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T07: Fix fingerprint generator error #361

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Merged
merged 2 commits into from
May 17, 2023
Merged

T07: Fix fingerprint generator error #361

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659a944
fix fp bug
hamzaibrahim21 May 16, 2023
2dcbc10
Merge branch 'dev' into 360-dev-branch-t007-does-not-execute
mbackenkoehler May 17, 2023
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84 changes: 42 additions & 42 deletions teachopencadd/talktorials/T007_compound_activity_machine_learning/talktorial.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -210,7 +210,7 @@
},
{
"cell_type": "code",
"execution_count": 32,
"execution_count": 28
"metadata": {},
"outputs": [],
"source": [
Expand Down Expand Up @@ -241,7 +241,7 @@
},
{
"cell_type": "code",
"execution_count": 33,
"execution_count": 29,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -265,7 +265,7 @@
},
{
"cell_type": "code",
"execution_count": 34,
"execution_count": 30,
"metadata": {},
"outputs": [
{
Expand Down Expand Up @@ -379,8 +379,8 @@
"</div>"
],
"text/plain": [
" molecule_chembl_id IC50 units smiles \\\n",
"0 CHEMBL63786 0.003 nM Brc1cccc(Nc2ncnc3cc4ccccc4cc23)c1 \n",
" molecule_chembl_id IC50 units smiles \n",
"0 CHEMBL63786 0.003 nM Brc1cccc(Nc2ncnc3cc4ccccc4cc23)c1 \\\n",
"1 CHEMBL35820 0.006 nM CCOc1cc2ncnc(Nc3cccc(Br)c3)c2cc1OCC \n",
"2 CHEMBL53711 0.006 nM CN(C)c1cc2c(Nc3cccc(Br)c3)ncnc2cn1 \n",
"3 CHEMBL66031 0.008 nM Brc1cccc(Nc2ncnc3cc4[nH]cnc4cc23)c1 \n",
Expand All @@ -394,7 +394,7 @@
"4 11.096910 329.027607 5 2 3.5726 True "
]
},
"execution_count": 34,
"execution_count": 30,
"metadata": {},
"output_type": "execute_result"
}
Expand All @@ -414,7 +414,7 @@
},
{
"cell_type": "code",
"execution_count": 35,
"execution_count": 31,
"metadata": {},
"outputs": [
{
Expand Down Expand Up @@ -487,7 +487,7 @@
"4 CHEMBL53753 CNc1cc2c(Nc3cccc(Br)c3)ncnc2cn1 11.096910"
]
},
"execution_count": 35,
"execution_count": 31,
"metadata": {},
"output_type": "execute_result"
}
Expand Down Expand Up @@ -522,7 +522,7 @@
},
{
"cell_type": "code",
"execution_count": 36,
"execution_count": 32,
"metadata": {},
"outputs": [
{
Expand All @@ -548,7 +548,7 @@
},
{
"cell_type": "code",
"execution_count": 37,
"execution_count": 33,
"metadata": {},
"outputs": [
{
Expand Down Expand Up @@ -627,7 +627,7 @@
"4 CHEMBL53753 CNc1cc2c(Nc3cccc(Br)c3)ncnc2cn1 11.096910 1.0"
]
},
"execution_count": 37,
"execution_count": 33,
"metadata": {},
"output_type": "execute_result"
}
Expand All @@ -652,7 +652,7 @@
},
{
"cell_type": "code",
"execution_count": 38,
"execution_count": 34,
"metadata": {},
"outputs": [],
"source": [
Expand Down Expand Up @@ -685,10 +685,10 @@
" return np.array(MACCSkeys.GenMACCSKeys(mol))\n",
" if method == \"morgan2\":\n",
" fpg = rdFingerprintGenerator.GetMorganGenerator(radius=2, fpSize=n_bits)\n",
" return np.array(fpg.GetCountFingerprint(mol))\n",
" return np.array(fpg.GetFingerprint(mol))\n",
" if method == \"morgan3\":\n",
" fpg = rdFingerprintGenerator.GetMorganGenerator(radius=3, fpSize=n_bits)\n",
" return np.array(fpg.GetCountFingerprint(mol))\n",
" return np.array(fpg.GetFingerprint(mol))\n",
" else:\n",
" # NBVAL_CHECK_OUTPUT\n",
" print(f\"Warning: Wrong method specified: {method}. Default will be used instead.\")\n",
Expand All @@ -697,7 +697,7 @@
},
{
"cell_type": "code",
"execution_count": 39,
"execution_count": 35,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -706,7 +706,7 @@
},
{
"cell_type": "code",
"execution_count": 40,
"execution_count": 36,
"metadata": {},
"outputs": [
{
Expand Down Expand Up @@ -767,8 +767,8 @@
"</div>"
],
"text/plain": [
" molecule_chembl_id smiles pIC50 active \\\n",
"0 CHEMBL63786 Brc1cccc(Nc2ncnc3cc4ccccc4cc23)c1 11.522879 1.0 \n",
" molecule_chembl_id smiles pIC50 active \n",
"0 CHEMBL63786 Brc1cccc(Nc2ncnc3cc4ccccc4cc23)c1 11.522879 1.0 \\\n",
"1 CHEMBL35820 CCOc1cc2ncnc(Nc3cccc(Br)c3)c2cc1OCC 11.221849 1.0 \n",
"2 CHEMBL53711 CN(C)c1cc2c(Nc3cccc(Br)c3)ncnc2cn1 11.221849 1.0 \n",
"\n",
Expand All @@ -778,7 +778,7 @@
"2 [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ... "
]
},
"execution_count": 40,
"execution_count": 36,
"metadata": {},
"output_type": "execute_result"
}
Expand Down Expand Up @@ -821,7 +821,7 @@
},
{
"cell_type": "code",
"execution_count": 10,
"execution_count": 37,
"metadata": {},
"outputs": [],
"source": [
Expand Down Expand Up @@ -884,7 +884,7 @@
},
{
"cell_type": "code",
"execution_count": 11,
"execution_count": 38,
"metadata": {},
"outputs": [],
"source": [
Expand Down Expand Up @@ -940,7 +940,7 @@
},
{
"cell_type": "code",
"execution_count": 12,
"execution_count": 39,
"metadata": {},
"outputs": [],
"source": [
Expand Down Expand Up @@ -986,7 +986,7 @@
},
{
"cell_type": "code",
"execution_count": 13,
"execution_count": 40,
"metadata": {},
"outputs": [
{
Expand Down Expand Up @@ -1035,7 +1035,7 @@
},
{
"cell_type": "code",
"execution_count": 14,
"execution_count": 41,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -1049,7 +1049,7 @@
},
{
"cell_type": "code",
"execution_count": 15,
"execution_count": 42,
"metadata": {},
"outputs": [
{
Expand All @@ -1069,7 +1069,7 @@
},
{
"cell_type": "code",
"execution_count": 16,
"execution_count": 43,
"metadata": {},
"outputs": [
{
Expand Down Expand Up @@ -1101,7 +1101,7 @@
},
{
"cell_type": "code",
"execution_count": 17,
"execution_count": 44,
"metadata": {
"scrolled": true
},
Expand All @@ -1126,7 +1126,7 @@
},
{
"cell_type": "code",
"execution_count": 18,
"execution_count": 45,
"metadata": {
"tags": [
"nbsphinx-thumbnail"
Expand Down Expand Up @@ -1161,7 +1161,7 @@
},
{
"cell_type": "code",
"execution_count": 19,
"execution_count": 46,
"metadata": {
"scrolled": true
},
Expand All @@ -1186,7 +1186,7 @@
},
{
"cell_type": "code",
"execution_count": 20,
"execution_count": 47,
"metadata": {},
"outputs": [
{
Expand Down Expand Up @@ -1226,7 +1226,7 @@
},
{
"cell_type": "code",
"execution_count": 21,
"execution_count": 48,
"metadata": {},
"outputs": [],
"source": [
Expand Down Expand Up @@ -1315,7 +1315,7 @@
},
{
"cell_type": "code",
"execution_count": 22,
"execution_count": 49,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -1331,7 +1331,7 @@
},
{
"cell_type": "code",
"execution_count": 23,
"execution_count": 50,
"metadata": {},
"outputs": [
{
Expand All @@ -1345,7 +1345,7 @@
"Mean sensitivity: 0.88 \tand std : 0.02 \n",
"Mean specificity: 0.76 \tand std : 0.01 \n",
"Mean AUC: 0.89 \tand std : 0.01 \n",
"Time taken : 1.56s\n",
"Time taken : 1.77s\n",
"\n",
"\n",
"======= \n",
Expand All @@ -1354,7 +1354,7 @@
"Mean sensitivity: 0.90 \tand std : 0.01 \n",
"Mean specificity: 0.76 \tand std : 0.00 \n",
"Mean AUC: 0.89 \tand std : 0.01 \n",
"Time taken : 21.25s\n",
"Time taken : 16.12s\n",
"\n",
"\n",
"======= \n",
Expand All @@ -1363,7 +1363,7 @@
"Mean sensitivity: 0.86 \tand std : 0.01 \n",
"Mean specificity: 0.73 \tand std : 0.01 \n",
"Mean AUC: 0.87 \tand std : 0.00 \n",
"Time taken : 4.91s\n",
"Time taken : 4.64s\n",
"\n"
]
}
Expand All @@ -1384,7 +1384,7 @@
},
{
"cell_type": "code",
"execution_count": 24,
"execution_count": 51,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -1394,7 +1394,7 @@
},
{
"cell_type": "code",
"execution_count": 25,
"execution_count": 52,
"metadata": {},
"outputs": [
{
Expand Down Expand Up @@ -1466,7 +1466,7 @@
"2 [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ... "
]
},
"execution_count": 25,
"execution_count": 52,
"metadata": {},
"output_type": "execute_result"
}
Expand All @@ -1487,7 +1487,7 @@
},
{
"cell_type": "code",
"execution_count": 26,
"execution_count": 53,
"metadata": {},
"outputs": [
{
Expand All @@ -1501,7 +1501,7 @@
"Mean sensitivity: 0.90 \tand std : 0.01 \n",
"Mean specificity: 0.81 \tand std : 0.00 \n",
"Mean AUC: 0.92 \tand std : 0.01 \n",
"Time taken : 5.85s\n",
"Time taken : 6.80s\n",
"\n",
"\n",
"=======\n",
Expand All @@ -1510,7 +1510,7 @@
"Mean sensitivity: 0.84 \tand std : 0.01 \n",
"Mean specificity: 0.77 \tand std : 0.00 \n",
"Mean AUC: 0.88 \tand std : 0.01 \n",
"Time taken : 34.01s\n",
"Time taken : 56.66s\n",
"\n"
]
}
Expand Down