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Update CASP15 notebook
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@amorehead
amorehead committed Jan 28, 2025
1 parent 117130a commit 4d9a85f
Showing 1 changed file with 20 additions and 15 deletions.
35 changes: 20 additions & 15 deletions notebooks/casp15_inference_results_plotting.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -72,12 +72,13 @@
" \"vina_p2rank\",\n",
" \"diffdock\",\n",
" \"dynamicbind\",\n",
" \"neuralplexer\",\n",
" \"rfaa\",\n",
" \"chai-lab_ss\",\n",
" \"chai-lab\",\n",
" \"alphafold3_ss\",\n",
" \"alphafold3\",\n",
" \"neuralplexer3_ss\",\n",
" \"neuralplexer3\",\n",
"]\n",
"max_num_repeats_per_method = 3\n",
"\n",
Expand All @@ -86,24 +87,26 @@
" \"vina_p2rank\": \"P2Rank-Vina\",\n",
" \"diffdock\": \"DiffDock-L\",\n",
" \"dynamicbind\": \"DynamicBind\",\n",
" \"neuralplexer\": \"NeuralPLexer\",\n",
" \"rfaa\": \"RoseTTAFold-AA\",\n",
" \"chai-lab_ss\": \"Chai-1-Single-Seq\",\n",
" \"chai-lab\": \"Chai-1\",\n",
" \"alphafold3_ss\": \"AF3-Single-Seq\",\n",
" \"alphafold3\": \"AF3\",\n",
" \"neuralplexer3_ss\": \"NP3-Single-Seq\",\n",
" \"neuralplexer3\": \"NP3\",\n",
"}\n",
"\n",
"method_category_mapping = {\n",
" \"vina_p2rank\": \"Conventional blind\",\n",
" \"diffdock\": \"DL-based blind\",\n",
" \"dynamicbind\": \"DL-based blind\",\n",
" \"neuralplexer\": \"DL-based blind\",\n",
" \"rfaa\": \"DL-based blind\",\n",
" \"chai-lab_ss\": \"DL-based blind\",\n",
" \"chai-lab\": \"DL-based blind\",\n",
" \"alphafold3_ss\": \"DL-based blind\",\n",
" \"alphafold3\": \"DL-based blind\",\n",
" \"neuralplexer3_ss\": \"DL-based blind\",\n",
" \"neuralplexer3\": \"DL-based blind\",\n",
"}"
]
},
Expand Down Expand Up @@ -549,7 +552,7 @@
"colors = [\"#FB8072\", \"#BEBADA\", \"#FCCDE5\"]\n",
"\n",
"bar_width = 0.5\n",
"r1 = [item - 0.5 for item in range(2, 20, 2)]\n",
"r1 = [item - 0.5 for item in range(2, 22, 2)]\n",
"r2 = [x + bar_width for x in r1]\n",
"r3 = [x + bar_width for x in r2]\n",
"\n",
Expand Down Expand Up @@ -796,7 +799,7 @@
" # 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_xlim(1, 19 + 0.1)\n",
" axis.set_xlim(1, 21 + 0.1)\n",
" axis.set_ylim(0, 125)\n",
"\n",
" axis.bar_label(casp15_rmsd_lt2_bar, fmt=\"{:,.1f}\", label_type=\"center\")\n",
Expand All @@ -810,21 +813,22 @@
" axis.grid(axis=\"y\", color=\"#EAEFF8\")\n",
" axis.set_axisbelow(True)\n",
"\n",
" axis.set_xticks([2, 2 + 1e-3, 4, 6, 8, 10, 11, 12, 14, 16, 18])\n",
" axis.set_xticks([2, 2 + 1e-3, 4, 6, 8, 10, 12, 12 + 1e-3, 14, 16, 18, 20])\n",
" axis.set_xticks([1 + 0.1], minor=True)\n",
" axis.set_xticklabels(\n",
" [\n",
" \"P2Rank-Vina\",\n",
" \"Conventional blind\",\n",
" \"DiffDock-L\",\n",
" \"DynamicBind\",\n",
" \"NeuralPLexer\",\n",
" \"RoseTTAFold-AA\",\n",
" \"DL-based blind\",\n",
" \"Chai-1-Single-Seq\",\n",
" \"Chai-1\",\n",
" \"DL-based blind\",\n",
" \"AF3-Single-Seq\",\n",
" \"AF3\",\n",
" \"NP3-Single-Seq\",\n",
" \"NP3\",\n",
" ]\n",
" )\n",
"\n",
Expand All @@ -836,7 +840,7 @@
" axis.tick_params(axis=\"y\", which=\"major\", left=\"off\", right=\"on\", color=\"#EAEFF8\")\n",
"\n",
" # vertical alignment of xtick labels\n",
" vert_alignments = [0.0, -0.1, 0.0, 0.0, 0.0, 0.0, -0.1, 0.0, 0.0, 0.0, 0.0]\n",
" vert_alignments = [0.0, -0.1, 0.0, 0.0, 0.0, 0.0, 0.0, -0.1, 0.0, 0.0, 0.0, 0.0]\n",
" for tick, y in zip(axis.get_xticklabels(), vert_alignments):\n",
" tick.set_y(y)\n",
"\n",
Expand Down Expand Up @@ -939,7 +943,7 @@
"colors = [\"#FB8072\", \"#BEBADA\"]\n",
"\n",
"bar_width = 0.75\n",
"r1 = [item - 0.25 for item in range(2, 20, 2)]\n",
"r1 = [item - 0.25 for item in range(2, 22, 2)]\n",
"r2 = [x + bar_width for x in r1]\n",
"\n",
"for complex_type in [\"single\", \"multi\"]:\n",
Expand Down Expand Up @@ -1122,7 +1126,7 @@
" # add labels, titles, ticks, etc.\n",
" axis.set_xlabel(f\"{complex_type.title()}-ligand blind docking ({complex_license})\")\n",
" axis.set_ylabel(\"Percentage of complex predictions\")\n",
" axis.set_xlim(1, 19 + 0.1)\n",
" axis.set_xlim(1, 21 + 0.1)\n",
" axis.set_ylim(0, 100)\n",
"\n",
" axis.bar_label(casp15_pb_valid_bar, fmt=\"{:,.1f}\", label_type=\"center\")\n",
Expand All @@ -1135,21 +1139,22 @@
" axis.grid(axis=\"y\", color=\"#EAEFF8\")\n",
" axis.set_axisbelow(True)\n",
"\n",
" axis.set_xticks([2, 2 + 1e-3, 4, 6, 8, 10, 11, 12, 14, 16, 18])\n",
" axis.set_xticks([2, 2 + 1e-3, 4, 6, 8, 10, 12, 12 + 1e-3, 14, 16, 18, 20])\n",
" axis.set_xticks([1 + 0.1], minor=True)\n",
" axis.set_xticklabels(\n",
" [\n",
" \"P2Rank-Vina\",\n",
" \"Conventional blind\",\n",
" \"DiffDock-L\",\n",
" \"DynamicBind\",\n",
" \"NeuralPLexer\",\n",
" \"RoseTTAFold-AA\",\n",
" \"DL-based blind\",\n",
" \"Chai-1-Single-Seq\",\n",
" \"Chai-1\",\n",
" \"DL-based blind\",\n",
" \"AF3-Single-Seq\",\n",
" \"AF3\",\n",
" \"NP3-Single-Seq\",\n",
" \"NP3\",\n",
" ]\n",
" )\n",
"\n",
Expand All @@ -1161,7 +1166,7 @@
" axis.tick_params(axis=\"y\", which=\"major\", left=\"off\", right=\"on\", color=\"#EAEFF8\")\n",
"\n",
" # vertical alignment of xtick labels\n",
" vert_alignments = [0.0, -0.1, 0.0, 0.0, 0.0, 0.0, -0.1, 0.0, 0.0, 0.0, 0.0]\n",
" vert_alignments = [0.0, -0.1, 0.0, 0.0, 0.0, 0.0, 0.0, -0.1, 0.0, 0.0, 0.0, 0.0]\n",
" for tick, y in zip(axis.get_xticklabels(), vert_alignments):\n",
" tick.set_y(y)\n",
"\n",
Expand Down

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