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ptosco/Set_chirality_from_atom_parity_flags.ipynb

Last active December 16, 2022 06:42
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Set chirality from atom parity flags
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Set_chirality_from_atom_parity_flags.ipynb
{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"import sys\n",
"from rdkit import Chem\n",
"from rdkit.Chem.Draw import IPythonConsole"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"First I load in a ChEMBL molecule which features chirality information in both the atom and the bond block. The RDKit reads both, but uses only the bond block information to set atom chiralities:"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"molBondInfo = Chem.MolFromMolBlock(\"\"\"\\\n",
"CHEMBL440060\n",
" 11280716012D 1 1.00000 0.00000 0\n",
"\n",
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" 54 55 1 0 0 0\n",
" 55 56 2 0 0 0\n",
" 28 29 1 0 0 0\n",
"192193 1 0 0 0\n",
"193194 1 0 0 0\n",
"194195 2 0 0 0\n",
"193196 1 1 0 0\n",
"196197 1 0 0 0\n",
"197198 1 0 0 0\n",
"198199 1 0 0 0\n",
"194184 1 0 0 0\n",
"186176 1 0 0 0\n",
"178167 1 0 0 0\n",
"169163 1 0 0 0\n",
"165158 1 0 0 0\n",
"160153 1 0 0 0\n",
"155143 1 0 0 0\n",
"145135 1 0 0 0\n",
"137131 1 0 0 0\n",
"133126 1 0 0 0\n",
"128121 1 0 0 0\n",
"123112 1 0 0 0\n",
"114104 1 0 0 0\n",
"106 96 1 0 0 0\n",
" 98 85 1 0 0 0\n",
" 87 76 1 0 0 0\n",
" 78 68 1 0 0 0\n",
" 70 57 1 0 0 0\n",
" 59 53 1 0 0 0\n",
" 55 44 1 0 0 0\n",
" 46 36 1 0 0 0\n",
" 38 32 1 0 0 0\n",
" 34 30 1 0 0 0\n",
" 29 30 1 0 0 0\n",
" 29200 1 0 0 0\n",
"200 26 1 0 0 0\n",
" 30 31 1 0 0 0\n",
"200201 2 0 0 0\n",
" 31 27 1 0 0 0\n",
" 29202 1 1 0 0\n",
" 13 16 1 1 0 0\n",
" 25203 1 0 0 0\n",
"203 18 1 0 0 0\n",
"104105 1 0 0 0\n",
"203204 2 0 0 0\n",
"105106 1 0 0 0\n",
" 25205 1 1 0 0\n",
" 20 12 1 0 0 0\n",
" 14 1 1 0 0 0\n",
"106107 2 0 0 0\n",
" 3206 1 0 0 0\n",
"M END\n",
"> <chembl_id>\n",
"CHEMBL440060\n",
"\n",
"$$$$\n",
"\"\"\")"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"image/png": 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fL4Vg2seFkFU8pfhS1tSOHTuKbqekpCAhIUFrWTRtXyZmvLL2dFpVilmaBgcOoLe5OZKT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\n",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x20392cfa260>"
]
},
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"molBondInfo"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"c1 = Chem.FindMolChiralCenters(molBondInfo)"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"[(1, 'S'),\n",
" (12, 'S'),\n",
" (24, 'S'),\n",
" (28, 'S'),\n",
" (36, 'S'),\n",
" (44, 'S'),\n",
" (57, 'S'),\n",
" (68, 'S'),\n",
" (76, 'S'),\n",
" (85, 'S'),\n",
" (96, 'S'),\n",
" (104, 'S'),\n",
" (112, 'S'),\n",
" (121, 'S'),\n",
" (126, 'S'),\n",
" (135, 'S'),\n",
" (143, 'S'),\n",
" (153, 'S'),\n",
" (158, 'S'),\n",
" (167, 'S'),\n",
" (170, 'S'),\n",
" (175, 'S'),\n",
" (183, 'S'),\n",
" (186, 'R'),\n",
" (190, 'S')]"
]
},
"execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"c1"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Now I intentionally remove chirality information from the bond block, while I leave it in the atom block."
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"molNoBondInfo = Chem.MolFromMolBlock(\"\"\"\\\n",
"CHEMBL440060\n",
" 11280716012D 1 1.00000 0.00000 0\n",
"\n",
"206208 0 1 0 999 V2000\n",
" 2.0792 -0.9500 0.0000 N 0 0 0 0 0 0 0 0 0\n",
" 1.4671 -0.5958 0.0000 C 0 0 2 0 0 0 0 0 0\n",
" 0.8510 -0.9500 0.0000 C 0 0 0 0 0 0 0 0 0\n",
" 0.8510 -1.6583 0.0000 O 0 0 0 0 0 0 0 0 0\n",
" 1.4671 0.1125 0.0000 C 0 0 0 0 0 0 0 0 0\n",
" 0.8510 0.4667 0.0000 C 0 0 0 0 0 0 0 0 0\n",
" 0.8510 1.1750 0.0000 C 0 0 0 0 0 0 0 0 0\n",
" 0.2444 1.5292 0.0000 N 0 0 0 0 0 0 0 0 0\n",
" -0.3695 1.1758 0.0000 C 0 0 0 0 0 0 0 0 0\n",
" -0.9825 1.5300 0.0000 N 0 0 0 0 0 0 0 0 0\n",
" -0.3704 0.4683 0.0000 N 0 0 0 0 0 0 0 0 0\n",
" 3.9167 -0.5958 0.0000 N 0 0 0 0 0 0 0 0 0\n",
" 3.3046 -0.9500 0.0000 C 0 0 2 0 0 0 0 0 0\n",
" 2.6885 -0.5958 0.0000 C 0 0 0 0 0 0 0 0 0\n",
" 2.6885 0.1125 0.0000 O 0 0 0 0 0 0 0 0 0\n",
" 3.3046 -1.6583 0.0000 C 0 0 0 0 0 0 0 0 0\n",
" 2.6885 -2.0125 0.0000 O 0 0 0 0 0 0 0 0 0\n",
" 5.7583 -0.9500 0.0000 N 0 0 0 0 0 0 0 0 0\n",
" 5.1463 -0.5958 0.0000 C 0 0 0 0 0 0 0 0 0\n",
" 4.5301 -0.9500 0.0000 C 0 0 0 0 0 0 0 0 0\n",
" 4.5301 -1.6583 0.0000 O 0 0 0 0 0 0 0 0 0\n",
" 6.7292 1.2084 0.0000 C 0 0 0 0 0 0 0 0 0\n",
" 6.0209 1.2084 0.0000 C 0 0 0 0 0 0 0 0 0\n",
" 5.8016 0.5367 0.0000 C 0 0 0 0 0 0 0 0 0\n",
" 6.3750 0.1167 0.0000 C 0 0 2 0 0 0 0 0 0\n",
" 6.9484 0.5367 0.0000 N 0 0 3 0 0 0 0 0 0\n",
" 9.1053 1.2248 0.0000 C 0 0 0 0 0 0 0 0 0\n",
" 8.3970 1.2248 0.0000 C 0 0 0 0 0 0 0 0 0\n",
" 8.1777 0.5532 0.0000 C 0 0 2 0 0 0 0 0 0\n",
" 8.7512 0.1331 0.0000 N 0 0 3 0 0 0 0 0 0\n",
" 9.3245 0.5532 0.0000 C 0 0 0 0 0 0 0 0 0\n",
" 9.9758 -0.5748 0.0000 N 0 0 0 0 0 0 0 0 0\n",
" 9.3638 -0.9290 0.0000 C 0 0 0 0 0 0 0 0 0\n",
" 8.7524 -0.5752 0.0000 C 0 0 0 0 0 0 0 0 0\n",
" 8.1406 -0.9321 0.0000 O 0 0 0 0 0 0 0 0 0\n",
" 11.8171 -0.9296 0.0000 N 0 0 0 0 0 0 0 0 0\n",
" 11.2051 -0.5754 0.0000 C 0 0 2 0 0 0 0 0 0\n",
" 10.5889 -0.9296 0.0000 C 0 0 0 0 0 0 0 0 0\n",
" 10.5889 -1.6379 0.0000 O 0 0 0 0 0 0 0 0 0\n",
" 11.2116 0.1254 0.0000 C 0 0 0 0 0 0 0 0 0\n",
" 11.8278 0.4796 0.0000 C 0 0 3 0 0 0 0 0 0\n",
" 11.8278 1.1879 0.0000 C 0 0 0 0 0 0 0 0 0\n",
" 12.4398 0.1254 0.0000 C 0 0 0 0 0 0 0 0 0\n",
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"M END\n",
"> <chembl_id>\n",
"CHEMBL440060\n",
"\n",
"$$$$\n",
"\"\"\")"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"The RDKit reads, but ignores, the atom parity flags; in fact, there are no perceived chiral centers:"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
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nZ37++WfNj9PyO7NmKOhW3DuVKYQ5yXWEwrxypjT/ZWTYK1WqcEcpGjduzPte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\nupoFVjcAAAAASUVORK5CYII=\n",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x20392f80120>"
]
},
"execution_count": 7,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"molNoBondInfo"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"[]"
]
},
"execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"Chem.FindMolChiralCenters(molNoBondInfo)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"According to http://c4.cabrillo.edu/404/ctfile.pdf and to https://www.chemaxon.com/marvin-archive/latest/help/sci/parity.html, I can set the atom chiral tags based on the atom parity information:\n",
"\n",
"1 (odd) --> clockwise\n",
"\n",
"2 (even) --> counterclockwise\n",
"\n",
"3 (either or unmarked) --> unspecified"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"for a in molNoBondInfo.GetAtoms():\n",
" if (a.HasProp('molParity')):\n",
" p = int(a.GetProp('molParity'))\n",
" if (p == 1):\n",
" a.SetChiralTag(Chem.rdchem.ChiralType.CHI_TETRAHEDRAL_CW)\n",
" elif (p == 2):\n",
" a.SetChiralTag(Chem.rdchem.ChiralType.CHI_TETRAHEDRAL_CCW)\n",
" elif (p == 3):\n",
" a.SetChiralTag(Chem.rdchem.ChiralType.CHI_UNSPECIFIED)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Now chirality is set, and I can access the CIP information calling `Chem.FindMolChiralCenters()`.\n",
"\n",
"I can thus reproduce the same chirality as in the previous case."
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"image/png": 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tWrUq+lm2TINzqFrOkpeXh+7duxdlGV/Yd5WxdxQXQlYujIzM0bVrNyQmJgqO\n1aSbiWiJzRVr5QGAbS8A6pt2A8CBAwdgYmICmUyGvLw8bNq0Se34Q4cOwcXFBXv2iKjiGuY5cuQI\nLCwsYGJigry8PPzvf/8Tfg2xNMySkJCAnJwcVKtWDbm5uTh69ChkMpn28jBWzrgQMq0QOqT5zeBx\nuJZmARcXFwQEBAgulivUzURjhQvHAgULxwo/JTg4GGlpaYiPj0ffvn2xfv16pdlv3bqFkSNHokeP\nHujcuTPatWun9TyjRo3C7du3cfPmTcyePRvnz5+Hr68vUlJShF9Ly1lcXFxw+/Zt3LlzB8uWLYOh\noSHatGmDo0ePavSyog+DFztyyxflM13gQsi0Rt0hTduGtug6ahP27t2L6OhoNGnSBKGhocjJycHy\n5Zn4+ecST9D2VPtSLBxblN3WFps2bcK+fftey/78+XMEBgbC3t4e9+7dQ1xcHEJDQ2Fubq6zPNWq\nVUNgYCDi4+NhamqKZs2aifqHhS6yGBoaws/PD1euXClayd7X1xfXrl0T/dJiDoMn7wYGF/xDyPGq\n6E0zJp6eZ62yCkKT7iF5eXm0ePFisrCwIGdnZ+rY8T8UHv5Cv29ApLy8PPr999+pZs2a1KhRI3Jw\ncKDIyEi95dm3bx85OjqSt7c3ZWZm6i0HEdHFixepe/fuVL9+fbp7967geI07zkQS6e+TZhUZ7xEy\nrRJzSNPQ0BCPHz9Gx44dsWbNGhgY7MHjx0v1FVkjhoaGGD9+PCIiInDt2jXEx8fDx0f83qW2de/e\nHWfOnEFUVBSSk4UnAOmSk5MT9u3bB3Nzc43OYYr5m9njD0i2vzqVyZg2Geo7AKtgCg5pfiYwbGjt\n2nhJhFatWuEHe3tUF3M48S1SvWAldiMjIz0nURTnt4nGn4nA38wef6BnuOK2BACFlSEcY0q8Xf8F\nsXeWbQAQUOz2PwW3A4oGAGEBr8a7Pn4M3LoFAGiXkgI0bFhOSdnbQpO/GS5+TJf40CjTqmHDAFFH\n6GbPBn77TXH7r78AvhatUsrKAnr1AviafKZPXAiZoIyMDDx8+FDU2PXrgbQ0oYvKk4HeNQErK0Un\nE2tr4B07NPo2ycrK0neEUsvPJ8TEELKyRDYiYEwHuBAyQbNnz0bv3r0Fv3BfvnwJIgm+/aYTsn/5\nRfXAUnR5YcrJg4LwaceO+o5RanJ5Bp48MQCQqu8orBLjQsjUOnPmDMLCwnDmzBmMGjVKZQuxzMxM\n/Pjjj/Dw8EDQlCkwbdJE9UZL0eXlbWNlZfVWtBYzcHfH+t9+Q/fu3fHLL2F48EDfiRRLb/311xZc\nFGgB9Pw5sHTpRtja2iI4eAXS0sonH2MlcSFkKuXn58Pf37+ofVZERATmzp372hiZTIYVK1bAzs4O\na9euRdeWLeHSqxfQt6/qDZeiy8vbpmHDhvj999/L6dXUNMXu1AkWrVujZ4sWePasMzp1AuRy/XZt\nmTJlCtq2nY8pUwpeSkkWANi0CThxwgsTJkxARsYn8PZWPZ47zjBd4kLIVMrPz8e3336L8ePHo2nT\npgCAhQsXYs2aNQCAgwcPolWrVpg1axYCAgKwbt06fHXzJpBaeJhLxRd4Gbq8qPpSrdCEDiWnpGB4\nfDwmT7bGnj1A4Vq5+ura8v777+Onn9pg165X9ynLMmoU8L//OWLcuHGYNs0Q27apH18e2VnlxJdP\nMJWqVKmCAQMGYMCAAQCAu3fv4tChQzh+/DiOHTuGDRs2YNKkSZgxY8arVeh37QIKVzcv/AL3wat/\n0gfYArAF/hG3DOaNGzdw4cIl5Ob2gKen4r4TkwB/eyDMTqtv9+2V2LzYdQaFh5JtXz3u5IRakZHw\nKrFafEgSkGgH7Cl25HmSHTCp4Ha7kGKXMOwBsppH4f59J1hbW2sltomJ+iyFfyY9emTgxYuJOHbs\nMBRXCmqe3b7YpTmMaYr3CJlo9erVw/DhwxEUFIRVq1Zh9+7dWLhw4asiCLz6dgPKfC7wxo0b6NOn\nD6ZN+xYzZwL//qu4X9nqFBWamEPJBsr/U9aka8uyUaMQExOj3exqshSaN6829u49/MbCx9xxhpUX\nLoRMY3l5RujYcTEaNBBYX7CM5wIPH05GtWoWuHr1LFJSgB49Xj2m6ku1QirDoWSh5uVFXVvCgdtP\nyhq0dFk+/BCoVk3y5gMaZBe5njBjSkmISNwxKsYKPHiguPTv5k3AxkbdyGTA0w44AQB+GrcH6dkT\naNr0BWrXXopnz2Zj1izg0Rpgdy/FEdbkUEVbrn/4sJhW2NjYYOnSpejfv7++ozBWrvgcIdOYpSWQ\nni7mGnjx5wKVmTULMDPLx4wZh1Gr1iy8fCl5oy3XpAjg+nXggw9K/TKMsUqOD40yjSSHAl6/AhYW\ngEGqmqnthb+omvavZvuFs0K96gJhx2rgj94H8OEPElhavtr+8uXLERsbi9BQYO3al1p+lxVHbm4u\nnjzR9THPAqH+QNHfQeEfheZ/A0lJSTh06JDOYjJWEhdCpjExU9sBlLqDjLrtZ2Zn4vC6EZg+fTru\n3r2Lzz/fib//FjhXWYkFBwfDx8cHL1680E8ADf8GHj58iNGjR+Ozzz7TX2ZW6XAhZBpTNmtzkl3B\nP/qLT2Ap5axR1du/imotPsTtW7E4ceIE+vTpgydPkpGTk40BAwbg+vXrZXtjFcyDBw+waNEinDp1\nCv3790dubq7ScVlZWQgMDESNGjXg5ORUhle8CNgVTuqZpLhLw7+BWrVq4cWLF0hLS8PixYvLkIUx\n8bgQslJRNrU9Kysb8l/+LprarnzWqLhDZSW3H3j0FqpXd8ewPi0wZGosbG1t8eWXX2LevHkYP348\nMjIy4OTkhPnz52vYhFrzQ3e6o90ss2bNwrNnzwAomh8MGTKkqEsQABARIiIi4OjoiL///htz586F\nvb19GbI0B5IK9/5CFHeJnDmckZGBjRs3QiqVIiQkBDKZDCEhIbh27VopszAmHhdCVjpKprYHBQXh\nUmQEqmU+VtyhbNq/2ENlJbZfo64Ndu3ahXU/r0Nmxl20bdsWx44dQ0xMDKZPn46DBw9ix44d2Lhx\nI+zt7bF27VqImhD9NjUA12IWuVwOV1dXDB48GDYFU3u3bduGr776CkSEc+fOoUOHDhg9ejRGjRqF\n+Ph4DBo0SPtZVF368eQJMGgQHickAFAU5UmTJuHChQvo1KkTZsyYgV9++QXm5uZv1/9HrGIixrTk\n6dOnFBubRCSTEeXlKR/k51fslySikEjR25fLiTZt2kk1atSg/v3709OnT98Yk5ubS4MHDyZjY2Nq\n2bIl+fn50d9//616o2XII0Z0dDT5+fkV/SxcuFAvWW7dukWbNm2iSZMm0bfffkuGhob0xRdf0P37\n98s9CxERPXhAL/z96T1TUzp69CgREcXGxlJWVlb5Z2GVHu8RMq05fPgwevbsjWMjRgDLlysfVIaL\n7NeuvYvp0+dgwYIF2Lp1q2JvoQRjY2N4eXlBKpXi6tWrWLduHXJyclRvVMcNwE1MTLBu3bqin9u3\nb+slS/369TFo0CAEBwcjJiYGEydOxIoVK1CnTp1yzwIAsLKC2fLl+GT4cAQHBwMA3NzcYGpqWv5Z\nWKXH1xEyrTI2zsQFV1d4DRumfEDAfxXne3oCiovsxV8NP2RIbQwdegZGRkZqx/Xs2RMvX766pKJr\n166qB5chjxgtWrTAggULin5v37693rIUZ2VlpX5AOWWpXbs2Hj9+/FZkYZUXF0KmNRKJBESEr6dN\nUzOq9BfZGxsbixrXuHFjTClcA0hQ2S76F1K1atW3JotmOAurPPjQKCt/+fmAnx9w5w5w7RowdqzW\nX2Lv3r3o168fDh8+LDx4wQLgn38Ut/38FL3jtCglJQX9+vVDeHi48OB16xQ/ALBoEXDkiFazaGT/\nfmD+fMXtFSuAguW39CI5GRg5UnE7KgqYM0d/WViFw4WQaU3hHqEgmUzxxZqeDjx8qLithuiFWotx\ncHDAqFGjYGtrC0GbNwOXLytmJa5YATx6pNUstWvXxqhRo+Dh4SGc5ehRxQ8AbNsGFMyq1FYWjVy5\nAuzbp7h98iRw5oza4TrNk5YGbNhQsJ3kV7nKmoUX92XgQsj04KVEgppVqiBBIsEZiQS1lU2QKEF0\nN5sCjRo1Qr9+/YouHVDHy8QEaw0MgIJccSWWAyprFnNzc/Tr1w8tWrQQHBtgaIgAQ8UZC29jY6xQ\nsbxSabOU9EhN0V9KhHYF/7AZQ4TxIv6RU5Y8aWlpkMvlSh87SQTDgseWE8FdxThNs/DivgzgQsi0\nyMrKClZWVjh8WP2adgYGBujSqxeeZuRhztylaO3lJbht0d1sALx8+RJBQUEYN24cli9fjfx89dtu\n26ED6tnYYOjQGWjeujXMa9TQWhYAiIiIgL+/P775ZjoyMtQXE8eWLeHYsiWmTg2FyXvvwUagm7im\nWQ4cOICnT5/CyckJjx49gr29PY4dO6Z0282aNYOPjw8WLfob9+/fh4uLi9osmuZJTExEdHQ02rRp\nA7lcjh49ehTNIC3J0tISI0eOxK5dMdi4cRc6dOjwxpiSRyPEZLENKFgrmhf3rdS4EDKt8fDwQM+e\nPTF9ej5+/131OENDQ2zevBkODjaoXl2GqKgoTJw4Eenp6Wq3L2ah1p07d6J58+YIDQ1F1apVsWuX\ncdGpJVWCgoLQuXNn1K0LnD59GpMnT0ZSkvpWYGKyxMXFoWPHjhgzZgyMjIxw69Z7aNNGgmLNXd7g\n7+8Pf39/2NmZ4fTp05g9ezaOFh4qLUOWpKQk9OnTB76+vujatSu6deuG7777Dq6urvBS8Q+Rbt26\nYc6cOXB3t8L16zcQGBiI1atXq9xrE5snPT0dEyZMgIuLC2xsbDBq1CisXr0at27dwhdffKF0m02a\nNMGqVavQrJklpNI8hIWFYd68ea91EVq7di3+LVy9WYPPhhf3ZVwImVYtXLgQ69d7YdAg4fM0tZ/W\nRs3263H8+HHExirapi1ZsgQvX75EejohKEjxpVVEzUKtTx9eQa9evfDpp5/i448/RmJiIn7++Wes\nXz+saL6HujxSqRQ/j1uCATOvwtzcHE5OTggICEBGRgby8gjBwYpmKGKy5GSmISAgAG3atEGdOnWQ\nkJCA3377DevWfYeICEAqFf5sxnb9Ar7TktG9e3d0794dvr6+SE1NBQBERBDOnROXJS/3BQIDA+Hs\n7AwiQkJCApYsWYLLly9jzZo1CA4OFszSrVFXeH55AYGBgZgxYwZat25dtBd58KAMW7aUeFEVefJl\n+bh0IhxNmzbFiRMncPDgQWzcuBFmZmaYM2cOFi1ahEdrzNVmsYUtmvjux44dO7BlyxbY2dkhPDwc\ncrkcq1atwuTJk0VlKcSL+zIA3FmG6U5SCBFA5BdJRElEfiGK+0KSCgco7iMikslk9Oeff5K1tTXZ\n2dmRvb0jeXk9o4cPhV9n8eKlZGRkQp9++induHFDK3kOHjxIzs7OZGlpSU2aNCEvrwt0+rRwlqio\nKKpevS59+OGHdFrNEzTJcunSJfLx8aEqVapQmzZtyNt7Na1bJ5zl+vXrVKtWE3J2dqaDBw++9tjO\nnTtp+vTpGmd5/PgxffXVV2RkZETt27enLl0m0qJFwlny8vLIycmDrK2t6c8//ySZTFb0WGJiIg0c\nOJBkMplGWXJzcykoKIjMzc2pa9euJJFICABt3bpVOBBjxfAeIdMpseeMDAwMMGbMGFy9ehXDhg3D\nzJnTEB1tpliDUIUVK1agW7duaNHiQ/Tt64u6deuiQYMGWsnj7e2NuLg4LFiwAKNHj8aePU3QurXq\n7cbFxcHCwgI1a9pj+PCPYWhoiNbqnqBBlqZNmyIyMhJbt27F5MmTsXZtd6jqVwAAOTk5MDY2RkrK\nPYwdOx4pKSnw9vZ+bYyvry+WLFmicZZatWrht99+Q1xcHDw9PREWNgEzZ6p9m2jVqhX++usvTJky\nC2lpaXBzc4NBsUlAzZo1Q0RERNF9YrMYGxtj6tSpSEpKQlxcHMLDwxEREcHLNzGNcSFkOifmPE2h\n6tWr49GjRzA3N3/ty1KZJlIp+ltawsfHHR/b2qJt1apazSOVSmFqaornz5/DzMxM7TbfI8IUe3u4\nuNTHp+08MEhV67JSZgEAHx8ffPrpp6hXr57abUoB/OTujqb1amBMXy8satVK61kaN26M9evX4wOB\nyTwAML5JEzQzNcXoUb3xk7s7LARm5WqaxdLSEgYGBqhXrx4GDhyIESNGCG6fseK4EDLdEzhPUxwR\nYefOndixY4fg2C5ZWRhfcN5syKNH+ESoVVcp8uzYsQNbt24VHNdEJsOc06cBAB2yszEhWeQKCRpk\nEcuICAExMagnk6Fxfj4mnjyp9SwHDhzAzZs3ceLECcGxX1y+DI/sbEgKcjVQN1uoFFkYKzN9H5tl\nrLjTp08TAKpZsyblqVrBolBSElHhua8zZ4hiY7WaJTs7m6pXr04AKDExUf3g9HSiTZsUt1NTifbv\n12oWjchkRLt2ET1/TvTkCdHu3Vp/iTFjxhAAmjJlivDgI0eIbt1S3N61iygjQ+t5LC0tabcO3ier\nHHiPkJWKmC4dymYjCincE0xPT1d5fVvRBj+zA7p2VUz3c3cH3NzK8I7edODAATx//vy1XCqz9K4J\nDB6syNKoEdCtm1aziJcMeEkBX1+g+lSgRg2gZ0+tvoJcLsfu3bsBQMTecjIwqyNgY6P4bHr3Bt57\nT6t5GCsrLoRMa5R16dC000jxgqO2+JTDYq1vUxbRyiHLP//8gwcPHgAArl+/jvj4eL3mYaysuBCy\nUhPTpUPZDEBVHj58CIlEAhsbG7i5ueHWrVuqByc2f3UFtG0vAOovgC+Nu3fvws3NDW5ubpDJZHj2\n7JnesohWhiypqakICgp6bQkrZeLj49G4cWPY2dnBzc0N58+f10kesWJiYmBlZYUaAh2BGFOFCyEr\nNbFdOkrOAFQmKysLy5YtQ0pKChwcHHDs2DFseeNK7WLKYbHWyMhIxMbGIjY2FqdPn8Z7qg7pvU0L\nx5Yhy61btxAaGgpnZ+eiQ58lnT17FuvXr8ejR48wc+ZMxMbGqp+lqcPP5vbt2xg2bBg6duyI7t27\no127dtrbOKtc9H2Skr2blF3kHOlHBcfAiOD3+pikEKJ2BRdCx8e/mldCpLi4+4MPPiBbW1vaVPwB\n9QmI2hV7Mb2qOFkyMzNp3rx5ZGpqSt7e3hQfH09ERI8ePaKJEyeSoaEhjRgxgu7du1cueZTJysqi\nxYsXU/Xq1alLly504cIFrWyXVV4SIjHr5jCmPRs3AkuWZKJKlR7Iz8/FlStX8N133yEgIED04rtM\nt65fv45vvvkGO3bsQJ8+fbB//360bNkSISEhcNPypCRNnDp1CoMGDYKJiQmCgoLQt29fvWVhFQcX\nQlbu8vLy0LatBzw82iI/Px9xcXE4I7DWHdOPqKgoDB8+HDNnzsTEiRMhEXExvC4NGDAA5ubmWL58\nOf+jiWmNob4DsEqICLXT0zD5q6+Qk5WFbz79VN+JmApeXl64f/8+OnfurPciCADvv/8S3t4duAgy\nreJCyMqdERH237gByOWAXI6916/rOxJ7R4wbdx+1a+foOwarYLgQsvJnaAjMnw9YWwN5eShaJ4kx\nAVZWE2Bq6qzvGKyC4ULIylky0MEOOAFg7m2AwoBvv9V3KPZW24MbZ3tC0Um2HWya/wNx7dUZE4ev\nI2TlizuNMA3lPtwO0+YENzeCm9t/Ya7vQKzC4ULIytfb1IWFCZJIJKhWrRqkUqneMphYfQNcl+Ds\nWQnOnv0MGXpLwioqPjTKyldhpxEfFHQasdd3IqaGkZFRUeNxvclIgokDQXH14h7cuLEHaOgj8CTG\nxOPrCFk5SwY8C84Rwk9xjpAxNXIz/HE9ORyKdecV5witTPQcilUoXAgZY2+djIwMpKXtQ+PGg/Ud\nhVUCfI6QMfbWMTY2RmTkKRCpXwmDMW3gPULGGGOVGu8RMsYYq9S4EDLGGKvUuBAyxhir1LgQMsYY\nq9S4EDLGGKvUuBAyxhir1LgQMsYYq9S4EDLGGKvUuBAyxhir1LgQMsYYq9S4EDLGGKvUuBAyxhir\n1LgQMsYYq9S4EDLGGKvUuBAyxhir1LgQMsYYq9T+H1csd+RMIpjiAAAAAElFTkSuQmCC\n",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x20392f80120>"
]
},
"execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"molNoBondInfo"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"c2 = Chem.FindMolChiralCenters(molNoBondInfo)"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"[(1, 'S'),\n",
" (12, 'S'),\n",
" (24, 'S'),\n",
" (28, 'S'),\n",
" (36, 'S'),\n",
" (44, 'S'),\n",
" (57, 'S'),\n",
" (68, 'S'),\n",
" (76, 'S'),\n",
" (85, 'S'),\n",
" (96, 'S'),\n",
" (104, 'S'),\n",
" (112, 'S'),\n",
" (121, 'S'),\n",
" (126, 'S'),\n",
" (135, 'S'),\n",
" (143, 'S'),\n",
" (153, 'S'),\n",
" (158, 'S'),\n",
" (167, 'S'),\n",
" (170, 'S'),\n",
" (175, 'S'),\n",
" (183, 'S'),\n",
" (186, 'R'),\n",
" (190, 'S')]"
]
},
"execution_count": 12,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"c2"
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"True"
]
},
"execution_count": 13,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"c1 == c2"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {
"collapsed": true
},
"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": "3.5.1"
}
},
"nbformat": 4,
"nbformat_minor": 0
}
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