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huichenggonghuichenggong
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correct the cylinder definition
1 parent 7c359a9 commit 0ebb470

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-49
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‎tutorial/01_sfilter_tutorial.ipynb

Lines changed: 36 additions & 49 deletions
Original file line numberDiff line numberDiff line change
@@ -395,13 +395,13 @@
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},
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{
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"cell_type": "code",
398-
"execution_count": 11,
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"execution_count": 13,
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"id": "4898aaa3-926a-4c15-9c4f-29acd0a3425a",
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"metadata": {},
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"outputs": [],
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"source": [
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"# Do the same with water\n",
404-
"wat = u.select_atoms(\"resname SOL\")\n",
404+
"wat = u.select_atoms(\"resname SOL and name OW\")\n",
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"site_occu_wat = []\n",
406406
"for ts in u.trajectory:\n",
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" wat_array = sf.state_detect(wat, s5_z_cutoff, r_cutoff, s0_r_cutoff) \n",
@@ -410,7 +410,7 @@
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},
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{
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"cell_type": "code",
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"execution_count": 12,
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"execution_count": 14,
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"id": "421c3e83-05f9-4b31-84c9-be3950713483",
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"metadata": {},
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"outputs": [
@@ -446,12 +446,12 @@
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" <tbody>\n",
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" <tr>\n",
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" <th>0</th>\n",
449-
" <td>[56425, 60299, 60300, 60301]</td>\n",
449+
" <td>[60299]</td>\n",
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" <td>[]</td>\n",
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" <td>[]</td>\n",
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" <td>[]</td>\n",
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" <td>[]</td>\n",
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" <td>[31255, 32579, 32580, 32581, 40145, 40146, 401...</td>\n",
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" <td>[40145, 44588]</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>1</th>\n",
@@ -460,7 +460,7 @@
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" <td>[]</td>\n",
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" <td>[]</td>\n",
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" <td>[]</td>\n",
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" <td>[36476, 36477, 39977, 39978, 39979, 41862, 522...</td>\n",
463+
" <td>[61961]</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>2</th>\n",
@@ -469,113 +469,100 @@
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" <td>[]</td>\n",
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" <td>[]</td>\n",
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" <td>[]</td>\n",
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" <td>[36476, 36477, 36478, 37471, 41862, 47115, 490...</td>\n",
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" <td>[49097, 51185, 51449]</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>3</th>\n",
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" <td>[35385, 35386, 48137, 48138]</td>\n",
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" <td>[48137]</td>\n",
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" <td>[]</td>\n",
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" <td>[]</td>\n",
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" <td>[]</td>\n",
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" <td>[]</td>\n",
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" <td>[31295, 31296, 31297, 37469, 37471, 40427, 404...</td>\n",
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" <td>[31295, 43874, 55148, 58355]</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>4</th>\n",
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" <td>[35384, 35385, 35386, 42595, 50423, 50424]</td>\n",
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" <td>[35384, 50423]</td>\n",
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" <td>[]</td>\n",
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" <td>[]</td>\n",
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" <td>[]</td>\n",
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" <td>[]</td>\n",
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" <td>[37016, 37017, 37018, 38117, 38118, 38119, 399...</td>\n",
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" <td>[37016, 49463]</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>5</th>\n",
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" <td>[42764, 42765, 42766, 47197, 53675, 53676, 53677]</td>\n",
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" <td>[42764, 53675]</td>\n",
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" <td>[]</td>\n",
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" <td>[]</td>\n",
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" <td>[]</td>\n",
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" <td>[]</td>\n",
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" <td>[30694, 36476, 36477, 36478, 36844, 37470, 384...</td>\n",
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" <td>[40154, 48152, 58601]</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>6</th>\n",
503-
" <td>[55301, 55302]</td>\n",
503+
" <td>[55301]</td>\n",
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" <td>[]</td>\n",
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" <td>[]</td>\n",
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" <td>[]</td>\n",
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" <td>[]</td>\n",
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" <td>[30692, 30693, 30694, 38414, 38415, 38416, 390...</td>\n",
508+
" <td>[38414, 39023, 59456]</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>7</th>\n",
512-
" <td>[41922, 41923, 43610, 43611, 43612]</td>\n",
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" <td>[43610]</td>\n",
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" <td>[]</td>\n",
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" <td>[]</td>\n",
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" <td>[]</td>\n",
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" <td>[]</td>\n",
517-
" <td>[30692, 30693, 30694, 32579, 32580, 32581, 364...</td>\n",
517+
" <td>[37358, 39977, 40088]</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>8</th>\n",
521-
" <td>[37128, 41121, 41122, 54627]</td>\n",
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" <td>[]</td>\n",
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" <td>[]</td>\n",
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" <td>[]</td>\n",
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" <td>[]</td>\n",
526-
" <td>[32580, 39023, 39025, 40088, 40089, 40090, 547...</td>\n",
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" <td>[]</td>\n",
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" <td>[40088, 55916]</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>9</th>\n",
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" <td>[33339, 37620, 41318, 41319, 41320]</td>\n",
530+
" <td>[41318]</td>\n",
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" <td>[]</td>\n",
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" <td>[]</td>\n",
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" <td>[]</td>\n",
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" <td>[]</td>\n",
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" <td>[30775, 33674, 33675, 33676, 37121, 37122, 371...</td>\n",
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" <td>[33674, 37121]</td>\n",
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" </tr>\n",
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" <tr>\n",
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" <th>10</th>\n",
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" <td>[34520, 38763]</td>\n",
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" <td>[34520]</td>\n",
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" <td>[]</td>\n",
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" <td>[]</td>\n",
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" <td>[]</td>\n",
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" <td>[]</td>\n",
544-
" <td>[32392, 33140, 33141, 33142, 33674, 33675, 336...</td>\n",
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" <td>[33140, 33674, 55745]</td>\n",
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" </tr>\n",
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" </tbody>\n",
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"</table>\n",
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"</div>"
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],
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"text/plain": [
551-
" S0 S1 S2 S3 S4 \\\n",
552-
"0 [56425, 60299, 60300, 60301] [] [] [] [] \n",
553-
"1 [] [] [] [] [] \n",
554-
"2 [] [] [] [] [] \n",
555-
"3 [35385, 35386, 48137, 48138] [] [] [] [] \n",
556-
"4 [35384, 35385, 35386, 42595, 50423, 50424] [] [] [] [] \n",
557-
"5 [42764, 42765, 42766, 47197, 53675, 53676, 53677] [] [] [] [] \n",
558-
"6 [55301, 55302] [] [] [] [] \n",
559-
"7 [41922, 41923, 43610, 43611, 43612] [] [] [] [] \n",
560-
"8 [37128, 41121, 41122, 54627] [] [] [] [] \n",
561-
"9 [33339, 37620, 41318, 41319, 41320] [] [] [] [] \n",
562-
"10 [34520, 38763] [] [] [] [] \n",
563-
"\n",
564-
" SCav \n",
565-
"0 [31255, 32579, 32580, 32581, 40145, 40146, 401... \n",
566-
"1 [36476, 36477, 39977, 39978, 39979, 41862, 522... \n",
567-
"2 [36476, 36477, 36478, 37471, 41862, 47115, 490... \n",
568-
"3 [31295, 31296, 31297, 37469, 37471, 40427, 404... \n",
569-
"4 [37016, 37017, 37018, 38117, 38118, 38119, 399... \n",
570-
"5 [30694, 36476, 36477, 36478, 36844, 37470, 384... \n",
571-
"6 [30692, 30693, 30694, 38414, 38415, 38416, 390... \n",
572-
"7 [30692, 30693, 30694, 32579, 32580, 32581, 364... \n",
573-
"8 [32580, 39023, 39025, 40088, 40089, 40090, 547... \n",
574-
"9 [30775, 33674, 33675, 33676, 37121, 37122, 371... \n",
575-
"10 [32392, 33140, 33141, 33142, 33674, 33675, 336... "
551+
" S0 S1 S2 S3 S4 SCav\n",
552+
"0 [60299] [] [] [] [] [40145, 44588]\n",
553+
"1 [] [] [] [] [] [61961]\n",
554+
"2 [] [] [] [] [] [49097, 51185, 51449]\n",
555+
"3 [48137] [] [] [] [] [31295, 43874, 55148, 58355]\n",
556+
"4 [35384, 50423] [] [] [] [] [37016, 49463]\n",
557+
"5 [42764, 53675] [] [] [] [] [40154, 48152, 58601]\n",
558+
"6 [55301] [] [] [] [] [38414, 39023, 59456]\n",
559+
"7 [43610] [] [] [] [] [37358, 39977, 40088]\n",
560+
"8 [] [] [] [] [] [40088, 55916]\n",
561+
"9 [41318] [] [] [] [] [33674, 37121]\n",
562+
"10 [34520] [] [] [] [] [33140, 33674, 55745]"
576563
]
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},
578-
"execution_count": 12,
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"execution_count": 14,
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"metadata": {},
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"output_type": "execute_result"
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}

‎tutorial/SF_definition.jpg

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