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janash committed Jul 2, 2024
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232 changes: 217 additions & 15 deletions _sources/chapters/EC_class_ligands_search.ipynb
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},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 1,
"id": "7f7f7135",
"metadata": {},
"outputs": [],
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},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 2,
"id": "e331ecd9",
"metadata": {},
"outputs": [],
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"['1AQ7', '1AUJ', '1AZ8', '1BJV', '1BTW', '1BTX', '1BTZ', '1C1S', '1C1T', '1C2D']\n"
]
},
{
"data": {
"text/plain": [
"180"
]
},
"execution_count": 2,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# There will be three components to the query, which will be labeled q1, q2 and q3.\n",
"\n",
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},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 3,
"id": "b4d77b9e",
"metadata": {},
"outputs": [],
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"There are 112 ligands for EC Number 3.4.21.4 in this list. Here is a list of the first 10 ligands.\n"
]
},
{
"data": {
"text/plain": [
"['0CA', '0CB', '0KV', '0ZG', '0ZW', '0ZX', '0ZY', '10U', '11U', '12U']"
]
},
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"molResultL = list(query(\"mol_definition\"))\n",
"print(\"There are\",len(molResultL), \"ligands for EC Number\", ECnumber, \"in this list. Here is a list of the first 10 ligands.\")\n",
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},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 4,
"id": "ffb3d082",
"metadata": {},
"outputs": [],
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},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 5,
"id": "9cbf3513",
"metadata": {},
"outputs": [],
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},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 6,
"id": "b7043e37",
"metadata": {},
"outputs": [],
"outputs": [
{
"data": {
"text/plain": [
"200"
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# check to see that the file downloaded properly. A status code of 200 means everything is okay.\n",
"\n",
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},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 7,
"id": "096a56da",
"metadata": {},
"outputs": [],
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},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 8,
"id": "c9d9c2e4",
"metadata": {},
"outputs": [],
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"@<TRIPOS>MOLECULE\n",
"11U\n",
" 59 61 0 0 0\n",
"SMALL\n",
"NO_CHARGES\n",
"\n",
"@<TRIPOS>ATOM\n",
" 1 C1 2.4220 0.4070 0.3360 C.2 1 11U_ideal 0.0000\n",
" 2 O1 2.0060 -0.6420 0.7800 O.2 1 11U_ideal 0.0000\n",
" 3 C2 3.8690 0.5350 -0.0630 C.3 1 11U_ideal 0.0000\n",
" 4 N1 4.5590 -0.7380 0.1810 N.3 1 11U_ideal 0.0000\n",
" 5 C3 5.9760 -0.6510 -0.1970 C.3 1 11U_ideal 0.0000\n",
" 6 C4 6.7790 -0.0680 0.9670 C.3 1 11U_ideal 0.0000\n",
" 7 C5 8.2550 0.0240 0.5730 C.3 1 11U_ideal 0.0000\n",
" 8 C6 8.7810 -1.3740 0.2400 C.3 1 11U_ideal 0.0000\n",
" 9 C7 7.9780 -1.9570 -0.9250 C.3 1 11U_ideal 0.0000\n",
" 10 C8 6.5020 -2.0480 -0.5310 C.3 1 11U_ideal 0.0000\n",
" 11 N2 1.5890 1.4580 0.1990 N.am 1 11U_ideal 0.0000\n",
" 12 C9 0.1600 1.4690 0.5420 C.3 1 11U_ideal 0.0000\n",
" 13 C10 -0.5770 0.4580 -0.2980 C.2 1 11U_ideal 0.0000\n",
" 14 O2 0.0270 -0.2120 -1.1080 O.2 1 11U_ideal 0.0000\n",
" 15 C11 -0.3710 2.8880 0.2460 C.3 1 11U_ideal 0.0000\n",
" 16 C12 0.9140 3.7560 0.2780 C.3 1 11U_ideal 0.0000\n",
" 17 C13 1.9600 2.7850 -0.3250 C.3 1 11U_ideal 0.0000\n",
" 18 N3 -1.9070 0.2990 -0.1490 N.am 1 11U_ideal 0.0000\n",
" 19 C14 -2.6230 -0.6850 -0.9660 C.3 1 11U_ideal 0.0000\n",
" 20 C15 -4.0860 -0.6660 -0.6070 C.ar 1 11U_ideal 0.0000\n",
" 21 C16 -4.5620 -1.4980 0.3910 C.ar 1 11U_ideal 0.0000\n",
" 22 C17 -5.9000 -1.4810 0.7270 C.ar 1 11U_ideal 0.0000\n",
" 23 C18 -6.7750 -0.6300 0.0520 C.ar 1 11U_ideal 0.0000\n",
" 24 C19 -8.2130 -0.6110 0.4050 C.2 1 11U_ideal 0.0000\n",
" 25 N4 -9.0280 0.1840 -0.2270 N.2 1 11U_ideal 0.0000\n",
" 26 N5 -8.6890 -1.4350 1.4020 N.pl3 1 11U_ideal 0.0000\n",
" 27 C20 -6.2910 0.2030 -0.9560 C.ar 1 11U_ideal 0.0000\n",
" 28 C21 -4.9490 0.1800 -1.2800 C.ar 1 11U_ideal 0.0000\n",
" 29 H1 3.9330 0.7860 -1.1220 H 1 11U_ideal 0.0000\n",
" 30 H2 4.3400 1.3220 0.5260 H 1 11U_ideal 0.0000\n",
" 31 H3 4.4590 -1.0250 1.1430 H 1 11U_ideal 0.0000\n",
" 32 H4 6.0800 -0.0050 -1.0690 H 1 11U_ideal 0.0000\n",
" 33 H5 6.4040 0.9280 1.2050 H 1 11U_ideal 0.0000\n",
" 34 H6 6.6750 -0.7130 1.8390 H 1 11U_ideal 0.0000\n",
" 35 H7 8.8270 0.4390 1.4030 H 1 11U_ideal 0.0000\n",
" 36 H8 8.3590 0.6690 -0.2990 H 1 11U_ideal 0.0000\n",
" 37 H9 8.6770 -2.0190 1.1120 H 1 11U_ideal 0.0000\n",
" 38 H10 9.8320 -1.3090 -0.0410 H 1 11U_ideal 0.0000\n",
" 39 H11 8.3530 -2.9520 -1.1620 H 1 11U_ideal 0.0000\n",
" 40 H12 8.0820 -1.3110 -1.7970 H 1 11U_ideal 0.0000\n",
" 41 H13 6.3980 -2.6930 0.3420 H 1 11U_ideal 0.0000\n",
" 42 H14 5.9300 -2.4630 -1.3600 H 1 11U_ideal 0.0000\n",
" 43 H15 0.0300 1.2400 1.6000 H 1 11U_ideal 0.0000\n",
" 44 H16 -1.0720 3.2080 1.0170 H 1 11U_ideal 0.0000\n",
" 45 H17 -0.8360 2.9240 -0.7390 H 1 11U_ideal 0.0000\n",
" 46 H18 1.1770 4.0280 1.3010 H 1 11U_ideal 0.0000\n",
" 47 H19 0.8020 4.6440 -0.3440 H 1 11U_ideal 0.0000\n",
" 48 H20 2.9630 3.0560 0.0040 H 1 11U_ideal 0.0000\n",
" 49 H21 1.9020 2.7930 -1.4130 H 1 11U_ideal 0.0000\n",
" 50 H22 -2.3900 0.8350 0.4990 H 1 11U_ideal 0.0000\n",
" 51 H23 -2.5040 -0.4370 -2.0200 H 1 11U_ideal 0.0000\n",
" 52 H24 -2.2160 -1.6780 -0.7780 H 1 11U_ideal 0.0000\n",
" 53 H25 -3.8840 -2.1590 0.9100 H 1 11U_ideal 0.0000\n",
" 54 H26 -6.2690 -2.1270 1.5090 H 1 11U_ideal 0.0000\n",
" 55 H27 -9.9700 0.1960 0.0040 H 1 11U_ideal 0.0000\n",
" 56 H28 -8.0820 -2.0270 1.8720 H 1 11U_ideal 0.0000\n",
" 57 H29 -9.6310 -1.4220 1.6330 H 1 11U_ideal 0.0000\n",
" 58 H30 -6.9630 0.8640 -1.4820 H 1 11U_ideal 0.0000\n",
" 59 H31 -4.5730 0.8240 -2.0610 H 1 11U_ideal 0.0000\n",
"@<TRIPOS>BOND\n",
" 1 1 11 am\n",
" 2 11 17 1\n",
" 3 11 12 1\n",
" 4 1 2 2\n",
" 5 1 3 1\n",
" 6 16 17 1\n",
" 7 15 16 1\n",
" 8 12 15 1\n",
" 9 12 13 1\n",
" 10 13 18 am\n",
" 11 13 14 2\n",
" 12 18 19 1\n",
" 13 19 20 1\n",
" 14 20 28 ar\n",
" 15 20 21 ar\n",
" 16 27 28 ar\n",
" 17 23 27 ar\n",
" 18 23 24 1\n",
" 19 22 23 ar\n",
" 20 24 25 2\n",
" 21 24 26 1\n",
" 22 21 22 ar\n",
" 23 3 4 1\n",
" 24 4 5 1\n",
" 25 5 10 1\n",
" 26 5 6 1\n",
" 27 9 10 1\n",
" 28 8 9 1\n",
" 29 7 8 1\n",
" 30 6 7 1\n",
" 31 3 29 1\n",
" 32 3 30 1\n",
" 33 17 48 1\n",
" 34 17 49 1\n",
" 35 16 46 1\n",
" 36 16 47 1\n",
" 37 15 44 1\n",
" 38 15 45 1\n",
" 39 12 43 1\n",
" 40 18 50 1\n",
" 41 19 51 1\n",
" 42 19 52 1\n",
" 43 28 59 1\n",
" 44 27 58 1\n",
" 45 25 55 1\n",
" 46 26 56 1\n",
" 47 26 57 1\n",
" 48 22 54 1\n",
" 49 21 53 1\n",
" 50 4 31 1\n",
" 51 5 32 1\n",
" 52 10 41 1\n",
" 53 10 42 1\n",
" 54 9 39 1\n",
" 55 9 40 1\n",
" 56 8 37 1\n",
" 57 8 38 1\n",
" 58 7 35 1\n",
" 59 7 36 1\n",
" 60 6 33 1\n",
" 61 6 34 1\n",
"\n"
]
}
],
"source": [
"# Now we use these commands to read the file and make sure it downloaded properly. As an alternative, we\n",
"# could go to the ligands folder in our Jupyter desktop and click on res11U.mol2 to make sure it looks correct.\n",
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},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 9,
"id": "b85d927b",
"metadata": {},
"outputs": [],
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},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 10,
"id": "8b9106d8",
"metadata": {},
"outputs": [],
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"There are 173 structures from EC Number 1.1.1.1 that have bound ligands with molecular weights between 400 and 700).\n",
"There are 11 unique ligands for structures with EC Number 1.1.1.1 in this list. Here is a list of the 11 ligands.\n"
]
},
{
"data": {
"text/plain": [
"['022', 'APR', 'CHD', 'CND', 'COD', 'NAD', 'NAI', 'NAJ', 'PAD', 'TAD', 'WKZ']"
]
},
"execution_count": 10,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"### Solution\n",
"\n",
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