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mcwitt/py3Dmol-mapping-demo.ipynb

Created March 6, 2023 20:29
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Demo of using py3Dmol to visualize atom mappings
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py3Dmol-mapping-demo.ipynb
{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"id": "e41bccde-100f-40b1-b748-eafb91231422",
"metadata": {},
"outputs": [],
"source": [
"%config InlineBackend.figure_format = \"retina\""
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "f1cc9c93-07ef-4329-b669-89081a7e884f",
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"\n",
" <script type=\"application/javascript\" id=\"jupyter_black\">\n",
" function jb_set_cell(\n",
" jb_formatted_code\n",
" ) {\n",
" for (var cell of Jupyter.notebook.get_cells()) {\n",
" if (cell.input_prompt_number == \"*\") {\n",
" cell.set_text(jb_formatted_code)\n",
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],
"text/plain": [
"<IPython.core.display.HTML object>"
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},
"metadata": {},
"output_type": "display_data"
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],
"source": [
"import jupyter_black\n",
"jupyter_black.load(lab=False)"
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "a92c06fc",
"metadata": {},
"outputs": [],
"source": [
"from itertools import cycle\n",
"import json\n",
"\n",
"import matplotlib.pyplot as plt\n",
"import py3Dmol\n",
"from rdkit import Chem\n",
"from timemachine.fe.utils import get_mol_name, read_sdf"
]
},
{
"cell_type": "code",
"execution_count": 4,
"id": "66d96f39",
"metadata": {},
"outputs": [],
"source": [
"mols_by_name = {\n",
" get_mol_name(m): m\n",
" for m in read_sdf(\"datasets/public/merck/hif2a/hif2a_5tbm_blocker_43.sdf\")\n",
"}"
]
},
{
"cell_type": "code",
"execution_count": 5,
"id": "51a22baf",
"metadata": {},
"outputs": [],
"source": [
"with open(\"datasets/public/merck/hif2a/hif2a_5tbm_blocker_43_edges.json\", \"r\") as f:\n",
" edges = json.load(f)"
]
},
{
"cell_type": "code",
"execution_count": 6,
"id": "3d87a337",
"metadata": {},
"outputs": [],
"source": [
"from timemachine.fe.atom_mapping import get_cores"
]
},
{
"cell_type": "code",
"execution_count": 7,
"id": "ffe487a7",
"metadata": {},
"outputs": [],
"source": [
"mol_a_name, mol_b_name = edges[0]\n",
"mol_a, mol_b = mols_by_name[mol_a_name], mols_by_name[mol_b_name]"
]
},
{
"cell_type": "code",
"execution_count": 8,
"id": "25e014a0",
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"WARNING:jax._src.lib.xla_bridge:No GPU/TPU found, falling back to CPU. (Set TF_CPP_MIN_LOG_LEVEL=0 and rerun for more info.)\n"
]
}
],
"source": [
"core = get_cores(\n",
" mol_a,\n",
" mol_b,\n",
" ring_cutoff=0.12,\n",
" chain_cutoff=0.2,\n",
" max_visits=1e7,\n",
" connected_core=True,\n",
" max_cores=1e6,\n",
" enforce_core_core=True,\n",
" complete_rings=True,\n",
" enforce_chiral=True,\n",
" min_threshold=0,\n",
")[0]"
]
},
{
"cell_type": "code",
"execution_count": 9,
"id": "58e0bbb8",
"metadata": {},
"outputs": [],
"source": [
"matplotlib_colors = plt.rcParams[\"axes.prop_cycle\"].by_key()[\"color\"]\n",
"\n",
"\n",
"def view_mapping_3d(mol_a, mol_b, core=None, colors=matplotlib_colors):\n",
" view = py3Dmol.view(viewergrid=(1, 2) if core is None else (2, 2))\n",
"\n",
" def addMol(mol, **kwargs):\n",
" view.addModel(Chem.MolToMolBlock(mol), \"mol\", **kwargs)\n",
"\n",
" addMol(mol_a, viewer=(0, 0))\n",
" addMol(mol_b, viewer=(0, 1))\n",
"\n",
" # second row (colored according to mapping)\n",
" if core is not None:\n",
" addMol(mol_a, viewer=(1, 0))\n",
" addMol(mol_b, viewer=(1, 1))\n",
"\n",
" view.setStyle({\"stick\": {}})\n",
"\n",
" if core is not None:\n",
" for (ia, ib), color in zip(core.tolist(), cycle(colors)):\n",
" view.setStyle({\"serial\": ia}, {\"stick\": {\"color\": color}}, viewer=(1, 0))\n",
" view.setStyle({\"serial\": ib}, {\"stick\": {\"color\": color}}, viewer=(1, 1))\n",
"\n",
" view.zoomTo()\n",
" return view.render()"
]
},
{
"cell_type": "code",
"execution_count": 10,
"id": "bb9a0fc4",
"metadata": {},
"outputs": [
{
"data": {
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You need to install the 3dmol extension: <br>\n <tt>jupyter labextension install jupyterlab_3dmol</tt></p>\n </div>\n<script>\n\nvar loadScriptAsync = function(uri){\n return new Promise((resolve, reject) => {\n //this is to ignore the existence of requirejs amd\n var savedexports, savedmodule;\n if (typeof exports !== 'undefined') savedexports = exports;\n else exports = {}\n if (typeof module !== 'undefined') savedmodule = module;\n else module = {}\n\n var tag = document.createElement('script');\n tag.src = uri;\n tag.async = true;\n tag.onload = () => {\n exports = savedexports;\n module = savedmodule;\n resolve();\n };\n var firstScriptTag = document.getElementsByTagName('script')[0];\n firstScriptTag.parentNode.insertBefore(tag, firstScriptTag);\n});\n};\n\nif(typeof $3Dmolpromise === 'undefined') {\n$3Dmolpromise = null;\n $3Dmolpromise = loadScriptAsync('https://cdnjs.cloudflare.com/ajax/libs/3Dmol/2.0.1/3Dmol-min.js');\n}\n\nvar viewer_1678134532070877 = null;\nvar warn = document.getElementById(\"3dmolwarning_1678134532070877\");\nif(warn) {\n warn.parentNode.removeChild(warn);\n}\n$3Dmolpromise.then(function() {\nvar viewergrid_1678134532070877 = null;\nviewergrid_1678134532070877 = $3Dmol.createViewerGrid(document.getElementById(\"3dmolviewer_1678134532070877\"),{rows: 2, cols: 2, control_all: true},{backgroundColor:\"white\"});\nviewer_1678134532070877 = viewergrid_1678134532070877[0][0];\nviewergrid_1678134532070877[0][0].zoomTo();viewergrid_1678134532070877[0][1].zoomTo();viewergrid_1678134532070877[1][0].zoomTo();viewergrid_1678134532070877[1][1].zoomTo();\tviewergrid_1678134532070877[0][0].addModel(\"338\\n RDKit 3D\\n\\n 37 39 0 0 1 0 0 0 0 0999 V2000\\n 27.6451 1.5396 -11.1263 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 27.1573 0.3054 -11.6394 C 0 0 2 0 0 0 0 0 0 0 0 0\\n 26.5145 0.3811 -13.0370 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 25.0296 0.6292 -12.8066 C 0 0 1 0 0 0 0 0 0 0 0 0\\n 24.8033 -0.0375 -11.4699 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 26.0149 -0.2195 -10.7892 C 0 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27.5283 -1.0639 -8.5710 S 0 0 0 0 0 0 0 0 0 0 0 0\\n 27.2110 -1.9989 -7.4925 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 28.6000 -1.3708 -9.5178 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 27.0777 1.2809 -13.8505 F 0 0 0 0 0 0 0 0 0 0 0 0\\n 18.0176 1.9927 -8.6784 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 24.8400 1.9615 -12.6525 F 0 0 0 0 0 0 0 0 0 0 0 0\\n 26.6372 -0.7929 -13.6486 F 0 0 0 0 0 0 0 0 0 0 0 0\\n 27.9360 0.4657 -7.8636 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 28.3611 1.8550 -11.6954 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 27.9701 -0.4195 -11.7119 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 24.3886 0.2707 -13.6271 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 24.7736 -1.4789 -7.8939 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 22.6914 -1.2459 -9.1138 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 21.2074 -2.5951 -11.9425 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 17.8099 -1.4198 -9.7083 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 21.0016 1.3428 -10.2620 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 27.2694 0.7696 -7.1547 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 28.1746 1.1824 -8.5552 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1 2 1 0\\n 1 28 1 0\\n 2 3 1 0\\n 2 6 1 0\\n 2 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"\tviewergrid_1678134532070877[0][1].addModel(\"165\\n RDKit 3D\\n\\n 39 41 0 0 1 0 0 0 0 0999 V2000\\n 27.5836 1.5568 -11.1222 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 27.1600 0.2656 -11.6609 C 0 0 2 0 0 0 0 0 0 0 0 0\\n 26.5184 0.3567 -13.0592 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 25.0297 0.5910 -12.8413 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 24.8052 -0.0654 -11.5002 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 26.0146 -0.2437 -10.8064 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 26.0168 -0.7770 -9.5128 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 24.7994 -1.0910 -8.8981 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 23.6068 -0.9245 -9.5924 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 23.5979 -0.4259 -10.8920 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 22.4815 -0.2804 -11.6866 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 21.2483 -0.5736 -11.1926 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 20.6741 -1.8286 -11.3993 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 19.4240 -2.1099 -10.8753 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 18.8513 -3.3170 -11.0668 F 0 0 0 0 0 0 0 0 0 0 0 0\\n 18.7373 -1.1448 -10.1406 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 19.2884 0.1262 -9.9662 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 18.5751 1.1667 -9.2345 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 20.5446 0.3954 -10.4628 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 27.5234 -1.0682 -8.5880 S 0 0 0 0 0 0 0 0 0 0 0 0\\n 27.2169 -1.9994 -7.4943 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 28.5933 -1.3900 -9.5234 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 27.9099 0.6030 -7.8462 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 27.0617 1.2852 -13.8476 F 0 0 0 0 0 0 0 0 0 0 0 0\\n 26.6509 -0.8260 -13.6655 F 0 0 0 0 0 0 0 0 0 0 0 0\\n 18.0232 1.9902 -8.6670 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 28.1780 1.3732 -10.3208 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 28.2339 1.9505 -11.7936 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 27.9972 -0.4377 -11.7205 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 24.4163 0.1879 -13.6481 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 24.8098 1.6549 -12.7768 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 24.7791 -1.4892 -7.9000 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 22.6845 -1.2350 -9.1033 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 21.2126 -2.5935 -11.9444 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 17.8017 -1.4265 -9.7043 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 21.0067 1.3483 -10.2588 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 28.8501 0.4838 -7.3200 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 27.1027 0.8984 -7.1794 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 28.0467 1.3492 -8.6202 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1 2 1 0\\n 1 27 1 0\\n 1 28 1 0\\n 2 3 1 0\\n 2 6 1 0\\n 2 29 1 6\\n 3 4 1 0\\n 3 24 1 0\\n 3 25 1 0\\n 4 5 1 0\\n 4 30 1 0\\n 4 31 1 0\\n 5 6 2 0\\n 5 10 1 0\\n 6 7 1 0\\n 7 8 2 0\\n 7 20 1 0\\n 8 9 1 0\\n 8 32 1 0\\n 9 10 2 0\\n 9 33 1 0\\n 10 11 1 0\\n 11 12 1 0\\n 12 13 2 0\\n 12 19 1 0\\n 13 14 1 0\\n 13 34 1 0\\n 14 15 1 0\\n 14 16 2 0\\n 16 17 1 0\\n 16 35 1 0\\n 17 18 1 0\\n 17 19 2 0\\n 18 26 3 0\\n 19 36 1 0\\n 20 21 2 0\\n 20 22 2 0\\n 20 23 1 0\\n 23 37 1 0\\n 23 38 1 0\\n 23 39 1 0\\nM END\\n\",\"mol\");\n",
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"\tviewergrid_1678134532070877[1][1].addModel(\"165\\n RDKit 3D\\n\\n 39 41 0 0 1 0 0 0 0 0999 V2000\\n 27.5836 1.5568 -11.1222 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 27.1600 0.2656 -11.6609 C 0 0 2 0 0 0 0 0 0 0 0 0\\n 26.5184 0.3567 -13.0592 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 25.0297 0.5910 -12.8413 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 24.8052 -0.0654 -11.5002 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 26.0146 -0.2437 -10.8064 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 26.0168 -0.7770 -9.5128 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 24.7994 -1.0910 -8.8981 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 23.6068 -0.9245 -9.5924 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 23.5979 -0.4259 -10.8920 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 22.4815 -0.2804 -11.6866 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 21.2483 -0.5736 -11.1926 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 20.6741 -1.8286 -11.3993 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 19.4240 -2.1099 -10.8753 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 18.8513 -3.3170 -11.0668 F 0 0 0 0 0 0 0 0 0 0 0 0\\n 18.7373 -1.1448 -10.1406 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 19.2884 0.1262 -9.9662 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 18.5751 1.1667 -9.2345 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 20.5446 0.3954 -10.4628 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 27.5234 -1.0682 -8.5880 S 0 0 0 0 0 0 0 0 0 0 0 0\\n 27.2169 -1.9994 -7.4943 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 28.5933 -1.3900 -9.5234 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 27.9099 0.6030 -7.8462 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 27.0617 1.2852 -13.8476 F 0 0 0 0 0 0 0 0 0 0 0 0\\n 26.6509 -0.8260 -13.6655 F 0 0 0 0 0 0 0 0 0 0 0 0\\n 18.0232 1.9902 -8.6670 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 28.1780 1.3732 -10.3208 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 28.2339 1.9505 -11.7936 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 27.9972 -0.4377 -11.7205 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 24.4163 0.1879 -13.6481 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 24.8098 1.6549 -12.7768 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 24.7791 -1.4892 -7.9000 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 22.6845 -1.2350 -9.1033 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 21.2126 -2.5935 -11.9444 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 17.8017 -1.4265 -9.7043 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 21.0067 1.3483 -10.2588 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 28.8501 0.4838 -7.3200 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 27.1027 0.8984 -7.1794 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 28.0467 1.3492 -8.6202 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1 2 1 0\\n 1 27 1 0\\n 1 28 1 0\\n 2 3 1 0\\n 2 6 1 0\\n 2 29 1 6\\n 3 4 1 0\\n 3 24 1 0\\n 3 25 1 0\\n 4 5 1 0\\n 4 30 1 0\\n 4 31 1 0\\n 5 6 2 0\\n 5 10 1 0\\n 6 7 1 0\\n 7 8 2 0\\n 7 20 1 0\\n 8 9 1 0\\n 8 32 1 0\\n 9 10 2 0\\n 9 33 1 0\\n 10 11 1 0\\n 11 12 1 0\\n 12 13 2 0\\n 12 19 1 0\\n 13 14 1 0\\n 13 34 1 0\\n 14 15 1 0\\n 14 16 2 0\\n 16 17 1 0\\n 16 35 1 0\\n 17 18 1 0\\n 17 19 2 0\\n 18 26 3 0\\n 19 36 1 0\\n 20 21 2 0\\n 20 22 2 0\\n 20 23 1 0\\n 23 37 1 0\\n 23 38 1 0\\n 23 39 1 0\\nM END\\n\",\"mol\");\n",
"\tviewergrid_1678134532070877[0][0].setStyle({\"stick\": {}});\n",
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{
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]
},
"execution_count": 10,
"metadata": {},
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],
"source": [
"view_mapping_3d(mol_a, mol_b, core)"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "0cd742b1",
"metadata": {},
"outputs": [],
"source": []
}
],
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