{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "A notebook to visualize some of the test systems in the C++ test code from `Code/GraphMol/RGroupDecomposition/testRGroupDecomp.cpp`" ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [], "source": [ "from rdkit import Chem\n", "from rdkit.Chem import AllChem\n", "from rdkit.Chem.Draw import IPythonConsole\n", "IPythonConsole.ipython_useSVG=True\n", "from rdkit.Chem.rdRGroupDecomposition import RGroupDecomposition, RGroupDecompositionParameters, \\\n", " RGroupMatching, RGroupScore, RGroupLabels, RGroupCoreAlignment\n", "import pandas as pd\n", "from rdkit.Chem import PandasTools\n", "from collections import OrderedDict\n", "from IPython.display import HTML\n", "from rdkit import rdBase\n", "from io import StringIO\n", "from rdkit.Chem import Draw\n", "rdBase.DisableLog(\"rdApp.debug\")" ] }, { "cell_type": "code", "execution_count": 2, "metadata": { "scrolled": true }, "outputs": [], "source": [ "\n", "def decomp(options):\n", " options.removeHydrogensPostMatch = True\n", " decomp = RGroupDecomposition(cores, options)\n", " for mol in mols:\n", " decomp.Add(mol)\n", " decomp.Process()\n", " cols = decomp.GetRGroupsAsColumns()\n", " return cols\n", "\n", "def show_decomp(cols, input_core=None):\n", " if input_core:\n", " if isinstance(input_core, list):\n", " cols['Input core'] = input_core\n", " else:\n", " cols['Input core'] = [input_core] * len(mols)\n", " cols['Mol'] = mols\n", " df = pd.DataFrame(cols);\n", " PandasTools.ChangeMoleculeRendering(df)\n", " return HTML(df.to_html())\n", "\n", "# for when we can't display structures (\"non-ring aromatic\")\n", "def show_decomp_smiles(cols):\n", " cols['mol'] = mols\n", " for c in cols:\n", " cols[c] = ['{}:{}'.format(c, Chem.MolToSmiles(m)) for m in cols[c]]\n", " df = pd.DataFrame(cols);\n", " PandasTools.ChangeMoleculeRendering(df)\n", " return HTML(df.to_html())\n", "\n", "def print_rows(options):\n", " decomp = RGroupDecomposition(cores, options)\n", " for mol in mols:\n", " decomp.Add(mol)\n", " decomp.Process()\n", " rows = decomp.GetRGroupsAsRows()\n", " for i, r in enumerate(rows):\n", " labels = ['{}:{}'.format(l, Chem.MolToSmiles(r[l])) for l in r]\n", " print('\"{}\",'.format(' '.join(labels)))\n", " " ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### testSDFGRoupMultiCoreNoneShouldMatch\n", "\n", "Cores, compounds and python code " ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "data": { "image/svg+xml": [ "\n", "\n", " \n", " \n", " \n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "" ], "text/plain": [ "" ] }, "execution_count": 3, "metadata": {}, "output_type": "execute_result" } ], "source": [ "sdcores = \"\"\"\n", "Mrv1813 05061918272D \n", "\n", " 13 14 0 0 0 0 999 V2000\n", " -1.1505 0.0026 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " -1.1505 -0.8225 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " -0.4360 -1.2350 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n", " 0.2784 -0.8225 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " 0.2784 0.0026 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n", " -0.4360 0.4151 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " -1.9354 0.2575 0.0000 A 0 0 0 0 0 0 0 0 0 0 0 0\n", " -2.4202 -0.4099 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " -1.9354 -1.0775 0.0000 A 0 0 0 0 0 0 0 0 0 0 0 0\n", " 0.9907 -1.2333 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0\n", " -0.4360 1.2373 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n", " 0.2784 1.6497 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0\n", " -3.2452 -0.4098 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0\n", " 6 1 1 0 0 0 0\n", " 1 7 1 0 0 0 0\n", " 1 2 1 0 0 0 0\n", " 2 3 1 0 0 0 0\n", " 9 2 1 0 0 0 0\n", " 3 4 1 0 0 0 0\n", " 4 5 1 0 0 0 0\n", " 4 10 1 0 0 0 0\n", " 5 6 1 0 0 0 0\n", " 6 11 1 0 0 0 0\n", " 7 8 1 0 0 0 0\n", " 8 13 1 0 0 0 0\n", " 8 9 1 0 0 0 0\n", " 11 12 1 0 0 0 0\n", "M RGP 3 10 1 12 2 13 3\n", "M END\n", "$$$$\n", "\n", " Mrv1813 05061918272D \n", "\n", " 13 14 0 0 0 0 999 V2000\n", " 6.9524 0.1684 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " 6.9524 -0.6567 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " 7.6668 -1.0692 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " 8.3813 -0.6567 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " 8.3813 0.1684 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n", " 7.6668 0.5809 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " 6.1674 0.4233 0.0000 A 0 0 0 0 0 0 0 0 0 0 0 0\n", " 5.6827 -0.2441 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " 6.1674 -0.9117 0.0000 A 0 0 0 0 0 0 0 0 0 0 0 0\n", " 9.0935 -1.0675 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0\n", " 7.6668 1.4031 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n", " 8.3813 1.8155 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0\n", " 4.8576 -0.2440 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0\n", " 6 1 1 0 0 0 0\n", " 1 7 1 0 0 0 0\n", " 1 2 1 0 0 0 0\n", " 2 3 1 0 0 0 0\n", " 9 2 1 0 0 0 0\n", " 3 4 1 0 0 0 0\n", " 4 5 1 0 0 0 0\n", " 4 10 1 0 0 0 0\n", " 5 6 1 0 0 0 0\n", " 6 11 1 0 0 0 0\n", " 7 8 1 0 0 0 0\n", " 8 13 1 0 0 0 0\n", " 8 9 1 0 0 0 0\n", " 11 12 1 0 0 0 0\n", "M RGP 3 10 1 12 2 13 3\n", "M END\n", "$$$$)CTAB\"\"\"\n", "\n", "supplier = Chem.SDMolSupplier()\n", "supplier.SetData(sdcores)\n", "cores = [x for x in supplier]\n", "for core in cores:\n", " AllChem.Compute2DCoords(core)\n", "Draw.MolsToGridImage(cores)" ] }, { "cell_type": "code", "execution_count": 4, "metadata": { "scrolled": false }, "outputs": [ { "data": { "image/svg+xml": [ "\n", "\n", " \n", " \n", " \n", " \n", " \n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "" ], "text/plain": [ "" ] }, "execution_count": 4, "metadata": {}, "output_type": "execute_result" } ], "source": [ "sdmols=\"\"\"CTAB(\n", " Mrv1813 05061918322D \n", "\n", " 15 17 0 0 0 0 999 V2000\n", " 0.1742 0.6899 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " 0.8886 0.2774 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " 0.8886 -0.5476 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " 0.1742 -0.9601 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n", " 0.1742 -1.7851 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " 0.8886 -2.1976 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n", " 0.8886 -3.0226 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " 0.1742 -3.4351 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n", " -0.5403 -3.0226 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " -1.3249 -3.2775 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n", " -1.8099 -2.6101 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " -1.3249 -1.9426 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " -0.5403 -2.1976 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " -0.5403 -0.5476 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " -0.5403 0.2774 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " 1 2 1 0 0 0 0\n", " 1 15 1 0 0 0 0\n", " 2 3 1 0 0 0 0\n", " 3 4 1 0 0 0 0\n", " 4 5 1 0 0 0 0\n", " 4 14 1 0 0 0 0\n", " 5 6 1 0 0 0 0\n", " 5 13 1 0 0 0 0\n", " 6 7 1 0 0 0 0\n", " 7 8 1 0 0 0 0\n", " 8 9 1 0 0 0 0\n", " 9 10 1 0 0 0 0\n", " 9 13 1 0 0 0 0\n", " 10 11 1 0 0 0 0\n", " 11 12 1 0 0 0 0\n", " 12 13 1 0 0 0 0\n", " 14 15 1 0 0 0 0\n", "M END\n", "$$$$\n", "\n", " Mrv1813 05061918322D \n", "\n", " 14 15 0 0 0 0 999 V2000\n", " 6.4368 0.3002 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " 5.7223 -0.1123 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n", " 5.7223 -0.9373 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " 6.4368 -1.3498 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n", " 6.4368 -2.1748 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " 5.7223 -2.5873 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n", " 5.0078 -2.1748 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " 4.2232 -2.4297 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0\n", " 3.7383 -1.7623 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " 4.2232 -1.0949 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " 3.9683 -0.3102 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " 3.1613 -0.1387 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " 4.5203 0.3029 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " 5.0078 -1.3498 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " 1 2 1 0 0 0 0\n", " 2 3 1 0 0 0 0\n", " 3 4 1 0 0 0 0\n", " 3 14 1 0 0 0 0\n", " 4 5 1 0 0 0 0\n", " 5 6 1 0 0 0 0\n", " 6 7 1 0 0 0 0\n", " 7 8 1 0 0 0 0\n", " 7 14 1 0 0 0 0\n", " 8 9 1 0 0 0 0\n", " 9 10 1 0 0 0 0\n", " 10 11 1 0 0 0 0\n", " 10 14 1 0 0 0 0\n", " 11 13 1 0 0 0 0\n", " 11 12 1 0 0 0 0\n", "M END\n", "$$$$\n", "\n", " Mrv1813 05061918322D \n", "\n", " 14 15 0 0 0 0 999 V2000\n", " 0.8289 -7.9643 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " 0.1144 -8.3768 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n", " 0.1144 -9.2018 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " 0.8289 -9.6143 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n", " 0.8289 -10.4393 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " 0.1144 -10.8518 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " -0.6000 -10.4393 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " -1.3847 -10.6942 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0\n", " -1.8696 -10.0268 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " -1.3847 -9.3593 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " -1.6396 -8.5747 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " -2.4466 -8.4032 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " -1.0876 -7.9616 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " -0.6000 -9.6143 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " 1 2 1 0 0 0 0\n", " 2 3 1 0 0 0 0\n", " 3 4 1 0 0 0 0\n", " 3 14 1 0 0 0 0\n", " 4 5 1 0 0 0 0\n", " 5 6 1 0 0 0 0\n", " 6 7 1 0 0 0 0\n", " 7 8 1 0 0 0 0\n", " 7 14 1 0 0 0 0\n", " 8 9 1 0 0 0 0\n", " 9 10 1 0 0 0 0\n", " 10 11 1 0 0 0 0\n", " 10 14 1 0 0 0 0\n", " 11 13 1 0 0 0 0\n", " 11 12 1 0 0 0 0\n", "M END\n", "$$$$\n", "\n", " Mrv1813 05061918322D \n", "\n", " 12 13 0 0 0 0 999 V2000\n", " 5.3295 -8.1871 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " 5.5844 -7.4025 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n", " 5.0995 -6.7351 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " 5.5844 -6.0676 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n", " 6.3690 -6.3226 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " 7.0835 -5.9101 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " 7.0835 -5.0851 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n", " 7.7980 -6.3226 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n", " 7.7980 -7.1476 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " 8.5124 -7.5601 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n", " 7.0835 -7.5601 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " 6.3690 -7.1476 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " 1 2 1 0 0 0 0\n", " 2 3 1 0 0 0 0\n", " 2 12 1 0 0 0 0\n", " 3 4 1 0 0 0 0\n", " 4 5 1 0 0 0 0\n", " 5 12 1 0 0 0 0\n", " 5 6 1 0 0 0 0\n", " 6 7 1 0 0 0 0\n", " 6 8 1 0 0 0 0\n", " 8 9 1 0 0 0 0\n", " 9 10 1 0 0 0 0\n", " 9 11 1 0 0 0 0\n", " 11 12 1 0 0 0 0\n", "M END\n", "$$$$)CTAB\"\"\"\n", "supplier = Chem.SDMolSupplier()\n", "supplier.SetData(sdmols)\n", "mols = [x for x in supplier]\n", "for mol in mols:\n", " AllChem.Compute2DCoords(mol)\n", "Draw.MolsToGridImage(mols)" ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
CoreR1R2R4R5R6Input coreMol
0\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/
1\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/
2\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/
3\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/
" ], "text/plain": [ "" ] }, "execution_count": 5, "metadata": {}, "output_type": "execute_result" } ], "source": [ "options = RGroupDecompositionParameters()\n", "options.onlyMatchAtRGroups = False\n", "options.removeHydrogensPostMatch = True\n", "cols = decomp(options)\n", "show_decomp(cols, [cores[0], cores[0], cores[1], cores[1]])" ] }, { "cell_type": "code", "execution_count": 6, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\"Core:C1C([*:6])C2C(N([*:2])[*:4])NC([*:1])NC2N1[*:5] R1:[H][*:1] R2:C(CC[*:2])CC[*:4] R4:C(CC[*:2])CC[*:4] R5:[H][*:5] R6:[H][*:6]\",\n", "\"Core:C1SC2NC([*:1])NC(N([*:2])[*:4])C2C1[*:6] R1:[H][*:1] R2:C[*:2] R4:[H][*:4] R6:CC(C)[*:6]\",\n", "\"Core:C1SC2CC([*:1])NC(N([*:2])[*:4])C2C1[*:6] R1:[H][*:1] R2:C[*:2] R4:[H][*:4] R6:CC(C)[*:6]\",\n", "\"Core:C1C2C(C(N([*:2])[*:4])NC1[*:1])N([*:6])CN2[*:5] R1:O[*:1] R2:[H][*:2] R4:[H][*:4] R5:C[*:5] R6:[H][*:6]\",\n" ] } ], "source": [ "print_rows(options)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### testMultiCorePreLabelled" ] }, { "cell_type": "code", "execution_count": 7, "metadata": { "scrolled": true }, "outputs": [ { "data": { "image/svg+xml": [ "\n", "\n", " \n", " \n", " \n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "" ], "text/plain": [ "" ] }, "execution_count": 7, "metadata": {}, "output_type": "execute_result" } ], "source": [ "sdcores = \"\"\"CTAB(\n", " RDKit 2D\n", "\n", " 9 9 0 0 0 0 0 0 0 0999 V2000\n", " 1.1100 -1.3431 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n", " 1.5225 -0.6286 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " 0.9705 -0.0156 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " 0.2168 -0.3511 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n", " 0.3029 -1.1716 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " 1.1419 0.7914 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " 0.5289 1.3431 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n", " 1.9266 1.0463 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0\n", " -0.4976 0.0613 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0\n", " 1 2 1 0\n", " 2 3 2 0\n", " 3 4 1 0\n", " 4 5 1 0\n", " 1 5 2 0\n", " 3 6 1 0\n", " 6 7 2 0\n", " 6 8 1 0\n", " 4 9 1 0\n", "M RGP 2 8 1 9 2\n", "V 8 *\n", "V 9 *\n", "M END\n", "$$$$\n", "\n", " RDKit 2D\n", "\n", " 12 13 0 0 0 0 0 0 0 0999 V2000\n", " -6.5623 0.3977 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0\n", " -5.8478 -0.0147 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " -5.1333 0.3977 0.0000 A 0 0 0 0 0 0 0 0 0 0 0 0\n", " -4.4188 -0.0147 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " -4.4188 -0.8397 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " -5.1333 -1.2522 0.0000 A 0 0 0 0 0 0 0 0 0 0 0 0\n", " -5.8478 -0.8397 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " -3.7044 -1.2522 0.0000 A 0 0 0 0 0 0 0 0 0 0 0 0\n", " -3.7044 0.3977 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n", " -2.9899 -0.0147 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " -2.9899 -0.8397 0.0000 A 0 0 0 0 0 0 0 0 0 0 0 0\n", " -2.2754 0.3978 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0\n", " 3 4 1 0\n", " 4 5 2 0\n", " 5 6 1 0\n", " 6 7 2 0\n", " 2 3 2 0\n", " 2 7 1 0\n", " 9 10 2 0\n", " 10 11 1 0\n", " 8 11 2 0\n", " 8 5 1 0\n", " 4 9 1 0\n", " 10 12 1 0\n", " 1 2 1 0\n", "M RGP 2 1 2 12 1\n", "V 1 *\n", "V 12 *\n", "M END\n", "$$$$\n", ")CTAB\"\"\"\n", "\n", "supplier = Chem.SDMolSupplier()\n", "supplier.SetData(sdcores)\n", "cores = [x for x in supplier]\n", "for core in cores:\n", " AllChem.Compute2DCoords(core)\n", "Draw.MolsToGridImage(cores)" ] }, { "cell_type": "code", "execution_count": 8, "metadata": { "scrolled": true }, "outputs": [ { "data": { "image/svg+xml": [ "\n", "\n", " \n", " \n", " \n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "" ], "text/plain": [ "" ] }, "execution_count": 8, "metadata": {}, "output_type": "execute_result" } ], "source": [ "smiles = [\"CNC(=O)C1=CN=CN1CC\", \"Fc1ccc2ccc(Br)nc2n1\"]\n", "mols = [Chem.MolFromSmiles(s) for s in smiles]\n", "Draw.MolsToGridImage(mols)" ] }, { "cell_type": "code", "execution_count": 9, "metadata": { "scrolled": false }, "outputs": [ { "data": { "text/html": [ "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
CoreR1R2Input coreMol
0\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/
1\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/
" ], "text/plain": [ "" ] }, "execution_count": 9, "metadata": {}, "output_type": "execute_result" } ], "source": [ "options = RGroupDecompositionParameters()\n", "options.labels = RGroupLabels.AutoDetect\n", "options.alignment = RGroupCoreAlignment.MCS\n", "options.onlyMatchAtRGroups = True\n", "cols = decomp(options)\n", "show_decomp(cols, cores)" ] }, { "cell_type": "code", "execution_count": 10, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\"Core:O=C(c1cncn1[*:2])[*:1] R1:CN[*:1] R2:CC[*:2]\",\n", "\"Core:c1cc2ccc([*:2])nc2nc1[*:1] R1:F[*:1] R2:Br[*:2]\",\n" ] } ], "source": [ "print_rows(options)" ] }, { "cell_type": "code", "execution_count": 11, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
CoreR1R2Input coreMol
0\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/
1\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/
" ], "text/plain": [ "" ] }, "execution_count": 11, "metadata": {}, "output_type": "execute_result" } ], "source": [ "options = RGroupDecompositionParameters()\n", "options.labels = RGroupLabels.MDLRGroupLabels | RGroupLabels.RelabelDuplicateLabels\n", "options.alignment = RGroupCoreAlignment.MCS\n", "options.onlyMatchAtRGroups = True\n", "cols=decomp(options)\n", "show_decomp(cols, cores)" ] }, { "cell_type": "code", "execution_count": 12, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\"Core:O=C(c1cncn1[*:2])[*:1] R1:CN[*:1] R2:CC[*:2]\",\n", "\"Core:c1cc2ccc([*:2])nc2nc1[*:1] R1:F[*:1] R2:Br[*:2]\",\n" ] } ], "source": [ "print_rows(options)" ] }, { "cell_type": "code", "execution_count": 13, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
CoreR1R2Input coreMol
0\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/
1\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/
" ], "text/plain": [ "" ] }, "execution_count": 13, "metadata": {}, "output_type": "execute_result" } ], "source": [ "options = RGroupDecompositionParameters()\n", "options.labels = RGroupLabels.AutoDetect\n", "options.alignment = RGroupCoreAlignment.NoAlignment\n", "options.onlyMatchAtRGroups = True\n", "cols=decomp(options)\n", "show_decomp(cols, cores)" ] }, { "cell_type": "code", "execution_count": 14, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\"Core:O=C(c1cncn1[*:2])[*:1] R1:CN[*:1] R2:CC[*:2]\",\n", "\"Core:c1cc2ccc([*:2])nc2nc1[*:1] R1:F[*:1] R2:Br[*:2]\",\n" ] } ], "source": [ "print_rows(options)" ] }, { "cell_type": "code", "execution_count": 15, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
CoreR1R2Input coreMol
0\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/
1\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/
" ], "text/plain": [ "" ] }, "execution_count": 15, "metadata": {}, "output_type": "execute_result" } ], "source": [ "options = RGroupDecompositionParameters()\n", "options.labels = RGroupLabels.MDLRGroupLabels | RGroupLabels.RelabelDuplicateLabels\n", "options.alignment = RGroupCoreAlignment.NoAlignment\n", "options.onlyMatchAtRGroups = True\n", "cols=decomp(options)\n", "show_decomp(cols, cores)" ] }, { "cell_type": "code", "execution_count": 16, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\"Core:O=C(c1cncn1[*:2])[*:1] R1:CN[*:1] R2:CC[*:2]\",\n", "\"Core:c1cc2ccc([*:2])nc2nc1[*:1] R1:F[*:1] R2:Br[*:2]\",\n" ] } ], "source": [ "print_rows(options)" ] }, { "cell_type": "code", "execution_count": 17, "metadata": {}, "outputs": [], "source": [ "for core in cores:\n", " for atom in core.GetAtoms():\n", " if atom.HasProp(\"_MolFileRLabel\"):\n", " atom.ClearProp(\"_MolFileRLabel\")\n", " if atom.GetIsotope():\n", " atom.SetIsotope(0)\n", " if atom.GetAtomMapNum():\n", " print(\"atom map num\")\n", " atom.SetAtomMapNum(0)\n", " " ] }, { "cell_type": "code", "execution_count": 18, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
CoreR1R2Input coreMol
0\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/
1\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/
" ], "text/plain": [ "" ] }, "execution_count": 18, "metadata": {}, "output_type": "execute_result" } ], "source": [ "options = RGroupDecompositionParameters()\n", "options.labels = RGroupLabels.AutoDetect\n", "options.alignment = RGroupCoreAlignment.MCS\n", "options.onlyMatchAtRGroups = True\n", "cols=decomp(options)\n", "show_decomp(cols, cores)" ] }, { "cell_type": "code", "execution_count": 19, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\"Core:O=C(c1cncn1[*:2])[*:1] R1:CN[*:1] R2:CC[*:2]\",\n", "\"Core:c1cc2ccc([*:2])nc2nc1[*:1] R1:Br[*:1] R2:F[*:2]\",\n" ] } ], "source": [ "print_rows(options)" ] }, { "cell_type": "code", "execution_count": 20, "metadata": { "scrolled": false }, "outputs": [ { "data": { "text/html": [ "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
CoreR1R2Input coreMol
0\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/
1\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/
" ], "text/plain": [ "" ] }, "execution_count": 20, "metadata": {}, "output_type": "execute_result" } ], "source": [ "options = RGroupDecompositionParameters()\n", "options.labels = RGroupLabels.DummyAtomLabels | RGroupLabels.RelabelDuplicateLabels\n", "options.alignment = RGroupCoreAlignment.MCS\n", "options.onlyMatchAtRGroups = True\n", "cols=decomp(options)\n", "show_decomp(cols, cores)" ] }, { "cell_type": "code", "execution_count": 21, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\"Core:O=C(c1cncn1[*:2])[*:1] R1:CN[*:1] R2:CC[*:2]\",\n", "\"Core:c1cc2ccc([*:2])nc2nc1[*:1] R1:Br[*:1] R2:F[*:2]\",\n" ] } ], "source": [ "print_rows(options)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### testMatchOnAnyAtom" ] }, { "cell_type": "code", "execution_count": 22, "metadata": {}, "outputs": [ { "data": { "image/svg+xml": [ "\n", "\n", " \n", " \n", " \n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "" ], "text/plain": [ "" ] }, "execution_count": 22, "metadata": {}, "output_type": "execute_result" } ], "source": [ "block=\"\"\"\n", " Mrv2008 01192109352D \n", "\n", " 12 12 0 0 0 0 999 V2000\n", " 3.7389 -3.2028 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " 4.5640 -3.2028 0.0000 A 0 0 0 0 0 0 0 0 0 0 0 0\n", " 4.9764 -2.4884 0.0000 A 0 0 0 0 0 0 0 0 0 0 0 0\n", " 4.5640 -1.7739 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " 3.7389 -1.7739 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " 3.3265 -2.4884 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " 2.5015 -2.4884 0.0000 A 0 0 0 0 0 0 0 0 0 0 0 0\n", " 3.3265 -3.9172 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0\n", " 5.8014 -2.4884 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0\n", " 2.0890 -1.7739 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " 2.5015 -1.0595 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n", " 1.2640 -1.7739 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0\n", " 5 6 8 0 0 0 0\n", " 4 5 8 0 0 0 0\n", " 3 4 8 0 0 0 0\n", " 2 3 8 0 0 0 0\n", " 1 2 8 0 0 0 0\n", " 1 6 8 0 0 0 0\n", " 6 7 1 0 0 0 0\n", " 1 8 1 0 0 0 0\n", " 3 9 1 0 0 0 0\n", " 7 10 1 0 0 0 0\n", " 10 11 2 0 0 0 0\n", " 10 12 1 0 0 0 0\n", "M RGP 3 8 2 9 3 12 1\n", "M END\n", "\"\"\"\n", "core=Chem.MolFromMolBlock(block)\n", "AllChem.Compute2DCoords(core)\n", "smiles = 'O=C(NC1CCN(c2ncccc2[N+](=O)[O-])CC1)c1cc(Cl)c(Cl)[nH]1'\n", "cores = [core]\n", "mols = [Chem.MolFromSmiles(smiles)]\n", "Draw.MolsToGridImage([cores[0], mols[0]], subImgSize=(300, 300))" ] }, { "cell_type": "code", "execution_count": 23, "metadata": { "scrolled": true }, "outputs": [ { "data": { "text/html": [ "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
CoreR1R3Input coreMol
0\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/
" ], "text/plain": [ "" ] }, "execution_count": 23, "metadata": {}, "output_type": "execute_result" } ], "source": [ "options = RGroupDecompositionParameters()\n", "options.onlyMatchAtRGroups = False\n", "cols=decomp(options)\n", "show_decomp(cols, core)" ] }, { "cell_type": "code", "execution_count": 24, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\"Core:O=C(NC1CCN([*:3])CC1)[*:1] R1:Clc1cc([*:1])[nH]c1Cl R3:O=[N+]([O-])c1cccnc1[*:3]\",\n" ] } ], "source": [ "print_rows(options)" ] }, { "cell_type": "code", "execution_count": 25, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
CoreR1R3Input coreMol
0\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/
" ], "text/plain": [ "" ] }, "execution_count": 25, "metadata": {}, "output_type": "execute_result" } ], "source": [ "options = RGroupDecompositionParameters()\n", "options.onlyMatchAtRGroups = True\n", "cols=decomp(options)\n", "show_decomp(cols, core)" ] }, { "cell_type": "code", "execution_count": 26, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\"Core:O=C(NC1CCN([*:3])CC1)[*:1] R1:Clc1cc([*:1])[nH]c1Cl R3:O=[N+]([O-])c1cccnc1[*:3]\",\n" ] } ], "source": [ "print_rows(options)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### testRingMatching3\n", "\n", "The default scoring function does not arrange the R groups correctly. " ] }, { "cell_type": "code", "execution_count": 63, "metadata": { "scrolled": false }, "outputs": [ { "data": { "text/html": [ "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
CoreR1R2R3R4R5Input coreMol
0\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/
1\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/
2\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/
" ], "text/plain": [ "" ] }, "execution_count": 63, "metadata": {}, "output_type": "execute_result" } ], "source": [ "cores = [Chem.MolFromSmarts(\"*1***[*:1]1\")]\n", "cores = [Chem.MolFromSmarts(\"*1****1([*:1])\")]\n", "smi = [\"c1cocc1CCl\", \"c1c[nH]cc1CI\", \"c1cscc1CF\"]\n", "mols = [Chem.MolFromSmiles(s) for s in smi]\n", "options = RGroupDecompositionParameters()\n", "#options.scoreMethod = RGroupScore.FingerprintVariance\n", "options.removeHydrogensPostMatch = True\n", "options.removeAllHydrogenRGroups = False\n", "options.onlyMatchAtRGroups = False\n", "options.allowNonTerminalRGroups = True;\n", "cols=decomp(options)\n", "show_decomp(cols, cores[0])" ] }, { "cell_type": "code", "execution_count": 28, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\"Core:c1cc([*:1])co1 R1:ClC[*:1]\",\n", "\"Core:c1cc([*:1])c[nH]1 R1:IC[*:1]\",\n", "\"Core:c1cc([*:1])cs1 R1:FC[*:1]\",\n" ] } ], "source": [ "print_rows(options)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### testGithub3402" ] }, { "cell_type": "code", "execution_count": 29, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
CoreR1Input coreMol
0\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/
" ], "text/plain": [ "" ] }, "execution_count": 29, "metadata": {}, "output_type": "execute_result" } ], "source": [ "cores = [Chem.MolFromSmarts(\"[$(C-!@[a])](=O)(Cl)\")]\n", "mols = [Chem.MolFromSmiles(\"c1ccccc1C(=O)Cl\")]\n", "options = RGroupDecompositionParameters()\n", "cols=decomp(options)\n", "show_decomp(cols, cores[0])\n", " " ] }, { "cell_type": "code", "execution_count": 30, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\"Core:O=C(Cl)[*:1] R1:c1ccc([*:1])cc1\",\n" ] } ], "source": [ "print_rows(options)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### singleAtomBridge\n", "\n", "This test is currently broken. It is clear from the core and molecule what the decomposition should be." ] }, { "cell_type": "code", "execution_count": 31, "metadata": { "scrolled": false }, "outputs": [ { "data": { "text/html": [ "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
CoreR1Input coreMol
0\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/
" ], "text/plain": [ "" ] }, "execution_count": 31, "metadata": {}, "output_type": "execute_result" } ], "source": [ "mols = [Chem.MolFromSmiles('C1CC2NC12')]\n", "cores = [Chem.MolFromSmiles('C1([*:1])C([*:2])CC1')]\n", "options = RGroupDecompositionParameters()\n", "options.onlyMatchAtRGroups = True\n", "cols=decomp(options)\n", "show_decomp(cols, cores[0])\n" ] }, { "cell_type": "code", "execution_count": 32, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\"Core:C1CC([*:1])C1 R1:N([*:1])[*:1]\",\n" ] } ], "source": [ "print_rows(options)" ] }, { "cell_type": "code", "execution_count": 33, "metadata": { "scrolled": true }, "outputs": [ { "data": { "text/html": [ "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
CoreR1Input coreMol
0\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/
" ], "text/plain": [ "" ] }, "execution_count": 33, "metadata": {}, "output_type": "execute_result" } ], "source": [ "mols = [Chem.MolFromSmiles('C1CC2NC12')]\n", "cores = [Chem.MolFromSmiles('C1([*:1])CCC1')]\n", "options = RGroupDecompositionParameters()\n", "cols=decomp(options)\n", "show_decomp(cols, cores[0])" ] }, { "cell_type": "code", "execution_count": 34, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\"Core:C1CC([*:1])C1 R1:N([*:1])[*:1]\",\n" ] } ], "source": [ "print_rows(options)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### testRingMatching" ] }, { "cell_type": "code", "execution_count": 35, "metadata": { "scrolled": false }, "outputs": [ { "data": { "text/html": [ "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
CoreInput coreMol
0\"Mol\"/\"Mol\"/\"Mol\"/
1\"Mol\"/\"Mol\"/\"Mol\"/
2\"Mol\"/\"Mol\"/\"Mol\"/
" ], "text/plain": [ "" ] }, "execution_count": 35, "metadata": {}, "output_type": "execute_result" } ], "source": [ "cores = [Chem.MolFromSmiles(\"c1ccc[1*]1\")]\n", "smi = [\"c1cocc1\", \"c1c[nH]cc1\", \"c1cscc1\"]\n", "mols = [Chem.MolFromSmiles(s) for s in smi]\n", "options = RGroupDecompositionParameters()\n", "options.allowNonTerminalRGroups = True;\n", "cols=decomp(options)\n", "show_decomp(cols, cores[0])" ] }, { "cell_type": "code", "execution_count": 36, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\"Core:c1ccoc1\",\n", "\"Core:c1cc[nH]c1\",\n", "\"Core:c1ccsc1\",\n" ] } ], "source": [ "print_rows(options)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### testRingMatching2" ] }, { "cell_type": "code", "execution_count": 37, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
CoreR2Input coreMol
0\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/
1\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/
2\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/
" ], "text/plain": [ "" ] }, "execution_count": 37, "metadata": {}, "output_type": "execute_result" } ], "source": [ "cores = [Chem.MolFromSmarts(\"*1***[*:1]1C[*:2]\")]\n", "smi = [\"c1cocc1CCl\", \"c1c[nH]cc1CI\", \"c1cscc1CF\"]\n", "mols = [Chem.MolFromSmiles(s) for s in smi]\n", "options = RGroupDecompositionParameters()\n", "options.allowNonTerminalRGroups = True;\n", "cols=decomp(options)\n", "show_decomp(cols, cores[0])" ] }, { "cell_type": "code", "execution_count": 38, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\"Core:c1cc(C[*:2])co1 R2:Cl[*:2]\",\n", "\"Core:c1cc(C[*:2])c[nH]1 R2:I[*:2]\",\n", "\"Core:c1cc(C[*:2])cs1 R2:F[*:2]\",\n" ] } ], "source": [ "print_rows(options)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### testCoreWithRGroupAdjQuery" ] }, { "cell_type": "code", "execution_count": 39, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
CoreR1R2Input coreMol
0\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/
" ], "text/plain": [ "" ] }, "execution_count": 39, "metadata": {}, "output_type": "execute_result" } ], "source": [ "block = \"\"\"\n", " RDKit 2D\n", "\n", " 10 10 0 0 0 0 0 0 0 0999 V2000\n", " -3.6689 -0.8582 0.0000 R# 0 0 0 0 0 1 0 0 0 0 0 0\n", " -2.2421 -1.3211 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n", " -1.1279 -0.3169 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " -1.4403 1.1502 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " -0.3261 2.1543 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " 1.1007 1.6914 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " 1.4132 0.2243 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " 0.2989 -0.7798 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " 2.8400 -0.2386 0.0000 Q 0 0 0 0 0 0 0 0 0 0 0 0\n", " 3.1525 -1.7057 0.0000 R# 0 0 0 0 0 1 0 0 0 0 0 0\n", " 1 2 1 0\n", " 2 3 1 0\n", " 3 4 2 0\n", " 4 5 1 0\n", " 5 6 2 0\n", " 6 7 1 0\n", " 7 8 2 0\n", " 7 9 1 0\n", " 9 10 1 0\n", " 8 3 1 0\n", "M RGP 2 1 1 10 2\n", "M END\n", "$$$$\n", "\"\"\"\n", "\n", "core=Chem.MolFromMolBlock(block)\n", "AllChem.Compute2DCoords(core)\n", "smiles = 'CNc1cccc(c1)OC1CCC1'\n", "cores = [core]\n", "mols = [Chem.MolFromSmiles(smiles)]\n", "options = RGroupDecompositionParameters()\n", "options.onlyMatchAtRGroups = True\n", "cols=decomp(options)\n", "show_decomp(cols, cores[0])" ] }, { "cell_type": "code", "execution_count": 40, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\"Core:c1cc(N[*:1])cc(O[*:2])c1 R1:C[*:1] R2:C1CC([*:2])C1\",\n" ] } ], "source": [ "print_rows(options)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### test_userLabels" ] }, { "cell_type": "code", "execution_count": 41, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
CoreR1R5R6Input coreMol
0\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/
" ], "text/plain": [ "" ] }, "execution_count": 41, "metadata": {}, "output_type": "execute_result" } ], "source": [ "smi = \"C(Cl)N(N)O(O)\"\n", "mols = [Chem.MolFromSmiles(smi)]\n", "smarts = 'C([*:1])N([*:5])O([*:6])'\n", "cores = [Chem.MolFromSmarts(smarts)]\n", "options = RGroupDecompositionParameters()\n", "cols=decomp(options)\n", "show_decomp(cols, cores[0])" ] }, { "cell_type": "code", "execution_count": 42, "metadata": { "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\"Core:C(N(O[*:6])[*:5])[*:1] R1:Cl[*:1] R5:N[*:5] R6:O[*:6]\",\n" ] } ], "source": [ "print_rows(options)" ] }, { "cell_type": "code", "execution_count": 43, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
CoreR4R5R6Input coreMol
0\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/
" ], "text/plain": [ "" ] }, "execution_count": 43, "metadata": {}, "output_type": "execute_result" } ], "source": [ "smarts = 'C([*:4])N([*:5])O([*:6])'\n", "cores = [Chem.MolFromSmarts(smarts)]\n", "options = RGroupDecompositionParameters()\n", "cols=decomp(options)\n", "show_decomp(cols, cores[0])" ] }, { "cell_type": "code", "execution_count": 44, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\"Core:C(N(O[*:6])[*:5])[*:4] R4:Cl[*:4] R5:N[*:5] R6:O[*:6]\",\n" ] } ], "source": [ "print_rows(options)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### testGeminalRGroups" ] }, { "cell_type": "code", "execution_count": 45, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
CoreR5R6Input coreMol
0\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/
1\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/
2\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/
" ], "text/plain": [ "" ] }, "execution_count": 45, "metadata": {}, "output_type": "execute_result" } ], "source": [ "block=\"\"\"\n", " RDKit 2D\n", "\n", " 8 8 0 0 0 0 0 0 0 0999 V2000\n", " -0.6026 1.2267 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " -1.3171 0.8142 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " -1.3171 -0.0108 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " -0.6026 -0.4232 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " 0.1118 -0.0108 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " 0.1118 0.8142 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n", " -1.0714 1.7839 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0\n", " -0.0506 1.8398 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0\n", " 2 3 1 0 0 0 0\n", " 3 4 1 0 0 0 0\n", " 4 5 1 0 0 0 0\n", " 5 6 1 0 0 0 0\n", " 1 2 1 0 0 0 0\n", " 1 6 1 0 0 0 0\n", " 1 7 1 0 0 0 0\n", " 1 8 1 0 0 0 0\n", "M RGP 2 7 5 8 6\n", "M END\n", "\"\"\"\n", "\n", "core=Chem.MolFromMolBlock(block)\n", "AllChem.Compute2DCoords(core)\n", "smi = [\"C1CCCCC12CC2\", \"C1CCCCC1(C)C\", \"C1CCCCC1(Cl)Br\"]\n", "cores = [core]\n", "mols = [Chem.MolFromSmiles(s) for s in smi]\n", "options = RGroupDecompositionParameters()\n", "options.onlyMatchAtRGroups = True\n", "options.scoreMethod = RGroupScore.FingerprintVariance\n", "cols=decomp(options)\n", "show_decomp(cols, cores[0])\n" ] }, { "cell_type": "code", "execution_count": 46, "metadata": { "scrolled": true }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\"Core:C1CCC([*:5])([*:6])CC1 R5:C(C[*:6])[*:5] R6:C(C[*:6])[*:5]\",\n", "\"Core:C1CCC([*:5])([*:6])CC1 R5:C[*:5] R6:C[*:6]\",\n", "\"Core:C1CCC([*:5])([*:6])CC1 R5:Br[*:5] R6:Cl[*:6]\",\n" ] } ], "source": [ "print_rows(options)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "### testUserMatchTypes" ] }, { "cell_type": "code", "execution_count": 47, "metadata": { "scrolled": true }, "outputs": [ { "data": { "text/html": [ "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
CoreR1R2Input coreMol
0\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/
" ], "text/plain": [ "" ] }, "execution_count": 47, "metadata": {}, "output_type": "execute_result" } ], "source": [ "cores = [Chem.MolFromSmiles('C1CCCCC1[*:1]')]\n", "mols = [Chem.MolFromSmiles('C1CCCCC1(N)(O)')]\n", "options = RGroupDecompositionParameters()\n", "options.scoreMethod = RGroupScore.FingerprintVariance\n", "options.onlyMatchAtRGroups = False\n", "cols=decomp(options)\n", "show_decomp(cols, cores[0])" ] }, { "cell_type": "code", "execution_count": 48, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\"Core:C1CCC([*:1])([*:2])CC1 R1:O[*:1] R2:N[*:2]\",\n" ] } ], "source": [ "print_rows(options)" ] }, { "cell_type": "code", "execution_count": 49, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
CoreR1R2Input coreMol
0\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/
" ], "text/plain": [ "" ] }, "execution_count": 49, "metadata": {}, "output_type": "execute_result" } ], "source": [ "cores = [Chem.MolFromSmiles('C1CCCCC1([*:1])([*:2])')]\n", "options = RGroupDecompositionParameters()\n", "options.scoreMethod = RGroupScore.FingerprintVariance\n", "options.onlyMatchAtRGroups = False\n", "cols=decomp(options)\n", "show_decomp(cols, cores[0])" ] }, { "cell_type": "code", "execution_count": 50, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\"Core:C1CCC([*:1])([*:2])CC1 R1:O[*:1] R2:N[*:2]\",\n" ] } ], "source": [ "print_rows(options)" ] }, { "cell_type": "code", "execution_count": 51, "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
CoreR1R2Input coreMol
0\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/\"Mol\"/
" ], "text/plain": [ "" ] }, "execution_count": 51, "metadata": {}, "output_type": "execute_result" } ], "source": [ "cores = [Chem.MolFromSmiles('C1CCCC[*:2]1[*:1]')]\n", "options = RGroupDecompositionParameters()\n", "options.allowNonTerminalRGroups = True;\n", "options.scoreMethod = RGroupScore.FingerprintVariance\n", "options.onlyMatchAtRGroups = False\n", "cols=decomp(options)\n", "show_decomp(cols, cores[0])" ] }, { "cell_type": "code", "execution_count": 52, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\"Core:C1CCC([*:1])([*:2])CC1 R1:O[*:1] R2:N[*:2]\",\n" ] } ], "source": [ "print_rows(options)" ] } ], "metadata": { "kernelspec": { "display_name": "Python (conda rdkit_build)", "language": "python", "name": "rdkit_build" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.8.3" } }, "nbformat": 4, "nbformat_minor": 1 }