Skip to content

1.0.0 #16

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 2 commits into from
Nov 4, 2025
Merged

1.0.0 #16

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
2f3c512
Add dot plots to bar plots for CASP15 docking success rates
amorehead Nov 4, 2025
4191849
Bump to version 1.0.0
amorehead Nov 4, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
6 changes: 6 additions & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,3 +1,9 @@
### 1.0.0 - 11/04/2025

**Changes**:

- Added dot plots on top of bar plots for improved clarity in CASP15 results.

### 0.7.1 - 08/11/2025

**Changes**:
Expand Down
2 changes: 1 addition & 1 deletion docs/source/conf.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@
# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
project = "PoseBench"
author = "Alex Morehead"
release = "0.7.1"
release = "1.0.0"
copyright = f"{datetime.datetime.now().year}, {author}"

# -- General configuration ---------------------------------------------------
Expand Down
Binary file modified notebooks/casp15_all_multi_ligand_relaxed_rmsd_lt2_bar_chart.png
View file
Open in desktop
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified notebooks/casp15_all_single_ligand_relaxed_rmsd_lt2_bar_chart.png
View file
Open in desktop
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
109 changes: 106 additions & 3 deletions notebooks/casp15_inference_results_plotting.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,7 @@
"import numpy as np\n",
"import pandas as pd\n",
"import seaborn as sns\n",
"from matplotlib.ticker import FuncFormatter\n",
"\n",
"from posebench.analysis.inference_analysis_casp import (\n",
" CASP_BUST_TEST_COLUMNS,\n",
Expand Down Expand Up @@ -304,7 +305,18 @@
" :param method: Method name.\n",
" :return: Method category.\n",
" \"\"\"\n",
" return method_category_mapping.get(method, \"DL-based blind\")"
" return method_category_mapping.get(method, \"DL-based blind\")\n",
"\n",
"\n",
"def percent_angstrom_formatter(x, pos):\n",
" \"\"\"\n",
" Format function for percent/angstrom axis.\n",
"\n",
" :param x: Value.\n",
" :param pos: Position.\n",
" :return: Formatted string.\n",
" \"\"\"\n",
" return f\"{x:.0f}% / Å\""
]
},
{
Expand Down Expand Up @@ -799,17 +811,108 @@
" width=bar_width,\n",
" )\n",
"\n",
" # extract raw RMSD values for each method and condition\n",
" for method_idx, method in enumerate(method_mapping.values()):\n",
" # get unrelaxed RMSD values grouped by target\n",
" unrelaxed_rmsd_by_target = {}\n",
" relaxed_rmsd_by_target = {}\n",
"\n",
" for repeat_index in range(1, max_num_repeats_per_method + 1):\n",
" # unrelaxed data\n",
" casp15_unrelaxed = (\n",
" globals()[f\"scoring_results_table_{repeat_index}\"][\n",
" (\n",
" globals()[f\"scoring_results_table_{repeat_index}\"][\"dataset\"]\n",
" == \"CASP15 set\"\n",
" )\n",
" & (\n",
" globals()[f\"scoring_results_table_{repeat_index}\"][\"post-processing\"]\n",
" == \"none\"\n",
" )\n",
" & (globals()[f\"scoring_results_table_{repeat_index}\"][\"method\"] == method)\n",
" ]\n",
" .groupby(\"target\")\n",
" .agg({\"rmsd\": \"mean\"})\n",
" )\n",
"\n",
" # relaxed data\n",
" casp15_relaxed = (\n",
" globals()[f\"scoring_results_table_{repeat_index}\"][\n",
" (\n",
" globals()[f\"scoring_results_table_{repeat_index}\"][\"dataset\"]\n",
" == \"CASP15 set\"\n",
" )\n",
" & (\n",
" globals()[f\"scoring_results_table_{repeat_index}\"][\"post-processing\"]\n",
" == \"energy minimization\"\n",
" )\n",
" & (globals()[f\"scoring_results_table_{repeat_index}\"][\"method\"] == method)\n",
" ]\n",
" .groupby(\"target\")\n",
" .agg({\"rmsd\": \"mean\"})\n",
" )\n",
"\n",
" # accumulate values by target\n",
" for target, rmsd_value in casp15_unrelaxed.iterrows():\n",
" if target not in unrelaxed_rmsd_by_target:\n",
" unrelaxed_rmsd_by_target[target] = []\n",
" unrelaxed_rmsd_by_target[target].append(rmsd_value[\"rmsd\"])\n",
"\n",
" for target, rmsd_value in casp15_relaxed.iterrows():\n",
" if target not in relaxed_rmsd_by_target:\n",
" relaxed_rmsd_by_target[target] = []\n",
" relaxed_rmsd_by_target[target].append(rmsd_value[\"rmsd\"])\n",
"\n",
" # calculate average RMSD across repeats for each target\n",
" unrelaxed_rmsd_averages = [\n",
" np.mean(values) for values in unrelaxed_rmsd_by_target.values()\n",
" ]\n",
" relaxed_rmsd_averages = [np.mean(values) for values in relaxed_rmsd_by_target.values()]\n",
"\n",
" # overlay unrelaxed RMSD points (averaged per target)\n",
" if len(unrelaxed_rmsd_averages) > 0:\n",
" # add small random jitter for better visibility when points overlap\n",
" x_positions = np.random.normal(r1[method_idx], 0.05, len(unrelaxed_rmsd_averages))\n",
" # clamp RMSD values at 100\n",
" clamped_rmsd = [min(val, 100) for val in unrelaxed_rmsd_averages]\n",
" axis.scatter(\n",
" x_positions,\n",
" clamped_rmsd,\n",
" alpha=0.6,\n",
" s=20,\n",
" color=\"darkred\",\n",
" edgecolors=\"black\",\n",
" linewidth=0.5,\n",
" zorder=10,\n",
" ) # higher zorder to appear on top\n",
"\n",
" # overlay relaxed RMSD points (averaged per target)\n",
" if len(relaxed_rmsd_averages) > 0:\n",
" x_positions = np.random.normal(r2[method_idx], 0.05, len(relaxed_rmsd_averages))\n",
" # clamp RMSD values at 100\n",
" clamped_rmsd = [min(val, 100) for val in relaxed_rmsd_averages]\n",
" axis.scatter(\n",
" x_positions,\n",
" clamped_rmsd,\n",
" alpha=0.6,\n",
" s=20,\n",
" color=\"purple\",\n",
" edgecolors=\"black\",\n",
" linewidth=0.5,\n",
" zorder=10,\n",
" )\n",
"\n",
" # add labels, titles, ticks, etc.\n",
" axis.set_xlabel(f\"{complex_type.title()}-ligand blind docking ({complex_license})\")\n",
" axis.set_ylabel(\"Percentage of predictions\")\n",
" axis.set_ylabel(\"Percentage of predictions / RMSD (Å)\")\n",
" axis.set_xlim(1, 23 + 0.1)\n",
" axis.set_ylim(0, 125)\n",
"\n",
" axis.bar_label(casp15_rmsd_lt2_bar, fmt=\"{:,.1f}\", label_type=\"center\")\n",
" axis.bar_label(casp15_relaxed_rmsd_lt_2_bar, fmt=\"{:,.1f}\", label_type=\"center\")\n",
" axis.bar_label(casp15_plif_wm_bar, fmt=\"{:,.1f}\", label_type=\"center\")\n",
"\n",
" axis.yaxis.set_major_formatter(mtick.PercentFormatter())\n",
" axis.yaxis.set_major_formatter(FuncFormatter(percent_angstrom_formatter))\n",
"\n",
" axis.set_yticks([0, 20, 40, 60, 80, 100])\n",
" axis.axhline(y=0, color=\"#EAEFF8\")\n",
Expand Down
Binary file modified notebooks/casp15_public_multi_ligand_relaxed_rmsd_lt2_bar_chart.png
View file
Open in desktop
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified notebooks/casp15_public_single_ligand_relaxed_rmsd_lt2_bar_chart.png
View file
Open in desktop
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
2 changes: 1 addition & 1 deletion pyproject.toml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
[project]
name = "posebench"
version = "0.7.1"
version = "1.0.0"
description = "Comprehensive benchmarking of protein-ligand structure prediction methods"
authors = [
{ name = "Alex Morehead", email = "acmwhb@umsystem.edu" }
Expand Down
Loading