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feat: add apo features #66

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56b2d13
feat: add apo features
yusuf1759 Sep 26, 2024
336ba7a
feat: add apo to holo mask
yusuf1759 Sep 30, 2024
48d0e09
fix: linting and typing
yusuf1759 Sep 30, 2024
18157a5
fix: update featurizer
yusuf1759 Oct 1, 2024
eb8da01
test: add tests
yusuf1759 Oct 3, 2024
1955b18
chore: type hinting
yusuf1759 Oct 3, 2024
2e01e83
chore: add apo linked file
yusuf1759 Oct 3, 2024
5d62a80
chore: add apo linked file
yusuf1759 Oct 3, 2024
2054c78
fix: tests
yusuf1759 Oct 3, 2024
d771872
chore: fix linting again
yusuf1759 Oct 3, 2024
8322aed
fix: failing tests
yusuf1759 Oct 3, 2024
1496e70
'chore: cleaning up docs and var names'
OleinikovasV Oct 22, 2024
6b817ec
chore: cleanup structure.py
yusuf1759 Nov 27, 2024
77497a5
fix: type hinting
yusuf1759 Nov 27, 2024
a609483
fix: type hinting again
yusuf1759 Nov 27, 2024
71ef2ad
feat: update notebook
yusuf1759 Dec 9, 2024
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3,467 changes: 3,387 additions & 80 deletions docs/examples/2_query_filter_index.ipynb
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233 changes: 218 additions & 15 deletions docs/examples/3_access_system_files.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@
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Expand All @@ -36,9 +36,28 @@
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{
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"execution_count": 2,
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"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"2024-11-27 10:18:44,563 | plinder.core.utils.cpl.download_paths:24 | INFO : runtime succeeded: 0.00s\n",
"2024-11-27 10:18:44,563 | plinder.core.utils.cpl.download_paths:24 | INFO : runtime succeeded: 0.00s\n"
]
},
{
"data": {
"text/plain": [
"{'1.W': '/Users/yusuf/.local/share/plinder/2024-06/v2/systems/4agi__1__1.C__1.W/ligand_files/1.W.sdf'}"
]
},
"execution_count": 2,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"plinder_system.ligand_sdfs"
]
Expand All @@ -52,9 +71,31 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 3,
"metadata": {},
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"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"2024-11-27 10:18:44,693 | plinder.core.utils.cpl.download_paths:24 | INFO : runtime succeeded: 0.00s\n",
"2024-11-27 10:18:44,693 | plinder.core.utils.cpl.download_paths:24 | INFO : runtime succeeded: 0.00s\n",
"2024-11-27 10:18:44,694 | plinder.core.index.utils:148 | INFO : loading entries from 1 zips\n",
"2024-11-27 10:18:44,700 | plinder.core.index.utils:163 | INFO : loaded 1 entries\n",
"2024-11-27 10:18:44,700 | plinder.core.index.utils.load_entries:24 | INFO : runtime succeeded: 0.11s\n"
]
},
{
"data": {
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"{'1.W': 'C[Se][C@@H]1O[C@@H](C)[C@@H](O)[C@@H](O)[C@@H]1O'}"
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},
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"plinder_system.smiles"
]
Expand All @@ -75,9 +116,21 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 4,
"metadata": {},
"outputs": [],
"outputs": [
{
"data": {
"text/plain": [
"('/Users/yusuf/.local/share/plinder/2024-06/v2/systems/4agi__1__1.C__1.W/receptor.pdb',\n",
" '/Users/yusuf/.local/share/plinder/2024-06/v2/systems/4agi__1__1.C__1.W/receptor.cif')"
]
},
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"plinder_system.receptor_pdb, plinder_system.receptor_cif"
]
Expand All @@ -91,9 +144,20 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 5,
"metadata": {},
"outputs": [],
"outputs": [
{
"data": {
"text/plain": [
"{'1.C': 'A'}"
]
},
"execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"plinder_system.chain_mapping"
]
Expand All @@ -107,9 +171,21 @@
},
{
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"execution_count": 6,
"metadata": {},
"outputs": [],
"outputs": [
{
"data": {
"text/plain": [
"('/Users/yusuf/.local/share/plinder/2024-06/v2/systems/4agi__1__1.C__1.W/sequences.fasta',\n",
" {'1.C': 'MSTPGAQQVLFRTGIAAVNSTNHLRVYFQDVYGSIRESLYEGSWANGTEKNVIGNAKLGSPVAATSKELKHIRVYTLTEGNTLQEFAYDSGTGWYNGGLGGAKFQVAPYSXIAAVFLAGTDALQLRIYAQKPDNTIQEYMWNGDGWKEGTNLGGALPGTGIGATSFRYTDYNGPSIRIWFQTDDLKLVQRAYDPHKGWYPDLVTIFDRAPPRTAIAATSFGAGNSSIYMRIYFVNSDNTIWQVCWDHGKGYHDKGTITPVIQGSEVAIISWGSFANNGPDLRLYFQNGTYISAVSEWVWNRAHGSQLGRSALPPA'})"
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"plinder_system.sequences_fasta, plinder_system.sequences"
]
Expand All @@ -127,18 +203,145 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 7,
"metadata": {},
"outputs": [],
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"2024-11-27 10:18:45,149 | plinder.core.utils.cpl.download_paths:24 | INFO : runtime succeeded: 0.17s\n",
"2024-11-27 10:18:45,546 | plinder.core.scores.links.query_links:24 | INFO : runtime succeeded: 0.72s\n"
]
}
],
"source": [
"link_info = plinder_system.linked_structures"
]
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 8,
"metadata": {},
"outputs": [],
"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>id</th>\n",
" <th>pocket_fident</th>\n",
" <th>lddt</th>\n",
" <th>bb_lddt</th>\n",
" <th>lddt_lp_ave</th>\n",
" <th>lddt_pli_ave</th>\n",
" <th>bisy_rmsd_ave</th>\n",
" <th>sort_score</th>\n",
" <th>kind</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>4uou_B</td>\n",
" <td>100.0</td>\n",
" <td>0.972682</td>\n",
" <td>0.994065</td>\n",
" <td>0.987813</td>\n",
" <td>0.989777</td>\n",
" <td>0.159702</td>\n",
" <td>2.40</td>\n",
" <td>apo</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
" <td>4uou_C</td>\n",
" <td>100.0</td>\n",
" <td>0.973562</td>\n",
" <td>0.994687</td>\n",
" <td>0.967287</td>\n",
" <td>0.951068</td>\n",
" <td>0.194233</td>\n",
" <td>2.40</td>\n",
" <td>apo</td>\n",
" </tr>\n",
" <tr>\n",
" <th>2</th>\n",
" <td>4uou_D</td>\n",
" <td>100.0</td>\n",
" <td>0.973604</td>\n",
" <td>0.994235</td>\n",
" <td>0.972579</td>\n",
" <td>0.973048</td>\n",
" <td>0.101252</td>\n",
" <td>2.40</td>\n",
" <td>apo</td>\n",
" </tr>\n",
" <tr>\n",
" <th>3</th>\n",
" <td>4uou_A</td>\n",
" <td>100.0</td>\n",
" <td>0.967257</td>\n",
" <td>0.994800</td>\n",
" <td>0.976908</td>\n",
" <td>0.963504</td>\n",
" <td>0.214243</td>\n",
" <td>2.40</td>\n",
" <td>apo</td>\n",
" </tr>\n",
" <tr>\n",
" <th>4</th>\n",
" <td>Q4WW81_A</td>\n",
" <td>100.0</td>\n",
" <td>0.982275</td>\n",
" <td>0.998587</td>\n",
" <td>0.999679</td>\n",
" <td>0.997273</td>\n",
" <td>0.126228</td>\n",
" <td>98.57</td>\n",
" <td>pred</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" id pocket_fident lddt bb_lddt lddt_lp_ave lddt_pli_ave \\\n",
"0 4uou_B 100.0 0.972682 0.994065 0.987813 0.989777 \n",
"1 4uou_C 100.0 0.973562 0.994687 0.967287 0.951068 \n",
"2 4uou_D 100.0 0.973604 0.994235 0.972579 0.973048 \n",
"3 4uou_A 100.0 0.967257 0.994800 0.976908 0.963504 \n",
"4 Q4WW81_A 100.0 0.982275 0.998587 0.999679 0.997273 \n",
"\n",
" bisy_rmsd_ave sort_score kind \n",
"0 0.159702 2.40 apo \n",
"1 0.194233 2.40 apo \n",
"2 0.101252 2.40 apo \n",
"3 0.214243 2.40 apo \n",
"4 0.126228 98.57 pred "
]
},
"execution_count": 8,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"link_info[\n",
" [\n",
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