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"cells": [
{
"cell_type": "markdown",
"id": "a8256e57",
"metadata": {},
"source": [
"# SI Figure S15: per-solute RMSE with delta-22 composite coefficients applied\n",
"\n",
"Per-solute ¹H and ¹³C RMSE for the natural-products / olefin-isomer test set with delta-22\n",
"coefficients applied (reproduces Figure 5C in ¹H, plus the ¹³C analogue), plus fitting-RMSE\n",
"comparisons across coefficient choices, feature-space coverage by solvent, delta-22-plane residuals,\n",
"and the RMSE distribution shift by solvent."
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "64581ad1",
"metadata": {},
"outputs": [],
"source": [
"import os, sys\n",
"\n",
"# make the in-repo modules importable (not pip-installed)\n",
"REPO = os.path.abspath(\"../..\")\n",
"for _p in (\"data/applications\", \"data/delta22\", \"analysis/code\", \"analysis/code/shared\"):\n",
" sys.path.insert(0, os.path.join(REPO, _p))"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "206af146",
"metadata": {},
"outputs": [],
"source": [
"import matplotlib.pyplot as plt\n",
"\n",
"from applications_reader import Applications\n",
"import applications\n",
"import applications_plots\n",
"import delta22\n",
"import paths"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "69c8b5ee",
"metadata": {},
"outputs": [],
"source": [
"DATA = os.path.join(REPO, \"data\", \"applications\")\n",
"DELTA22_HDF5 = paths.dataset_file(\"delta22\", root=REPO)\n",
"DELTA22_XLSX = os.path.join(REPO, \"data\", \"delta22\", \"delta22_experimental.xlsx\")\n",
"\n",
"def figure_path(name):\n",
" os.makedirs(\"figures\", exist_ok=True)\n",
" return os.path.join(\"figures\", name)"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "9cde73dc",
"metadata": {},
"outputs": [],
"source": [
"loader = Applications(paths.dataset_file(\"applications\", root=REPO),\n",
" os.path.join(DATA, \"applications_experimental.xlsx\"))\n",
"\n",
"# assemble the feature table and run the composite-model fits + bootstrap\n",
"query_df_nn = applications.build_query_df_nn(loader)\n",
"site_counts = (query_df_nn.drop_duplicates(subset=[\"solute\", \"nucleus\", \"site\"])\n",
" .groupby([\"solute\", \"nucleus\"]).size().unstack(fill_value=0))\n",
"\n",
"per_solute = applications.per_solute_fits(query_df_nn) # \"scaled to solute\" baseline\n",
"all_solute = applications.per_solvent_fits(query_df_nn) # \"scaled to test set\" full fit\n",
"\n",
"seed = applications.build_bootstrap_seed_coeffs(loader)\n",
"bootstrap_rmses = {}\n",
"for nuc in [\"H\", \"C\"]:\n",
" preds = applications.apply_bootstrap_params_to_full_dataset(query_df_nn, seed[nuc], nucleus=nuc)\n",
" bootstrap_rmses[nuc] = applications.compute_solute_rmses(preds)"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "d218de52",
"metadata": {},
"outputs": [],
"source": [
"# published solute order (isomers, then the two pyridines, then the natural products); matches\n",
"# main-text Figure 5D. delta-22 is drawn first by the box-plot engine, so it is not listed here.\n",
"S15_SOLUTE_ORDER = [\"isomer_1E\", \"isomer_1Z\", \"isomer_2E\", \"isomer_2Z\", \"isomer_3E\", \"isomer_3Z\",\n",
" \"isomer_4N\", \"isomer_4O\", \"vomicine\", \"prednisone\", \"peptide\", \"flavone\",\n",
" \"dihydrotanshinone_I\"]"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "85097f2d",
"metadata": {},
"outputs": [],
"source": [
"# 1H panel (reproduces Figure 5C)\n",
"applications_plots.plot_nps_on_boxplot_delta22_simplified(\n",
" loader.rmse_distribution(\"H\"), bootstrap_rmses[\"H\"], per_solute[\"H\"],\n",
" nucleus=\"H\", formulas=[\"stationary_plus_qcd + openMM\"], colors=[\"#61a89a\"],\n",
" site_counts=site_counts, formula_remap=applications.FORMULA_REMAP,\n",
" solute_remap=applications.SOLUTE_DISPLAY, solute_order=S15_SOLUTE_ORDER,\n",
" solute_color_remap=applications.PEPTIDE_HIGHLIGHT_H,\n",
" figsize=(14, 8), box_width=0.20, box_gap=0.1,\n",
" show_baseline=True, baseline_annotation_text=\"Scaled to solute\",\n",
" baseline_annotation_x=0.215, baseline_annotation_y=0.39,\n",
" show_full_fit_line=True, full_fit_line_label=\"Scaled to Test Set\", full_fit_line_label_x=0.835,\n",
" all_solute_fitting_results=all_solute,\n",
" max_bar_height=0.06, site_count_axis_mode=\"inset\", site_count_inset_area_frac=0.1,\n",
" site_count_inset_axis_offset=-0.06, site_count_inset_axis_label_pad=0.045,\n",
" save_path=figure_path(\"si_figure_s15_1H.png\"),\n",
")"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "973af7b2",
"metadata": {},
"outputs": [],
"source": [
"# 13C panel\n",
"applications_plots.plot_nps_on_boxplot_delta22_simplified(\n",
" loader.rmse_distribution(\"C\"), bootstrap_rmses[\"C\"], per_solute[\"C\"],\n",
" nucleus=\"C\", formulas=[\"stationary_plus_op_vib + openMM\"], colors=[\"#61a89a\"],\n",
" site_counts=site_counts, formula_remap=applications.FORMULA_REMAP,\n",
" solute_remap=applications.SOLUTE_DISPLAY, solute_order=S15_SOLUTE_ORDER,\n",
" solute_color_remap=applications.PEPTIDE_HIGHLIGHT_C,\n",
" figsize=(14, 8), box_width=0.20, box_gap=0.1,\n",
" show_baseline=True, baseline_annotation_text=\"Scaled to solute\",\n",
" baseline_annotation_x=0.28, baseline_annotation_y=0.355,\n",
" show_full_fit_line=True, full_fit_line_label=\"Scaled to Test Set\", full_fit_line_label_x=0.98,\n",
" all_solute_fitting_results=all_solute,\n",
" max_bar_height=0.8, site_count_axis_mode=\"inset\", site_count_inset_area_frac=0.1,\n",
" site_count_inset_axis_offset=-0.06, site_count_inset_axis_label_pad=0.045,\n",
" save_path=figure_path(\"si_figure_s15_13C.png\"),\n",
")"
]
},
{
"cell_type": "markdown",
"id": "f079c075",
"metadata": {},
"source": [
"## Fitting RMSE Comparisons (chloroform)\n",
"\n",
"Per-solute RMSE under three coefficient choices (Scaled to Solute / Scaled to Test Set / Extrapolated\n",
"from delta22)."
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "11ea3200",
"metadata": {},
"outputs": [],
"source": [
"for nucleus, formula in [(\"H\", \"stationary_plus_qcd + openMM\"), (\"C\", \"stationary_plus_op_vib + openMM\")]:\n",
" table = applications.fitting_rmse_comparison_table(query_df_nn, per_solute, all_solute, bootstrap_rmses[nucleus],\n",
" nucleus, \"chloroform\", formula)\n",
" table = table.rename(index=applications.SOLUTE_DISPLAY)\n",
" order = [applications.SOLUTE_DISPLAY.get(k, k) for k in S15_SOLUTE_ORDER] # published order; peptide has no chloroform data\n",
" table = table.reindex([n for n in order if n in table.index])\n",
" print(f\"--- {nucleus} ---\")\n",
" display(table.round(3))\n",
" applications_plots.plot_fitting_rmse_comparison_bars(\n",
" table, nucleus, \"chloroform\",\n",
" save_path=figure_path(f\"si_figure_s15_fitting_rmse_comparisons_{'1H' if nucleus == 'H' else '13C'}.png\"))\n",
"plt.show()"
]
},
{
"cell_type": "markdown",
"id": "47773c94",
"metadata": {},
"source": [
"## Feature Space Coverage by Solvent\n",
"\n",
"Test-set vs delta-22 mean-centered feature values across the four explicit-solvent solvents."
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "fa1de7fe",
"metadata": {},
"outputs": [],
"source": [
"delta22_query_df_nn = delta22.add_composite_columns(delta22.load_query_df_nn(\n",
" DELTA22_HDF5, DELTA22_XLSX, verbose=False))"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "a19b095b",
"metadata": {},
"outputs": [],
"source": [
"_FEATURE_X_LABELS = {\n",
" \"H\": \"Gas-Phase Shielding + QCD Correction (centered, ppm)\",\n",
" \"C\": \"Gas-Phase Shielding + OpenMM Vibrational Correction (centered, ppm)\",\n",
"}\n",
"for nucleus in [\"H\", \"C\"]:\n",
" coverage = applications.feature_space_coverage_table(query_df_nn, delta22_query_df_nn, nucleus)\n",
" applications_plots.plot_feature_space_coverage_grid(\n",
" coverage, nucleus, _FEATURE_X_LABELS[nucleus],\n",
" save_path=figure_path(f\"si_figure_s15_feature_space_coverage_{'1H' if nucleus == 'H' else '13C'}.png\"))\n",
"plt.show()"
]
},
{
"cell_type": "markdown",
"id": "5d7bc6b3",
"metadata": {},
"source": [
"## Residuals for Delta22 Fitting Coefficients\n",
"\n",
"Residuals of a delta-22-only 2-feature plane applied to both delta-22 and the test set, vs\n",
"experimental shielding."
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "8dea4de5",
"metadata": {},
"outputs": [],
"source": [
"for nucleus in [\"H\", \"C\"]:\n",
" residuals = applications.delta22_plane_residuals_table(query_df_nn, delta22_query_df_nn, nucleus)\n",
" applications_plots.plot_delta22_plane_residuals_grid(\n",
" residuals, nucleus,\n",
" save_path=figure_path(f\"si_figure_s15_delta22_plane_residuals_{'1H' if nucleus == 'H' else '13C'}.png\"))\n",
"plt.show()"
]
},
{
"cell_type": "markdown",
"id": "3fd43b43",
"metadata": {},
"source": [
"## Distribution Shift by Solvent\n",
"\n",
"Per-solvent mean test-set RMSE under the three coefficient choices."
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "24d4b26e",
"metadata": {},
"outputs": [],
"source": [
"for nucleus, formula in [(\"H\", \"stationary_plus_qcd + openMM\"), (\"C\", \"stationary_plus_op_vib + openMM\")]:\n",
" shift = applications.distribution_shift_by_solvent_table(per_solute, all_solute, bootstrap_rmses[nucleus],\n",
" nucleus, formula)\n",
" print(f\"--- {nucleus} ---\")\n",
" display(shift.round(3))\n",
" applications_plots.plot_distribution_shift_by_solvent_bars(\n",
" shift, nucleus,\n",
" save_path=figure_path(f\"si_figure_s15_distribution_shift_by_solvent_{'1H' if nucleus == 'H' else '13C'}.png\"))\n",
"plt.show()"
]
}
],
"metadata": {
"language_info": {
"name": "python"
}
},
"nbformat": 4,
"nbformat_minor": 5
}
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