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custom/1_3 completed
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@kabu00002
kabu00002 committed Apr 16, 2024
1 parent 8fa0ee2 commit 61048be
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144 changes: 72 additions & 72 deletions notebooks/custom_kinfraglib/1_2_custom_filters_drug_likeness.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -53,7 +53,7 @@
},
{
"cell_type": "code",
"execution_count": 23,
"execution_count": 44,
"id": "e21ff76d-e6b9-41d5-8c99-9c8cf331111d",
"metadata": {},
"outputs": [],
Expand All @@ -68,7 +68,7 @@
},
{
"cell_type": "code",
"execution_count": 24,
"execution_count": 45,
"id": "b0b98f88-8429-47fa-9ca6-9b4d2c225119",
"metadata": {},
"outputs": [
Expand All @@ -88,7 +88,7 @@
},
{
"cell_type": "code",
"execution_count": 25,
"execution_count": 46,
"id": "ca329332-8304-46ad-85da-291709385db3",
"metadata": {},
"outputs": [],
Expand All @@ -107,7 +107,7 @@
},
{
"cell_type": "code",
"execution_count": 26,
"execution_count": 47,
"id": "b69f472d-063d-4897-84d0-ca03fb9d5129",
"metadata": {},
"outputs": [],
Expand All @@ -129,7 +129,7 @@
},
{
"cell_type": "code",
"execution_count": 27,
"execution_count": 48,
"id": "839a6067-16d4-4077-9252-cceb56261fc8",
"metadata": {},
"outputs": [],
Expand All @@ -139,7 +139,7 @@
},
{
"cell_type": "code",
"execution_count": 28,
"execution_count": 49,
"id": "67852002-8ed8-4230-813e-492a590df8d3",
"metadata": {},
"outputs": [
Expand All @@ -149,7 +149,7 @@
"dict_keys(['AP', 'FP', 'SE', 'GA', 'B1', 'B2', 'X'])"
]
},
"execution_count": 28,
"execution_count": 49,
"metadata": {},
"output_type": "execute_result"
}
Expand All @@ -161,7 +161,7 @@
},
{
"cell_type": "code",
"execution_count": 29,
"execution_count": 50,
"id": "1d8ce30a-c2c9-4305-a1a5-139898306744",
"metadata": {},
"outputs": [
Expand All @@ -171,7 +171,7 @@
"(9505, 15)"
]
},
"execution_count": 29,
"execution_count": 50,
"metadata": {},
"output_type": "execute_result"
}
Expand All @@ -196,7 +196,7 @@
},
{
"cell_type": "code",
"execution_count": 30,
"execution_count": 51,
"id": "ed3c2041-0404-4711-bdac-c36a85e2940c",
"metadata": {},
"outputs": [],
Expand All @@ -206,7 +206,7 @@
},
{
"cell_type": "code",
"execution_count": 31,
"execution_count": 52,
"id": "c712bf41-00fc-4713-ad12-a2d2723f7bd4",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -426,7 +426,7 @@
"4 [SE] [AP=SE] "
]
},
"execution_count": 31,
"execution_count": 52,
"metadata": {},
"output_type": "execute_result"
}
Expand All @@ -446,7 +446,7 @@
},
{
"cell_type": "code",
"execution_count": 32,
"execution_count": 53,
"id": "8c710616-304e-4696-97f5-3d4792f7f885",
"metadata": {},
"outputs": [],
Expand Down Expand Up @@ -495,7 +495,7 @@
},
{
"cell_type": "code",
"execution_count": 33,
"execution_count": 54,
"id": "e19dad22-c75e-4c4d-8ac7-26438445a28d",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -545,7 +545,7 @@
},
{
"cell_type": "code",
"execution_count": 34,
"execution_count": 55,
"id": "a31c893f-f85d-455a-9fe3-9c01f81050f1",
"metadata": {},
"outputs": [],
Expand All @@ -563,7 +563,7 @@
},
{
"cell_type": "code",
"execution_count": 35,
"execution_count": 56,
"id": "493c4061-4a42-47b2-8e80-dc831baa97a7",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -789,7 +789,7 @@
"4 [SE] [AP=SE] 1 "
]
},
"execution_count": 35,
"execution_count": 56,
"metadata": {},
"output_type": "execute_result"
}
Expand All @@ -809,7 +809,7 @@
},
{
"cell_type": "code",
"execution_count": 36,
"execution_count": 57,
"id": "f6aedaa5-af5d-4454-b0b5-0815310f745d",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -897,7 +897,7 @@
"Total 3505 2470 1035"
]
},
"execution_count": 36,
"execution_count": 57,
"metadata": {},
"output_type": "execute_result"
}
Expand All @@ -916,7 +916,7 @@
"num_fragments_ro3 = pd.concat(\n",
" [\n",
" num_fragments_ro3,\n",
" pd.DataFrame(num_fragments_ro3.sum().rename(\"Total\")).T\n",
" num_fragments_ro3.sum().rename(\"Total\").to_frame().T\n",
" ],\n",
" axis=0\n",
")\n",
Expand Down Expand Up @@ -952,7 +952,7 @@
},
{
"cell_type": "code",
"execution_count": 37,
"execution_count": 58,
"id": "c954d397-c471-4091-9ad5-d956e9d3cdce",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -996,7 +996,7 @@
},
{
"cell_type": "code",
"execution_count": 38,
"execution_count": 59,
"id": "e4b4015d-f41c-429d-9fd3-07a4faa0ae12",
"metadata": {},
"outputs": [],
Expand All @@ -1014,7 +1014,7 @@
},
{
"cell_type": "code",
"execution_count": 39,
"execution_count": 60,
"id": "736f1790-40c5-4cbc-bc82-08d778fba09a",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -1255,7 +1255,7 @@
"[5 rows x 21 columns]"
]
},
"execution_count": 39,
"execution_count": 60,
"metadata": {},
"output_type": "execute_result"
}
Expand All @@ -1275,7 +1275,7 @@
},
{
"cell_type": "code",
"execution_count": 40,
"execution_count": 61,
"id": "c64b76c9-7c7d-41c1-9ecf-e2227498d280",
"metadata": {},
"outputs": [
Expand Down Expand Up @@ -1363,7 +1363,7 @@
"Total 3505 2665 840"
]
},
"execution_count": 40,
"execution_count": 61,
"metadata": {},
"output_type": "execute_result"
}
Expand All @@ -1380,7 +1380,7 @@
")\n",
"num_fragments_qed = pd.concat(\n",
" [num_fragments_qed,\n",
" pd.DataFrame(num_fragments_qed.sum().rename(\"Total\")).T],\n",
" num_fragments_qed.sum().rename(\"Total\").to_frame().T],\n",
" axis=0\n",
")\n",
"num_fragments_qed\n",
Expand Down Expand Up @@ -1411,7 +1411,7 @@
},
{
"cell_type": "code",
"execution_count": 41,
"execution_count": 62,
"id": "2ee5ec2d-4520-4b85-9ead-06ce2f2e95dc",
"metadata": {},
"outputs": [],
Expand All @@ -1423,7 +1423,7 @@
},
{
"cell_type": "code",
"execution_count": 42,
"execution_count": 63,
"id": "4346069b-b2bf-4d18-a0e9-53f53ca3b7ce",
"metadata": {},
"outputs": [
Expand All @@ -1432,75 +1432,75 @@
"text/html": [
"<style type=\"text/css\">\n",
"</style>\n",
"<table id=\"T_f33e3\">\n",
"<table id=\"T_07946\">\n",
" <caption>drug likeness filters</caption>\n",
" <thead>\n",
" <tr>\n",
" <th class=\"blank level0\" >&nbsp;</th>\n",
" <th id=\"T_f33e3_level0_col0\" class=\"col_heading level0 col0\" >pre-filtered</th>\n",
" <th id=\"T_f33e3_level0_col1\" class=\"col_heading level0 col1\" >accepted by 2</th>\n",
" <th id=\"T_f33e3_level0_col2\" class=\"col_heading level0 col2\" >accepted by 1</th>\n",
" <th id=\"T_f33e3_level0_col3\" class=\"col_heading level0 col3\" >accepted by 0</th>\n",
" <th id=\"T_07946_level0_col0\" class=\"col_heading level0 col0\" >pre-filtered</th>\n",
" <th id=\"T_07946_level0_col1\" class=\"col_heading level0 col1\" >accepted by 2</th>\n",
" <th id=\"T_07946_level0_col2\" class=\"col_heading level0 col2\" >accepted by 1</th>\n",
" <th id=\"T_07946_level0_col3\" class=\"col_heading level0 col3\" >accepted by 0</th>\n",
" </tr>\n",
" </thead>\n",
" <tbody>\n",
" <tr>\n",
" <th id=\"T_f33e3_level0_row0\" class=\"row_heading level0 row0\" >AP</th>\n",
" <td id=\"T_f33e3_row0_col0\" class=\"data row0 col0\" >1201</td>\n",
" <td id=\"T_f33e3_row0_col1\" class=\"data row0 col1\" >541</td>\n",
" <td id=\"T_f33e3_row0_col2\" class=\"data row0 col2\" >588</td>\n",
" <td id=\"T_f33e3_row0_col3\" class=\"data row0 col3\" >72</td>\n",
" <th id=\"T_07946_level0_row0\" class=\"row_heading level0 row0\" >AP</th>\n",
" <td id=\"T_07946_row0_col0\" class=\"data row0 col0\" >1201</td>\n",
" <td id=\"T_07946_row0_col1\" class=\"data row0 col1\" >541</td>\n",
" <td id=\"T_07946_row0_col2\" class=\"data row0 col2\" >588</td>\n",
" <td id=\"T_07946_row0_col3\" class=\"data row0 col3\" >72</td>\n",
" </tr>\n",
" <tr>\n",
" <th id=\"T_f33e3_level0_row1\" class=\"row_heading level0 row1\" >FP</th>\n",
" <td id=\"T_f33e3_row1_col0\" class=\"data row1 col0\" >1100</td>\n",
" <td id=\"T_f33e3_row1_col1\" class=\"data row1 col1\" >546</td>\n",
" <td id=\"T_f33e3_row1_col2\" class=\"data row1 col2\" >507</td>\n",
" <td id=\"T_f33e3_row1_col3\" class=\"data row1 col3\" >47</td>\n",
" <th id=\"T_07946_level0_row1\" class=\"row_heading level0 row1\" >FP</th>\n",
" <td id=\"T_07946_row1_col0\" class=\"data row1 col0\" >1100</td>\n",
" <td id=\"T_07946_row1_col1\" class=\"data row1 col1\" >546</td>\n",
" <td id=\"T_07946_row1_col2\" class=\"data row1 col2\" >507</td>\n",
" <td id=\"T_07946_row1_col3\" class=\"data row1 col3\" >47</td>\n",
" </tr>\n",
" <tr>\n",
" <th id=\"T_f33e3_level0_row2\" class=\"row_heading level0 row2\" >SE</th>\n",
" <td id=\"T_f33e3_row2_col0\" class=\"data row2 col0\" >743</td>\n",
" <td id=\"T_f33e3_row2_col1\" class=\"data row2 col1\" >439</td>\n",
" <td id=\"T_f33e3_row2_col2\" class=\"data row2 col2\" >285</td>\n",
" <td id=\"T_f33e3_row2_col3\" class=\"data row2 col3\" >19</td>\n",
" <th id=\"T_07946_level0_row2\" class=\"row_heading level0 row2\" >SE</th>\n",
" <td id=\"T_07946_row2_col0\" class=\"data row2 col0\" >743</td>\n",
" <td id=\"T_07946_row2_col1\" class=\"data row2 col1\" >439</td>\n",
" <td id=\"T_07946_row2_col2\" class=\"data row2 col2\" >285</td>\n",
" <td id=\"T_07946_row2_col3\" class=\"data row2 col3\" >19</td>\n",
" </tr>\n",
" <tr>\n",
" <th id=\"T_f33e3_level0_row3\" class=\"row_heading level0 row3\" >GA</th>\n",
" <td id=\"T_f33e3_row3_col0\" class=\"data row3 col0\" >355</td>\n",
" <td id=\"T_f33e3_row3_col1\" class=\"data row3 col1\" >206</td>\n",
" <td id=\"T_f33e3_row3_col2\" class=\"data row3 col2\" >134</td>\n",
" <td id=\"T_f33e3_row3_col3\" class=\"data row3 col3\" >15</td>\n",
" <th id=\"T_07946_level0_row3\" class=\"row_heading level0 row3\" >GA</th>\n",
" <td id=\"T_07946_row3_col0\" class=\"data row3 col0\" >355</td>\n",
" <td id=\"T_07946_row3_col1\" class=\"data row3 col1\" >206</td>\n",
" <td id=\"T_07946_row3_col2\" class=\"data row3 col2\" >134</td>\n",
" <td id=\"T_07946_row3_col3\" class=\"data row3 col3\" >15</td>\n",
" </tr>\n",
" <tr>\n",
" <th id=\"T_f33e3_level0_row4\" class=\"row_heading level0 row4\" >B1</th>\n",
" <td id=\"T_f33e3_row4_col0\" class=\"data row4 col0\" >47</td>\n",
" <td id=\"T_f33e3_row4_col1\" class=\"data row4 col1\" >23</td>\n",
" <td id=\"T_f33e3_row4_col2\" class=\"data row4 col2\" >23</td>\n",
" <td id=\"T_f33e3_row4_col3\" class=\"data row4 col3\" >1</td>\n",
" <th id=\"T_07946_level0_row4\" class=\"row_heading level0 row4\" >B1</th>\n",
" <td id=\"T_07946_row4_col0\" class=\"data row4 col0\" >47</td>\n",
" <td id=\"T_07946_row4_col1\" class=\"data row4 col1\" >23</td>\n",
" <td id=\"T_07946_row4_col2\" class=\"data row4 col2\" >23</td>\n",
" <td id=\"T_07946_row4_col3\" class=\"data row4 col3\" >1</td>\n",
" </tr>\n",
" <tr>\n",
" <th id=\"T_f33e3_level0_row5\" class=\"row_heading level0 row5\" >B2</th>\n",
" <td id=\"T_f33e3_row5_col0\" class=\"data row5 col0\" >59</td>\n",
" <td id=\"T_f33e3_row5_col1\" class=\"data row5 col1\" >29</td>\n",
" <td id=\"T_f33e3_row5_col2\" class=\"data row5 col2\" >30</td>\n",
" <td id=\"T_f33e3_row5_col3\" class=\"data row5 col3\" >0</td>\n",
" <th id=\"T_07946_level0_row5\" class=\"row_heading level0 row5\" >B2</th>\n",
" <td id=\"T_07946_row5_col0\" class=\"data row5 col0\" >59</td>\n",
" <td id=\"T_07946_row5_col1\" class=\"data row5 col1\" >29</td>\n",
" <td id=\"T_07946_row5_col2\" class=\"data row5 col2\" >30</td>\n",
" <td id=\"T_07946_row5_col3\" class=\"data row5 col3\" >0</td>\n",
" </tr>\n",
" <tr>\n",
" <th id=\"T_f33e3_level0_row6\" class=\"row_heading level0 row6\" >Total</th>\n",
" <td id=\"T_f33e3_row6_col0\" class=\"data row6 col0\" >3505</td>\n",
" <td id=\"T_f33e3_row6_col1\" class=\"data row6 col1\" >1784</td>\n",
" <td id=\"T_f33e3_row6_col2\" class=\"data row6 col2\" >1567</td>\n",
" <td id=\"T_f33e3_row6_col3\" class=\"data row6 col3\" >154</td>\n",
" <th id=\"T_07946_level0_row6\" class=\"row_heading level0 row6\" >Total</th>\n",
" <td id=\"T_07946_row6_col0\" class=\"data row6 col0\" >3505</td>\n",
" <td id=\"T_07946_row6_col1\" class=\"data row6 col1\" >1784</td>\n",
" <td id=\"T_07946_row6_col2\" class=\"data row6 col2\" >1567</td>\n",
" <td id=\"T_07946_row6_col3\" class=\"data row6 col3\" >154</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n"
],
"text/plain": [
"<pandas.io.formats.style.Styler at 0x7fabab511130>"
"<pandas.io.formats.style.Styler at 0x7fabab4ffe20>"
]
},
"execution_count": 42,
"execution_count": 63,
"metadata": {},
"output_type": "execute_result"
}
Expand All @@ -1525,7 +1525,7 @@
},
{
"cell_type": "code",
"execution_count": 43,
"execution_count": 64,
"id": "ba548049-9271-4467-820e-c842b86eedcc",
"metadata": {},
"outputs": [
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