Skip to content

Instantly share code, notes, and snippets.

@iwatobipen

iwatobipen/shape_align.ipynb

Created September 23, 2024 10:03
Show Gist options

  • Select an option

    Learn more about clone URLs
  • Save iwatobipen/43e5ecf1049f6adeb27c5e4cfc6b3f7f to your computer and use it in GitHub Desktop.

Select an option

Learn more about clone URLs
Save iwatobipen/43e5ecf1049f6adeb27c5e4cfc6b3f7f to your computer and use it in GitHub Desktop.
Download ZIP
Display the source blob
Display the rendered blob
Raw
shape_align.ipynb
{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"id": "b267482a-ba1e-4c99-acee-b58abe1126d8",
"metadata": {
"execution": {
"iopub.execute_input": "2024-09-23T07:40:00.232595Z",
"iopub.status.busy": "2024-09-23T07:40:00.232272Z",
"iopub.status.idle": "2024-09-23T07:40:00.489714Z",
"shell.execute_reply": "2024-09-23T07:40:00.488690Z",
"shell.execute_reply.started": "2024-09-23T07:40:00.232567Z"
}
},
"outputs": [],
"source": [
"import rdkit\n",
"from rdkit import Chem\n",
"from rdkit.Chem import rdDistGeom\n",
"from rdkit.Chem.Draw import IPythonConsole\n",
"import copy\n",
"IPythonConsole.ipython_3d = True"
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "fec23cf5-3a79-45df-b16a-411bb1a69e79",
"metadata": {
"execution": {
"iopub.execute_input": "2024-09-23T07:40:00.490739Z",
"iopub.status.busy": "2024-09-23T07:40:00.490480Z",
"iopub.status.idle": "2024-09-23T07:40:00.495647Z",
"shell.execute_reply": "2024-09-23T07:40:00.494911Z",
"shell.execute_reply.started": "2024-09-23T07:40:00.490718Z"
}
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"2024.09.1b1\n"
]
}
],
"source": [
"print(rdkit.__version__)"
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "7ebaf9a6-ac4d-45a5-bef5-495aede3ff82",
"metadata": {
"execution": {
"iopub.execute_input": "2024-09-23T07:40:13.253547Z",
"iopub.status.busy": "2024-09-23T07:40:13.253095Z",
"iopub.status.idle": "2024-09-23T07:40:13.297678Z",
"shell.execute_reply": "2024-09-23T07:40:13.295937Z",
"shell.execute_reply.started": "2024-09-23T07:40:13.253499Z"
}
},
"outputs": [],
"source": [
"ms = [m for m in Chem.SDMolSupplier('./cdk2.sdf', removeHs=False)]\n",
"ms2 = copy.deepcopy(ms)"
]
},
{
"cell_type": "code",
"execution_count": 4,
"id": "1bc1c24b-b9fc-428c-aa97-1c1c1dd63ed1",
"metadata": {
"execution": {
"iopub.execute_input": "2024-09-23T07:40:23.862333Z",
"iopub.status.busy": "2024-09-23T07:40:23.861939Z",
"iopub.status.idle": "2024-09-23T07:40:23.869364Z",
"shell.execute_reply": "2024-09-23T07:40:23.867818Z",
"shell.execute_reply.started": "2024-09-23T07:40:23.862289Z"
}
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"47\n",
"46\n"
]
}
],
"source": [
"print(len(ms2))\n",
"ref = ms2.pop(0)\n",
"print(len(ms2))"
]
},
{
"cell_type": "code",
"execution_count": 5,
"id": "dc1fe605-44cb-4014-a108-778bf223799e",
"metadata": {
"execution": {
"iopub.execute_input": "2024-09-23T07:40:32.427731Z",
"iopub.status.busy": "2024-09-23T07:40:32.427040Z",
"iopub.status.idle": "2024-09-23T07:40:32.436327Z",
"shell.execute_reply": "2024-09-23T07:40:32.435257Z",
"shell.execute_reply.started": "2024-09-23T07:40:32.427686Z"
}
},
"outputs": [
{
"data": {
"application/3dmoljs_load.v0": "<div id=\"3dmolviewer_17270772324307446\" style=\"position: relative; width: 400px; height: 400px;\">\n <p id=\"3dmolwarning_17270772324307446\" style=\"background-color:#ffcccc;color:black\">3Dmol.js failed to load for some reason. Please check your browser console for error messages.<br></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/2.4.0/3Dmol-min.js');\n}\n\nvar viewer_17270772324307446 = null;\nvar warn = document.getElementById(\"3dmolwarning_17270772324307446\");\nif(warn) {\n warn.parentNode.removeChild(warn);\n}\n$3Dmolpromise.then(function() {\nviewer_17270772324307446 = $3Dmol.createViewer(document.getElementById(\"3dmolviewer_17270772324307446\"),{backgroundColor:\"white\"});\nviewer_17270772324307446.zoomTo();\n\tviewer_17270772324307446.addModel(\"ZINC03814457\\n RDKit 3D\\n\\n 30 31 0 0 1 0 0 0 0 0999 V2000\\n 5.4230 -0.4412 0.7616 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.2434 0.3667 0.1880 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.5978 0.9630 -1.1852 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.9575 -0.4703 0.1074 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.9988 -1.6999 0.0580 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.6357 0.2975 0.0804 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.5374 -0.6063 0.0692 O 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.7229 -0.0532 0.0310 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.8848 -0.8592 -0.0106 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.1098 -0.1432 -0.0466 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -4.0854 -1.1212 -0.0831 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.4330 -2.2959 -0.0687 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.1041 -2.2310 -0.0241 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.2721 1.2054 -0.0433 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.0919 1.8123 -0.0064 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.8677 1.2990 0.0350 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.1448 3.1672 -0.0074 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.7118 -1.2538 0.0931 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.2974 0.1913 0.9136 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.1671 -0.8852 1.7247 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.0364 1.1881 0.8743 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.4832 1.5956 -1.1194 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.8059 0.1785 -1.9146 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.7887 1.5777 -1.5810 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.6085 0.9288 -0.8080 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.5821 0.9425 0.9579 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -5.0816 -0.9900 -0.1173 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.9506 -3.2459 -0.0915 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.0380 3.6039 0.1519 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.3036 3.6737 0.2145 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1 2 1 0\\n 1 18 1 0\\n 1 19 1 0\\n 1 20 1 0\\n 2 3 1 0\\n 2 4 1 0\\n 2 21 1 0\\n 3 22 1 0\\n 3 23 1 0\\n 3 24 1 0\\n 4 5 2 0\\n 4 6 1 0\\n 6 7 1 0\\n 6 25 1 0\\n 6 26 1 0\\n 7 8 1 0\\n 8 16 2 0\\n 8 9 1 0\\n 9 13 1 0\\n 9 10 2 0\\n 10 11 1 0\\n 10 14 1 0\\n 11 12 1 0\\n 11 27 1 0\\n 12 13 2 0\\n 12 28 1 0\\n 14 15 2 0\\n 15 16 1 0\\n 15 17 1 0\\n 17 29 1 0\\n 17 30 1 0\\nM END\\n\",\"sdf\");\n\tviewer_17270772324307446.setStyle({\"stick\": {}});\n\tviewer_17270772324307446.addModel(\"ZINC03814459\\n RDKit 3D\\n\\n 30 32 0 0 1 0 0 0 0 0999 V2000\\n 3.2069 2.4332 0.1683 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.9680 1.3361 0.0191 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.0936 0.2661 -0.0051 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.8080 0.8502 0.1384 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.8933 2.2332 0.2504 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.7321 -0.0685 0.1386 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.0086 -1.3940 0.0148 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.2734 -1.7772 -0.1068 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.3866 -1.0536 -0.1367 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.4572 -3.1158 -0.2204 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.5735 0.3558 0.2686 O 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.5971 -0.6310 0.2422 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.9575 0.0650 0.3723 C 0 0 2 0 0 0 0 0 0 0 0 0\\n -4.1165 -0.8888 0.6548 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -5.3322 -0.1496 0.1130 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -4.7364 0.9594 -0.7584 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.3578 0.6367 -0.8635 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.6300 3.4278 0.2204 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.9699 1.3070 -0.0571 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.3600 -3.4373 -0.5285 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.6460 -3.6786 -0.4180 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.4556 -1.3123 1.0829 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.5595 -1.2189 -0.6765 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.9193 0.8386 1.1419 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -4.2043 -1.1389 1.7124 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.9777 -1.8177 0.0998 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -5.9676 -0.8188 -0.4679 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -5.9361 0.2761 0.9151 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -5.2028 1.0183 -1.7422 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -4.8426 1.9307 -0.2727 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1 5 2 0\\n 1 2 1 0\\n 1 18 1 0\\n 2 3 1 0\\n 2 19 1 0\\n 3 9 2 0\\n 3 4 1 0\\n 4 5 1 0\\n 4 6 2 0\\n 6 7 1 0\\n 6 11 1 0\\n 7 8 2 0\\n 8 9 1 0\\n 8 10 1 0\\n 10 20 1 0\\n 10 21 1 0\\n 11 12 1 0\\n 12 13 1 0\\n 12 22 1 0\\n 12 23 1 0\\n 13 17 1 0\\n 13 14 1 0\\n 13 24 1 1\\n 14 15 1 0\\n 14 25 1 0\\n 14 26 1 0\\n 15 16 1 0\\n 15 27 1 0\\n 15 28 1 0\\n 16 17 1 0\\n 16 29 1 0\\n 16 30 1 0\\nM END\\n\",\"sdf\");\n\tviewer_17270772324307446.setStyle({\"stick\": {}});\n\tviewer_17270772324307446.zoomTo();\nviewer_17270772324307446.render();\n});\n</script>",
"text/html": [
"<div id=\"3dmolviewer_17270772324307446\" style=\"position: relative; width: 400px; height: 400px;\">\n",
" <p id=\"3dmolwarning_17270772324307446\" style=\"background-color:#ffcccc;color:black\">3Dmol.js failed to load for some reason. Please check your browser console for error messages.<br></p>\n",
" </div>\n",
"<script>\n",
"\n",
"var 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",
"\n",
"if(typeof $3Dmolpromise === 'undefined') {\n",
"$3Dmolpromise = null;\n",
" $3Dmolpromise = loadScriptAsync('https://cdnjs.cloudflare.com/ajax/libs/3Dmol/2.4.0/3Dmol-min.js');\n",
"}\n",
"\n",
"var viewer_17270772324307446 = null;\n",
"var warn = document.getElementById(\"3dmolwarning_17270772324307446\");\n",
"if(warn) {\n",
" warn.parentNode.removeChild(warn);\n",
"}\n",
"$3Dmolpromise.then(function() {\n",
"viewer_17270772324307446 = $3Dmol.createViewer(document.getElementById(\"3dmolviewer_17270772324307446\"),{backgroundColor:\"white\"});\n",
"viewer_17270772324307446.zoomTo();\n",
"\tviewer_17270772324307446.addModel(\"ZINC03814457\\n RDKit 3D\\n\\n 30 31 0 0 1 0 0 0 0 0999 V2000\\n 5.4230 -0.4412 0.7616 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.2434 0.3667 0.1880 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.5978 0.9630 -1.1852 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.9575 -0.4703 0.1074 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.9988 -1.6999 0.0580 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.6357 0.2975 0.0804 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.5374 -0.6063 0.0692 O 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.7229 -0.0532 0.0310 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.8848 -0.8592 -0.0106 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.1098 -0.1432 -0.0466 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -4.0854 -1.1212 -0.0831 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.4330 -2.2959 -0.0687 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.1041 -2.2310 -0.0241 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.2721 1.2054 -0.0433 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.0919 1.8123 -0.0064 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.8677 1.2990 0.0350 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.1448 3.1672 -0.0074 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.7118 -1.2538 0.0931 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.2974 0.1913 0.9136 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.1671 -0.8852 1.7247 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.0364 1.1881 0.8743 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.4832 1.5956 -1.1194 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.8059 0.1785 -1.9146 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.7887 1.5777 -1.5810 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.6085 0.9288 -0.8080 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.5821 0.9425 0.9579 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -5.0816 -0.9900 -0.1173 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.9506 -3.2459 -0.0915 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.0380 3.6039 0.1519 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.3036 3.6737 0.2145 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1 2 1 0\\n 1 18 1 0\\n 1 19 1 0\\n 1 20 1 0\\n 2 3 1 0\\n 2 4 1 0\\n 2 21 1 0\\n 3 22 1 0\\n 3 23 1 0\\n 3 24 1 0\\n 4 5 2 0\\n 4 6 1 0\\n 6 7 1 0\\n 6 25 1 0\\n 6 26 1 0\\n 7 8 1 0\\n 8 16 2 0\\n 8 9 1 0\\n 9 13 1 0\\n 9 10 2 0\\n 10 11 1 0\\n 10 14 1 0\\n 11 12 1 0\\n 11 27 1 0\\n 12 13 2 0\\n 12 28 1 0\\n 14 15 2 0\\n 15 16 1 0\\n 15 17 1 0\\n 17 29 1 0\\n 17 30 1 0\\nM END\\n\",\"sdf\");\n",
"\tviewer_17270772324307446.setStyle({\"stick\": {}});\n",
"\tviewer_17270772324307446.addModel(\"ZINC03814459\\n RDKit 3D\\n\\n 30 32 0 0 1 0 0 0 0 0999 V2000\\n 3.2069 2.4332 0.1683 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.9680 1.3361 0.0191 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.0936 0.2661 -0.0051 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.8080 0.8502 0.1384 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.8933 2.2332 0.2504 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.7321 -0.0685 0.1386 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.0086 -1.3940 0.0148 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.2734 -1.7772 -0.1068 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.3866 -1.0536 -0.1367 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.4572 -3.1158 -0.2204 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.5735 0.3558 0.2686 O 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.5971 -0.6310 0.2422 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.9575 0.0650 0.3723 C 0 0 2 0 0 0 0 0 0 0 0 0\\n -4.1165 -0.8888 0.6548 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -5.3322 -0.1496 0.1130 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -4.7364 0.9594 -0.7584 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.3578 0.6367 -0.8635 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.6300 3.4278 0.2204 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.9699 1.3070 -0.0571 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.3600 -3.4373 -0.5285 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.6460 -3.6786 -0.4180 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.4556 -1.3123 1.0829 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.5595 -1.2189 -0.6765 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.9193 0.8386 1.1419 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -4.2043 -1.1389 1.7124 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.9777 -1.8177 0.0998 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -5.9676 -0.8188 -0.4679 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -5.9361 0.2761 0.9151 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -5.2028 1.0183 -1.7422 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -4.8426 1.9307 -0.2727 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1 5 2 0\\n 1 2 1 0\\n 1 18 1 0\\n 2 3 1 0\\n 2 19 1 0\\n 3 9 2 0\\n 3 4 1 0\\n 4 5 1 0\\n 4 6 2 0\\n 6 7 1 0\\n 6 11 1 0\\n 7 8 2 0\\n 8 9 1 0\\n 8 10 1 0\\n 10 20 1 0\\n 10 21 1 0\\n 11 12 1 0\\n 12 13 1 0\\n 12 22 1 0\\n 12 23 1 0\\n 13 17 1 0\\n 13 14 1 0\\n 13 24 1 1\\n 14 15 1 0\\n 14 25 1 0\\n 14 26 1 0\\n 15 16 1 0\\n 15 27 1 0\\n 15 28 1 0\\n 16 17 1 0\\n 16 29 1 0\\n 16 30 1 0\\nM END\\n\",\"sdf\");\n",
"\tviewer_17270772324307446.setStyle({\"stick\": {}});\n",
"\tviewer_17270772324307446.zoomTo();\n",
"viewer_17270772324307446.render();\n",
"});\n",
"</script>"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"import py3Dmol\n",
"p = py3Dmol.view(width=400, height=400)\n",
"IPythonConsole.addMolToView(ref,p)\n",
"IPythonConsole.addMolToView(ms2[0],p)\n",
"p.zoomTo()\n",
"p.show()"
]
},
{
"cell_type": "code",
"execution_count": 10,
"id": "c96455ce-9a92-4a21-af82-f5fa068aaa1e",
"metadata": {
"execution": {
"iopub.execute_input": "2024-09-23T07:41:01.595139Z",
"iopub.status.busy": "2024-09-23T07:41:01.594641Z",
"iopub.status.idle": "2024-09-23T07:41:01.603097Z",
"shell.execute_reply": "2024-09-23T07:41:01.601493Z",
"shell.execute_reply.started": "2024-09-23T07:41:01.595097Z"
}
},
"outputs": [],
"source": [
"from rdkit.Chem import rdShapeAlign"
]
},
{
"cell_type": "code",
"execution_count": 11,
"id": "46c68337-6996-44b9-b890-2d942e5d61c7",
"metadata": {
"execution": {
"iopub.execute_input": "2024-09-23T07:41:01.922091Z",
"iopub.status.busy": "2024-09-23T07:41:01.921580Z",
"iopub.status.idle": "2024-09-23T07:41:01.930156Z",
"shell.execute_reply": "2024-09-23T07:41:01.928927Z",
"shell.execute_reply.started": "2024-09-23T07:41:01.922029Z"
}
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"(0.905364833658121, 0.7687866865068402)\n"
]
}
],
"source": [
"tpl = rdShapeAlign.AlignMol(ref, ms2[0])\n",
"print(tpl)"
]
},
{
"cell_type": "code",
"execution_count": 12,
"id": "9ed44361-76cc-4ec5-82ec-518776c424f8",
"metadata": {
"execution": {
"iopub.execute_input": "2024-09-23T07:41:02.475406Z",
"iopub.status.busy": "2024-09-23T07:41:02.474874Z",
"iopub.status.idle": "2024-09-23T07:41:02.483200Z",
"shell.execute_reply": "2024-09-23T07:41:02.482014Z",
"shell.execute_reply.started": "2024-09-23T07:41:02.475373Z"
}
},
"outputs": [
{
"data": {
"application/3dmoljs_load.v0": "<div id=\"3dmolviewer_17270772624778967\" style=\"position: relative; width: 400px; height: 400px;\">\n <p id=\"3dmolwarning_17270772624778967\" style=\"background-color:#ffcccc;color:black\">3Dmol.js failed to load for some reason. Please check your browser console for error messages.<br></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/2.4.0/3Dmol-min.js');\n}\n\nvar viewer_17270772624778967 = null;\nvar warn = document.getElementById(\"3dmolwarning_17270772624778967\");\nif(warn) {\n warn.parentNode.removeChild(warn);\n}\n$3Dmolpromise.then(function() {\nviewer_17270772624778967 = $3Dmol.createViewer(document.getElementById(\"3dmolviewer_17270772624778967\"),{backgroundColor:\"white\"});\nviewer_17270772624778967.zoomTo();\n\tviewer_17270772624778967.addModel(\"ZINC03814457\\n RDKit 3D\\n\\n 30 31 0 0 1 0 0 0 0 0999 V2000\\n 5.4230 -0.4412 0.7616 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.2434 0.3667 0.1880 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.5978 0.9630 -1.1852 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.9575 -0.4703 0.1074 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.9988 -1.6999 0.0580 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.6357 0.2975 0.0804 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.5374 -0.6063 0.0692 O 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.7229 -0.0532 0.0310 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.8848 -0.8592 -0.0106 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.1098 -0.1432 -0.0466 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -4.0854 -1.1212 -0.0831 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.4330 -2.2959 -0.0687 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.1041 -2.2310 -0.0241 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.2721 1.2054 -0.0433 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.0919 1.8123 -0.0064 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.8677 1.2990 0.0350 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.1448 3.1672 -0.0074 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.7118 -1.2538 0.0931 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.2974 0.1913 0.9136 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.1671 -0.8852 1.7247 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.0364 1.1881 0.8743 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.4832 1.5956 -1.1194 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.8059 0.1785 -1.9146 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.7887 1.5777 -1.5810 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.6085 0.9288 -0.8080 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.5821 0.9425 0.9579 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -5.0816 -0.9900 -0.1173 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.9506 -3.2459 -0.0915 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.0380 3.6039 0.1519 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.3036 3.6737 0.2145 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1 2 1 0\\n 1 18 1 0\\n 1 19 1 0\\n 1 20 1 0\\n 2 3 1 0\\n 2 4 1 0\\n 2 21 1 0\\n 3 22 1 0\\n 3 23 1 0\\n 3 24 1 0\\n 4 5 2 0\\n 4 6 1 0\\n 6 7 1 0\\n 6 25 1 0\\n 6 26 1 0\\n 7 8 1 0\\n 8 16 2 0\\n 8 9 1 0\\n 9 13 1 0\\n 9 10 2 0\\n 10 11 1 0\\n 10 14 1 0\\n 11 12 1 0\\n 11 27 1 0\\n 12 13 2 0\\n 12 28 1 0\\n 14 15 2 0\\n 15 16 1 0\\n 15 17 1 0\\n 17 29 1 0\\n 17 30 1 0\\nM END\\n\",\"sdf\");\n\tviewer_17270772624778967.setStyle({\"stick\": {}});\n\tviewer_17270772624778967.addModel(\"ZINC03814459\\n RDKit 3D\\n\\n 30 32 0 0 1 0 0 0 0 0999 V2000\\n -3.5053 -2.3291 -0.0243 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -4.2011 -1.1840 -0.1219 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.2676 -0.1660 -0.0782 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.0193 -0.8293 0.0475 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.1839 -2.2091 0.0831 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.8935 0.0251 0.1096 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.0930 1.3689 0.0552 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.3323 1.8295 -0.0594 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.4839 1.1733 -0.1409 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.4387 3.1805 -0.1019 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.3840 -0.4793 0.2308 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.4618 0.4474 0.2695 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.7787 -0.3310 0.3765 C 0 0 2 0 0 0 0 0 0 0 0 0\\n 3.9854 0.5385 0.7233 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.1650 -0.2386 0.1556 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.5201 -1.2633 -0.7814 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.1636 -0.8573 -0.8840 O 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.9845 -3.2992 -0.0311 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -5.1985 -1.0938 -0.2075 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.3174 3.5690 -0.4020 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.5944 3.7059 -0.2596 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.3471 1.0895 1.1443 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.4704 1.0850 -0.6161 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.6861 -1.1413 1.1023 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.0722 0.7260 1.7938 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.9071 1.5022 0.2182 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.8452 0.4235 -0.3809 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.7325 -0.7405 0.9399 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.9962 -1.2957 -1.7616 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.5645 -2.2636 -0.3482 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1 5 2 0\\n 1 2 1 0\\n 1 18 1 0\\n 2 3 1 0\\n 2 19 1 0\\n 3 9 2 0\\n 3 4 1 0\\n 4 5 1 0\\n 4 6 2 0\\n 6 7 1 0\\n 6 11 1 0\\n 7 8 2 0\\n 8 9 1 0\\n 8 10 1 0\\n 10 20 1 0\\n 10 21 1 0\\n 11 12 1 0\\n 12 13 1 0\\n 12 22 1 0\\n 12 23 1 0\\n 13 17 1 0\\n 13 14 1 0\\n 13 24 1 1\\n 14 15 1 0\\n 14 25 1 0\\n 14 26 1 0\\n 15 16 1 0\\n 15 27 1 0\\n 15 28 1 0\\n 16 17 1 0\\n 16 29 1 0\\n 16 30 1 0\\nM END\\n\",\"sdf\");\n\tviewer_17270772624778967.setStyle({\"stick\": {}});\n\tviewer_17270772624778967.zoomTo();\nviewer_17270772624778967.render();\n});\n</script>",
"text/html": [
"<div id=\"3dmolviewer_17270772624778967\" style=\"position: relative; width: 400px; height: 400px;\">\n",
" <p id=\"3dmolwarning_17270772624778967\" style=\"background-color:#ffcccc;color:black\">3Dmol.js failed to load for some reason. Please check your browser console for error messages.<br></p>\n",
" </div>\n",
"<script>\n",
"\n",
"var 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",
"\n",
"if(typeof $3Dmolpromise === 'undefined') {\n",
"$3Dmolpromise = null;\n",
" $3Dmolpromise = loadScriptAsync('https://cdnjs.cloudflare.com/ajax/libs/3Dmol/2.4.0/3Dmol-min.js');\n",
"}\n",
"\n",
"var viewer_17270772624778967 = null;\n",
"var warn = document.getElementById(\"3dmolwarning_17270772624778967\");\n",
"if(warn) {\n",
" warn.parentNode.removeChild(warn);\n",
"}\n",
"$3Dmolpromise.then(function() {\n",
"viewer_17270772624778967 = $3Dmol.createViewer(document.getElementById(\"3dmolviewer_17270772624778967\"),{backgroundColor:\"white\"});\n",
"viewer_17270772624778967.zoomTo();\n",
"\tviewer_17270772624778967.addModel(\"ZINC03814457\\n RDKit 3D\\n\\n 30 31 0 0 1 0 0 0 0 0999 V2000\\n 5.4230 -0.4412 0.7616 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.2434 0.3667 0.1880 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.5978 0.9630 -1.1852 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.9575 -0.4703 0.1074 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.9988 -1.6999 0.0580 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.6357 0.2975 0.0804 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.5374 -0.6063 0.0692 O 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.7229 -0.0532 0.0310 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.8848 -0.8592 -0.0106 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.1098 -0.1432 -0.0466 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -4.0854 -1.1212 -0.0831 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.4330 -2.2959 -0.0687 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.1041 -2.2310 -0.0241 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.2721 1.2054 -0.0433 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.0919 1.8123 -0.0064 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.8677 1.2990 0.0350 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.1448 3.1672 -0.0074 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.7118 -1.2538 0.0931 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.2974 0.1913 0.9136 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.1671 -0.8852 1.7247 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.0364 1.1881 0.8743 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.4832 1.5956 -1.1194 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.8059 0.1785 -1.9146 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.7887 1.5777 -1.5810 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.6085 0.9288 -0.8080 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.5821 0.9425 0.9579 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -5.0816 -0.9900 -0.1173 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.9506 -3.2459 -0.0915 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.0380 3.6039 0.1519 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.3036 3.6737 0.2145 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1 2 1 0\\n 1 18 1 0\\n 1 19 1 0\\n 1 20 1 0\\n 2 3 1 0\\n 2 4 1 0\\n 2 21 1 0\\n 3 22 1 0\\n 3 23 1 0\\n 3 24 1 0\\n 4 5 2 0\\n 4 6 1 0\\n 6 7 1 0\\n 6 25 1 0\\n 6 26 1 0\\n 7 8 1 0\\n 8 16 2 0\\n 8 9 1 0\\n 9 13 1 0\\n 9 10 2 0\\n 10 11 1 0\\n 10 14 1 0\\n 11 12 1 0\\n 11 27 1 0\\n 12 13 2 0\\n 12 28 1 0\\n 14 15 2 0\\n 15 16 1 0\\n 15 17 1 0\\n 17 29 1 0\\n 17 30 1 0\\nM END\\n\",\"sdf\");\n",
"\tviewer_17270772624778967.setStyle({\"stick\": {}});\n",
"\tviewer_17270772624778967.addModel(\"ZINC03814459\\n RDKit 3D\\n\\n 30 32 0 0 1 0 0 0 0 0999 V2000\\n -3.5053 -2.3291 -0.0243 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -4.2011 -1.1840 -0.1219 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.2676 -0.1660 -0.0782 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.0193 -0.8293 0.0475 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.1839 -2.2091 0.0831 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.8935 0.0251 0.1096 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.0930 1.3689 0.0552 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.3323 1.8295 -0.0594 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.4839 1.1733 -0.1409 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.4387 3.1805 -0.1019 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.3840 -0.4793 0.2308 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.4618 0.4474 0.2695 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.7787 -0.3310 0.3765 C 0 0 2 0 0 0 0 0 0 0 0 0\\n 3.9854 0.5385 0.7233 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.1650 -0.2386 0.1556 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.5201 -1.2633 -0.7814 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.1636 -0.8573 -0.8840 O 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.9845 -3.2992 -0.0311 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -5.1985 -1.0938 -0.2075 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.3174 3.5690 -0.4020 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.5944 3.7059 -0.2596 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.3471 1.0895 1.1443 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.4704 1.0850 -0.6161 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.6861 -1.1413 1.1023 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.0722 0.7260 1.7938 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.9071 1.5022 0.2182 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.8452 0.4235 -0.3809 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.7325 -0.7405 0.9399 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.9962 -1.2957 -1.7616 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.5645 -2.2636 -0.3482 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1 5 2 0\\n 1 2 1 0\\n 1 18 1 0\\n 2 3 1 0\\n 2 19 1 0\\n 3 9 2 0\\n 3 4 1 0\\n 4 5 1 0\\n 4 6 2 0\\n 6 7 1 0\\n 6 11 1 0\\n 7 8 2 0\\n 8 9 1 0\\n 8 10 1 0\\n 10 20 1 0\\n 10 21 1 0\\n 11 12 1 0\\n 12 13 1 0\\n 12 22 1 0\\n 12 23 1 0\\n 13 17 1 0\\n 13 14 1 0\\n 13 24 1 1\\n 14 15 1 0\\n 14 25 1 0\\n 14 26 1 0\\n 15 16 1 0\\n 15 27 1 0\\n 15 28 1 0\\n 16 17 1 0\\n 16 29 1 0\\n 16 30 1 0\\nM END\\n\",\"sdf\");\n",
"\tviewer_17270772624778967.setStyle({\"stick\": {}});\n",
"\tviewer_17270772624778967.zoomTo();\n",
"viewer_17270772624778967.render();\n",
"});\n",
"</script>"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"p = py3Dmol.view(width=400, height=400)\n",
"IPythonConsole.addMolToView(ref,p)\n",
"IPythonConsole.addMolToView(ms2[0],p)\n",
"p.zoomTo()\n",
"p.show()\n"
]
},
{
"cell_type": "code",
"execution_count": 14,
"id": "f194da9c-53db-4b59-aa62-392cea4e04f8",
"metadata": {
"execution": {
"iopub.execute_input": "2024-09-23T07:43:12.749722Z",
"iopub.status.busy": "2024-09-23T07:43:12.749292Z",
"iopub.status.idle": "2024-09-23T07:43:12.760547Z",
"shell.execute_reply": "2024-09-23T07:43:12.759359Z",
"shell.execute_reply.started": "2024-09-23T07:43:12.749695Z"
}
},
"outputs": [
{
"data": {
"text/plain": [
"1"
]
},
"execution_count": 14,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ms2[0].GetNumConformers()"
]
},
{
"cell_type": "code",
"execution_count": 21,
"id": "0eae33ea-7adf-4dbb-bdec-cd2d886f760d",
"metadata": {
"execution": {
"iopub.execute_input": "2024-09-23T07:45:27.051153Z",
"iopub.status.busy": "2024-09-23T07:45:27.050690Z",
"iopub.status.idle": "2024-09-23T07:45:27.276838Z",
"shell.execute_reply": "2024-09-23T07:45:27.275548Z",
"shell.execute_reply.started": "2024-09-23T07:45:27.051118Z"
}
},
"outputs": [
{
"data": {
"text/plain": [
"<rdkit.rdBase._vecti at 0x72bed6b1c740>"
]
},
"execution_count": 21,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"rdDistGeom.EmbedMultipleConfs(ms[0], numConfs=20, clearConfs=True)"
]
},
{
"cell_type": "code",
"execution_count": 22,
"id": "08f77d17-84f1-454b-9cb1-f917082ecb16",
"metadata": {
"execution": {
"iopub.execute_input": "2024-09-23T07:45:38.236333Z",
"iopub.status.busy": "2024-09-23T07:45:38.234728Z",
"iopub.status.idle": "2024-09-23T07:45:38.243330Z",
"shell.execute_reply": "2024-09-23T07:45:38.242244Z",
"shell.execute_reply.started": "2024-09-23T07:45:38.236264Z"
}
},
"outputs": [
{
"data": {
"text/plain": [
"20"
]
},
"execution_count": 22,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"ms[0].GetNumConformers()"
]
},
{
"cell_type": "code",
"execution_count": 27,
"id": "f4456b24-d967-4b5e-8576-f67916a68cfa",
"metadata": {
"execution": {
"iopub.execute_input": "2024-09-23T07:48:44.680904Z",
"iopub.status.busy": "2024-09-23T07:48:44.679270Z",
"iopub.status.idle": "2024-09-23T07:48:44.711472Z",
"shell.execute_reply": "2024-09-23T07:48:44.710061Z",
"shell.execute_reply.started": "2024-09-23T07:48:44.680843Z"
}
},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"confId:0 score (0.8542879129531401, 0.4722432197100978)\n",
"confId:1 score (0.8808902027340768, 0.6974905376016416)\n",
"confId:2 score (0.7898387669876854, 0.3063275887954462)\n",
"confId:3 score (0.880527544148696, 0.7116334899939337)\n",
"confId:4 score (0.8729775624069694, 0.6825306575010707)\n",
"confId:5 score (0.9864794077839071, 0.9088223949714581)\n",
"confId:6 score (0.9472298392448602, 0.957002197067338)\n",
"confId:7 score (0.9891675871193726, 0.9604732031905421)\n",
"confId:8 score (0.8516339003582291, 0.5572700904652848)\n",
"confId:9 score (0.9652758642776211, 0.9182496022437263)\n",
"confId:10 score (0.7516978303417313, 0.0634575518733277)\n",
"confId:11 score (0.8499156680566791, 0.47275013900866353)\n",
"confId:12 score (0.9356752093095162, 0.8260476532442919)\n",
"confId:13 score (0.829384550323322, 0.5760493696244279)\n",
"confId:14 score (0.8081998492544819, 0.3377250231859849)\n",
"confId:15 score (0.9790899262182409, 0.8649580663054487)\n",
"confId:16 score (0.8019988431966623, 0.5153725246983543)\n",
"confId:17 score (0.9806695644654704, 0.8556072570305334)\n",
"confId:18 score (0.8825032324900696, 0.7057761504893614)\n",
"confId:19 score (0.8643148020534952, 0.5201490819343806)\n"
]
}
],
"source": [
"for conf in ms[0].GetConformers():\n",
" tpl = rdShapeAlign.AlignMol(ref, ms[0], probeConfId=conf.GetId())\n",
" print(f\"confId:{conf.GetId()} score {tpl}\")"
]
},
{
"cell_type": "code",
"execution_count": 28,
"id": "54fae478-ba56-4727-8ed6-f897bc098e29",
"metadata": {
"execution": {
"iopub.execute_input": "2024-09-23T07:49:25.768101Z",
"iopub.status.busy": "2024-09-23T07:49:25.766902Z",
"iopub.status.idle": "2024-09-23T07:49:25.775410Z",
"shell.execute_reply": "2024-09-23T07:49:25.774343Z",
"shell.execute_reply.started": "2024-09-23T07:49:25.768071Z"
}
},
"outputs": [
{
"data": {
"application/3dmoljs_load.v0": "<div id=\"3dmolviewer_17270777657707818\" style=\"position: relative; width: 400px; height: 400px;\">\n <p id=\"3dmolwarning_17270777657707818\" style=\"background-color:#ffcccc;color:black\">3Dmol.js failed to load for some reason. Please check your browser console for error messages.<br></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/2.4.0/3Dmol-min.js');\n}\n\nvar viewer_17270777657707818 = null;\nvar warn = document.getElementById(\"3dmolwarning_17270777657707818\");\nif(warn) {\n warn.parentNode.removeChild(warn);\n}\n$3Dmolpromise.then(function() {\nviewer_17270777657707818 = $3Dmol.createViewer(document.getElementById(\"3dmolviewer_17270777657707818\"),{backgroundColor:\"white\"});\nviewer_17270777657707818.zoomTo();\n\tviewer_17270777657707818.addModel(\"ZINC03814457\\n RDKit 3D\\n\\n 30 31 0 0 1 0 0 0 0 0999 V2000\\n 5.4230 -0.4412 0.7616 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.2434 0.3667 0.1880 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.5978 0.9630 -1.1852 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.9575 -0.4703 0.1074 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.9988 -1.6999 0.0580 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.6357 0.2975 0.0804 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.5374 -0.6063 0.0692 O 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.7229 -0.0532 0.0310 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.8848 -0.8592 -0.0106 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.1098 -0.1432 -0.0466 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -4.0854 -1.1212 -0.0831 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.4330 -2.2959 -0.0687 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.1041 -2.2310 -0.0241 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.2721 1.2054 -0.0433 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.0919 1.8123 -0.0064 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.8677 1.2990 0.0350 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.1448 3.1672 -0.0074 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.7118 -1.2538 0.0931 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.2974 0.1913 0.9136 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.1671 -0.8852 1.7247 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.0364 1.1881 0.8743 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.4832 1.5956 -1.1194 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.8059 0.1785 -1.9146 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.7887 1.5777 -1.5810 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.6085 0.9288 -0.8080 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.5821 0.9425 0.9579 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -5.0816 -0.9900 -0.1173 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.9506 -3.2459 -0.0915 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.0380 3.6039 0.1519 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.3036 3.6737 0.2145 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1 2 1 0\\n 1 18 1 0\\n 1 19 1 0\\n 1 20 1 0\\n 2 3 1 0\\n 2 4 1 0\\n 2 21 1 0\\n 3 22 1 0\\n 3 23 1 0\\n 3 24 1 0\\n 4 5 2 0\\n 4 6 1 0\\n 6 7 1 0\\n 6 25 1 0\\n 6 26 1 0\\n 7 8 1 0\\n 8 16 2 0\\n 8 9 1 0\\n 9 13 1 0\\n 9 10 2 0\\n 10 11 1 0\\n 10 14 1 0\\n 11 12 1 0\\n 11 27 1 0\\n 12 13 2 0\\n 12 28 1 0\\n 14 15 2 0\\n 15 16 1 0\\n 15 17 1 0\\n 17 29 1 0\\n 17 30 1 0\\nM END\\n\",\"sdf\");\n\tviewer_17270777657707818.setStyle({\"stick\": {}});\n\tviewer_17270777657707818.addModel(\"ZINC03814457\\n RDKit 3D\\n\\n 30 31 0 0 1 0 0 0 0 0999 V2000\\n 4.6126 0.6441 1.5137 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.3380 -0.1984 0.2952 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.5855 0.5658 -0.9775 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.9567 -0.7534 0.2651 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.7212 -1.9535 0.2406 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.8119 0.1712 0.2646 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.5974 -0.5886 0.2333 O 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.6390 -0.0068 0.2254 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.7497 -0.8387 0.1944 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.0199 -0.2908 0.1854 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.9315 -1.2799 0.1546 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.2460 -2.4472 0.1442 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.9110 -2.1897 0.1683 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.1857 1.0600 0.2067 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.0902 1.8704 0.2370 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.8519 1.3323 0.2458 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.3204 3.2762 0.2584 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.3833 1.6927 1.2242 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.6817 0.5870 1.8035 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.9971 0.3221 2.3544 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.0993 -1.0223 0.3189 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.7470 -0.1166 -1.8372 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.5083 1.1799 -0.9044 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.7368 1.2442 -1.2081 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.8280 0.7588 -0.6771 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.8714 0.7864 1.1822 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -4.9779 -1.1720 0.1411 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.7153 -3.4253 0.1201 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.7476 3.6565 1.1399 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.0889 3.9115 -0.5371 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1 2 1 0\\n 1 18 1 0\\n 1 19 1 0\\n 1 20 1 0\\n 2 3 1 0\\n 2 4 1 0\\n 2 21 1 0\\n 3 22 1 0\\n 3 23 1 0\\n 3 24 1 0\\n 4 5 2 0\\n 4 6 1 0\\n 6 7 1 0\\n 6 25 1 0\\n 6 26 1 0\\n 7 8 1 0\\n 8 16 2 0\\n 8 9 1 0\\n 9 13 1 0\\n 9 10 2 0\\n 10 11 1 0\\n 10 14 1 0\\n 11 12 1 0\\n 11 27 1 0\\n 12 13 2 0\\n 12 28 1 0\\n 14 15 2 0\\n 15 16 1 0\\n 15 17 1 0\\n 17 29 1 0\\n 17 30 1 0\\nM END\\n\",\"sdf\");\n\tviewer_17270777657707818.setStyle({\"stick\": {}});\n\tviewer_17270777657707818.zoomTo();\nviewer_17270777657707818.render();\n});\n</script>",
"text/html": [
"<div id=\"3dmolviewer_17270777657707818\" style=\"position: relative; width: 400px; height: 400px;\">\n",
" <p id=\"3dmolwarning_17270777657707818\" style=\"background-color:#ffcccc;color:black\">3Dmol.js failed to load for some reason. Please check your browser console for error messages.<br></p>\n",
" </div>\n",
"<script>\n",
"\n",
"var 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",
"\n",
"if(typeof $3Dmolpromise === 'undefined') {\n",
"$3Dmolpromise = null;\n",
" $3Dmolpromise = loadScriptAsync('https://cdnjs.cloudflare.com/ajax/libs/3Dmol/2.4.0/3Dmol-min.js');\n",
"}\n",
"\n",
"var viewer_17270777657707818 = null;\n",
"var warn = document.getElementById(\"3dmolwarning_17270777657707818\");\n",
"if(warn) {\n",
" warn.parentNode.removeChild(warn);\n",
"}\n",
"$3Dmolpromise.then(function() {\n",
"viewer_17270777657707818 = $3Dmol.createViewer(document.getElementById(\"3dmolviewer_17270777657707818\"),{backgroundColor:\"white\"});\n",
"viewer_17270777657707818.zoomTo();\n",
"\tviewer_17270777657707818.addModel(\"ZINC03814457\\n RDKit 3D\\n\\n 30 31 0 0 1 0 0 0 0 0999 V2000\\n 5.4230 -0.4412 0.7616 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.2434 0.3667 0.1880 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.5978 0.9630 -1.1852 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.9575 -0.4703 0.1074 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.9988 -1.6999 0.0580 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.6357 0.2975 0.0804 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.5374 -0.6063 0.0692 O 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.7229 -0.0532 0.0310 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.8848 -0.8592 -0.0106 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.1098 -0.1432 -0.0466 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -4.0854 -1.1212 -0.0831 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.4330 -2.2959 -0.0687 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.1041 -2.2310 -0.0241 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.2721 1.2054 -0.0433 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.0919 1.8123 -0.0064 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.8677 1.2990 0.0350 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.1448 3.1672 -0.0074 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.7118 -1.2538 0.0931 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.2974 0.1913 0.9136 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.1671 -0.8852 1.7247 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.0364 1.1881 0.8743 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.4832 1.5956 -1.1194 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.8059 0.1785 -1.9146 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.7887 1.5777 -1.5810 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.6085 0.9288 -0.8080 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.5821 0.9425 0.9579 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -5.0816 -0.9900 -0.1173 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.9506 -3.2459 -0.0915 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.0380 3.6039 0.1519 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.3036 3.6737 0.2145 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1 2 1 0\\n 1 18 1 0\\n 1 19 1 0\\n 1 20 1 0\\n 2 3 1 0\\n 2 4 1 0\\n 2 21 1 0\\n 3 22 1 0\\n 3 23 1 0\\n 3 24 1 0\\n 4 5 2 0\\n 4 6 1 0\\n 6 7 1 0\\n 6 25 1 0\\n 6 26 1 0\\n 7 8 1 0\\n 8 16 2 0\\n 8 9 1 0\\n 9 13 1 0\\n 9 10 2 0\\n 10 11 1 0\\n 10 14 1 0\\n 11 12 1 0\\n 11 27 1 0\\n 12 13 2 0\\n 12 28 1 0\\n 14 15 2 0\\n 15 16 1 0\\n 15 17 1 0\\n 17 29 1 0\\n 17 30 1 0\\nM END\\n\",\"sdf\");\n",
"\tviewer_17270777657707818.setStyle({\"stick\": {}});\n",
"\tviewer_17270777657707818.addModel(\"ZINC03814457\\n RDKit 3D\\n\\n 30 31 0 0 1 0 0 0 0 0999 V2000\\n 4.6126 0.6441 1.5137 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.3380 -0.1984 0.2952 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.5855 0.5658 -0.9775 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.9567 -0.7534 0.2651 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.7212 -1.9535 0.2406 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.8119 0.1712 0.2646 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.5974 -0.5886 0.2333 O 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.6390 -0.0068 0.2254 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.7497 -0.8387 0.1944 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.0199 -0.2908 0.1854 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.9315 -1.2799 0.1546 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.2460 -2.4472 0.1442 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.9110 -2.1897 0.1683 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.1857 1.0600 0.2067 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.0902 1.8704 0.2370 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.8519 1.3323 0.2458 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.3204 3.2762 0.2584 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.3833 1.6927 1.2242 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.6817 0.5870 1.8035 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.9971 0.3221 2.3544 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.0993 -1.0223 0.3189 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.7470 -0.1166 -1.8372 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.5083 1.1799 -0.9044 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.7368 1.2442 -1.2081 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.8280 0.7588 -0.6771 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.8714 0.7864 1.1822 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -4.9779 -1.1720 0.1411 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.7153 -3.4253 0.1201 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.7476 3.6565 1.1399 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.0889 3.9115 -0.5371 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1 2 1 0\\n 1 18 1 0\\n 1 19 1 0\\n 1 20 1 0\\n 2 3 1 0\\n 2 4 1 0\\n 2 21 1 0\\n 3 22 1 0\\n 3 23 1 0\\n 3 24 1 0\\n 4 5 2 0\\n 4 6 1 0\\n 6 7 1 0\\n 6 25 1 0\\n 6 26 1 0\\n 7 8 1 0\\n 8 16 2 0\\n 8 9 1 0\\n 9 13 1 0\\n 9 10 2 0\\n 10 11 1 0\\n 10 14 1 0\\n 11 12 1 0\\n 11 27 1 0\\n 12 13 2 0\\n 12 28 1 0\\n 14 15 2 0\\n 15 16 1 0\\n 15 17 1 0\\n 17 29 1 0\\n 17 30 1 0\\nM END\\n\",\"sdf\");\n",
"\tviewer_17270777657707818.setStyle({\"stick\": {}});\n",
"\tviewer_17270777657707818.zoomTo();\n",
"viewer_17270777657707818.render();\n",
"});\n",
"</script>"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"p = py3Dmol.view(width=400, height=400)\n",
"IPythonConsole.addMolToView(ref,p)\n",
"IPythonConsole.addMolToView(ms[0],p,confId=9)\n",
"p.zoomTo()\n",
"p.show()"
]
},
{
"cell_type": "code",
"execution_count": 29,
"id": "f935c5ae-3f89-4ab8-b77b-6a53e821ecd5",
"metadata": {
"execution": {
"iopub.execute_input": "2024-09-23T07:49:38.237932Z",
"iopub.status.busy": "2024-09-23T07:49:38.237453Z",
"iopub.status.idle": "2024-09-23T07:49:38.248611Z",
"shell.execute_reply": "2024-09-23T07:49:38.246917Z",
"shell.execute_reply.started": "2024-09-23T07:49:38.237896Z"
}
},
"outputs": [
{
"data": {
"application/3dmoljs_load.v0": "<div id=\"3dmolviewer_17270777782416031\" style=\"position: relative; width: 400px; height: 400px;\">\n <p id=\"3dmolwarning_17270777782416031\" style=\"background-color:#ffcccc;color:black\">3Dmol.js failed to load for some reason. Please check your browser console for error messages.<br></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/2.4.0/3Dmol-min.js');\n}\n\nvar viewer_17270777782416031 = null;\nvar warn = document.getElementById(\"3dmolwarning_17270777782416031\");\nif(warn) {\n warn.parentNode.removeChild(warn);\n}\n$3Dmolpromise.then(function() {\nviewer_17270777782416031 = $3Dmol.createViewer(document.getElementById(\"3dmolviewer_17270777782416031\"),{backgroundColor:\"white\"});\nviewer_17270777782416031.zoomTo();\n\tviewer_17270777782416031.addModel(\"ZINC03814457\\n RDKit 3D\\n\\n 30 31 0 0 1 0 0 0 0 0999 V2000\\n 5.4230 -0.4412 0.7616 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.2434 0.3667 0.1880 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.5978 0.9630 -1.1852 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.9575 -0.4703 0.1074 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.9988 -1.6999 0.0580 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.6357 0.2975 0.0804 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.5374 -0.6063 0.0692 O 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.7229 -0.0532 0.0310 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.8848 -0.8592 -0.0106 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.1098 -0.1432 -0.0466 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -4.0854 -1.1212 -0.0831 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.4330 -2.2959 -0.0687 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.1041 -2.2310 -0.0241 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.2721 1.2054 -0.0433 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.0919 1.8123 -0.0064 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.8677 1.2990 0.0350 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.1448 3.1672 -0.0074 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.7118 -1.2538 0.0931 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.2974 0.1913 0.9136 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.1671 -0.8852 1.7247 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.0364 1.1881 0.8743 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.4832 1.5956 -1.1194 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.8059 0.1785 -1.9146 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.7887 1.5777 -1.5810 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.6085 0.9288 -0.8080 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.5821 0.9425 0.9579 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -5.0816 -0.9900 -0.1173 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.9506 -3.2459 -0.0915 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.0380 3.6039 0.1519 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.3036 3.6737 0.2145 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1 2 1 0\\n 1 18 1 0\\n 1 19 1 0\\n 1 20 1 0\\n 2 3 1 0\\n 2 4 1 0\\n 2 21 1 0\\n 3 22 1 0\\n 3 23 1 0\\n 3 24 1 0\\n 4 5 2 0\\n 4 6 1 0\\n 6 7 1 0\\n 6 25 1 0\\n 6 26 1 0\\n 7 8 1 0\\n 8 16 2 0\\n 8 9 1 0\\n 9 13 1 0\\n 9 10 2 0\\n 10 11 1 0\\n 10 14 1 0\\n 11 12 1 0\\n 11 27 1 0\\n 12 13 2 0\\n 12 28 1 0\\n 14 15 2 0\\n 15 16 1 0\\n 15 17 1 0\\n 17 29 1 0\\n 17 30 1 0\\nM END\\n\",\"sdf\");\n\tviewer_17270777782416031.setStyle({\"stick\": {}});\n\tviewer_17270777782416031.addModel(\"ZINC03814457\\n RDKit 3D\\n\\n 30 31 0 0 1 0 0 0 0 0999 V2000\\n 3.9527 1.4430 -0.5345 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.7506 0.5532 0.6702 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.6320 -0.6604 0.5979 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.3338 0.1079 0.7805 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.6341 0.3573 1.7456 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.7809 -0.6751 -0.3585 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.4506 -1.0550 -0.1805 O 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.6208 -0.1914 -0.0019 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.8877 -0.7493 0.1617 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.9929 0.0853 0.3442 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -4.0941 -0.6980 0.4774 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.6871 -1.9900 0.3805 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.3386 -2.0116 0.1878 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.8080 1.4196 0.3581 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.5774 1.9486 0.1988 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.4912 1.1510 0.0201 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.4673 3.3727 0.2260 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.8497 0.8857 -1.4831 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.9690 1.8815 -0.4567 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.2333 2.2785 -0.5119 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.0219 1.1245 1.5735 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.2524 -1.3976 1.3587 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.6656 -0.4227 0.9053 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.6217 -1.1755 -0.3777 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.3779 -1.6074 -0.4588 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.9061 -0.0601 -1.2646 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -5.0879 -0.3717 0.6287 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -4.2902 -2.8942 0.4391 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.8057 3.8706 0.8838 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.0761 3.9274 -0.4413 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1 2 1 0\\n 1 18 1 0\\n 1 19 1 0\\n 1 20 1 0\\n 2 3 1 0\\n 2 4 1 0\\n 2 21 1 0\\n 3 22 1 0\\n 3 23 1 0\\n 3 24 1 0\\n 4 5 2 0\\n 4 6 1 0\\n 6 7 1 0\\n 6 25 1 0\\n 6 26 1 0\\n 7 8 1 0\\n 8 16 2 0\\n 8 9 1 0\\n 9 13 1 0\\n 9 10 2 0\\n 10 11 1 0\\n 10 14 1 0\\n 11 12 1 0\\n 11 27 1 0\\n 12 13 2 0\\n 12 28 1 0\\n 14 15 2 0\\n 15 16 1 0\\n 15 17 1 0\\n 17 29 1 0\\n 17 30 1 0\\nM END\\n\",\"sdf\");\n\tviewer_17270777782416031.setStyle({\"stick\": {}});\n\tviewer_17270777782416031.zoomTo();\nviewer_17270777782416031.render();\n});\n</script>",
"text/html": [
"<div id=\"3dmolviewer_17270777782416031\" style=\"position: relative; width: 400px; height: 400px;\">\n",
" <p id=\"3dmolwarning_17270777782416031\" style=\"background-color:#ffcccc;color:black\">3Dmol.js failed to load for some reason. Please check your browser console for error messages.<br></p>\n",
" </div>\n",
"<script>\n",
"\n",
"var 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",
"\n",
"if(typeof $3Dmolpromise === 'undefined') {\n",
"$3Dmolpromise = null;\n",
" $3Dmolpromise = loadScriptAsync('https://cdnjs.cloudflare.com/ajax/libs/3Dmol/2.4.0/3Dmol-min.js');\n",
"}\n",
"\n",
"var viewer_17270777782416031 = null;\n",
"var warn = document.getElementById(\"3dmolwarning_17270777782416031\");\n",
"if(warn) {\n",
" warn.parentNode.removeChild(warn);\n",
"}\n",
"$3Dmolpromise.then(function() {\n",
"viewer_17270777782416031 = $3Dmol.createViewer(document.getElementById(\"3dmolviewer_17270777782416031\"),{backgroundColor:\"white\"});\n",
"viewer_17270777782416031.zoomTo();\n",
"\tviewer_17270777782416031.addModel(\"ZINC03814457\\n RDKit 3D\\n\\n 30 31 0 0 1 0 0 0 0 0999 V2000\\n 5.4230 -0.4412 0.7616 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.2434 0.3667 0.1880 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.5978 0.9630 -1.1852 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.9575 -0.4703 0.1074 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.9988 -1.6999 0.0580 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.6357 0.2975 0.0804 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.5374 -0.6063 0.0692 O 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.7229 -0.0532 0.0310 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.8848 -0.8592 -0.0106 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.1098 -0.1432 -0.0466 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -4.0854 -1.1212 -0.0831 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.4330 -2.2959 -0.0687 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.1041 -2.2310 -0.0241 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.2721 1.2054 -0.0433 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.0919 1.8123 -0.0064 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.8677 1.2990 0.0350 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.1448 3.1672 -0.0074 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.7118 -1.2538 0.0931 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 6.2974 0.1913 0.9136 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.1671 -0.8852 1.7247 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.0364 1.1881 0.8743 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.4832 1.5956 -1.1194 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.8059 0.1785 -1.9146 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.7887 1.5777 -1.5810 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.6085 0.9288 -0.8080 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.5821 0.9425 0.9579 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -5.0816 -0.9900 -0.1173 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.9506 -3.2459 -0.0915 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.0380 3.6039 0.1519 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.3036 3.6737 0.2145 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1 2 1 0\\n 1 18 1 0\\n 1 19 1 0\\n 1 20 1 0\\n 2 3 1 0\\n 2 4 1 0\\n 2 21 1 0\\n 3 22 1 0\\n 3 23 1 0\\n 3 24 1 0\\n 4 5 2 0\\n 4 6 1 0\\n 6 7 1 0\\n 6 25 1 0\\n 6 26 1 0\\n 7 8 1 0\\n 8 16 2 0\\n 8 9 1 0\\n 9 13 1 0\\n 9 10 2 0\\n 10 11 1 0\\n 10 14 1 0\\n 11 12 1 0\\n 11 27 1 0\\n 12 13 2 0\\n 12 28 1 0\\n 14 15 2 0\\n 15 16 1 0\\n 15 17 1 0\\n 17 29 1 0\\n 17 30 1 0\\nM END\\n\",\"sdf\");\n",
"\tviewer_17270777782416031.setStyle({\"stick\": {}});\n",
"\tviewer_17270777782416031.addModel(\"ZINC03814457\\n RDKit 3D\\n\\n 30 31 0 0 1 0 0 0 0 0999 V2000\\n 3.9527 1.4430 -0.5345 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.7506 0.5532 0.6702 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.6320 -0.6604 0.5979 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.3338 0.1079 0.7805 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.6341 0.3573 1.7456 O 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.7809 -0.6751 -0.3585 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.4506 -1.0550 -0.1805 O 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.6208 -0.1914 -0.0019 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.8877 -0.7493 0.1617 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.9929 0.0853 0.3442 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -4.0941 -0.6980 0.4774 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -3.6871 -1.9900 0.3805 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.3386 -2.0116 0.1878 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.8080 1.4196 0.3581 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.5774 1.9486 0.1988 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.4912 1.1510 0.0201 N 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.4673 3.3727 0.2260 N 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.8497 0.8857 -1.4831 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.9690 1.8815 -0.4567 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 3.2333 2.2785 -0.5119 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.0219 1.1245 1.5735 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.2524 -1.3976 1.3587 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 5.6656 -0.4227 0.9053 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 4.6217 -1.1755 -0.3777 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.3779 -1.6074 -0.4588 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.9061 -0.0601 -1.2646 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -5.0879 -0.3717 0.6287 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -4.2902 -2.8942 0.4391 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.8057 3.8706 0.8838 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.0761 3.9274 -0.4413 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1 2 1 0\\n 1 18 1 0\\n 1 19 1 0\\n 1 20 1 0\\n 2 3 1 0\\n 2 4 1 0\\n 2 21 1 0\\n 3 22 1 0\\n 3 23 1 0\\n 3 24 1 0\\n 4 5 2 0\\n 4 6 1 0\\n 6 7 1 0\\n 6 25 1 0\\n 6 26 1 0\\n 7 8 1 0\\n 8 16 2 0\\n 8 9 1 0\\n 9 13 1 0\\n 9 10 2 0\\n 10 11 1 0\\n 10 14 1 0\\n 11 12 1 0\\n 11 27 1 0\\n 12 13 2 0\\n 12 28 1 0\\n 14 15 2 0\\n 15 16 1 0\\n 15 17 1 0\\n 17 29 1 0\\n 17 30 1 0\\nM END\\n\",\"sdf\");\n",
"\tviewer_17270777782416031.setStyle({\"stick\": {}});\n",
"\tviewer_17270777782416031.zoomTo();\n",
"viewer_17270777782416031.render();\n",
"});\n",
"</script>"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"p = py3Dmol.view(width=400, height=400)\n",
"IPythonConsole.addMolToView(ref,p)\n",
"IPythonConsole.addMolToView(ms[0],p,confId=19)\n",
"p.zoomTo()\n",
"p.show()"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "b32cf12f-6b17-46b5-8697-50e75c3df7ce",
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.9"
}
},
"nbformat": 4,
"nbformat_minor": 5
}
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment