-
-
Save leelasd/4f3c84e9f2aaf7cd8033fae5f1ecc7b3 to your computer and use it in GitHub Desktop.
3D-MCS.ipynb
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| { | |
| "cells": [ | |
| { | |
| "metadata": { | |
| "trusted": true | |
| }, | |
| "cell_type": "code", | |
| "source": "from rdkit import Chem\nfrom rdkit.Chem import rdFMCS\nfrom rdkit.Chem import Draw\nfrom rdkit.Chem import AllChem\nfrom rdkit.Chem.Draw import IPythonConsole", | |
| "execution_count": 1, | |
| "outputs": [ | |
| { | |
| "output_type": "stream", | |
| "text": "RDKit WARNING: [15:18:29] Enabling RDKit 2019.09.3 jupyter extensions\n", | |
| "name": "stderr" | |
| } | |
| ] | |
| }, | |
| { | |
| "metadata": { | |
| "trusted": true | |
| }, | |
| "cell_type": "code", | |
| "source": "m1 = Chem.MolFromSmiles('C1CCOC[C@H]1O')\nm2 = Chem.MolFromSmiles('C1CCOC[C@@H]1O')\nDraw.MolsToGridImage((m1,m2))", | |
| "execution_count": 2, | |
| "outputs": [ | |
| { | |
| "output_type": "execute_result", | |
| "execution_count": 2, | |
| "data": { | |
| "text/plain": "<PIL.PngImagePlugin.PngImageFile image mode=RGB size=600x200 at 0x7F6554222DD0>", | |
| "image/png": "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\n" | |
| }, | |
| "metadata": {} | |
| } | |
| ] | |
| }, | |
| { | |
| "metadata": {}, | |
| "cell_type": "markdown", | |
| "source": "## Setup\n\nFor the purposes of this demo, get a scaffold conformation to work with and then generate conformation of each of the two molecules where the core atoms match the scaffold" | |
| }, | |
| { | |
| "metadata": { | |
| "trusted": true | |
| }, | |
| "cell_type": "code", | |
| "source": "IPythonConsole.ipython_3d=True", | |
| "execution_count": 3, | |
| "outputs": [] | |
| }, | |
| { | |
| "metadata": { | |
| "trusted": true | |
| }, | |
| "cell_type": "code", | |
| "source": "scaffold = Chem.AddHs(Chem.MolFromSmiles('C1CCOCC1'))\nAllChem.EmbedMolecule(scaffold,randomSeed=0xf00d)\nscaffold", | |
| "execution_count": 4, | |
| "outputs": [ | |
| { | |
| "output_type": "display_data", | |
| "data": { | |
| "application/3dmoljs_load.v0": "<div id=\"3dmolviewer_15790115101965034\" style=\"position: relative; width: 400px; height: 400px\">\n <p id=\"3dmolwarning_15790115101965034\" style=\"background-color:#ffcccc;color:black\">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). 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 var tag = document.createElement('script');\n tag.src = uri;\n tag.async = true;\n tag.onload = () => {\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://3dmol.csb.pitt.edu/build/3Dmol.js');\n}\n\nvar viewer_15790115101965034 = null;\nvar warn = document.getElementById(\"3dmolwarning_15790115101965034\");\nif(warn) {\n warn.parentNode.removeChild(warn);\n}\n$3Dmolpromise.then(function() {\nviewer_15790115101965034 = $3Dmol.createViewer($(\"#3dmolviewer_15790115101965034\"),{backgroundColor:\"white\"});\n\tviewer_15790115101965034.removeAllModels();\n\tviewer_15790115101965034.addModel(\"\\n RDKit 3D\\n\\n 16 16 0 0 0 0 0 0 0 0999 V2000\\n -0.1962 -1.1869 -0.1225 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.2056 -0.6189 -0.1426 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.1140 0.8654 -0.4324 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.2410 1.5262 0.4081 O 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.0622 1.0494 0.1937 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.0766 -0.3532 0.8156 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.6188 -0.9877 -1.1475 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.2345 -2.2475 0.1311 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.7420 -0.8308 0.7942 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.7110 -1.0839 -1.0329 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.7880 0.9848 -1.4963 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.1182 1.3483 -0.3039 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.1506 0.8998 -0.9141 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.8338 1.6917 0.6053 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.6484 -0.3200 1.8426 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.0989 -0.7365 0.8019 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1 2 1 0\\n 2 3 1 0\\n 3 4 1 0\\n 4 5 1 0\\n 5 6 1 0\\n 6 1 1 0\\n 1 7 1 0\\n 1 8 1 0\\n 2 9 1 0\\n 2 10 1 0\\n 3 11 1 0\\n 3 12 1 0\\n 5 13 1 0\\n 5 14 1 0\\n 6 15 1 0\\n 6 16 1 0\\nM END\\n\",\"sdf\");\n\tviewer_15790115101965034.setStyle({\"stick\": {}});\n\tviewer_15790115101965034.setBackgroundColor(\"0xeeeeee\");\n\tviewer_15790115101965034.zoomTo();\nviewer_15790115101965034.render();\n});\n</script>", | |
| "text/html": "<div id=\"3dmolviewer_15790115101965034\" style=\"position: relative; width: 400px; height: 400px\">\n <p id=\"3dmolwarning_15790115101965034\" style=\"background-color:#ffcccc;color:black\">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). 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 var tag = document.createElement('script');\n tag.src = uri;\n tag.async = true;\n tag.onload = () => {\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://3dmol.csb.pitt.edu/build/3Dmol.js');\n}\n\nvar viewer_15790115101965034 = null;\nvar warn = document.getElementById(\"3dmolwarning_15790115101965034\");\nif(warn) {\n warn.parentNode.removeChild(warn);\n}\n$3Dmolpromise.then(function() {\nviewer_15790115101965034 = $3Dmol.createViewer($(\"#3dmolviewer_15790115101965034\"),{backgroundColor:\"white\"});\n\tviewer_15790115101965034.removeAllModels();\n\tviewer_15790115101965034.addModel(\"\\n RDKit 3D\\n\\n 16 16 0 0 0 0 0 0 0 0999 V2000\\n -0.1962 -1.1869 -0.1225 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.2056 -0.6189 -0.1426 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.1140 0.8654 -0.4324 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.2410 1.5262 0.4081 O 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.0622 1.0494 0.1937 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.0766 -0.3532 0.8156 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.6188 -0.9877 -1.1475 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.2345 -2.2475 0.1311 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.7420 -0.8308 0.7942 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.7110 -1.0839 -1.0329 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.7880 0.9848 -1.4963 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.1182 1.3483 -0.3039 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.1506 0.8998 -0.9141 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.8338 1.6917 0.6053 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.6484 -0.3200 1.8426 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.0989 -0.7365 0.8019 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1 2 1 0\\n 2 3 1 0\\n 3 4 1 0\\n 4 5 1 0\\n 5 6 1 0\\n 6 1 1 0\\n 1 7 1 0\\n 1 8 1 0\\n 2 9 1 0\\n 2 10 1 0\\n 3 11 1 0\\n 3 12 1 0\\n 5 13 1 0\\n 5 14 1 0\\n 6 15 1 0\\n 6 16 1 0\\nM END\\n\",\"sdf\");\n\tviewer_15790115101965034.setStyle({\"stick\": {}});\n\tviewer_15790115101965034.setBackgroundColor(\"0xeeeeee\");\n\tviewer_15790115101965034.zoomTo();\nviewer_15790115101965034.render();\n});\n</script>" | |
| }, | |
| "metadata": {} | |
| }, | |
| { | |
| "output_type": "execute_result", | |
| "execution_count": 4, | |
| "data": { | |
| "text/plain": "<rdkit.Chem.rdchem.Mol at 0x7f6527881170>", | |
| "text/html": "", | |
| "image/png": "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\n" | |
| }, | |
| "metadata": {} | |
| } | |
| ] | |
| }, | |
| { | |
| "metadata": { | |
| "trusted": true | |
| }, | |
| "cell_type": "code", | |
| "source": "scaff_noh = Chem.RemoveHs(scaffold)\nscaff_conf = scaff_noh.GetConformer()\nmatch_m1 = m1.GetSubstructMatch(scaff_noh)\nm1_map = {}\nfor i,idx in enumerate(match_m1):\n m1_map[idx]=scaff_conf.GetAtomPosition(i)\nm1_h = Chem.AddHs(m1)\n# generating conformations that match core atoms works best using random coordinates:\nAllChem.EmbedMolecule(m1_h,randomSeed=0xf00d,coordMap=m1_map,useRandomCoords=True)\nm1_h", | |
| "execution_count": 5, | |
| "outputs": [ | |
| { | |
| "output_type": "display_data", | |
| "data": { | |
| "application/3dmoljs_load.v0": "<div id=\"3dmolviewer_1579011510461295\" style=\"position: relative; width: 400px; height: 400px\">\n <p id=\"3dmolwarning_1579011510461295\" style=\"background-color:#ffcccc;color:black\">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). 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 var tag = document.createElement('script');\n tag.src = uri;\n tag.async = true;\n tag.onload = () => {\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://3dmol.csb.pitt.edu/build/3Dmol.js');\n}\n\nvar viewer_1579011510461295 = null;\nvar warn = document.getElementById(\"3dmolwarning_1579011510461295\");\nif(warn) {\n warn.parentNode.removeChild(warn);\n}\n$3Dmolpromise.then(function() {\nviewer_1579011510461295 = $3Dmol.createViewer($(\"#3dmolviewer_1579011510461295\"),{backgroundColor:\"white\"});\n\tviewer_1579011510461295.removeAllModels();\n\tviewer_1579011510461295.addModel(\"\\n RDKit 3D\\n\\n 17 17 0 0 0 0 0 0 0 0999 V2000\\n -0.1962 -1.1869 -0.1225 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.2056 -0.6189 -0.1426 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.1140 0.8654 -0.4324 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.2410 1.5262 0.4081 O 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.0622 1.0494 0.1937 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.0766 -0.3532 0.8156 C 0 0 1 0 0 0 0 0 0 0 0 0\\n -2.3579 -0.8739 0.7665 O 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.2320 -2.2492 0.1104 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.6163 -0.9902 -1.1479 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.7156 -0.8228 0.8038 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.7130 -1.0789 -1.0250 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.1199 1.3436 -0.2866 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.8421 0.9705 -1.4939 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.7539 1.7313 0.7098 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.2857 0.9638 -0.8802 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.6534 -0.3308 1.8315 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.7518 -0.9702 1.6783 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1 2 1 0\\n 2 3 1 0\\n 3 4 1 0\\n 4 5 1 0\\n 5 6 1 0\\n 6 7 1 0\\n 6 1 1 0\\n 1 8 1 0\\n 1 9 1 0\\n 2 10 1 0\\n 2 11 1 0\\n 3 12 1 0\\n 3 13 1 0\\n 5 14 1 0\\n 5 15 1 0\\n 6 16 1 1\\n 7 17 1 0\\nM END\\n\",\"sdf\");\n\tviewer_1579011510461295.setStyle({\"stick\": {}});\n\tviewer_1579011510461295.setBackgroundColor(\"0xeeeeee\");\n\tviewer_1579011510461295.zoomTo();\nviewer_1579011510461295.render();\n});\n</script>", | |
| "text/html": "<div id=\"3dmolviewer_1579011510461295\" style=\"position: relative; width: 400px; height: 400px\">\n <p id=\"3dmolwarning_1579011510461295\" style=\"background-color:#ffcccc;color:black\">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). 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 var tag = document.createElement('script');\n tag.src = uri;\n tag.async = true;\n tag.onload = () => {\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://3dmol.csb.pitt.edu/build/3Dmol.js');\n}\n\nvar viewer_1579011510461295 = null;\nvar warn = document.getElementById(\"3dmolwarning_1579011510461295\");\nif(warn) {\n warn.parentNode.removeChild(warn);\n}\n$3Dmolpromise.then(function() {\nviewer_1579011510461295 = $3Dmol.createViewer($(\"#3dmolviewer_1579011510461295\"),{backgroundColor:\"white\"});\n\tviewer_1579011510461295.removeAllModels();\n\tviewer_1579011510461295.addModel(\"\\n RDKit 3D\\n\\n 17 17 0 0 0 0 0 0 0 0999 V2000\\n -0.1962 -1.1869 -0.1225 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.2056 -0.6189 -0.1426 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.1140 0.8654 -0.4324 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.2410 1.5262 0.4081 O 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.0622 1.0494 0.1937 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.0766 -0.3532 0.8156 C 0 0 1 0 0 0 0 0 0 0 0 0\\n -2.3579 -0.8739 0.7665 O 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.2320 -2.2492 0.1104 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.6163 -0.9902 -1.1479 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.7156 -0.8228 0.8038 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.7130 -1.0789 -1.0250 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.1199 1.3436 -0.2866 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.8421 0.9705 -1.4939 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.7539 1.7313 0.7098 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.2857 0.9638 -0.8802 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.6534 -0.3308 1.8315 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.7518 -0.9702 1.6783 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1 2 1 0\\n 2 3 1 0\\n 3 4 1 0\\n 4 5 1 0\\n 5 6 1 0\\n 6 7 1 0\\n 6 1 1 0\\n 1 8 1 0\\n 1 9 1 0\\n 2 10 1 0\\n 2 11 1 0\\n 3 12 1 0\\n 3 13 1 0\\n 5 14 1 0\\n 5 15 1 0\\n 6 16 1 1\\n 7 17 1 0\\nM END\\n\",\"sdf\");\n\tviewer_1579011510461295.setStyle({\"stick\": {}});\n\tviewer_1579011510461295.setBackgroundColor(\"0xeeeeee\");\n\tviewer_1579011510461295.zoomTo();\nviewer_1579011510461295.render();\n});\n</script>" | |
| }, | |
| "metadata": {} | |
| }, | |
| { | |
| "output_type": "execute_result", | |
| "execution_count": 5, | |
| "data": { | |
| "text/plain": "<rdkit.Chem.rdchem.Mol at 0x7f652788cb70>", | |
| "text/html": "", | |
| "image/png": "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\n" | |
| }, | |
| "metadata": {} | |
| } | |
| ] | |
| }, | |
| { | |
| "metadata": { | |
| "trusted": true | |
| }, | |
| "cell_type": "code", | |
| "source": "match_m2 = m2.GetSubstructMatch(scaff_noh)\nm2_map = {}\nfor i,idx in enumerate(match_m2):\n m2_map[idx]=scaff_conf.GetAtomPosition(i)\nm2_h = Chem.AddHs(m2)\n# generating conformations that match core atoms works best using random coordinates:\nAllChem.EmbedMolecule(m2_h,randomSeed=0xf00d,coordMap=m2_map,useRandomCoords=True)\nm2_h", | |
| "execution_count": 6, | |
| "outputs": [ | |
| { | |
| "output_type": "display_data", | |
| "data": { | |
| "application/3dmoljs_load.v0": "<div id=\"3dmolviewer_15790115107964318\" style=\"position: relative; width: 400px; height: 400px\">\n <p id=\"3dmolwarning_15790115107964318\" style=\"background-color:#ffcccc;color:black\">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). 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 var tag = document.createElement('script');\n tag.src = uri;\n tag.async = true;\n tag.onload = () => {\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://3dmol.csb.pitt.edu/build/3Dmol.js');\n}\n\nvar viewer_15790115107964318 = null;\nvar warn = document.getElementById(\"3dmolwarning_15790115107964318\");\nif(warn) {\n warn.parentNode.removeChild(warn);\n}\n$3Dmolpromise.then(function() {\nviewer_15790115107964318 = $3Dmol.createViewer($(\"#3dmolviewer_15790115107964318\"),{backgroundColor:\"white\"});\n\tviewer_15790115107964318.removeAllModels();\n\tviewer_15790115107964318.addModel(\"\\n RDKit 3D\\n\\n 17 17 0 0 0 0 0 0 0 0999 V2000\\n -0.1962 -1.1869 -0.1225 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.2056 -0.6189 -0.1426 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.1140 0.8654 -0.4324 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.2410 1.5262 0.4081 O 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.0622 1.0494 0.1937 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.0766 -0.3532 0.8156 C 0 0 2 0 0 0 0 0 0 0 0 0\\n -0.5306 -0.3294 2.0874 O 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.1204 -2.1865 0.3691 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.6672 -1.2227 -1.1131 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.6259 -0.7701 0.8672 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.7849 -1.1120 -0.9170 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.1277 1.2835 -0.2934 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.7835 1.0401 -1.4695 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.7824 1.6779 0.7402 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.2873 0.9551 -0.8797 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.0886 -0.7846 0.8139 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.0381 0.5306 2.1899 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1 2 1 0\\n 2 3 1 0\\n 3 4 1 0\\n 4 5 1 0\\n 5 6 1 0\\n 6 7 1 0\\n 6 1 1 0\\n 1 8 1 0\\n 1 9 1 0\\n 2 10 1 0\\n 2 11 1 0\\n 3 12 1 0\\n 3 13 1 0\\n 5 14 1 0\\n 5 15 1 0\\n 6 16 1 1\\n 7 17 1 0\\nM END\\n\",\"sdf\");\n\tviewer_15790115107964318.setStyle({\"stick\": {}});\n\tviewer_15790115107964318.setBackgroundColor(\"0xeeeeee\");\n\tviewer_15790115107964318.zoomTo();\nviewer_15790115107964318.render();\n});\n</script>", | |
| "text/html": "<div id=\"3dmolviewer_15790115107964318\" style=\"position: relative; width: 400px; height: 400px\">\n <p id=\"3dmolwarning_15790115107964318\" style=\"background-color:#ffcccc;color:black\">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). 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 var tag = document.createElement('script');\n tag.src = uri;\n tag.async = true;\n tag.onload = () => {\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://3dmol.csb.pitt.edu/build/3Dmol.js');\n}\n\nvar viewer_15790115107964318 = null;\nvar warn = document.getElementById(\"3dmolwarning_15790115107964318\");\nif(warn) {\n warn.parentNode.removeChild(warn);\n}\n$3Dmolpromise.then(function() {\nviewer_15790115107964318 = $3Dmol.createViewer($(\"#3dmolviewer_15790115107964318\"),{backgroundColor:\"white\"});\n\tviewer_15790115107964318.removeAllModels();\n\tviewer_15790115107964318.addModel(\"\\n RDKit 3D\\n\\n 17 17 0 0 0 0 0 0 0 0999 V2000\\n -0.1962 -1.1869 -0.1225 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.2056 -0.6189 -0.1426 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.1140 0.8654 -0.4324 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.2410 1.5262 0.4081 O 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.0622 1.0494 0.1937 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.0766 -0.3532 0.8156 C 0 0 2 0 0 0 0 0 0 0 0 0\\n -0.5306 -0.3294 2.0874 O 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.1204 -2.1865 0.3691 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.6672 -1.2227 -1.1131 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.6259 -0.7701 0.8672 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.7849 -1.1120 -0.9170 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.1277 1.2835 -0.2934 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.7835 1.0401 -1.4695 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.7824 1.6779 0.7402 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.2873 0.9551 -0.8797 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -2.0886 -0.7846 0.8139 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.0381 0.5306 2.1899 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1 2 1 0\\n 2 3 1 0\\n 3 4 1 0\\n 4 5 1 0\\n 5 6 1 0\\n 6 7 1 0\\n 6 1 1 0\\n 1 8 1 0\\n 1 9 1 0\\n 2 10 1 0\\n 2 11 1 0\\n 3 12 1 0\\n 3 13 1 0\\n 5 14 1 0\\n 5 15 1 0\\n 6 16 1 1\\n 7 17 1 0\\nM END\\n\",\"sdf\");\n\tviewer_15790115107964318.setStyle({\"stick\": {}});\n\tviewer_15790115107964318.setBackgroundColor(\"0xeeeeee\");\n\tviewer_15790115107964318.zoomTo();\nviewer_15790115107964318.render();\n});\n</script>" | |
| }, | |
| "metadata": {} | |
| }, | |
| { | |
| "output_type": "execute_result", | |
| "execution_count": 6, | |
| "data": { | |
| "text/plain": "<rdkit.Chem.rdchem.Mol at 0x7f652788b670>", | |
| "text/html": "", | |
| "image/png": "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\n" | |
| }, | |
| "metadata": {} | |
| } | |
| ] | |
| }, | |
| { | |
| "metadata": {}, | |
| "cell_type": "markdown", | |
| "source": "## Now find the \"3D MCS\"" | |
| }, | |
| { | |
| "metadata": {}, | |
| "cell_type": "markdown", | |
| "source": "Now find the MCS and the corresponding atoms that are close to each other:" | |
| }, | |
| { | |
| "metadata": { | |
| "trusted": true | |
| }, | |
| "cell_type": "code", | |
| "source": "mcs = rdFMCS.FindMCS([m1_h,m2_h])\nprint(\"MCS:\",mcs.smartsString)\nmcs_mol = Chem.MolFromSmarts(mcs.smartsString)\nm1_match = m1_h.GetSubstructMatch(mcs_mol)\nm2_match = m2_h.GetSubstructMatch(mcs_mol)\nm1_conf = m1_h.GetConformer()\nm2_conf = m2_h.GetConformer()\nm1_ats = []\ntol = .3\nfor idx1,idx2 in zip(m1_match,m2_match):\n delt = m1_conf.GetAtomPosition(idx1)-m2_conf.GetAtomPosition(idx2)\n #print(idx1,idx2,delt.Length())\n if delt.Length()<=tol:\n m1_ats.append(idx1)\nprint(\"atoms:\",m1_ats)", | |
| "execution_count": 7, | |
| "outputs": [ | |
| { | |
| "output_type": "stream", | |
| "text": "MCS: [#6]1(-[#6](-[#6](-[#8]-[#6](-[#6]-1(-[#8]-[#1])-[#1])(-[#1])-[#1])(-[#1])-[#1])(-[#1])-[#1])(-[#1])-[#1]\natoms: [0, 1, 2, 3, 4, 5, 13, 14, 11, 12, 9, 10, 7, 8]\n", | |
| "name": "stdout" | |
| } | |
| ] | |
| }, | |
| { | |
| "metadata": { | |
| "trusted": true | |
| }, | |
| "cell_type": "code", | |
| "source": "mcs_3d_mol = Chem.RWMol(m1_h)\nfor i in range(m1_h.GetNumAtoms(),0,-1):\n idx = i-1\n if idx not in m1_ats:\n mcs_3d_mol.RemoveAtom(idx)\nmcs_3d_mol", | |
| "execution_count": 8, | |
| "outputs": [ | |
| { | |
| "output_type": "display_data", | |
| "data": { | |
| "application/3dmoljs_load.v0": "<div id=\"3dmolviewer_15790115111029403\" style=\"position: relative; width: 400px; height: 400px\">\n <p id=\"3dmolwarning_15790115111029403\" style=\"background-color:#ffcccc;color:black\">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). 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 var tag = document.createElement('script');\n tag.src = uri;\n tag.async = true;\n tag.onload = () => {\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://3dmol.csb.pitt.edu/build/3Dmol.js');\n}\n\nvar viewer_15790115111029403 = null;\nvar warn = document.getElementById(\"3dmolwarning_15790115111029403\");\nif(warn) {\n warn.parentNode.removeChild(warn);\n}\n$3Dmolpromise.then(function() {\nviewer_15790115111029403 = $3Dmol.createViewer($(\"#3dmolviewer_15790115111029403\"),{backgroundColor:\"white\"});\n\tviewer_15790115111029403.removeAllModels();\n\tviewer_15790115111029403.addModel(\"\\n RDKit 3D\\n\\n 14 14 0 0 0 0 0 0 0 0999 V2000\\n -0.1962 -1.1869 -0.1225 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.2056 -0.6189 -0.1426 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.1140 0.8654 -0.4324 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.2410 1.5262 0.4081 O 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.0622 1.0494 0.1937 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.0766 -0.3532 0.8156 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.2320 -2.2492 0.1104 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.6163 -0.9902 -1.1479 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.7156 -0.8228 0.8038 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.7130 -1.0789 -1.0250 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.1199 1.3436 -0.2866 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.8421 0.9705 -1.4939 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.7539 1.7313 0.7098 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.2857 0.9638 -0.8802 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1 2 1 0\\n 2 3 1 0\\n 3 4 1 0\\n 4 5 1 0\\n 6 5 1 6\\n 6 1 1 0\\n 1 7 1 0\\n 1 8 1 0\\n 2 9 1 0\\n 2 10 1 0\\n 3 11 1 0\\n 3 12 1 0\\n 5 13 1 0\\n 5 14 1 0\\nM END\\n\",\"sdf\");\n\tviewer_15790115111029403.setStyle({\"stick\": {}});\n\tviewer_15790115111029403.setBackgroundColor(\"0xeeeeee\");\n\tviewer_15790115111029403.zoomTo();\nviewer_15790115111029403.render();\n});\n</script>", | |
| "text/html": "<div id=\"3dmolviewer_15790115111029403\" style=\"position: relative; width: 400px; height: 400px\">\n <p id=\"3dmolwarning_15790115111029403\" style=\"background-color:#ffcccc;color:black\">You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). 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 var tag = document.createElement('script');\n tag.src = uri;\n tag.async = true;\n tag.onload = () => {\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://3dmol.csb.pitt.edu/build/3Dmol.js');\n}\n\nvar viewer_15790115111029403 = null;\nvar warn = document.getElementById(\"3dmolwarning_15790115111029403\");\nif(warn) {\n warn.parentNode.removeChild(warn);\n}\n$3Dmolpromise.then(function() {\nviewer_15790115111029403 = $3Dmol.createViewer($(\"#3dmolviewer_15790115111029403\"),{backgroundColor:\"white\"});\n\tviewer_15790115111029403.removeAllModels();\n\tviewer_15790115111029403.addModel(\"\\n RDKit 3D\\n\\n 14 14 0 0 0 0 0 0 0 0999 V2000\\n -0.1962 -1.1869 -0.1225 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.2056 -0.6189 -0.1426 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.1140 0.8654 -0.4324 C 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.2410 1.5262 0.4081 O 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.0622 1.0494 0.1937 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.0766 -0.3532 0.8156 C 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.2320 -2.2492 0.1104 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -0.6163 -0.9902 -1.1479 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.7156 -0.8228 0.8038 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1.7130 -1.0789 -1.0250 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 2.1199 1.3436 -0.2866 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 0.8421 0.9705 -1.4939 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.7539 1.7313 0.7098 H 0 0 0 0 0 0 0 0 0 0 0 0\\n -1.2857 0.9638 -0.8802 H 0 0 0 0 0 0 0 0 0 0 0 0\\n 1 2 1 0\\n 2 3 1 0\\n 3 4 1 0\\n 4 5 1 0\\n 6 5 1 6\\n 6 1 1 0\\n 1 7 1 0\\n 1 8 1 0\\n 2 9 1 0\\n 2 10 1 0\\n 3 11 1 0\\n 3 12 1 0\\n 5 13 1 0\\n 5 14 1 0\\nM END\\n\",\"sdf\");\n\tviewer_15790115111029403.setStyle({\"stick\": {}});\n\tviewer_15790115111029403.setBackgroundColor(\"0xeeeeee\");\n\tviewer_15790115111029403.zoomTo();\nviewer_15790115111029403.render();\n});\n</script>" | |
| }, | |
| "metadata": {} | |
| }, | |
| { | |
| "output_type": "execute_result", | |
| "execution_count": 8, | |
| "data": { | |
| "text/plain": "<rdkit.Chem.rdchem.RWMol at 0x7f65278871f0>", | |
| "text/html": "", | |
| "image/png": "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\n" | |
| }, | |
| "metadata": {} | |
| } | |
| ] | |
| }, | |
| { | |
| "metadata": { | |
| "trusted": true | |
| }, | |
| "cell_type": "code", | |
| "source": "Chem.MolToSmiles(mcs_3d_mol)", | |
| "execution_count": 9, | |
| "outputs": [ | |
| { | |
| "output_type": "execute_result", | |
| "execution_count": 9, | |
| "data": { | |
| "text/plain": "'[H]C1([H])CC([H])([H])C([H])([H])C([H])([H])O1'" | |
| }, | |
| "metadata": {} | |
| } | |
| ] | |
| }, | |
| { | |
| "metadata": { | |
| "trusted": true | |
| }, | |
| "cell_type": "code", | |
| "source": "", | |
| "execution_count": null, | |
| "outputs": [] | |
| } | |
| ], | |
| "metadata": { | |
| "kernelspec": { | |
| "name": "python3", | |
| "display_name": "Python 3", | |
| "language": "python" | |
| }, | |
| "language_info": { | |
| "name": "python", | |
| "version": "3.7.5", | |
| "mimetype": "text/x-python", | |
| "codemirror_mode": { | |
| "name": "ipython", | |
| "version": 3 | |
| }, | |
| "pygments_lexer": "ipython3", | |
| "nbconvert_exporter": "python", | |
| "file_extension": ".py" | |
| }, | |
| "gist": { | |
| "id": "", | |
| "data": { | |
| "description": "3D-MCS.ipynb", | |
| "public": true | |
| } | |
| } | |
| }, | |
| "nbformat": 4, | |
| "nbformat_minor": 2 | |
| } |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment