{"spec_id":"spectrum-nmr","library":"bokeh","language":"python","code":"\"\"\" anyplot.ai\nspectrum-nmr: NMR Spectrum (Nuclear Magnetic Resonance)\nLibrary: bokeh 3.9.0 | Python 3.13.13\nQuality: 92/100 | Updated: 2026-06-03\n\"\"\"\n\nimport os\nimport sys\nimport time\nfrom pathlib import Path\n\n\n# bokeh.py is the script name — remove its directory from sys.path so that\n# `import bokeh` resolves to the installed package, not this file itself.\n_here = os.path.dirname(os.path.abspath(__file__))\nsys.path[:] = [p for p in sys.path if os.path.abspath(p) != _here]\n\nimport numpy as np\nfrom bokeh.io import output_file, save\nfrom bokeh.models import ColumnDataSource, HoverTool, Label, Span\nfrom bokeh.plotting import figure\nfrom selenium import webdriver\nfrom selenium.webdriver.chrome.options import Options\n\n\n# Theme tokens\nTHEME = os.getenv(\"ANYPLOT_THEME\", \"light\")\nPAGE_BG = \"#FAF8F1\" if THEME == \"light\" else \"#1A1A17\"\nELEVATED_BG = \"#FFFDF6\" if THEME == \"light\" else \"#242420\"\nINK = \"#1A1A17\" if THEME == \"light\" else \"#F0EFE8\"\nINK_SOFT = \"#4A4A44\" if THEME == \"light\" else \"#B8B7B0\"\nINK_MUTED = \"#6B6A63\" if THEME == \"light\" else \"#A8A79F\"\n\n# Imprint palette — first series always #009E73\nBRAND = \"#009E73\"\n\n# Data - synthetic 1H NMR spectrum of ethanol (CH3-CH2-OH)\nnp.random.seed(42)\nppm = np.linspace(-0.5, 12.0, 6000)\nw = 0.008  # Lorentzian peak width\nj = 0.07  # J-coupling constant\n\n# TMS reference peak at 0 ppm (singlet)\nw_tms = 0.006\nspectrum = 0.3 * w_tms**2 / ((ppm - 0.0) ** 2 + w_tms**2)\n\n# CH3 triplet near 1.18 ppm (intensity ratio 1:2:1)\nspectrum += 0.5 * w**2 / ((ppm - (1.18 - j)) ** 2 + w**2)\nspectrum += 1.0 * w**2 / ((ppm - 1.18) ** 2 + w**2)\nspectrum += 0.5 * w**2 / ((ppm - (1.18 + j)) ** 2 + w**2)\n\n# OH singlet near 2.61 ppm\nspectrum += 0.4 * w**2 / ((ppm - 2.61) ** 2 + w**2)\n\n# CH2 quartet near 3.69 ppm (intensity ratio 1:3:3:1)\nspectrum += 0.3 * w**2 / ((ppm - (3.69 - 1.5 * j)) ** 2 + w**2)\nspectrum += 0.9 * w**2 / ((ppm - (3.69 - 0.5 * j)) ** 2 + w**2)\nspectrum += 0.9 * w**2 / ((ppm - (3.69 + 0.5 * j)) ** 2 + w**2)\nspectrum += 0.3 * w**2 / ((ppm - (3.69 + 1.5 * j)) ** 2 + w**2)\n\n# Subtle baseline noise\nspectrum += np.random.normal(0, 0.003, len(ppm))\nspectrum = np.maximum(spectrum, 0)\n\n# Molecular group label for each data point (enriches interactive tooltip)\n_peak_centers = [(0.0, \"TMS\"), (1.18, \"CH₃ triplet\"), (2.61, \"OH singlet\"), (3.69, \"CH₂ quartet\")]\ngroups = np.array([\"baseline\"] * len(ppm), dtype=object)\nfor _center, _name in _peak_centers:\n    groups[np.abs(ppm - _center) < 0.6] = _name\n\nsource = ColumnDataSource(data={\"ppm\": ppm, \"intensity\": spectrum, \"group\": groups})\n\n# Title with length-scaled fontsize (bokeh default '50pt' baseline at 67 chars)\ntitle_text = \"¹H NMR Spectrum of Ethanol · spectrum-nmr · python · bokeh · anyplot.ai\"\nn = len(title_text)\nratio = 67 / n if n > 67 else 1.0\ntitle_fontsize = f\"{max(34, round(50 * ratio))}pt\"\n\n# Figure: 3200×1800, reversed x-axis (NMR convention: high ppm on left)\np = figure(\n    width=3200,\n    height=1800,\n    title=title_text,\n    x_axis_label=\"Chemical Shift (ppm)\",\n    y_axis_label=\"Intensity (a.u.)\",\n    x_range=(12.0, -0.5),\n    toolbar_location=None,\n    min_border_bottom=160,\n    min_border_left=180,\n    min_border_top=110,\n    min_border_right=50,\n)\n\n# Subtle functional-group region shading (behind data layer)\n_region_coords = [(-0.25, 0.25), (0.90, 1.50), (2.20, 3.05), (3.30, 4.10)]\nfor r_left, r_right in _region_coords:\n    p.quad(top=1.45, bottom=-0.02, left=r_left, right=r_right, fill_color=BRAND, fill_alpha=0.06, line_color=None)\n\n# Filled area under spectrum — Imprint brand green with light alpha\np.varea(x=\"ppm\", y1=0, y2=\"intensity\", source=source, fill_color=BRAND, fill_alpha=0.12)\n\n# Spectrum line\np.line(x=\"ppm\", y=\"intensity\", source=source, line_color=BRAND, line_width=2.5)\n\n# TMS reference: dashed vertical line at 0 ppm\ntms_span = Span(\n    location=0.0, dimension=\"height\", line_color=INK_MUTED, line_width=1.5, line_dash=\"dashed\", line_alpha=0.7\n)\np.add_layout(tms_span)\n\n# Peak annotations with chemical shift values\npeak_labels = [\n    (0.0, 0.3, \"TMS\\n0.00 ppm\"),\n    (1.18, 1.0, \"CH₃ (triplet)\\n1.18 ppm\"),\n    (2.61, 0.4, \"OH (singlet)\\n2.61 ppm\"),\n    (3.69, 0.9, \"CH₂ (quartet)\\n3.69 ppm\"),\n]\nfor ppm_val, y_val, text in peak_labels:\n    p.add_layout(\n        Label(\n            x=ppm_val,\n            y=y_val + 0.06,\n            text=text,\n            text_font_size=\"22pt\",\n            text_color=INK,\n            text_font_style=\"bold\",\n            text_align=\"center\",\n        )\n    )\n\n# HoverTool for interactive HTML exploration\np.add_tools(\n    HoverTool(\n        tooltips=[(\"Group\", \"@group\"), (\"Chemical Shift\", \"@ppm{0.00} ppm\"), (\"Intensity\", \"@intensity{0.000}\")],\n        mode=\"vline\",\n    )\n)\n\n# Theme-adaptive chrome\np.background_fill_color = PAGE_BG\np.border_fill_color = PAGE_BG\np.outline_line_color = None  # L-shaped frame: axes only, no enclosing box\n\np.title.text_font_size = title_fontsize\np.title.text_color = INK\np.title.text_font_style = \"bold\"\n\np.xaxis.axis_label_text_font_size = \"42pt\"\np.yaxis.axis_label_text_font_size = \"42pt\"\np.xaxis.major_label_text_font_size = \"34pt\"\np.yaxis.major_label_text_font_size = \"34pt\"\np.xaxis.axis_label_text_color = INK\np.yaxis.axis_label_text_color = INK\np.xaxis.major_label_text_color = INK_SOFT\np.yaxis.major_label_text_color = INK_SOFT\np.xaxis.axis_line_color = INK_SOFT\np.yaxis.axis_line_color = INK_SOFT\np.xaxis.major_tick_line_color = INK_SOFT\np.yaxis.major_tick_line_color = INK_SOFT\np.xaxis.minor_tick_line_color = None\np.yaxis.minor_tick_line_color = None\n\n# Grid: y-axis only, very subtle\np.xgrid.grid_line_alpha = 0\np.ygrid.grid_line_color = INK\np.ygrid.grid_line_alpha = 0.12\n\n# Y range: zero baseline with headroom for peak labels\np.y_range.start = -0.02\np.y_range.end = 1.45\n\n# Save interactive HTML\noutput_file(f\"plot-{THEME}.html\")\nsave(p)\n\n# Screenshot via headless Chrome (export_png is broken on this system)\nW, H = 3200, 1800\nopts = Options()\nfor arg in (\n    \"--headless=new\",\n    \"--no-sandbox\",\n    \"--disable-dev-shm-usage\",\n    \"--disable-gpu\",\n    f\"--window-size={W},{H}\",\n    \"--hide-scrollbars\",\n):\n    opts.add_argument(arg)\ndriver = webdriver.Chrome(options=opts)\n# CDP override makes the inner viewport authoritative — --window-size alone\n# is reduced by Chrome UI chrome in headless mode (gives 1661 instead of 1800)\ndriver.execute_cdp_cmd(\n    \"Emulation.setDeviceMetricsOverride\", {\"width\": W, \"height\": H, \"deviceScaleFactor\": 1, \"mobile\": False}\n)\ndriver.get(f\"file://{Path(f'plot-{THEME}.html').resolve()}\")\ntime.sleep(3)\ndriver.save_screenshot(f\"plot-{THEME}.png\")\ndriver.quit()\n"}