From fd01552066abb9685f0888b666e2548413a9b5ab Mon Sep 17 00:00:00 2001 From: Diego Prada-Gracia Date: Fri, 17 May 2024 00:21:10 -0600 Subject: [PATCH] In process to fix the documentation of user/tools/basic/selection --- docs/contents/user/tools/basic/add.ipynb | 84 +- docs/contents/user/tools/basic/get.ipynb | 62 +- docs/contents/user/tools/basic/select.ipynb | 4618 +------------------ molsysmt/basic/select.py | 4 +- molsysmt/basic/selector/molsysmt.py | 25 +- sandbox/Tests.ipynb | 89 +- 6 files changed, 201 insertions(+), 4681 deletions(-) diff --git a/docs/contents/user/tools/basic/add.ipynb b/docs/contents/user/tools/basic/add.ipynb index c2fd76458..a848948eb 100644 --- a/docs/contents/user/tools/basic/add.ipynb +++ b/docs/contents/user/tools/basic/add.ipynb @@ -51,7 +51,7 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "baf4b256100046659e91d4b1486bb726", + "model_id": "93e79f3dca404cb28fb7196e33d8284f", "version_major": 2, "version_minor": 0 }, @@ -110,37 +110,37 @@ "text/html": [ "\n", - "\n", + "
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\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 5, @@ -197,37 +197,37 @@ "text/html": [ "\n", - "\n", + "
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\n" ], "text/plain": [ - "" + "" ] }, "execution_count": 7, @@ -265,7 +265,7 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "11f4a8b657ad49f0ac87d01d4e9803dc", + "model_id": "af7ce781ea86498791a623cc97f5311d", "version_major": 2, "version_minor": 0 }, diff --git a/docs/contents/user/tools/basic/get.ipynb b/docs/contents/user/tools/basic/get.ipynb index cb37ecedc..84cac7656 100644 --- a/docs/contents/user/tools/basic/get.ipynb +++ b/docs/contents/user/tools/basic/get.ipynb @@ -60,7 +60,7 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "1309a7c26df6419184a0bd625d446b63", + "model_id": "272b236d462449699d2381bf42333d3f", "version_major": 2, "version_minor": 0 }, @@ -93,39 +93,39 @@ "text/html": [ "\n", - "\n", + "
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" ], "text/latex": [ "$\\begin{pmatrix}\\end{pmatrix}\\ \\mathrm{nanometer}^{3}$" ], "text/plain": [ - "array([507.55092521]) " + "array([507.55094751]) " ] }, "execution_count": 57, diff --git a/docs/contents/user/tools/basic/select.ipynb b/docs/contents/user/tools/basic/select.ipynb index d2761e039..2ef36dd39 100644 --- a/docs/contents/user/tools/basic/select.ipynb +++ b/docs/contents/user/tools/basic/select.ipynb @@ -2,7 +2,7 @@ "cells": [ { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "metadata": { "editable": true, "slideshow": { @@ -190,6 +190,7 @@ "\n", "| Word | Equivalent |\n", "|---|---|\n", + "| \"all\" | Any *element* in the system where *element* is given by the input argument ``element``|\n", "| \"index\" or \"indices\" | \"*element*_index\" where *element* is given by the input argument ``element``|\n", "| \"id\" or \"ids\" | \"*element*_id\" where *element* is given by the input argument ``element``|\n", "| \"name\" or \"names\" | \"*element*_name\" where *element* is given by the input argument ``element``|\n", @@ -232,38 +233,25 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "application/vnd.jupyter.widget-view+json": { - "model_id": "001157aa157c4e8790a109af13aa2cfc", - "version_major": 2, - "version_minor": 0 - }, - "text/plain": [] - }, - "metadata": {}, - "output_type": "display_data" - } - ], + "outputs": [], "source": [ "import molsysmt as msm" ] }, { "cell_type": "code", - "execution_count": 3, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ - "molecular_system = msm.convert('1TCD', to_form='molsysmt.MolSys')" + "molecular_system = msm.convert('1TCD')" ] }, { "cell_type": "code", - "execution_count": 4, + "execution_count": null, "metadata": { "editable": true, "slideshow": { @@ -273,18 +261,7 @@ "remove-input" ] }, - "outputs": [ - { - "data": { - "text/plain": [ - "[1, 4, 10, 13, 17]" - ] - }, - "execution_count": 4, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "# Atoms with name CA or CB and id < 20\n", "msm.select(molecular_system, element='atom', selection='atom_name in [\"CA\",\"CB\"] and atom_id<20')" @@ -302,1020 +279,9 @@ }, { "cell_type": "code", - 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" 1191,\n", - " 1192,\n", - " 1193,\n", - " 1194,\n", - " 1195,\n", - " 1196,\n", - " 1199,\n", - " 1201,\n", - " 1202,\n", - " 1205,\n", - " 1207,\n", - " 1208,\n", - " 1209,\n", - " 1210,\n", - " 1211,\n", - " 1212,\n", - " 1213,\n", - " 1216,\n", - " 1218,\n", - " 1219,\n", - " 1220,\n", - " 1223,\n", - " 1225,\n", - " 1226,\n", - " 1227,\n", - " 1230,\n", - " 1232,\n", - " 1233,\n", - " 1234,\n", - " 1235,\n", - " 1238,\n", - " 1240,\n", - " 1243,\n", - " 1245,\n", - " 1246,\n", - " 1247,\n", - " 1248,\n", - " 1249,\n", - " 1250,\n", - " 1251,\n", - " 1252,\n", - " 1255,\n", - " 1257,\n", - " 1258,\n", - " 1259,\n", - " 1260,\n", - " 1261,\n", - " 1264,\n", - " 1266,\n", - " 1267,\n", - " 1268,\n", - " 1271,\n", - " 1273,\n", - " 1274,\n", - " 1275,\n", - " 1278,\n", - " 1280,\n", - " 1281,\n", - " 1282,\n", - " 1283,\n", - " 1284,\n", - " 1285,\n", - " 1286,\n", - " 1287,\n", - " 1288,\n", - " 1289,\n", - " 1292,\n", - " 1294,\n", - " 1297,\n", - " 1299,\n", - " 1300,\n", - " 1301,\n", - " 1302,\n", - " 1305,\n", - " 1306,\n", - " 1309,\n", - " 1311,\n", - " 1312,\n", - " 1313,\n", - " 1316,\n", - " 1317,\n", - " 1320,\n", - " 1322,\n", - " 1323,\n", - " 1324,\n", - " 1325,\n", - " 1326,\n", - " 1329,\n", - " 1331,\n", - " 1332,\n", - " 1333,\n", - " 1336,\n", - " 1338,\n", - " 1341,\n", - " 1343,\n", - " 1344,\n", - " 1345,\n", - " 1348,\n", - " 1350,\n", - " 1351,\n", - " 1352,\n", - " 1355,\n", - " 1357,\n", - " 1358,\n", - " 1359,\n", - " 1360,\n", - " 1361,\n", - " 1364,\n", - " 1366,\n", - " 1367,\n", - " 1368,\n", - " 1369,\n", - " 1370,\n", - " 1373,\n", - " 1375,\n", - " 1378,\n", - " 1380,\n", - " 1381,\n", - " 1382,\n", - " 1383,\n", - " 1384,\n", - " 1387,\n", - " 1389,\n", - " 1390,\n", - " 1391,\n", - " 1392,\n", - " 1393,\n", - " 1396,\n", - " 1398,\n", - " 1399,\n", - " 1400,\n", - " 1403,\n", - " 1405,\n", - " 1406,\n", - " 1407,\n", - " 1408,\n", - " 1409,\n", - " 1410,\n", - " 1413,\n", - " 1415,\n", - " 1416,\n", - " 1417,\n", - " 1418,\n", - " 1419,\n", - " 1422,\n", - " 1424,\n", - " 1425,\n", - " 1426,\n", - " 1427,\n", - " 1430,\n", - " 1432,\n", - " 1433,\n", - " 1434,\n", - " 1435,\n", - " 1438,\n", - " 1440,\n", - " 1441,\n", - " 1442,\n", - " 1443,\n", - " 1444,\n", - " 1445,\n", - " 1446,\n", - " 1449,\n", - " 1451,\n", - " 1452,\n", - " 1453,\n", - " 1454,\n", - " 1455,\n", - " 1456,\n", - " 1457,\n", - " 1460,\n", - " 1462,\n", - " 1463,\n", - " 1464,\n", - " 1465,\n", - " 1466,\n", - " 1467,\n", - " 1468,\n", - " 1469,\n", - " 1470,\n", - " 1471,\n", - " 1474,\n", - " 1476,\n", - " 1477,\n", - " 1478,\n", - " 1481,\n", - " 1483,\n", - " 1484,\n", - " 1485,\n", - " 1486,\n", - " 1487,\n", - " 1488,\n", - " 1489,\n", - " 1492,\n", - " 1494,\n", - " 1495,\n", - " 1498,\n", - " 1500,\n", - " 1501,\n", - " 1502,\n", - " 1503,\n", - " 1504,\n", - " 1507,\n", - " 1509,\n", - " 1510,\n", - " 1511,\n", - " 1512,\n", - " 1515,\n", - " 1516,\n", - " 1519,\n", - " 1521,\n", - " 1522,\n", - " 1523,\n", - " 1526,\n", - " 1528,\n", - " 1529,\n", - " 1530,\n", - " 1531,\n", - " 1534,\n", - " 1536,\n", - " 1537,\n", - " 1538,\n", - " 1539,\n", - " 1542,\n", - " 1544,\n", - " 1547,\n", - " 1549,\n", - " 1552,\n", - " 1554,\n", - " 1555,\n", - " 1556,\n", - " 1557,\n", - " 1558,\n", - " 1561,\n", - " 1563,\n", - " 1564,\n", - " 1565,\n", - " 1566,\n", - " 1569,\n", - " 1571,\n", - " 1572,\n", - " 1573,\n", - " 1574,\n", - " 1575,\n", - " 1576,\n", - " 1577,\n", - " 1580,\n", - " 1582,\n", - " 1583,\n", - " 1584,\n", - " 1585,\n", - " 1588,\n", - " 1590,\n", - " 1591,\n", - " 1592,\n", - " 1593,\n", - " 1596,\n", - " 1598,\n", - " 1599,\n", - " 1600,\n", - " 1601,\n", - " 1602,\n", - " 1603,\n", - " 1604,\n", - " 1605,\n", - " 1608,\n", - " 1609,\n", - " 1612,\n", - " 1613,\n", - " 1616,\n", - " 1618,\n", - " ...]" - ] - }, - "execution_count": 8, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "# Atoms not named CA, CB or C\n", "msm.select(molecular_system, 'atom_name!=[\"CA\",\"CB\",\"C\"]')" @@ -3418,188 +351,13 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": null, "metadata": { "tags": [ "scroll-output" ] }, - "outputs": [ - { - "data": { - "text/plain": [ - "[3818,\n", - " 3819,\n", - " 3820,\n", - " 3821,\n", - " 3822,\n", - " 3823,\n", - " 3824,\n", - " 3825,\n", - " 3826,\n", - " 3827,\n", - " 3828,\n", - " 3829,\n", - " 3830,\n", - " 3831,\n", - " 3832,\n", - " 3833,\n", - " 3834,\n", - " 3835,\n", - " 3836,\n", - " 3837,\n", - " 3838,\n", - " 3839,\n", - " 3840,\n", - " 3841,\n", - " 3842,\n", - " 3843,\n", - " 3844,\n", - " 3845,\n", - " 3846,\n", - " 3847,\n", - " 3848,\n", - " 3849,\n", - " 3850,\n", - " 3851,\n", - " 3852,\n", - " 3853,\n", - " 3854,\n", - " 3855,\n", - " 3856,\n", - " 3857,\n", - " 3858,\n", - " 3859,\n", - " 3860,\n", - " 3861,\n", - " 3862,\n", - " 3863,\n", - " 3864,\n", - " 3865,\n", - " 3866,\n", - " 3867,\n", - " 3868,\n", - " 3869,\n", - " 3870,\n", - " 3871,\n", - " 3872,\n", - " 3873,\n", - " 3874,\n", - " 3875,\n", - " 3876,\n", - " 3877,\n", - " 3878,\n", - " 3879,\n", - " 3880,\n", - " 3881,\n", - " 3882,\n", - " 3883,\n", - " 3884,\n", - " 3885,\n", - " 3886,\n", - " 3887,\n", - " 3888,\n", - " 3889,\n", - " 3890,\n", - " 3891,\n", - " 3892,\n", - " 3893,\n", - " 3894,\n", - " 3895,\n", - " 3896,\n", - " 3897,\n", - " 3898,\n", - " 3899,\n", - " 3900,\n", - " 3901,\n", - " 3902,\n", - " 3903,\n", - " 3904,\n", - " 3905,\n", - " 3906,\n", - " 3907,\n", - " 3908,\n", - " 3909,\n", - " 3910,\n", - " 3911,\n", - " 3912,\n", - " 3913,\n", - " 3914,\n", - " 3915,\n", - " 3916,\n", - " 3917,\n", - " 3918,\n", - " 3919,\n", - " 3920,\n", - " 3921,\n", - " 3922,\n", - " 3923,\n", - " 3924,\n", - " 3925,\n", - " 3926,\n", - " 3927,\n", - " 3928,\n", - " 3929,\n", - " 3930,\n", - " 3931,\n", - " 3932,\n", - " 3933,\n", - " 3934,\n", - " 3935,\n", - " 3936,\n", - " 3937,\n", - " 3938,\n", - " 3939,\n", - " 3940,\n", - " 3941,\n", - " 3942,\n", - " 3943,\n", - " 3944,\n", - " 3945,\n", - " 3946,\n", - " 3947,\n", - " 3948,\n", - " 3949,\n", - " 3950,\n", - " 3951,\n", - " 3952,\n", - " 3953,\n", - " 3954,\n", - " 3955,\n", - " 3956,\n", - " 3957,\n", - " 3958,\n", - " 3959,\n", - " 3960,\n", - " 3961,\n", - " 3962,\n", - " 3963,\n", - " 3964,\n", - " 3965,\n", - " 3966,\n", - " 3967,\n", - " 3968,\n", - " 3969,\n", - " 3970,\n", - " 3971,\n", - " 3972,\n", - " 3973,\n", - " 3974,\n", - " 3975,\n", - " 3976,\n", - " 3977,\n", - " 3978,\n", - " 3979,\n", - " 3980,\n", - " 3981,\n", - " 3982]" - ] - }, - "execution_count": 9, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "# Atoms belonging to molecules of type water.\n", "msm.select(molecular_system, 'molecule_type==\"water\"')" @@ -3607,20 +365,9 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[25, 26, 27, 28, 29, 30, 31]" - ] - }, - "execution_count": 10, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "# Heavy atoms belonging to molecules of type protein.\n", "msm.select(molecular_system, 'molecule_type==\"protein\" and atom_type!=\"H\" and group_index==3')" @@ -3628,27 +375,16 @@ }, { "cell_type": "code", - "execution_count": 11, + "execution_count": null, "metadata": { "tags": [ "scroll-output" ] }, - "outputs": [ - { - "data": { - "text/plain": [ - "[]" - ] - }, - "execution_count": 11, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "# Atoms belonging to residues named GLY, ALA or VAL in chain id A.\n", - "msm.select(molecular_system, 'group_name==[\"GLY\",\"ALA\",\"VAL\"] and chain_id==\"A\"')" + "msm.select(molecular_system, 'group_name==[\"GLY\",\"ALA\",\"VAL\"] and chain_name==\"A\"')" ] }, { @@ -3660,20 +396,9 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[10, 11, 12, 13]" - ] - }, - "execution_count": 12, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "msm.select(molecular_system, selection=[10,11,12,13])" ] @@ -3689,25 +414,9 @@ }, { "cell_type": "code", - "execution_count": 13, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "array([ 5, 6, 7, 27, 28, 39, 50, 60, 61, 64, 70, 107, 111,\n", - " 113, 115, 116, 133, 137, 138, 145, 146, 148, 155, 162, 168, 175,\n", - " 180, 200, 201, 213, 216, 233, 245, 254, 255, 256, 276, 277, 288,\n", - " 299, 309, 310, 313, 319, 356, 360, 362, 364, 365, 382, 386, 387,\n", - " 394, 395, 397, 404, 411, 417, 424, 429, 449, 450, 462, 465, 482,\n", - " 494])" - ] - }, - "execution_count": 13, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "# Groups with name \"ALA\"\n", "msm.select(molecular_system, element='group', selection='group_name==\"ALA\"')" @@ -3715,20 +424,9 @@ }, { "cell_type": "code", - "execution_count": 14, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "array([4, 5, 9])" - ] - }, - "execution_count": 14, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "# Groups of atoms index 34, 44 or 64\n", "msm.select(molecular_system, element='group', selection='atom_index==[34,44,64]')" @@ -3736,61 +434,27 @@ }, { "cell_type": "code", - "execution_count": 15, + "execution_count": null, "metadata": { "tags": [ "scroll-output" ] }, - "outputs": [ - { - "data": { - "text/plain": [ - "[]" - ] - }, - "execution_count": 15, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "# Groups belonging to chain id A or C and molecule of type anything but water\n", - "msm.select(molecular_system, element='group', selection='chain_id in [\"A\", \"C\"] and molecule_type!=\"water\"')" + "msm.select(molecular_system, element='group', selection='chain_name in [\"A\", \"C\"] and molecule_type!=\"water\"')" ] }, { "cell_type": "code", - "execution_count": 16, + "execution_count": null, "metadata": { "tags": [ "scroll-output" ] }, - "outputs": [ - { - "data": { - "text/plain": [ - "array([ 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,\n", - " 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27,\n", - " 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40,\n", - " 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53,\n", - " 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66,\n", - " 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79,\n", - " 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92,\n", - " 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105,\n", - " 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118,\n", - " 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131,\n", - " 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144,\n", - " 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157,\n", - " 158, 159, 160, 161, 162, 163, 164, 165, 166])" - ] - }, - "execution_count": 16, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "# Molecules of type water\n", "msm.select(molecular_system, 'molecule_type==\"water\"', element='molecule')" @@ -3798,20 +462,9 @@ }, { "cell_type": "code", - "execution_count": 17, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "array([2, 3])" - ] - }, - "execution_count": 17, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "# Chains with molecules of type water\n", "msm.select(molecular_system, 'molecule_type==\"water\"', element='chain')" @@ -3819,20 +472,9 @@ }, { "cell_type": "code", - "execution_count": 18, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[42, 43, 44, 45]" - ] - }, - "execution_count": 18, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "# Bonds in group index 5\n", "msm.select(molecular_system, 'group_index==5', element='bond')" @@ -3847,40 +489,18 @@ }, { "cell_type": "code", - "execution_count": 19, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11]" - ] - }, - "execution_count": 19, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "msm.select(molecular_system, element='group', selection=[0,1,2,3,4,5,6,7,8,9,10,11])" ] }, { "cell_type": "code", - "execution_count": 20, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[3900, 3910, 3920]" - ] - }, - "execution_count": 20, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "msm.select(molecular_system, element='molecule', selection=[3900, 3910, 3920])" ] @@ -3896,42 +516,9 @@ }, { "cell_type": "code", - "execution_count": 21, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[77,\n", - " 78,\n", - " 79,\n", - " 80,\n", - " 81,\n", - " 82,\n", - " 83,\n", - " 84,\n", - " 85,\n", - " 86,\n", - " 87,\n", - " 88,\n", - " 89,\n", - " 90,\n", - " 91,\n", - " 92,\n", - " 93,\n", - " 94,\n", - " 95,\n", - " 96,\n", - " 97,\n", - " 98,\n", - " 99]" - ] - }, - "execution_count": 21, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "# Atoms in groups with indices 10, 11 or 12.\n", "indices = [10,11,12]\n", @@ -3940,20 +527,9 @@ }, { "cell_type": "code", - "execution_count": 22, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[10, 11, 12, 16, 17, 18, 19, 25, 26, 27, 28]" - ] - }, - "execution_count": 22, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "# Atoms named CA, C, O or N in groups with indices 10 to 29.\n", "indices = list(range(10,30))\n", @@ -3963,20 +539,9 @@ }, { "cell_type": "code", - "execution_count": 23, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "array([ 0, 100, 200])" - ] - }, - "execution_count": 23, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "# Groups with indices equal to 0, 100 or 200\n", "indices = [0,100,200]\n", @@ -3994,81 +559,27 @@ }, { "cell_type": "code", - "execution_count": 25, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[89,\n", - " 480,\n", - " 489,\n", - " 527,\n", - " 547,\n", - " 550,\n", - " 552,\n", - " 554,\n", - " 557,\n", - " 566,\n", - " 600,\n", - " 723,\n", - " 734,\n", - " 3818,\n", - " 3819,\n", - " 3820,\n", - " 3833,\n", - " 3836,\n", - " 3854,\n", - " 3866,\n", - " 3870,\n", - " 3872]" - ] - }, - "execution_count": 25, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "msm.select(molecular_system, 'chain_name==\"A\" within 0.3 nm of chain_name==\"B\"')" ] }, { "cell_type": "code", - "execution_count": 26, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[119, 213, 473, 531, 654, 696, 799, 1049]" - ] - }, - "execution_count": 26, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "msm.select(molecular_system, '(atom_name==\"N\" and chain_name==\"A\") within 3 angstroms of (atom_type==\"O\" and molecule_type==\"water\")')" ] }, { "cell_type": "code", - "execution_count": 27, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "array([10, 42, 62, 72, 73])" - ] - }, - "execution_count": 27, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "msm.select(molecular_system, '(atom_name==\"CA\" and chain_name==\"A\") within 0.5 nm of (atom_name==\"CA\" and chain_name==\"B\")',\n", " element='group')" @@ -4083,20 +594,9 @@ }, { "cell_type": "code", - "execution_count": 28, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[1521, 1522, 1723, 1724, 3882]" - ] - }, - "execution_count": 28, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "msm.select(molecular_system, 'chain_name==\"A\" not within 7.8 nanometers of chain_name==\"B\"')" ] @@ -4110,82 +610,18 @@ }, { "cell_type": "code", - "execution_count": 29, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[89,\n", - " 480,\n", - " 489,\n", - " 527,\n", - " 547,\n", - " 550,\n", - " 552,\n", - " 554,\n", - " 557,\n", - " 566,\n", - " 600,\n", - " 723,\n", - " 734,\n", - " 3818,\n", - " 3819,\n", - " 3820,\n", - " 3833,\n", - " 3836,\n", - " 3854,\n", - " 3866,\n", - " 3870,\n", - " 3872]" - ] - }, - "execution_count": 29, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "msm.select(molecular_system, 'chain_name==\"A\" within 0.3 nm without pbc of chain_name==\"B\"')" ] }, { "cell_type": "code", - "execution_count": 30, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[89,\n", - " 480,\n", - " 489,\n", - " 527,\n", - " 547,\n", - " 550,\n", - " 552,\n", - " 554,\n", - " 557,\n", - " 566,\n", - " 600,\n", - " 723,\n", - " 734,\n", - " 3818,\n", - " 3819,\n", - " 3820,\n", - " 3833,\n", - " 3836,\n", - " 3854,\n", - " 3866,\n", - " 3870,\n", - " 3872]" - ] - }, - "execution_count": 30, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "msm.select(molecular_system, 'chain_name==\"A\" within 0.3 nm with pbc of chain_name==\"B\"')" ] @@ -4201,894 +637,26 @@ }, { "cell_type": "code", - 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"metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "msm.select(molecular_system, '(atom_type==\"O\" and chain_name==\"A\") bonded to (atom_type==\"C\" and chain_name==\"A\")')" ] @@ -5102,20 +670,9 @@ }, { "cell_type": "code", - "execution_count": 33, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[363, 1714, 2275, 3626]" - ] - }, - "execution_count": 33, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "msm.select(molecular_system, '(all not bonded to atom_type==[\"H\",\"N\",\"C\",\"O\"]) and molecule_type==\"protein\"')" ] @@ -5129,20 +686,9 @@ }, { "cell_type": "code", - "execution_count": 34, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "[119, 213, 473, 531, 654, 696, 799, 1049]" - ] - }, - "execution_count": 34, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "msm.select(molecular_system, '((atom_name==\"N\" and chain_name==\"A\") bonded to atom_type==\"C\") within 3 angstroms of (atom_type==\"O\" and molecule_type==\"water\")')" ] @@ -5160,31 +706,9 @@ }, { "cell_type": "code", - "execution_count": 35, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "/home/diego/repos@uibcdf/MolSysMT/molsysmt/basic/selector/molsysmt.py:249: RuntimeWarning: Engine has switched to 'python' because numexpr does not support extension array dtypes. Please set your engine to python manually.\n", - " output = aux_df.query(tmp_selection).index.to_list()\n" - ] - }, - { - "data": { - "text/plain": [ - "[array([86, 87, 88, 89, 90, 91]),\n", - " array([273, 274, 275, 276, 277, 278]),\n", - " array([880, 881, 882, 883, 884, 885]),\n", - " array([943, 944, 945, 946, 947, 948])]" - ] - }, - "execution_count": 35, - "metadata": {}, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "msm.select(molecular_system, 'all in groups of molecule_index==0 and group_name==\"CYS\"')" ] @@ -5219,7 +743,7 @@ "outputs": [], "source": [ "msm.select(molecular_system, element='group',\n", - " selection='group_name==\"ALA\" in components of molecule_name==\"Triosephosphate isomerase\"')" + " selection='group_name==\"ALA\" in components of molecule_name==\"TRIOSEPHOSPHATE ISOMERASE\"')" ] }, { diff --git a/molsysmt/basic/select.py b/molsysmt/basic/select.py index 96a17cb95..a43f99390 100644 --- a/molsysmt/basic/select.py +++ b/molsysmt/basic/select.py @@ -173,14 +173,14 @@ def select(molecular_system, selection='all', structure_indices='all', element=' for aux_atom_indices in atom_indices: temp_output_indices = getattr(_dict_modules[aux_form], f'get_{element}_index_from_atom')(aux_item, indices=aux_atom_indices) - output_indices.append(np.unique(temp_output_indices)) + output_indices.append(np.unique(temp_output_indices).tolist()) else: aux_item, aux_form = where_is_attribute(molecular_system, element+'_index', skip_digestion=True) output_indices = getattr(_dict_modules[aux_form], f'get_{element}_index_from_atom')(aux_item, indices=atom_indices) - output_indices = np.unique(output_indices) + output_indices = np.unique(output_indices).tolist() elif element == 'bond': diff --git a/molsysmt/basic/selector/molsysmt.py b/molsysmt/basic/selector/molsysmt.py index eb182b730..891b20ffa 100644 --- a/molsysmt/basic/selector/molsysmt.py +++ b/molsysmt/basic/selector/molsysmt.py @@ -245,8 +245,7 @@ def select_standard(item, selection): left_on='chain_index', right_index=True) tmp_selection = tmp_selection.replace('atom_index','index') - - output = aux_df.query(tmp_selection).index.to_list() + output = aux_df.query(tmp_selection, engine='python').index.to_list() del aux_df @@ -365,8 +364,10 @@ def select_in_elements_of(molecular_system, selection): aafter = 'all' kwarg = {_element_index[element_1]: True} - pre_output = get(molecular_system, element=element_2, selection=aafter, **kwarg) - mask = get(molecular_system, element=element_1, selection=bbefore, index=True) + pre_output = get(molecular_system, element=element_2, selection=aafter, skip_digestion=True, + **kwarg) + mask = get(molecular_system, element=element_1, selection=bbefore, skip_digestion=True, + **kwarg) output_2 = [np.intersect1d(ii, mask) for ii in pre_output] output_2 = [ii for ii in output_2 if ii.shape[0] > 0] @@ -379,9 +380,10 @@ def select_in_elements_of(molecular_system, selection): for aux_after in output_2: - pre_output = get(molecular_system, element=element_1, selection=aux_after, atom_index=True) - aux_output = [np.intersect1d(ii, mask) for ii in pre_output] - aux_output = [ii for ii in aux_output if ii.shape[0] > 0] + pre_output = get(molecular_system, element=element_1, selection=aux_after, skip_digestion=True, + atom_index=True) + aux_output = [np.intersect1d(ii, mask).tolist() for ii in pre_output] + aux_output = [ii for ii in aux_output if len(ii) > 0] output.append(aux_output) return output @@ -398,10 +400,11 @@ def select_in_elements_of(molecular_system, selection): if after == '': after = 'all' - pre_output = get(molecular_system, element=element_1, selection=after, atom_index=True) - mask = select(molecular_system, selection=before) - output = [np.intersect1d(ii, mask) for ii in pre_output] - output = [ii for ii in output if ii.shape[0] > 0] + pre_output = get(molecular_system, element=element_1, selection=after, skip_digestion=True, + atom_index=True) + mask = select(molecular_system, selection=before, skip_digestion=True) + output = [np.intersect1d(ii, mask).tolist() for ii in pre_output] + output = [ii for ii in output if len(ii) > 0] return output diff --git a/sandbox/Tests.ipynb b/sandbox/Tests.ipynb index 059bfbd9d..c9bac8a02 100644 --- a/sandbox/Tests.ipynb +++ b/sandbox/Tests.ipynb @@ -21,7 +21,7 @@ { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "ae19204960324f488659c71a1908e20e", + "model_id": "a4e8fb7ba002470d881083ff62b26554", "version_major": 2, "version_minor": 0 }, @@ -37,74 +37,67 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 2, "id": "4cdc4f01-cba8-494c-b029-e3cb4e801786", "metadata": {}, "outputs": [], "source": [ - "molsys = msm.convert('1L2Y')" + "molsys = msm.convert('1TCD')" ] }, { "cell_type": "code", - "execution_count": 5, - "id": "4ab7563b-7b41-44f9-b5d3-e8994ed39734", + "execution_count": 3, + "id": "b02a20f2-e896-4f69-9075-fc92642fafb0", "metadata": {}, "outputs": [ { - "data": { - "text/html": [ - "\n", - "\n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - "
formn_atomsn_groupsn_componentsn_chainsn_moleculesn_entitiesn_peptidesn_structures
molsysmt.MolSys304201111138
\n" - ], - "text/plain": [ - "" - ] - }, - "execution_count": 5, - "metadata": {}, - "output_type": "execute_result" + "name": "stdout", + "output_type": "stream", + "text": [ + "CPU times: user 51.9 s, sys: 381 ms, total: 52.3 s\n", + "Wall time: 52.4 s\n" + ] } ], "source": [ - "msm.info(molsys)" + "%%time\n", + "sel1 = msm.select(molsys, 'all in groups of all in components of all')" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "d2ef1e2d-a120-4ed1-82f5-c18c1a4aa30b", + "metadata": {}, + "outputs": [], + "source": [ + "sel2 = msm.select(molsys, 'all in groups of all in components')" ] }, { "cell_type": "code", "execution_count": null, - "id": "086feead-0abc-4431-978a-f0e337a0eeda", + "id": "f3513c99-3b57-452b-b57d-a01b30e692bb", "metadata": {}, "outputs": [], - "source": [] + "source": [ + "sel2" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "5ab33dbf-a8b9-427a-969e-56bacc8a72a2", + "metadata": {}, + "outputs": [], + "source": [ + "sel1 = msm.select(molecular_system, 'all in groups of all in components of all')\n", + "sel2 = msm.select(molecular_system, 'all in groups of all in components')\n", + "sel3 = msm.select(molecular_system, 'all in groups in components of all')\n", + "sel4 = msm.select(molecular_system, 'all in groups in components')\n", + "sel5 = msm.select(molecular_system, 'in groups in components')" + ] } ], "metadata": {