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hadim/2022.07 M2D2.ipynb

Last active June 27, 2022 18:32
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2022.07 M2D2.ipynb
{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"id": "1ab1ed6a-868d-483c-8d5b-345cb84c72a8",
"metadata": {},
"outputs": [],
"source": [
"import tempfile\n",
"import numpy as np\n",
"\n",
"# Only a single import is needed (similar to Pandas and Numpy)\n",
"import datamol as dm"
]
},
{
"cell_type": "markdown",
"id": "7bd2ff4a-9da1-4ae2-b95a-1ec3ee1868d4",
"metadata": {},
"source": [
"## `dm.mol`"
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "e687c648-9345-4cf9-bbe6-598443e53b53",
"metadata": {},
"outputs": [
{
"data": {
"image/png": 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\n",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x7f35cdc30400>"
]
},
"execution_count": 2,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"mol = dm.to_mol(\"CC(=O)OC1=CC=CC=C1C(=O)O\")\n",
"mol"
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "c5008433-e2dd-4920-9f0d-3c71716e180e",
"metadata": {},
"outputs": [
{
"data": {
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"<!-- END OF HEADER -->\n",
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"</svg>"
],
"text/plain": [
"<IPython.core.display.SVG object>"
]
},
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"mol = dm.to_mol(\"CC(=O)OC1=CC=CC=C1C(=O)O\")\n",
"mol2 = dm.randomize_atoms(mol)\n",
"dm.to_image([mol, mol2], indices=True)"
]
},
{
"cell_type": "code",
"execution_count": 4,
"id": "bc56a6d0-c4e2-4260-955f-9d171790c6a8",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'ef3ab3a6ad681393e4a948a5014b5264'"
]
},
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# Copy a molecule\n",
"mol = dm.to_mol(\"CC(=O)OC1=CC=CC=C1C(=O)O\")\n",
"copied_mol = dm.copy_mol(mol)\n",
"\n",
"# Check two mols are the same\n",
"assert dm.same_mol(mol, copied_mol) == True\n",
"\n",
"# Generate a unique id for your molecule\n",
"dm.unique_id(mol)"
]
},
{
"cell_type": "code",
"execution_count": 5,
"id": "1cbb8db9-c8ff-49b8-be71-8cc3d683f7eb",
"metadata": {},
"outputs": [
{
"data": {
"image/png": 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\n",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x7f35cda6fd60>"
]
},
"execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"mol = dm.to_mol(\"O=c1ccnc(c1)-c1cnc2cc3ccnc3cc12\", sanitize=False)\n",
"mol"
]
},
{
"cell_type": "code",
"execution_count": 6,
"id": "5e13bf67-117f-4d63-81ea-0257e06fb85b",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"O=c1cc[nH]c(C2=CN=c3cc4c(cc32)=NC=C4)c1\n"
]
},
{
"data": {
"image/png": 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\n",
"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x7f35cda6ff40>"
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"with dm.without_rdkit_log():\n",
" mol = dm.sanitize_mol(mol)\n",
"\n",
"print(dm.to_smiles(mol))\n",
"mol"
]
},
{
"cell_type": "code",
"execution_count": 7,
"id": "a225d8fa-05d7-4b8b-81fb-868fe462336b",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"{'a_float': 2.658, 'a_string': 'hello mol', 'a_boolean': False}"
]
},
"execution_count": 7,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"mol = dm.to_mol(\"CC(=O)OC1=CC=CC=C1C(=O)O\")\n",
"\n",
"props = dict(a_float=2.658, a_string=\"hello mol\", a_boolean=False)\n",
"mol = dm.set_mol_props(mol, props)\n",
"\n",
"mol.GetPropsAsDict()"
]
},
{
"cell_type": "code",
"execution_count": 8,
"id": "fa7e6681-cddc-4e8c-960d-dabe975edac3",
"metadata": {},
"outputs": [
{
"data": {
"image/png": 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"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x7f35cda90220>"
]
},
"execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"mol = dm.to_mol(\"[Na]OC1=CC2CCCCC2N=C1\")\n",
"mol"
]
},
{
"cell_type": "code",
"execution_count": 9,
"id": "91a011a0-08a4-41f9-9bd0-c6ef326291e8",
"metadata": {},
"outputs": [
{
"data": {
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"<!-- END OF HEADER -->\n",
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"<IPython.core.display.SVG object>"
]
},
"execution_count": 9,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"mol = dm.to_mol(\"OC1=CC2CCCCC2[N:1]=C1\")\n",
"variants = dm.enumerate_tautomers(mol, n_variants=10)\n",
"\n",
"dm.to_image([mol] + variants, legends=[\"original\", \"variant #1\", \"variant #2\"])"
]
},
{
"cell_type": "markdown",
"id": "e007f2f9-7512-4e2d-9de0-574ed1f90fc0",
"metadata": {},
"source": [
"## `dm.convert`"
]
},
{
"cell_type": "code",
"execution_count": 10,
"id": "f98521a1-1b4e-4a1c-8566-adb5ae6fc002",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"SMILES: CC(=O)Oc1ccccc1C(=O)O\n",
"SELFIES: [C][C][=Branch1][C][=O][O][C][=C][C][=C][C][=C][Ring1][=Branch1][C][=Branch1][C][=O][O]\n",
"Inchi: InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12)\n",
"Inchikey: BSYNRYMUTXBXSQ-UHFFFAOYSA-N\n"
]
}
],
"source": [
"mol = dm.to_mol(\"CC(=O)OC1=CC=CC=C1C(=O)O\")\n",
"\n",
"# To SMILES\n",
"print(f\"SMILES: {dm.to_smiles(mol)}\")\n",
"\n",
"# To SELFIES\n",
"print(f\"SELFIES: {dm.to_selfies(mol)}\")\n",
"\n",
"# To Inchi\n",
"print(f\"Inchi: {dm.to_inchi(mol)}\")\n",
"\n",
"# To Inchikey\n",
"print(f\"Inchikey: {dm.to_inchikey(mol)}\")\n",
"\n",
"# From Inchi\n",
"assert dm.same_mol(mol, dm.from_inchi(\"InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12)\"))\n",
"\n",
"# From SELFIES\n",
"assert dm.same_mol(\n",
" mol,\n",
" dm.from_selfies(\n",
" \"[C][C][=Branch1][C][=O][O][C][=C][C][=C][C][=C][Ring1][=Branch1][C][=Branch1][C][=O][O]\"\n",
" ),\n",
")"
]
},
{
"cell_type": "code",
"execution_count": 11,
"id": "09a020aa-fa5b-4c82-a751-adcf4a345df6",
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<style scoped>\n",
" .dataframe tbody tr th:only-of-type {\n",
" vertical-align: middle;\n",
" }\n",
"\n",
" .dataframe tbody tr th {\n",
" vertical-align: top;\n",
" }\n",
"\n",
" .dataframe thead th {\n",
" text-align: right;\n",
" }\n",
"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>iupac</th>\n",
" <th>smiles</th>\n",
" <th>expt</th>\n",
" <th>calc</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>4-methoxy-N,N-dimethyl-benzamide</td>\n",
" <td>CN(C)C(=O)c1ccc(cc1)OC</td>\n",
" <td>-11.01</td>\n",
" <td>-9.625</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>methanesulfonyl chloride</td>\n",
" <td>CS(=O)(=O)Cl</td>\n",
" <td>-4.87</td>\n",
" <td>-6.219</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>3-methylbut-1-ene</td>\n",
" <td>CC(C)C=C</td>\n",
" <td>1.83</td>\n",
" <td>2.452</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" iupac smiles expt calc\n",
"0 4-methoxy-N,N-dimethyl-benzamide CN(C)C(=O)c1ccc(cc1)OC -11.01 -9.625\n",
"1 methanesulfonyl chloride CS(=O)(=O)Cl -4.87 -6.219\n",
"2 3-methylbut-1-ene CC(C)C=C 1.83 2.452"
]
},
"execution_count": 11,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# Load the Freesolv dataset\n",
"df = dm.data.freesolv()\n",
"df.head(3)"
]
},
{
"cell_type": "code",
"execution_count": 12,
"id": "bff77a40-1a58-47c4-9c1a-4c9e9b793606",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"{'iupac': '4-methoxy-N,N-dimethyl-benzamide', 'expt': -11.01, 'calc': -9.625}\n"
]
},
{
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"</svg>"
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"text/plain": [
"<IPython.core.display.SVG object>"
]
},
"execution_count": 12,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# Convert the dataframe to a list of mols\n",
"mols = dm.from_df(df, smiles_column=\"smiles\")\n",
"\n",
"# Dataframe columns are preserved as mol properties\n",
"print(mols[0].GetPropsAsDict())\n",
"\n",
"dm.to_image(mols[:2])"
]
},
{
"cell_type": "code",
"execution_count": 14,
"id": "a560b5a9-f7a0-4c82-92d5-194f34debe79",
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<div>\n",
"<style scoped>\n",
" .dataframe tbody tr th:only-of-type {\n",
" vertical-align: middle;\n",
" }\n",
"\n",
" .dataframe tbody tr th {\n",
" vertical-align: top;\n",
" }\n",
"\n",
" .dataframe thead th {\n",
" text-align: right;\n",
" }\n",
"</style>\n",
"<table border=\"1\" class=\"dataframe\">\n",
" <thead>\n",
" <tr style=\"text-align: right;\">\n",
" <th></th>\n",
" <th>smiles</th>\n",
" <th>mol</th>\n",
" <th>iupac</th>\n",
" <th>expt</th>\n",
" <th>calc</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>COc1ccc(C(=O)N(C)C)cc1</td>\n",
" <td>&lt;img data-content=\"rdkit/molecule\" src=\"data:i...</td>\n",
" <td>4-methoxy-N,N-dimethyl-benzamide</td>\n",
" <td>-11.01</td>\n",
" <td>-9.625</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>CS(=O)(=O)Cl</td>\n",
" <td>&lt;img data-content=\"rdkit/molecule\" src=\"data:i...</td>\n",
" <td>methanesulfonyl chloride</td>\n",
" <td>-4.87</td>\n",
" <td>-6.219</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" smiles mol \\\n",
"0 COc1ccc(C(=O)N(C)C)cc1 <img data-content=\"rdkit/molecule\" src=\"data:i... \n",
"1 CS(=O)(=O)Cl <img data-content=\"rdkit/molecule\" src=\"data:i... \n",
"\n",
" iupac expt calc \n",
"0 4-methoxy-N,N-dimethyl-benzamide -11.01 -9.625 \n",
"1 methanesulfonyl chloride -4.87 -6.219 "
]
},
"execution_count": 14,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# Convert a list of molecule to a dataframe\n",
"df = dm.to_df(mols, mol_column=\"mol\")\n",
"df.head(2)"
]
},
{
"cell_type": "markdown",
"id": "f77aa4eb-e0c7-43a5-8c90-5f5aa999b741",
"metadata": {},
"source": [
"## `dm.io`"
]
},
{
"cell_type": "code",
"execution_count": 15,
"id": "288673fd-60db-4bc6-9ded-52a7eec997d8",
"metadata": {},
"outputs": [],
"source": [
"# Load the Freesolv dataset\n",
"df = dm.data.freesolv()\n",
"\n",
"# Save a dataframe or a list of molecules to an SDF file\n",
"_, fpath = tempfile.mkstemp()\n",
"dm.to_sdf(df, urlpath=fpath, smiles_column=\"smiles\")"
]
},
{
"cell_type": "code",
"execution_count": 17,
"id": "f10f249b-2d22-40d7-9a87-71b9bb7fbd62",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\n",
" RDKit 2D\n",
"\n",
" 13 13 0 0 0 0 0 0 0 0999 V2000\n",
" 5.2500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 3.7500 -1.2990 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 3.0000 -2.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 3.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 3.7500 1.2990 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n",
" 1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"
]
}
],
"source": [
"%%bash -s $fpath\n",
"head -n 10 $1"
]
},
{
"cell_type": "markdown",
"id": "708d926f-f335-4800-a88e-858044f3f841",
"metadata": {},
"source": [
"## `dm.cluster`"
]
},
{
"cell_type": "code",
"execution_count": 33,
"id": "7a3e8741-0fb6-40a6-9899-b14842f853a3",
"metadata": {},
"outputs": [
{
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},
"execution_count": 33,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# Get some mols\n",
"df = dm.data.freesolv()\n",
"mols = df[\"smiles\"].apply(dm.to_mol)\n",
"\n",
"# Cluster the mols\n",
"clusters, mol_clusters = dm.cluster_mols(mols, cutoff=0.5)\n",
"\n",
"# Cluster #1\n",
"dm.to_image(\n",
" mol_clusters[4],\n",
" mol_size=(100, 100),\n",
" n_cols=3,\n",
" max_mols=9,\n",
")"
]
},
{
"cell_type": "code",
"execution_count": 35,
"id": "8bb89551-89fe-4077-b8a7-2ad1c4340f95",
"metadata": {},
"outputs": [
{
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"</svg>"
],
"text/plain": [
"<IPython.core.display.SVG object>"
]
},
"execution_count": 35,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# Get some mols\n",
"df = dm.data.freesolv()\n",
"mols = df[\"smiles\"].apply(dm.to_mol)\n",
"\n",
"# Pick diverse molecules\n",
"indices, picks = dm.pick_diverse(mols, npick=9)\n",
"dm.to_image(picks, mol_size=(150, 100), n_cols=3)"
]
},
{
"cell_type": "markdown",
"id": "7d09c4e3-814e-4c1d-ab3c-faa577e5aa10",
"metadata": {},
"source": [
"## `dm.fragment`"
]
},
{
"cell_type": "code",
"execution_count": 36,
"id": "6d085a1a-babb-49ef-8f23-467464b9e0ab",
"metadata": {},
"outputs": [
{
"data": {
"image/png": 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"text/plain": [
"<rdkit.Chem.rdchem.Mol at 0x7f35c6655060>"
]
},
"execution_count": 36,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"mol = dm.to_mol(\"CCCOCc1cc(c2ncccc2)ccc1\")\n",
"mol"
]
},
{
"cell_type": "code",
"execution_count": 38,
"id": "ef8d4224-92b2-4842-8d4f-52230c64a2ea",
"metadata": {},
"outputs": [
{
"data": {
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"<!-- END OF HEADER -->\n",
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"<path class=\"bond-4 atom-4 atom-5\" d=\"M 67.2,248.9 L 59.4,235.3\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-4 atom-4 atom-5\" d=\"M 63.3,248.4 L 57.8,238.9\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-5 atom-5 atom-6\" d=\"M 59.4,235.3 L 43.7,235.3\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-6 atom-6 atom-7\" d=\"M 43.7,235.3 L 35.9,248.9\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-6 atom-6 atom-7\" d=\"M 45.3,238.9 L 39.8,248.4\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-7 atom-7 atom-8\" d=\"M 35.9,248.9 L 43.7,262.4\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-8 atom-8 atom-9\" d=\"M 43.7,262.4 L 50.4,262.4\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-8 atom-8 atom-9\" d=\"M 50.4,262.4 L 57.2,262.4\" style=\"fill:none;fill-rule:evenodd;stroke:#0000FF;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-8 atom-8 atom-9\" d=\"M 45.7,259.3 L 50.4,259.3\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-8 atom-8 atom-9\" d=\"M 50.4,259.3 L 55.1,259.3\" style=\"fill:none;fill-rule:evenodd;stroke:#0000FF;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-9 atom-3 atom-10\" d=\"M 82.8,248.9 L 90.6,235.3\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-10 atom-10 atom-11\" d=\"M 90.6,235.3 L 106.3,235.3\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-10 atom-10 atom-11\" d=\"M 93.0,238.5 L 103.9,238.5\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-11 atom-11 atom-0\" d=\"M 106.3,235.3 L 114.1,248.9\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-12 atom-9 atom-4\" d=\"M 60.9,259.7 L 64.1,254.3\" style=\"fill:none;fill-rule:evenodd;stroke:#0000FF;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-12 atom-9 atom-4\" d=\"M 64.1,254.3 L 67.2,248.9\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"atom-9\" d=\"M 58.4 260.2 L 59.8 262.6 Q 60.0 262.8, 60.2 263.2 Q 60.4 263.6, 60.4 263.7 L 60.4 260.2 L 61.0 260.2 L 61.0 264.7 L 60.4 264.7 L 58.9 262.1 Q 58.7 261.8, 58.5 261.4 Q 58.3 261.1, 58.3 261.0 L 58.3 264.7 L 57.7 264.7 L 57.7 260.2 L 58.4 260.2 \" fill=\"#0000FF\"/>\n",
"<path class=\"bond-0 atom-0 atom-1\" d=\"M 241.5,250.0 L 233.7,263.5\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-0 atom-0 atom-1\" d=\"M 237.6,250.5 L 232.1,260.0\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-1 atom-1 atom-2\" d=\"M 233.7,263.5 L 218.0,263.5\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-2 atom-2 atom-3\" d=\"M 218.0,263.5 L 214.9,258.1\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-2 atom-2 atom-3\" d=\"M 214.9,258.1 L 211.8,252.7\" style=\"fill:none;fill-rule:evenodd;stroke:#0000FF;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-2 atom-2 atom-3\" d=\"M 219.8,260.4 L 217.6,256.6\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-2 atom-2 atom-3\" d=\"M 217.6,256.6 L 215.4,252.8\" style=\"fill:none;fill-rule:evenodd;stroke:#0000FF;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-3 atom-3 atom-4\" d=\"M 211.8,247.3 L 214.9,241.9\" style=\"fill:none;fill-rule:evenodd;stroke:#0000FF;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-3 atom-3 atom-4\" d=\"M 214.9,241.9 L 218.0,236.5\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-4 atom-4 atom-5\" d=\"M 218.0,236.5 L 233.7,236.5\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-4 atom-4 atom-5\" d=\"M 220.4,239.6 L 231.3,239.6\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-5 atom-5 atom-0\" d=\"M 233.7,236.5 L 241.5,250.0\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"atom-3\" d=\"M 209.2 247.8 L 210.7 250.1 Q 210.8 250.4, 211.0 250.8 Q 211.3 251.2, 211.3 251.2 L 211.3 247.8 L 211.9 247.8 L 211.9 252.2 L 211.3 252.2 L 209.7 249.6 Q 209.5 249.3, 209.3 249.0 Q 209.1 248.7, 209.1 248.6 L 209.1 252.2 L 208.5 252.2 L 208.5 247.8 L 209.2 247.8 \" fill=\"#0000FF\"/>\n",
"<path class=\"bond-0 atom-0 atom-1\" d=\"M 326.2,250.1 L 341.0,245.0\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-1 atom-1 atom-2\" d=\"M 341.0,245.0 L 352.8,255.2\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-2 atom-2 atom-3\" d=\"M 352.8,255.2 L 359.0,253.1\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-2 atom-2 atom-3\" d=\"M 359.0,253.1 L 365.1,251.0\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-3 atom-3 atom-4\" d=\"M 370.2,252.3 L 374.8,256.3\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-3 atom-3 atom-4\" d=\"M 374.8,256.3 L 379.5,260.3\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-4 atom-4 atom-5\" d=\"M 379.5,260.3 L 394.2,255.1\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-5 atom-5 atom-6\" d=\"M 394.2,255.1 L 397.2,239.8\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-5 atom-5 atom-6\" d=\"M 397.7,253.4 L 399.8,242.7\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-6 atom-6 atom-7\" d=\"M 397.2,239.8 L 411.9,234.6\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-7 atom-7 atom-8\" d=\"M 411.9,234.6 L 423.8,244.9\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-7 atom-7 atom-8\" d=\"M 411.7,238.5 L 420.0,245.7\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-8 atom-8 atom-9\" d=\"M 423.8,244.9 L 420.8,260.2\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-9 atom-9 atom-10\" d=\"M 420.8,260.2 L 406.1,265.4\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-9 atom-9 atom-10\" d=\"M 417.6,258.0 L 407.3,261.6\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-10 atom-10 atom-5\" d=\"M 406.1,265.4 L 394.2,255.1\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"atom-3\" d=\"M 365.6 250.1 Q 365.6 249.0, 366.1 248.4 Q 366.6 247.8, 367.6 247.8 Q 368.6 247.8, 369.1 248.4 Q 369.6 249.0, 369.6 250.1 Q 369.6 251.2, 369.1 251.8 Q 368.6 252.4, 367.6 252.4 Q 366.6 252.4, 366.1 251.8 Q 365.6 251.2, 365.6 250.1 M 367.6 251.9 Q 368.3 251.9, 368.7 251.4 Q 369.0 251.0, 369.0 250.1 Q 369.0 249.2, 368.7 248.8 Q 368.3 248.3, 367.6 248.3 Q 366.9 248.3, 366.6 248.8 Q 366.2 249.2, 366.2 250.1 Q 366.2 251.0, 366.6 251.4 Q 366.9 251.9, 367.6 251.9 \" fill=\"#FF0000\"/>\n",
"</svg>"
],
"text/plain": [
"<IPython.core.display.SVG object>"
]
},
"execution_count": 38,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"with dm.without_rdkit_log():\n",
" frags = dm.fragment.brics(mol)\n",
"dm.to_image(frags, n_cols=3, mol_size=(150, 100))"
]
},
{
"cell_type": "markdown",
"id": "3c28a554-7d08-413c-9106-b344a9e4d989",
"metadata": {},
"source": [
"## `dm.scaffold`"
]
},
{
"cell_type": "code",
"execution_count": 54,
"id": "73e70b05-0e30-43fd-99ad-e51f0ae76472",
"metadata": {},
"outputs": [
{
"data": {
"image/svg+xml": [
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"<!-- END OF HEADER -->\n",
"<rect style=\"opacity:1.0;fill:#FFFFFF;stroke:none\" width=\"750.0\" height=\"200.0\" x=\"0.0\" y=\"0.0\"> </rect>\n",
"<path class=\"bond-0 atom-0 atom-1\" d=\"M 142.9,152.8 L 148.8,129.7\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-1 atom-1 atom-2\" d=\"M 148.8,129.7 L 171.8,123.2\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-2 atom-2 atom-3\" d=\"M 171.8,123.2 L 177.8,100.1\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-3 atom-3 atom-4\" d=\"M 177.8,100.1 L 200.8,93.6\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-3 atom-3 atom-4\" d=\"M 179.9,94.5 L 196.0,90.0\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-4 atom-4 atom-5\" d=\"M 200.8,93.6 L 206.7,70.5\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-5 atom-5 atom-6\" d=\"M 206.7,70.5 L 189.6,53.7\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-5 atom-5 atom-6\" d=\"M 200.8,71.4 L 188.9,59.7\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-6 atom-6 atom-7\" d=\"M 189.6,53.7 L 166.6,60.2\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-7 atom-7 atom-8\" d=\"M 166.6,60.2 L 160.7,83.4\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-7 atom-7 atom-8\" d=\"M 170.4,64.9 L 166.2,81.1\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-8 atom-6 atom-9\" d=\"M 189.6,53.7 L 192.0,44.3\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-8 atom-6 atom-9\" d=\"M 192.0,44.3 L 194.5,34.9\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-9 atom-5 atom-10\" d=\"M 206.7,70.5 L 216.3,67.8\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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"<path class=\"bond-10 atom-2 atom-11\" d=\"M 171.8,123.2 L 178.4,129.7\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-10 atom-2 atom-11\" d=\"M 178.4,129.7 L 185.0,136.1\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-11 atom-1 atom-12\" d=\"M 148.8,129.7 L 141.9,123.0\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-11 atom-1 atom-12\" d=\"M 141.9,123.0 L 135.1,116.2\" style=\"fill:none;fill-rule:evenodd;stroke:#0000FF;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-12 atom-12 atom-13\" d=\"M 132.8,108.8 L 135.2,99.3\" style=\"fill:none;fill-rule:evenodd;stroke:#0000FF;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-12 atom-12 atom-13\" d=\"M 135.2,99.3 L 137.6,89.8\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-13 atom-12 atom-14\" d=\"M 128.4,113.9 L 118.5,116.6\" style=\"fill:none;fill-rule:evenodd;stroke:#0000FF;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-13 atom-12 atom-14\" d=\"M 118.5,116.6 L 108.7,119.4\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-14 atom-14 atom-15\" d=\"M 111.0,120.0 L 108.6,129.5\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-14 atom-14 atom-15\" d=\"M 108.6,129.5 L 106.1,138.9\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-14 atom-14 atom-15\" d=\"M 106.4,118.8 L 103.9,128.3\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-14 atom-14 atom-15\" d=\"M 103.9,128.3 L 101.5,137.8\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-15 atom-14 atom-16\" d=\"M 108.7,119.4 L 102.1,112.9\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-15 atom-14 atom-16\" d=\"M 102.1,112.9 L 95.5,106.5\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-16 atom-16 atom-17\" d=\"M 87.7,103.8 L 78.1,106.4\" style=\"fill:none;fill-rule:evenodd;stroke:#FF0000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-16 atom-16 atom-17\" d=\"M 78.1,106.4 L 68.6,109.1\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-17 atom-17 atom-18\" d=\"M 68.6,109.1 L 51.5,92.4\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
"<path class=\"bond-18 atom-18 atom-19\" d=\"M 51.5,92.4 L 28.5,98.8\" style=\"fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:2.0px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1\"/>\n",
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"</svg>"
],
"text/plain": [
"<IPython.core.display.SVG object>"
]
},
"execution_count": 54,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# A molecule\n",
"mol = dm.to_mol(\"CC(C(C1=CC(=C(C=C1)O)O)O)N(C)C(=O)OCC2=CC=CC=C2\")\n",
"\n",
"# Extract the Murcko scaffold\n",
"scaffold = dm.to_scaffold_murcko(mol)\n",
"\n",
"# Extract the generic Murcko scaffold\n",
"scaffold_generic = dm.to_scaffold_murcko(mol, make_generic=True)\n",
"\n",
"legends = [\"Original\", \"Murcko Scaffold\", \"Generic Murcko Scaffold\"]\n",
"dm.to_image([mol, scaffold, scaffold_generic], legends=legends, mol_size=(250, 200))"
]
},
{
"cell_type": "markdown",
"id": "491aeee8-2ce5-4e59-8fcd-abc852e42c32",
"metadata": {},
"source": [
"## `dm.fp` and `dm.similarity`"
]
},
{
"cell_type": "code",
"execution_count": 58,
"id": "d1f2d102-e2bb-4b1f-b4e4-d0c0f20b027c",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"['maccs',\n",
" 'ecfp',\n",
" 'topological',\n",
" 'atompair',\n",
" 'rdkit',\n",
" 'pattern',\n",
" 'layered',\n",
" 'erg',\n",
" 'estate',\n",
" 'avalon-count',\n",
" 'rdkit-count',\n",
" 'ecfp-count',\n",
" 'fcfp-count',\n",
" 'topological-count',\n",
" 'atompair-count']"
]
},
"execution_count": 58,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"list(dm.list_supported_fingerprints().keys())"
]
},
{
"cell_type": "code",
"execution_count": 61,
"id": "d6503ac9-ad56-4799-9f3f-dd2b3fcd6dd0",
"metadata": {},
"outputs": [
{
"data": {
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"<!-- END OF HEADER -->\n",
"<rect style=\"opacity:1.0;fill:#FFFFFF;stroke:none\" width=\"600.0\" height=\"150.0\" x=\"0.0\" y=\"0.0\"> </rect>\n",
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"<path class=\"atom-2\" d=\"M 29.6 44.4 Q 29.6 41.9, 30.9 40.5 Q 32.1 39.1, 34.4 39.1 Q 36.6 39.1, 37.9 40.5 Q 39.1 41.9, 39.1 44.4 Q 39.1 46.9, 37.9 48.3 Q 36.6 49.7, 34.4 49.7 Q 32.1 49.7, 30.9 48.3 Q 29.6 46.9, 29.6 44.4 M 34.4 48.5 Q 35.9 48.5, 36.8 47.5 Q 37.6 46.4, 37.6 44.4 Q 37.6 42.3, 36.8 41.3 Q 35.9 40.3, 34.4 40.3 Q 32.8 40.3, 31.9 41.3 Q 31.1 42.3, 31.1 44.4 Q 31.1 46.4, 31.9 47.5 Q 32.8 48.5, 34.4 48.5 \" fill=\"#FF0000\"/>\n",
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"<path class=\"atom-2\" d=\"M 251.1 24.1 Q 251.1 21.6, 252.3 20.2 Q 253.5 18.8, 255.8 18.8 Q 258.1 18.8, 259.3 20.2 Q 260.5 21.6, 260.5 24.1 Q 260.5 26.6, 259.3 28.0 Q 258.1 29.4, 255.8 29.4 Q 253.5 29.4, 252.3 28.0 Q 251.1 26.6, 251.1 24.1 M 255.8 28.2 Q 257.4 28.2, 258.2 27.2 Q 259.1 26.1, 259.1 24.1 Q 259.1 22.0, 258.2 21.0 Q 257.4 20.0, 255.8 20.0 Q 254.2 20.0, 253.4 21.0 Q 252.5 22.0, 252.5 24.1 Q 252.5 26.1, 253.4 27.2 Q 254.2 28.2, 255.8 28.2 \" fill=\"#FF0000\"/>\n",
"<path class=\"atom-3\" d=\"M 276.8 81.5 Q 276.8 79.1, 278.0 77.7 Q 279.3 76.3, 281.6 76.3 Q 283.8 76.3, 285.1 77.7 Q 286.3 79.1, 286.3 81.5 Q 286.3 84.0, 285.0 85.4 Q 283.8 86.9, 281.6 86.9 Q 279.3 86.9, 278.0 85.4 Q 276.8 84.0, 276.8 81.5 M 281.6 85.7 Q 283.1 85.7, 284.0 84.6 Q 284.8 83.6, 284.8 81.5 Q 284.8 79.5, 284.0 78.5 Q 283.1 77.5, 281.6 77.5 Q 280.0 77.5, 279.1 78.5 Q 278.3 79.5, 278.3 81.5 Q 278.3 83.6, 279.1 84.6 Q 280.0 85.7, 281.6 85.7 \" fill=\"#FF0000\"/>\n",
"<path class=\"atom-10\" d=\"M 338.2 118.9 L 341.6 124.4 Q 341.9 124.9, 342.4 125.9 Q 343.0 126.9, 343.0 126.9 L 343.0 118.9 L 344.4 118.9 L 344.4 129.2 L 343.0 129.2 L 339.3 123.3 Q 338.9 122.6, 338.5 121.8 Q 338.0 121.0, 337.9 120.7 L 337.9 129.2 L 336.6 129.2 L 336.6 118.9 L 338.2 118.9 \" fill=\"#0000FF\"/>\n",
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"</svg>"
],
"text/plain": [
"<IPython.core.display.SVG object>"
]
},
"execution_count": 61,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"mol1 = dm.to_mol(\"CC(=O)Oc1ccccc1C(=O)O\")\n",
"mol2 = dm.to_mol(\"CC(=O)Oc1ccccc1N\")\n",
"mol3 = dm.to_mol(\"c1cc2ccccc2cc1\")\n",
"\n",
"dm.to_image([mol1, mol2, mol3], mol_size=(200, 150))"
]
},
{
"cell_type": "code",
"execution_count": 62,
"id": "f83cf126-ba22-4171-8afa-ca6e408777b0",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"array([[1, 1, 1, ..., 0, 0, 0],\n",
" [1, 0, 1, ..., 0, 0, 0],\n",
" [0, 0, 0, ..., 0, 0, 0]], dtype=uint8)"
]
},
"execution_count": 62,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# Compute fingerprints\n",
"fp1 = dm.to_fp(mol1, fp_type=\"ecfp\", nBits=2048)\n",
"fp2 = dm.to_fp(mol2, fp_type=\"ecfp\", nBits=2048)\n",
"fp3 = dm.to_fp(mol3, fp_type=\"ecfp\", nBits=2048)\n",
"\n",
"fps = np.array([fp1, fp2, fp3])\n",
"fps"
]
},
{
"cell_type": "code",
"execution_count": 64,
"id": "b6ad5924-351c-4938-9bf7-02a5271aa898",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"array([[1. , 0.325 , 0.08571429],\n",
" [0.325 , 1. , 0.1 ],\n",
" [0.08571429, 0.1 , 1. ]])"
]
},
"execution_count": 64,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# Compute distances/similarities\n",
"distances = dm.pdist([mol1, mol2, mol3], fp_type=\"ecfp\", nBits=2048)\n",
"similarities = 1 - distances\n",
"similarities"
]
},
{
"cell_type": "markdown",
"id": "d66b820f-c108-435a-b300-3afb82bade0b",
"metadata": {},
"source": [
"## `dm.conformers`"
]
},
{
"cell_type": "code",
"execution_count": 65,
"id": "95ea4295-f654-4224-8636-6b6a145214b4",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"18"
]
},
"execution_count": 65,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"mol = dm.to_mol(\"O=C(C)Oc1ccccc1C(=O)O\")\n",
"\n",
"# Generate conformers\n",
"mol = dm.conformers.generate(mol, n_confs=None, rms_cutoff=0.5, minimize_energy=False)\n",
"mol.GetNumConformers()"
]
},
{
"cell_type": "code",
"execution_count": 66,
"id": "6754e0cf-3ab4-48b6-acfe-ce529292d694",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"array([332.32744758, 332.9694191 , 327.6102489 , 336.34704967,\n",
" 330.68335373, 328.71789468, 334.26080305, 327.34812497,\n",
" 330.13868996, 331.51024942])"
]
},
"execution_count": 66,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# Compute SASA from conformers (not on windows)\n",
"sasa = dm.conformers.sasa(mol)\n",
"sasa[:10]"
]
},
{
"cell_type": "code",
"execution_count": 68,
"id": "1d20b74c-9c8d-40c8-a544-13687168770b",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"array([[4.67577303e-08, 8.90381000e-01, 1.28252725e+00, 4.15550972e-02],\n",
" [8.90381000e-01, 0.00000000e+00, 1.00286711e+00, 8.89637491e-01],\n",
" [1.28252725e+00, 1.00286711e+00, 0.00000000e+00, 1.28446123e+00],\n",
" [4.15550972e-02, 8.89637491e-01, 1.28446123e+00, 0.00000000e+00]])"
]
},
"execution_count": 68,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
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"\n",
"# A function to apply to every elements (molecule) of the input list\n",
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