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solving merge conflict
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@kabu00002
kabu00002 committed May 27, 2024
2 parents 17c7950 + 3c10589 commit cc98cdd
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147 changes: 43 additions & 104 deletions notebooks/custom_kinfraglib/1_1_custom_filters_unwanted_substructures.ipynb
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Original file line number Diff line number Diff line change
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"</div>"
],
"text/plain": [
" subpocket smiles \\\n",
"0 AP Nc1c[nH]c2ncccc12 \n",
"1 AP N/C(=C1\\C(=O)Nc2ccccc21)c1ccccc1 \n",
"2 AP CC1=C2/C(=N/c3ccccc3)N=CN=[N+]2C=C1 \n",
"3 AP Nc1ncnn2cccc12 \n",
"4 AP Cc1cc(N)[nH]n1 \n",
"\n",
" ROMol \\\n",
"0 <img data-content=\"rdkit/molecule\" src=\"data:i... \n",
"1 <img data-content=\"rdkit/molecule\" src=\"data:i... \n",
"2 <img data-content=\"rdkit/molecule\" src=\"data:i... \n",
"3 <img data-content=\"rdkit/molecule\" src=\"data:i... \n",
"4 <img data-content=\"rdkit/molecule\" src=\"data:i... \n",
"\n",
" ROMol_dummy \\\n",
"0 <img data-content=\"rdkit/molecule\" src=\"data:i... \n",
"1 <img data-content=\"rdkit/molecule\" src=\"data:i... \n",
"2 <img data-content=\"rdkit/molecule\" src=\"data:i... \n",
"3 <img data-content=\"rdkit/molecule\" src=\"data:i... \n",
"4 <img data-content=\"rdkit/molecule\" src=\"data:i... \n",
"\n",
" ROMol_original kinase family group \\\n",
"0 <img data-content=\"rdkit/molecule\" src=\"data:i... AAK1 NAK Other \n",
"1 <img data-content=\"rdkit/molecule\" src=\"data:i... AAK1 NAK Other \n",
"2 <img data-content=\"rdkit/molecule\" src=\"data:i... AAK1 NAK Other \n",
"3 <img data-content=\"rdkit/molecule\" src=\"data:i... AAK1 NAK Other \n",
"4 <img data-content=\"rdkit/molecule\" src=\"data:i... ABL1 Abl TK \n",
"\n",
" complex_pdb ligand_pdb alt chain \\\n",
"0 5l4q LKB A A \n",
"1 5te0 XIN A \n",
"2 8gmc YFV A \n",
"3 8gmd ZRR A \n",
"4 2f4j VX6 A \n",
"\n",
" atom_subpockets \\\n",
"0 AP AP AP AP AP AP AP AP AP AP AP AP AP AP AP F... \n",
"1 AP AP AP AP AP AP AP AP AP AP AP AP AP AP AP A... \n",
"2 AP AP AP AP AP AP AP AP AP AP AP AP AP AP AP A... \n",
"3 AP AP AP AP AP AP AP AP AP AP AP AP AP AP GA FP \n",
"4 AP AP AP AP AP AP AP AP AP AP AP AP AP SE \n",
"\n",
" atom_environments \\\n",
"0 16 16 16 16 16 16 16 16 16 16 16 16 16 5 5 na na \n",
"1 7 16 7 16 16 16 16 5 16 16 16 16 16 5 5 5 5 5 ... \n",
"2 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 16 4 4 4 4... \n",
"3 14 14 14 14 14 14 14 16 14 14 14 14 5 5 na na \n",
"4 5 5 14 14 14 14 14 14 14 8 8 8 8 na \n",
"\n",
" smiles_dummy fragment_count \\\n",
"0 [11*]c1cnc2[nH]cc(N[27*])c2c1 3 \n",
"1 [12*]N/C(=C1\\C(=O)Nc2cc([20*])ccc21)c1ccccc1 3 \n",
"2 [39*]c1cccc(/N=C2\\N=CN=[N+]3C=CC(C[42*])=C23)c1 1 \n",
"3 *Nc1ncnn2ccc([25*])c12 6 \n",
"4 [22*]Nc1cc(C)n[nH]1 10 \n",
"\n",
" connections connections_name \n",
"0 [FP, SE] [AP=FP, AP=SE] \n",
"1 [SE, GA] [AP=SE, AP=GA] \n",
"2 [FP, FP] [AP=FP, AP=FP] \n",
"3 [GA, FP] [AP=GA, AP=FP] \n",
"4 [SE] [AP=SE] "
"<IPython.core.display.HTML object>"
]
},
"execution_count": 32,
Expand All @@ -436,7 +375,7 @@
}
],
"source": [
"fragment_library[\"AP\"].head()"
"HTML(fragment_library[\"AP\"].head().to_html(notebook=True))"
]
},
{
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"text/html": [
"<style type=\"text/css\">\n",
"</style>\n",
"<table id=\"T_ca712\">\n",
"<table id=\"T_3cf0e\">\n",
" <caption>unwanted substrutcures filters</caption>\n",
" <thead>\n",
" <tr>\n",
" <th class=\"blank level0\" >&nbsp;</th>\n",
" <th id=\"T_ca712_level0_col0\" class=\"col_heading level0 col0\" >pre-filtered</th>\n",
" <th id=\"T_ca712_level0_col1\" class=\"col_heading level0 col1\" >accepted by 2</th>\n",
" <th id=\"T_ca712_level0_col2\" class=\"col_heading level0 col2\" >accepted by 1</th>\n",
" <th id=\"T_ca712_level0_col3\" class=\"col_heading level0 col3\" >accepted by 0</th>\n",
" <th id=\"T_3cf0e_level0_col0\" class=\"col_heading level0 col0\" >pre-filtered</th>\n",
" <th id=\"T_3cf0e_level0_col1\" class=\"col_heading level0 col1\" >accepted by 2</th>\n",
" <th id=\"T_3cf0e_level0_col2\" class=\"col_heading level0 col2\" >accepted by 1</th>\n",
" <th id=\"T_3cf0e_level0_col3\" class=\"col_heading level0 col3\" >accepted by 0</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th id=\"T_ca712_level0_row0\" class=\"row_heading level0 row0\" >AP</th>\n",
" <td id=\"T_ca712_row0_col0\" class=\"data row0 col0\" >1201</td>\n",
" <td id=\"T_ca712_row0_col1\" class=\"data row0 col1\" >942</td>\n",
" <td id=\"T_ca712_row0_col2\" class=\"data row0 col2\" >247</td>\n",
" <td id=\"T_ca712_row0_col3\" class=\"data row0 col3\" >12</td>\n",
" <th id=\"T_3cf0e_level0_row0\" class=\"row_heading level0 row0\" >AP</th>\n",
" <td id=\"T_3cf0e_row0_col0\" class=\"data row0 col0\" >1201</td>\n",
" <td id=\"T_3cf0e_row0_col1\" class=\"data row0 col1\" >942</td>\n",
" <td id=\"T_3cf0e_row0_col2\" class=\"data row0 col2\" >247</td>\n",
" <td id=\"T_3cf0e_row0_col3\" class=\"data row0 col3\" >12</td>\n",
" </tr>\n",
" <tr>\n",
" <th id=\"T_ca712_level0_row1\" class=\"row_heading level0 row1\" >FP</th>\n",
" <td id=\"T_ca712_row1_col0\" class=\"data row1 col0\" >1100</td>\n",
" <td id=\"T_ca712_row1_col1\" class=\"data row1 col1\" >895</td>\n",
" <td id=\"T_ca712_row1_col2\" class=\"data row1 col2\" >186</td>\n",
" <td id=\"T_ca712_row1_col3\" class=\"data row1 col3\" >19</td>\n",
" <th id=\"T_3cf0e_level0_row1\" class=\"row_heading level0 row1\" >FP</th>\n",
" <td id=\"T_3cf0e_row1_col0\" class=\"data row1 col0\" >1100</td>\n",
" <td id=\"T_3cf0e_row1_col1\" class=\"data row1 col1\" >895</td>\n",
" <td id=\"T_3cf0e_row1_col2\" class=\"data row1 col2\" >186</td>\n",
" <td id=\"T_3cf0e_row1_col3\" class=\"data row1 col3\" >19</td>\n",
" </tr>\n",
" <tr>\n",
" <th id=\"T_ca712_level0_row2\" class=\"row_heading level0 row2\" >SE</th>\n",
" <td id=\"T_ca712_row2_col0\" class=\"data row2 col0\" >743</td>\n",
" <td id=\"T_ca712_row2_col1\" class=\"data row2 col1\" >608</td>\n",
" <td id=\"T_ca712_row2_col2\" class=\"data row2 col2\" >129</td>\n",
" <td id=\"T_ca712_row2_col3\" class=\"data row2 col3\" >6</td>\n",
" <th id=\"T_3cf0e_level0_row2\" class=\"row_heading level0 row2\" >SE</th>\n",
" <td id=\"T_3cf0e_row2_col0\" class=\"data row2 col0\" >743</td>\n",
" <td id=\"T_3cf0e_row2_col1\" class=\"data row2 col1\" >608</td>\n",
" <td id=\"T_3cf0e_row2_col2\" class=\"data row2 col2\" >129</td>\n",
" <td id=\"T_3cf0e_row2_col3\" class=\"data row2 col3\" >6</td>\n",
" </tr>\n",
" <tr>\n",
" <th id=\"T_ca712_level0_row3\" class=\"row_heading level0 row3\" >GA</th>\n",
" <td id=\"T_ca712_row3_col0\" class=\"data row3 col0\" >355</td>\n",
" <td id=\"T_ca712_row3_col1\" class=\"data row3 col1\" >235</td>\n",
" <td id=\"T_ca712_row3_col2\" class=\"data row3 col2\" >113</td>\n",
" <td id=\"T_ca712_row3_col3\" class=\"data row3 col3\" >7</td>\n",
" <th id=\"T_3cf0e_level0_row3\" class=\"row_heading level0 row3\" >GA</th>\n",
" <td id=\"T_3cf0e_row3_col0\" class=\"data row3 col0\" >355</td>\n",
" <td id=\"T_3cf0e_row3_col1\" class=\"data row3 col1\" >235</td>\n",
" <td id=\"T_3cf0e_row3_col2\" class=\"data row3 col2\" >113</td>\n",
" <td id=\"T_3cf0e_row3_col3\" class=\"data row3 col3\" >7</td>\n",
" </tr>\n",
" <tr>\n",
" <th id=\"T_ca712_level0_row4\" class=\"row_heading level0 row4\" >B1</th>\n",
" <td id=\"T_ca712_row4_col0\" class=\"data row4 col0\" >47</td>\n",
" <td id=\"T_ca712_row4_col1\" class=\"data row4 col1\" >34</td>\n",
" <td id=\"T_ca712_row4_col2\" class=\"data row4 col2\" >13</td>\n",
" <td id=\"T_ca712_row4_col3\" class=\"data row4 col3\" >0</td>\n",
" <th id=\"T_3cf0e_level0_row4\" class=\"row_heading level0 row4\" >B1</th>\n",
" <td id=\"T_3cf0e_row4_col0\" class=\"data row4 col0\" >47</td>\n",
" <td id=\"T_3cf0e_row4_col1\" class=\"data row4 col1\" >34</td>\n",
" <td id=\"T_3cf0e_row4_col2\" class=\"data row4 col2\" >13</td>\n",
" <td id=\"T_3cf0e_row4_col3\" class=\"data row4 col3\" >0</td>\n",
" </tr>\n",
" <tr>\n",
" <th id=\"T_ca712_level0_row5\" class=\"row_heading level0 row5\" >B2</th>\n",
" <td id=\"T_ca712_row5_col0\" class=\"data row5 col0\" >59</td>\n",
" <td id=\"T_ca712_row5_col1\" class=\"data row5 col1\" >53</td>\n",
" <td id=\"T_ca712_row5_col2\" class=\"data row5 col2\" >6</td>\n",
" <td id=\"T_ca712_row5_col3\" class=\"data row5 col3\" >0</td>\n",
" <th id=\"T_3cf0e_level0_row5\" class=\"row_heading level0 row5\" >B2</th>\n",
" <td id=\"T_3cf0e_row5_col0\" class=\"data row5 col0\" >59</td>\n",
" <td id=\"T_3cf0e_row5_col1\" class=\"data row5 col1\" >53</td>\n",
" <td id=\"T_3cf0e_row5_col2\" class=\"data row5 col2\" >6</td>\n",
" <td id=\"T_3cf0e_row5_col3\" class=\"data row5 col3\" >0</td>\n",
" </tr>\n",
" <tr>\n",
" <th id=\"T_ca712_level0_row6\" class=\"row_heading level0 row6\" >Total</th>\n",
" <td id=\"T_ca712_row6_col0\" class=\"data row6 col0\" >3505</td>\n",
" <td id=\"T_ca712_row6_col1\" class=\"data row6 col1\" >2767</td>\n",
" <td id=\"T_ca712_row6_col2\" class=\"data row6 col2\" >694</td>\n",
" <td id=\"T_ca712_row6_col3\" class=\"data row6 col3\" >44</td>\n",
" <th id=\"T_3cf0e_level0_row6\" class=\"row_heading level0 row6\" >Total</th>\n",
" <td id=\"T_3cf0e_row6_col0\" class=\"data row6 col0\" >3505</td>\n",
" <td id=\"T_3cf0e_row6_col1\" class=\"data row6 col1\" >2767</td>\n",
" <td id=\"T_3cf0e_row6_col2\" class=\"data row6 col2\" >694</td>\n",
" <td id=\"T_3cf0e_row6_col3\" class=\"data row6 col3\" >44</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n"
],
"text/plain": [
"<pandas.io.formats.style.Styler at 0x7f9f1ea9e940>"
"<pandas.io.formats.style.Styler at 0x7f39661af550>"
]
},
"execution_count": 45,
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