ha="left",
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va="center",
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bbox={"boxstyle": "round,pad=0.3", "facecolor": "white", "edgecolor": "none", "alpha": 0.9},
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)
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# Style
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ax.set_xlabel("Reaction Coordinate", fontsize=20)
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ax.set_ylabel("Potential Energy (kJ/mol)", fontsize=20)
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ax.set_title("line-reaction-coordinate · matplotlib · pyplots.ai", fontsize=24, fontweight="medium")
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ax.tick_params(axis="both", labelsize=16)
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ax.set_xlim(-0.05, 1.22)
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ax.set_ylim(0, actual_peak + 25)
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ax.spines["top"].set_visible(False)
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ax.spines["right"].set_visible(False)
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ax.yaxis.grid(True, alpha=0.2, linewidth=0.8)
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ax.set_xticks([])
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plt.tight_layout()
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plt.savefig("plot.png", dpi=300, bbox_inches="tight")

‎plots/line-reaction-coordinate/metadata/matplotlib.yaml‎

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library: matplotlib
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specification_id: line-reaction-coordinate
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created: '2026-03-21T20:47:52Z'
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updated: '2026-03-21T20:51:34Z'
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generated_by: claude-opus-4-5-20251101
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workflow_run: 23388404489
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issue: 4409
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python_version: 3.14.3
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library_version: 3.10.8
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preview_url: https://storage.googleapis.com/pyplots-images/plots/line-reaction-coordinate/matplotlib/plot.png
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preview_thumb: https://storage.googleapis.com/pyplots-images/plots/line-reaction-coordinate/matplotlib/plot_thumb.png
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preview_html: null
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quality_score: 91
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review:
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strengths:
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- Excellent spec compliance — all required features (Ea arrow, ΔH arrow, labeled
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species, dashed reference lines) implemented precisely
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- Strong color-coded visual storytelling with intentional color assignments for
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each element
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- Clean scientific diagram aesthetic with appropriate spine removal and subtle grid
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- Deterministic, well-structured code with no unnecessary complexity
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weaknesses:
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- 'DQ-01: Only shows single-step reaction; could demonstrate richer feature coverage'
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- 'DE-01: Could push further toward publication quality with more refined typography
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or shading under the curve'
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image_description: The plot displays a reaction coordinate energy diagram with a
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smooth blue curve (#306998) tracing from reactants at 50 kJ/mol through a transition
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state peak at ~122 kJ/mol down to products at 20 kJ/mol. The title reads "line-reaction-coordinate
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· matplotlib · pyplots.ai" in medium-weight font. The y-axis is labeled "Potential
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Energy (kJ/mol)" and the x-axis "Reaction Coordinate" (with no tick marks, appropriate
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for arbitrary units). An orange double-headed arrow on the left shows Ea = 72
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kJ/mol between reactant level and peak, with a white-background label. A green
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double-headed arrow on the right shows ΔH = -30 kJ/mol between reactant and product
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levels. A red dot marks the transition state with a label above. Dashed gray reference
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lines extend at reactant (50) and product (20) energy levels. Top and right spines
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are removed, subtle y-axis grid at alpha=0.2. Clean, professional scientific diagram.
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criteria_checklist:
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visual_quality:
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score: 30
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max: 30
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items:
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- id: VQ-01
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name: Text Legibility
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score: 8
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max: 8
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passed: true
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comment: 'All font sizes explicitly set: title 24pt, axis labels 20pt, tick
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labels 16pt, annotations 16pt'
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- id: VQ-02
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name: No Overlap
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score: 6
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max: 6
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passed: true
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comment: All text labels well-positioned with no collisions
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- id: VQ-03
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name: Element Visibility
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score: 6
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max: 6
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passed: true
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comment: Line thickness 3.5, marker s=140, arrows linewidth=2 — all clearly
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visible
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- id: VQ-04
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name: Color Accessibility
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score: 4
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max: 4
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passed: true
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comment: Blue, orange, green, red — four distinct hues, colorblind-safe
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- id: VQ-05
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name: Layout & Canvas
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score: 4
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max: 4
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passed: true
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comment: Good canvas utilization, balanced margins
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- id: VQ-06
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name: Axis Labels & Title
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score: 2
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max: 2
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passed: true
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comment: Y-axis with units, x-axis appropriate for arbitrary reaction progress
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design_excellence:
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score: 15
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max: 20
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items:
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- id: DE-01
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name: Aesthetic Sophistication
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score: 5
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max: 8
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passed: true
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comment: Custom color palette with intentional color coding, white bbox backgrounds,
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good typography hierarchy
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- id: DE-02
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name: Visual Refinement
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score: 5
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max: 6
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passed: true
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comment: Spines removed, subtle grid, hidden x-ticks, clean whitespace
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- id: DE-03
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name: Data Storytelling
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score: 5
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max: 6
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passed: true
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comment: Color-coded arrows communicate Ea and ΔH as key insights, transition
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state highlighted
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spec_compliance:
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score: 15
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max: 15
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items:
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- id: SC-01
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name: Plot Type
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score: 5
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max: 5
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passed: true
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comment: 'Correct: smooth line plot for reaction coordinate energy diagram'
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- id: SC-02
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name: Required Features
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score: 4
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max: 4
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passed: true
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comment: 'All spec requirements met: labels, arrows, dashed lines, smooth
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curve'
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- id: SC-03
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name: Data Mapping
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score: 3
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max: 3
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passed: true
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comment: X=reaction coordinate, Y=potential energy, all data visible
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- id: SC-04
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name: Title & Legend
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score: 3
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max: 3
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passed: true
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comment: Correct title format, no legend needed for annotated single-series
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data_quality:
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score: 14
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max: 15
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items:
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- id: DQ-01
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name: Feature Coverage
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score: 5
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max: 6
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passed: true
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comment: Shows single-step exothermic reaction with all key features
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- id: DQ-02
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name: Realistic Context
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score: 5
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max: 5
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passed: true
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comment: Chemistry domain, values from spec example, neutral educational context
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- id: DQ-03
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name: Appropriate Scale
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score: 4
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max: 4
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passed: true
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comment: Realistic energy values for a chemical reaction
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code_quality:
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score: 10
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max: 10
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items:
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- id: CQ-01
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name: KISS Structure
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score: 3
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max: 3
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passed: true
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comment: 'Linear flow: imports → data → plot → annotations → styling → save'
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- id: CQ-02
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name: Reproducibility
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score: 2
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max: 2
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passed: true
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comment: Fully deterministic data, no randomness
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- id: CQ-03
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name: Clean Imports
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score: 2
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max: 2
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passed: true
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comment: All three imports used
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- id: CQ-04
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name: Code Elegance
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score: 2
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max: 2
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passed: true
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comment: Clean, well-organized, appropriate complexity
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- id: CQ-05
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name: Output & API
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score: 1
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max: 1
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passed: true
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comment: Saves as plot.png with dpi=300, bbox_inches=tight
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library_mastery:
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score: 7
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max: 10
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items:
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- id: LM-01
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name: Idiomatic Usage
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score: 4
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max: 5
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passed: true
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comment: Good use of ax methods, FancyArrowPatch, proper hlines
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- id: LM-02
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name: Distinctive Features
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score: 3
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max: 5
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passed: true
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comment: FancyArrowPatch with arrowstyle is distinctively matplotlib, bbox
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dict styling on text
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verdict: APPROVED
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impl_tags:
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dependencies: []
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techniques:
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- annotations
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- patches
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patterns:
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- data-generation
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dataprep: []
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styling:
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- grid-styling
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- edge-highlighting

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