Created
June 1, 2019 12:08
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hetero_suffle_Example
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| { | |
| "cells": [ | |
| { | |
| "cell_type": "code", | |
| "execution_count": 3, | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [ | |
| "import pprint\n", | |
| "from rdkit import Chem\n", | |
| "from rdkit.Chem import rdChemReactions\n", | |
| "from rdkit.Chem import AllChem\n", | |
| "from rdkit.Chem import RWMol\n", | |
| "from rdkit.Chem.Draw import IPythonConsole" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 4, | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [ | |
| "mol = Chem.AddHs(Chem.MolFromSmiles('Cc1ccccc1'))" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 5, | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "data": { | |
| "text/plain": [ | |
| "0" | |
| ] | |
| }, | |
| "execution_count": 5, | |
| "metadata": {}, | |
| "output_type": "execute_result" | |
| } | |
| ], | |
| "source": [ | |
| "AllChem.EmbedMolecule(mol)" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 6, | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "name": "stdout", | |
| "output_type": "stream", | |
| "text": [ | |
| "('\\n'\n", | |
| " ' RDKit 3D\\n'\n", | |
| " '\\n'\n", | |
| " ' 15 15 0 0 0 0 0 0 0 0999 V2000\\n'\n", | |
| " ' 2.1985 -0.1426 0.0619 C 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' 0.7133 -0.0733 0.0106 C 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' 0.0761 1.1546 0.1011 C 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' -1.2976 1.2884 0.0602 C 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' -2.0772 0.1594 -0.0761 C 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' -1.4454 -1.0663 -0.1665 C 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' -0.0700 -1.1998 -0.1256 C 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' 2.4632 -0.5975 1.0482 H 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' 2.6208 0.8583 0.0206 H 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' 2.6037 -0.8414 -0.7013 H 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' 0.7267 2.0352 0.2090 H 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' -1.7313 2.2955 0.1378 H 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' -3.1580 0.2587 -0.1088 H 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' -2.0514 -1.9718 -0.2751 H 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' 0.4286 -2.1575 -0.1960 H 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' 1 2 1 0\\n'\n", | |
| " ' 2 3 2 0\\n'\n", | |
| " ' 3 4 1 0\\n'\n", | |
| " ' 4 5 2 0\\n'\n", | |
| " ' 5 6 1 0\\n'\n", | |
| " ' 6 7 2 0\\n'\n", | |
| " ' 7 2 1 0\\n'\n", | |
| " ' 1 8 1 0\\n'\n", | |
| " ' 1 9 1 0\\n'\n", | |
| " ' 1 10 1 0\\n'\n", | |
| " ' 3 11 1 0\\n'\n", | |
| " ' 4 12 1 0\\n'\n", | |
| " ' 5 13 1 0\\n'\n", | |
| " ' 6 14 1 0\\n'\n", | |
| " ' 7 15 1 0\\n'\n", | |
| " 'M END\\n')\n" | |
| ] | |
| } | |
| ], | |
| "source": [ | |
| "mblock = Chem.MolToMolBlock(mol)\n", | |
| "pprint.pprint(mblock)" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 7, | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [ | |
| "rxn = rdChemReactions.ReactionFromSmarts('[c:1][H]>>[n:1]')" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 8, | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [ | |
| "ps = rxn.RunReactants((mol,))" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 9, | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "data": { | |
| "image/png": 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ZkHlsCQ6EEU0MHjx47ty5R44ciYuLO3jwIOk4FrNly5ZLly799NNPJrcuXLhw27Zt+fn5U6dO9fPzY7PZLi4uLi4ubDbbycmJw+E4Ojqy2WzjtDBHR0fj1ZmdJykpCQAiIyNZLFanvhGyOJzwhAAAHj9+PHjwYIPBkJuba3Jpki7q3r17fn5+zW2dNm3a/fv3lUplG1+NxWI5Ojoarx9r+oPJxoY/cLnc5l65tLRUKBTq9frHjx8bl2pGXQiWUfS7yMjIL7/8cv78+ampqaSzWMPp06ffeecdBweHtWvXuri46HQ6jUZTXl6u1WqNU261Wq1Wq62oqNBoNFqtVqPRdPAd7ezsnJ2de/XqxWaz2Wy2sbay2WxXV9fc3NwbN260cC0ZojMso+h3RUVFr732ml6vv3fv3rBhw0jH6VylpaUikUihUOzduzcqKqqNz9LpdNXV1cYi2/QHk42Ntrbw4o6OjlOnTv3+++8t8fmQVWEZRS8sX778888/nz179nfffUc6S+eaPXv2iRMnAgIC0tPTO2kmWVO1tbVVVVVqtdo44FWr1VVVVVqttrKy8vDhw7dv37axsXny5AmPx7NOHmQpWEbRC3K5fMCAATqd7s6dO8bJN93SwYMHly5dyuFw7t+/LxQKSccBADAYDFwut6KiYvz48Tdu3CAdB5kHp9+jF3g83ocffkhR1KZNm0hn6SwFBQWrVq0CgOTkZJrUUABgMpnGM/U3b97MyMggHQeZB0ej6CVlZWXGJe5v3rw5btw40nEs7PnCgO+++25aWhrpOI0NGDBALBbz+fzudEVZT4CjUfQSNze3FStWAMDGjRtJZ7G8bdu2Xb16VSAQfPHFF6SzmHDq1CkGgyGTyeLi4khnQWbA0ShqrLy83NvbW6VSXb58efLkyaTjWMy9e/fGjh2r1+vPnj371ltvkY5j2owZM86fP+/g4KBSqZqu8ofoCUejqDFXV9eVK1cCwIYNG0hnsZiampqwsLDa2tqoqCja1lAAOH78uJ2dXU1Nze7du0lnQW2Fo1FkwvO1jc+fPx8YGEg6jgWsXLlyz549gwYNys7Opvko79ChQxEREVwuNz8/3+QtCRDd4GgUmeDs7PzJJ58AwPr167vBH9pLly4lJCTY2tqmpKTQvIYCwJIlS6ZPn65SqWJjY0lnQW2CZRSZZlzbODs7u6tfV1NeXr548WKDwRATE9NVJsPev3+fwWAkJyc/ePDgeWNISIjVrhRAZsEyikxjsVhr1qwBgA0bNtBqbWNzffjhh0VFRePGjTMu1dwl2NnZ9enTp76+/u9//zvpLKh1WEZRs5YtW+bt7Z2Tk3P8+HHSWdrp5MmTR48edXJySklJsbGxIR3HDAKBwM3N7fLly6dOnSKdBbUCyyhqlr29fXR0NABs3Lixrq6OdByzyWSyyMhIANi9e7ePjw/pOOaxsbExXku2atWqVu+VjcjCMopasnjx4oEDB+bn5x85coR0FvNQFBUREfHs2bPAwMCIiAjSccxWUFBw584dLpcrkUgmTZoUHh5uXB4f0RBOeEKtSE1NXbhwoZeX16NHj+zt7UnHaauEhIQVK1a4ubk9ePDA09OTdBzzCIVCpVIpEAiqq6tramp69erFYDAUCkVVVRX+wtIQjkZRK0JDQ0UiUWFhofHev13Cw4cPjSeU9u3b1+VqqJFIJBKLxVKptKysTCKRiMViOl810MNhGUWtYDKZxsuZNm/erNPpSMdpXV1dXVhYmE6nW7JkifGmp12aUChsOk8LJz/RCpZR1LrZs2f7+fnJZLIDBw6QztK62NjYH374wdvbe9euXaSzoB4B7wyKWsdgMGJjY4ODg+Pi4pYsWeLi4tJcT7lcvnTpUk9PTz6f7+HhIRAI3N3dBQKBh4eHg4ODFaLeunUrPj6eyWQePny4s+/liZARllHUJkFBQWPHjr19+3ZSUlIL89gLCwv/+9//mtzEYrH4fD6Px2v6yOVy+Xx+x0NWVVUtWrSovr4+Ojp64sSJHX9BUprbYccdeXrCM/WordLT06dNm8bhcAoKCjgcjsk+z549u379ulwul8vlJSUlMplMoVBIpVKlUqnX61t4cTabbRy08vl8T09PHo/H4/Gej2rd3d3bknDZsmVffPHFiBEj7ty504UmFbRMKBRqtdqgoKCGjenp6VKpFH95aQLLKDLD5MmTr1y58umnn8bExJj7XIVCoVQqpVKpQqGQyWQlJSUNq61Wq23huXZ2dt9+++2sWbNa6HPx4sW33nrL3t4+KytLJBKZG4+2nk9+atiIk59oBcsoMsONGzdef/31Xr16SSQSy67hptPp5HK5TCZTqVTGHxo+KhSK//3vf2+88UZzTy8rKxOJRCUlJbt27TIultptCIVCDw+PrKysho0hISFpaWn4y0sTeGwUmeFPf/rT9OnTL168+K9//Ss+Pt6Cr+zo6NivX79+/fqZ3FpTU2Nr29J39a9//WtJScmECROMd0BByJpwwhMyz9atWxkMRmJiokKhsNqbOjg4tLCwyFdffZWWlubq6nrkyBEmE7/SyNrwO4fMM2rUqODg4Kqqqm3btpHOAgBQUFBg3ItPSkqizw2TUY+CZRSZbcuWLUwmc9++fVeuXKmsrCSYxGAwhIeHV1RUzJo1KzQ0lGCSzoOTn+gPTzGh9hg7dqxYLC4rKwMAFotlnPhpcjaol5dX5y30uW3btujoaD6f//PPP+NtixApWEaR2SQSiUgk0mq1r7766tOnT1udq+Tu7m5yNqjxGqd2T/D86aefxowZQ/MbJqOeAM/UI/MYDIbFixdrtdrQ0FDjIqQ6nc7kLKXnc5WkUqlUKm3uBVu4ukkgEDQ3z//5DZOXL1+ONRSRhaNRZB7jOp6enp65ubm9e/dutX9NTY1SqSwuLjY5916pVLa8rr6zs7PJq5uOHTt2+PBhX1/f7OxsNpttuc+HkNmwjCIzFBQUDBs2TKPRnDhxouVritpOpVI9H7o2GtVKpdLy8nKTz+rdu3d5efnt27dHjx5tkRgItRvu1KO2MhgMixYt0mg0CxYssFQNBQAul8vlcocMGWJyq1qtbnR5vkKhKC4uzsrKMhgMXesudai7wtEoaqs9e/asXLmSx+Pl5OS0ZXe+U33yySc7d+7885//fObMGbJJEMIyitpEIpEMHz5co9GcPHly5syZpONAWVlZ//79Kyoqrl692sK19ghZAU6/R617vjsfFhZGhxoKAG5ubsbL59evX086C+rpcDSKWrdr165Vq1bxeLzc3Fwul0s6zu/Ky8v79+//9OnTjIyMgIAA0nFQz4WjUdSKvLw844gvOTmZPjUUAFxdXVevXg0A0dHROBpABOFoFLXEYDBMnDjx+vXr4eHhNLzBsk6n8/HxkUql33//fXBwMOk4qIfC0Shqyc6dO69fv87n83fu3Ek6iwmOjo5r1qwBgHXr1hkMBtJxUA+Fo1HUrLy8PD8/P51Od+7cOdpecFlbW+vr61tQUHDs2LE5c+aQjoN6IhyNItMMBkNERIROp1uyZAltaygA2NvbGw/dbty4seXrShHqJFhGkWk7duy4fv26QCDYsWMH6SytCAsL8/X1zc/PT0lJIZ0F9US4U49MePjwoZ+fX01Nzblz5wIDA0nHad233347d+5coVD46NEjBwcH0nFQz4KjUdRYfX19WFhYdXV1REREl6ihAPD++++PGDGiqKjowIEDpLOgHgdHo6ix+Pj4f/7znwKBICcnp7nlPmnozJkzwcHBffr0EYvFLi4upOOgHgRHo+glv/7666ZNmxgMxqFDh7pQDQWAoKCgcePGlZaWJiUlkc6CehYcjaIX6urqxo8fn5WVtWzZsv3795OOY7ZLly5NmTKFw+FIJBJaXXCFujccjaIXCgsLlUqll5cX/c/OmxQQEPDmm2+q1erdu3eTzoJ6EByNopdUVlYWFhYOHTqUdJB2ysrKGjNmjJOTk1gsdnd3Jx0H9Qg4GkUvcXFx6bo1FAD8/f3ffvttjUazfft20llQT4FltIcSCoX+/v6NGkNCQhgMBpE8FhQXF8dkMpOTk4uLi0lnQT0CllHU3YhEopCQkOrq6q1bt5LOgnoELKOoG9q8ebOtre2hQ4fEYjHpLKj7wzuDom7Ix8cnPDxcr9ezWCzSWVD3h2fqeyihUKjVaoOCgho2pqenS6XS7vGVoCiqGxznRV0CjkZ7Lo1Gc+3atYYtarWaVBiLwxqKrAaPjfZcIpFI/DI6rytqrm48FQHRDZZRhBDqECyjCCHUIVhGEUKoQ/AUUw/V3CHC7nTosKCgIDw8vGHLrVu3SIVB3RhOeELdk1AoVCqVAoGgYaNCoaiqqsLvPLIsHI2ibkskEmVlZTVsCQkJSUtLI5UHdVd4bBQhhDoEyyhCCHUIllGEEOoQLKOoe+oJUxEQTfw/ENmWrNvw/MwAAAAASUVORK5CYII=\n", | |
| "text/plain": [ | |
| "<rdkit.Chem.rdchem.Mol at 0x1088d9138>" | |
| ] | |
| }, | |
| "execution_count": 9, | |
| "metadata": {}, | |
| "output_type": "execute_result" | |
| } | |
| ], | |
| "source": [ | |
| "ps[0][0]" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 10, | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "name": "stdout", | |
| "output_type": "stream", | |
| "text": [ | |
| "('\\n'\n", | |
| " ' RDKit 3D\\n'\n", | |
| " '\\n'\n", | |
| " ' 14 14 0 0 0 0 0 0 0 0999 V2000\\n'\n", | |
| " ' 0.0761 1.1546 0.1011 N 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' 0.7133 -0.0733 0.0106 C 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' -1.2976 1.2884 0.0602 C 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' 2.1985 -0.1426 0.0619 C 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' -0.0700 -1.1998 -0.1256 C 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' -2.0772 0.1594 -0.0761 C 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' -1.7313 2.2955 0.1378 H 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' 2.4632 -0.5975 1.0482 H 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' 2.6208 0.8583 0.0206 H 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' 2.6037 -0.8414 -0.7013 H 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' -1.4454 -1.0663 -0.1665 C 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' 0.4286 -2.1575 -0.1960 H 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' -3.1580 0.2587 -0.1088 H 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' -2.0514 -1.9718 -0.2751 H 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' 2 1 2 0\\n'\n", | |
| " ' 1 3 1 0\\n'\n", | |
| " ' 4 2 1 0\\n'\n", | |
| " ' 5 2 1 0\\n'\n", | |
| " ' 3 6 2 0\\n'\n", | |
| " ' 3 7 1 0\\n'\n", | |
| " ' 4 8 1 0\\n'\n", | |
| " ' 4 9 1 0\\n'\n", | |
| " ' 4 10 1 0\\n'\n", | |
| " ' 11 5 2 0\\n'\n", | |
| " ' 5 12 1 0\\n'\n", | |
| " ' 6 11 1 0\\n'\n", | |
| " ' 6 13 1 0\\n'\n", | |
| " ' 11 14 1 0\\n'\n", | |
| " 'M END\\n')\n" | |
| ] | |
| } | |
| ], | |
| "source": [ | |
| "pprint.pprint(Chem.MolToMolBlock(ps[0][0]))" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 22, | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [ | |
| "rxn2 = rdChemReactions.ReactionFromSmarts('[H:1]([c:2])>>[F:1]([c:2])')" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 26, | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [ | |
| "ps2 = rxn2.RunReactants((mol,))" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 27, | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "data": { | |
| "image/png": 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\n", | |
| "text/plain": [ | |
| "<rdkit.Chem.rdchem.Mol at 0x11a970d98>" | |
| ] | |
| }, | |
| "execution_count": 27, | |
| "metadata": {}, | |
| "output_type": "execute_result" | |
| } | |
| ], | |
| "source": [ | |
| "ps2[0][0]" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 28, | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "name": "stdout", | |
| "output_type": "stream", | |
| "text": [ | |
| "('\\n'\n", | |
| " ' RDKit 3D\\n'\n", | |
| " '\\n'\n", | |
| " ' 15 15 0 0 0 0 0 0 0 0999 V2000\\n'\n", | |
| " ' 0.7267 2.0352 0.2090 F 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' 0.0761 1.1546 0.1011 C 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' 0.7133 -0.0733 0.0106 C 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' -1.2976 1.2884 0.0602 C 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' 2.1985 -0.1426 0.0619 C 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' -0.0700 -1.1998 -0.1256 C 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' -2.0772 0.1594 -0.0761 C 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' -1.7313 2.2955 0.1378 H 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' 2.4632 -0.5975 1.0482 H 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' 2.6208 0.8583 0.0206 H 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' 2.6037 -0.8414 -0.7013 H 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' -1.4454 -1.0663 -0.1665 C 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' 0.4286 -2.1575 -0.1960 H 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' -3.1580 0.2587 -0.1088 H 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' -2.0514 -1.9718 -0.2751 H 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' 2 1 1 0\\n'\n", | |
| " ' 3 2 2 0\\n'\n", | |
| " ' 2 4 1 0\\n'\n", | |
| " ' 5 3 1 0\\n'\n", | |
| " ' 6 3 1 0\\n'\n", | |
| " ' 4 7 2 0\\n'\n", | |
| " ' 4 8 1 0\\n'\n", | |
| " ' 5 9 1 0\\n'\n", | |
| " ' 5 10 1 0\\n'\n", | |
| " ' 5 11 1 0\\n'\n", | |
| " ' 12 6 2 0\\n'\n", | |
| " ' 6 13 1 0\\n'\n", | |
| " ' 7 12 1 0\\n'\n", | |
| " ' 7 14 1 0\\n'\n", | |
| " ' 12 15 1 0\\n'\n", | |
| " 'M END\\n')\n" | |
| ] | |
| } | |
| ], | |
| "source": [ | |
| "pprint.pprint(Chem.MolToMolBlock(ps2[0][0]))" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 31, | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "name": "stdout", | |
| "output_type": "stream", | |
| "text": [ | |
| "('\\n'\n", | |
| " ' RDKit 3D\\n'\n", | |
| " '\\n'\n", | |
| " ' 15 15 0 0 0 0 0 0 0 0999 V2000\\n'\n", | |
| " ' 2.1985 -0.1426 0.0619 C 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' 0.7133 -0.0733 0.0106 C 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' 0.0761 1.1546 0.1011 C 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' -1.2976 1.2884 0.0602 C 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' -2.0772 0.1594 -0.0761 C 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' -1.4454 -1.0663 -0.1665 C 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' -0.0700 -1.1998 -0.1256 C 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' 2.4632 -0.5975 1.0482 H 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' 2.6208 0.8583 0.0206 H 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' 2.6037 -0.8414 -0.7013 H 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' 0.7267 2.0352 0.2090 H 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' -1.7313 2.2955 0.1378 H 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' -3.1580 0.2587 -0.1088 H 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' -2.0514 -1.9718 -0.2751 H 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' 0.4286 -2.1575 -0.1960 H 0 0 0 0 0 0 0 0 0 0 0 0\\n'\n", | |
| " ' 1 2 1 0\\n'\n", | |
| " ' 2 3 2 0\\n'\n", | |
| " ' 3 4 1 0\\n'\n", | |
| " ' 4 5 2 0\\n'\n", | |
| " ' 5 6 1 0\\n'\n", | |
| " ' 6 7 2 0\\n'\n", | |
| " ' 7 2 1 0\\n'\n", | |
| " ' 1 8 1 0\\n'\n", | |
| " ' 1 9 1 0\\n'\n", | |
| " ' 1 10 1 0\\n'\n", | |
| " ' 3 11 1 0\\n'\n", | |
| " ' 4 12 1 0\\n'\n", | |
| " ' 5 13 1 0\\n'\n", | |
| " ' 6 14 1 0\\n'\n", | |
| " ' 7 15 1 0\\n'\n", | |
| " 'M END\\n')\n" | |
| ] | |
| } | |
| ], | |
| "source": [ | |
| "pprint.pprint(Chem.MolToMolBlock(mol))" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": null, | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [] | |
| } | |
| ], | |
| "metadata": { | |
| "kernelspec": { | |
| "display_name": "Python 3", | |
| "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": "3.6.8" | |
| } | |
| }, | |
| "nbformat": 4, | |
| "nbformat_minor": 2 | |
| } |
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