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 @@
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+ " form | \n",
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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 @@
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- " n_proteins | \n",
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+ " form | \n",
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+ " molsysmt.MolSys | \n",
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+ "Magnitude | [[[4.3709999999999996 0.0 0.0] [0.0 7.765 0.0] [0.0 0.0 14.953999999999997]]] |
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"$\\begin{pmatrix} & & \\end{pmatrix}\\ \\mathrm{nanometer}$"
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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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- " 542,\n",
- " 543,\n",
- " 544,\n",
- " 545,\n",
- " 546,\n",
- " 547,\n",
- " 548,\n",
- " 549,\n",
- " 550,\n",
- " 551,\n",
- " 552,\n",
- " 553,\n",
- " 554,\n",
- " 555,\n",
- " 556,\n",
- " 557,\n",
- " 558,\n",
- " 559,\n",
- " 560,\n",
- " 561,\n",
- " 562,\n",
- " 563,\n",
- " 564,\n",
- " 565,\n",
- " 566,\n",
- " 567,\n",
- " 568,\n",
- " 569,\n",
- " 570,\n",
- " 571,\n",
- " 572,\n",
- " 573,\n",
- " 574,\n",
- " 575,\n",
- " 576,\n",
- " 577,\n",
- " 578,\n",
- " 579,\n",
- " 580,\n",
- " 581,\n",
- " 582,\n",
- " 583,\n",
- " 584,\n",
- " 585,\n",
- " 586,\n",
- " 587,\n",
- " 588,\n",
- " 589,\n",
- " 590,\n",
- " 591,\n",
- " 592,\n",
- " 593,\n",
- " 594,\n",
- " 595,\n",
- " 596,\n",
- " 597,\n",
- " 598,\n",
- " 599,\n",
- " 600,\n",
- " 601,\n",
- " 602,\n",
- " 603,\n",
- " 604,\n",
- " 605,\n",
- " 606,\n",
- " 607,\n",
- " 608,\n",
- " 609,\n",
- " 610,\n",
- " 611,\n",
- " 612,\n",
- " 613,\n",
- " 614,\n",
- " 615,\n",
- " 616,\n",
- " 617,\n",
- " 618,\n",
- " 619,\n",
- " 620,\n",
- " 621,\n",
- " 622,\n",
- " 623,\n",
- " 624,\n",
- " 625,\n",
- " 626,\n",
- " 627,\n",
- " 628,\n",
- " 629,\n",
- " 630,\n",
- " 631,\n",
- " 632,\n",
- " 633,\n",
- " 634,\n",
- " 635,\n",
- " 636,\n",
- " 637,\n",
- " 638,\n",
- " 639,\n",
- " 640,\n",
- " 641,\n",
- " 642,\n",
- " 643,\n",
- " 644,\n",
- " 645,\n",
- " 646,\n",
- " 647,\n",
- " 648,\n",
- " 649,\n",
- " 650,\n",
- " 651,\n",
- " 652,\n",
- " 653,\n",
- " 654,\n",
- " 655,\n",
- " 656,\n",
- " 657,\n",
- " 658,\n",
- " 659,\n",
- " 660,\n",
- " 661,\n",
- " 662,\n",
- " 663,\n",
- " 664,\n",
- " 665,\n",
- " 666,\n",
- " 667,\n",
- " 668,\n",
- " 669,\n",
- " 670,\n",
- " 671,\n",
- " 672,\n",
- " 673,\n",
- " 674,\n",
- " 675,\n",
- " 676,\n",
- " 677,\n",
- " 678,\n",
- " 679,\n",
- " 680,\n",
- " 681,\n",
- " 682,\n",
- " 683,\n",
- " 684,\n",
- " 685,\n",
- " 686,\n",
- " 687,\n",
- " 688,\n",
- " 689,\n",
- " 690,\n",
- " 691,\n",
- " 692,\n",
- " 693,\n",
- " 694,\n",
- " 695,\n",
- " 696,\n",
- " 697,\n",
- " 698,\n",
- " 699,\n",
- " 700,\n",
- " 701,\n",
- " 702,\n",
- " 703,\n",
- " 704,\n",
- " 705,\n",
- " 706,\n",
- " 707,\n",
- " 708,\n",
- " 709,\n",
- " 710,\n",
- " 711,\n",
- " 712,\n",
- " 713,\n",
- " 714,\n",
- " 715,\n",
- " 716,\n",
- " 717,\n",
- " 718,\n",
- " 719,\n",
- " 720,\n",
- " 721,\n",
- " 722,\n",
- " 723,\n",
- " 724,\n",
- " 725,\n",
- " 726,\n",
- " 727,\n",
- " 728,\n",
- " 729,\n",
- " 730,\n",
- " 731,\n",
- " 732,\n",
- " 733,\n",
- " 734,\n",
- " 735,\n",
- " 736,\n",
- " 737,\n",
- " 738,\n",
- " 739,\n",
- " 740,\n",
- " 741,\n",
- " 742,\n",
- " 743,\n",
- " 744,\n",
- " 745,\n",
- " 746,\n",
- " 747,\n",
- " 748,\n",
- " 749,\n",
- " 750,\n",
- " 751,\n",
- " 752,\n",
- " 753,\n",
- " 754,\n",
- " 755,\n",
- " 756,\n",
- " 757,\n",
- " 758,\n",
- " 759,\n",
- " 760,\n",
- " 761,\n",
- " 762,\n",
- " 763,\n",
- " 764,\n",
- " 765,\n",
- " 766,\n",
- " 767,\n",
- " 768,\n",
- " 769,\n",
- " 770,\n",
- " 771,\n",
- " 772,\n",
- " 773,\n",
- " 774,\n",
- " 775,\n",
- " 776,\n",
- " 777,\n",
- " 778,\n",
- " 779,\n",
- " 780,\n",
- " 781,\n",
- " 782,\n",
- " 783,\n",
- " 784,\n",
- " 785,\n",
- " 786,\n",
- " 787,\n",
- " 788,\n",
- " 789,\n",
- " 790,\n",
- " 791,\n",
- " 792,\n",
- " 793,\n",
- " 794,\n",
- " 795,\n",
- " 796,\n",
- " 797,\n",
- " 798,\n",
- " 799,\n",
- " 800,\n",
- " 801,\n",
- " 802,\n",
- " 803,\n",
- " 804,\n",
- " 805,\n",
- " 806,\n",
- " 807,\n",
- " 808,\n",
- " 809,\n",
- " 810,\n",
- " 811,\n",
- " 812,\n",
- " 813,\n",
- " 814,\n",
- " 815,\n",
- " 816,\n",
- " 817,\n",
- " 818,\n",
- " 819,\n",
- " 820,\n",
- " 821,\n",
- " 822,\n",
- " 823,\n",
- " 824,\n",
- " 825,\n",
- " 826,\n",
- " 827,\n",
- " 828,\n",
- " 829,\n",
- " 830,\n",
- " 831,\n",
- " 832,\n",
- " 833,\n",
- " 834,\n",
- " 835,\n",
- " 836,\n",
- " 837,\n",
- " 838,\n",
- " 839,\n",
- " 840,\n",
- " 841,\n",
- " 842,\n",
- " 843,\n",
- " 844,\n",
- " 845,\n",
- " 846,\n",
- " 847,\n",
- " 848,\n",
- " 849,\n",
- " 850,\n",
- " 851,\n",
- " 852,\n",
- " 853,\n",
- " 854,\n",
- " 855,\n",
- " 856,\n",
- " 857,\n",
- " 858,\n",
- " 859,\n",
- " 860,\n",
- " 861,\n",
- " 862,\n",
- " 863,\n",
- " 864,\n",
- " 865,\n",
- " 866,\n",
- " 867,\n",
- " 868,\n",
- " 869,\n",
- " 870,\n",
- " 871,\n",
- " 872,\n",
- " 873,\n",
- " 874,\n",
- " 875,\n",
- " 876,\n",
- " 877,\n",
- " 878,\n",
- " 879,\n",
- " 880,\n",
- " 881,\n",
- " 882,\n",
- " 883,\n",
- " 884,\n",
- " 885,\n",
- " 886,\n",
- " 887,\n",
- " 888,\n",
- " 889,\n",
- " 890,\n",
- " 891,\n",
- " 892,\n",
- " 893,\n",
- " 894,\n",
- " 895,\n",
- " 896,\n",
- " 897,\n",
- " 898,\n",
- " 899,\n",
- " 900,\n",
- " 901,\n",
- " 902,\n",
- " 903,\n",
- " 904,\n",
- " 905,\n",
- " 906,\n",
- " 907,\n",
- " 908,\n",
- " 909,\n",
- " 910,\n",
- " 911,\n",
- " 912,\n",
- " 913,\n",
- " 914,\n",
- " 915,\n",
- " 916,\n",
- " 917,\n",
- " 918,\n",
- " 919,\n",
- " 920,\n",
- " 921,\n",
- " 922,\n",
- " 923,\n",
- " 924,\n",
- " 925,\n",
- " 926,\n",
- " 927,\n",
- " 928,\n",
- " 929,\n",
- " 930,\n",
- " 931,\n",
- " 932,\n",
- " 933,\n",
- " 934,\n",
- " 935,\n",
- " 936,\n",
- " 937,\n",
- " 938,\n",
- " 939,\n",
- " 940,\n",
- " 941,\n",
- " 942,\n",
- " 943,\n",
- " 944,\n",
- " 945,\n",
- " 946,\n",
- " 947,\n",
- " 948,\n",
- " 949,\n",
- " 950,\n",
- " 951,\n",
- " 952,\n",
- " 953,\n",
- " 954,\n",
- " 955,\n",
- " 956,\n",
- " 957,\n",
- " 958,\n",
- " 959,\n",
- " 960,\n",
- " 961,\n",
- " 962,\n",
- " 963,\n",
- " 964,\n",
- " 965,\n",
- " 966,\n",
- " 967,\n",
- " 968,\n",
- " 969,\n",
- " 970,\n",
- " 971,\n",
- " 972,\n",
- " 973,\n",
- " 974,\n",
- " 975,\n",
- " 976,\n",
- " 977,\n",
- " 978,\n",
- " 979,\n",
- " 980,\n",
- " 981,\n",
- " 982,\n",
- " 983,\n",
- " 984,\n",
- " 985,\n",
- " 986,\n",
- " 987,\n",
- " 988,\n",
- " 989,\n",
- " 990,\n",
- " 991,\n",
- " 992,\n",
- " 993,\n",
- " 994,\n",
- " 995,\n",
- " 996,\n",
- " 997,\n",
- " 998,\n",
- " 999,\n",
- " ...]"
- ]
- },
- "execution_count": 5,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
+ "outputs": [],
"source": [
"# Heavy atoms\n",
"msm.select(molecular_system, 'not atom_type==\"H\"')"
@@ -1340,20 +306,9 @@
},
{
"cell_type": "code",
- "execution_count": 6,
+ "execution_count": null,
"metadata": {},
- "outputs": [
- {
- "data": {
- "text/plain": [
- "[0, 1, 2]"
- ]
- },
- "execution_count": 6,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
+ "outputs": [],
"source": [
"msm.select(molecular_system, element='atom', selection=[0,1,2])"
]
@@ -1369,1020 +324,9 @@
},
{
"cell_type": "code",
- "execution_count": 7,
+ "execution_count": null,
"metadata": {},
- "outputs": [
- {
- "data": {
- "text/plain": [
- "[2,\n",
- " 4,\n",
- " 5,\n",
- " 6,\n",
- " 7,\n",
- " 11,\n",
- " 13,\n",
- " 14,\n",
- " 15,\n",
- " 18,\n",
- " 20,\n",
- " 21,\n",
- " 22,\n",
- " 27,\n",
- " 29,\n",
- " 30,\n",
- " 31,\n",
- " 34,\n",
- " 36,\n",
- " 37,\n",
- " 38,\n",
- " 39,\n",
- " 42,\n",
- " 44,\n",
- " 47,\n",
- " 49,\n",
- " 52,\n",
- " 54,\n",
- " 57,\n",
- " 59,\n",
- " 60,\n",
- " 65,\n",
- " 67,\n",
- " 68,\n",
- " 69,\n",
- " 70,\n",
- " 72,\n",
- " 73,\n",
- " 74,\n",
- " 75,\n",
- " 76,\n",
- " 79,\n",
- " 81,\n",
- " 82,\n",
- " 83,\n",
- " 84,\n",
- " 88,\n",
- " 90,\n",
- " 94,\n",
- " 96,\n",
- " 97,\n",
- " 102,\n",
- " 106,\n",
- " 108,\n",
- " 112,\n",
- " 114,\n",
- " 115,\n",
- " 116,\n",
- " 121,\n",
- " 123,\n",
- " 127,\n",
- " 129,\n",
- " 130,\n",
- " 131,\n",
- " 132,\n",
- " 135,\n",
- " 137,\n",
- " 138,\n",
- " 139,\n",
- " 140,\n",
- " 143,\n",
- " 145,\n",
- " 146,\n",
- " 147,\n",
- " 150,\n",
- " 152,\n",
- " 153,\n",
- " 154,\n",
- " 157,\n",
- " 159,\n",
- " 160,\n",
- " 161,\n",
- " 162,\n",
- " 165,\n",
- " 167,\n",
- " 168,\n",
- " 169,\n",
- " 170,\n",
- " 173,\n",
- " 175,\n",
- " 176,\n",
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- " 182,\n",
- " 184,\n",
- " 186,\n",
- " 189,\n",
- " 191,\n",
- " 192,\n",
- " 193,\n",
- " 194,\n",
- " 197,\n",
- " 199,\n",
- " 200,\n",
- " 205,\n",
- " 207,\n",
- " 210,\n",
- " 212,\n",
- " 215,\n",
- " 217,\n",
- " 219,\n",
- " 222,\n",
- " 224,\n",
- " 225,\n",
- " 226,\n",
- " 227,\n",
- " 228,\n",
- " 229,\n",
- " 230,\n",
- " 233,\n",
- " 235,\n",
- " 236,\n",
- " 241,\n",
- " 243,\n",
- " 244,\n",
- " 246,\n",
- " 247,\n",
- " 251,\n",
- " 253,\n",
- " 254,\n",
- " 259,\n",
- " 261,\n",
- " 262,\n",
- " 263,\n",
- " 266,\n",
- " 268,\n",
- " 269,\n",
- " 270,\n",
- " 275,\n",
- " 277,\n",
- " 281,\n",
- " 283,\n",
- " 284,\n",
- " 285,\n",
- " 288,\n",
- " 290,\n",
- " 291,\n",
- " 292,\n",
- " 295,\n",
- " 297,\n",
- " 300,\n",
- " 302,\n",
- " 303,\n",
- " 304,\n",
- " 307,\n",
- " 309,\n",
- " 311,\n",
- " 314,\n",
- " 316,\n",
- " 317,\n",
- " 318,\n",
- " 319,\n",
- " 320,\n",
- " 321,\n",
- " 322,\n",
- " 325,\n",
- " 327,\n",
- " 328,\n",
- " 329,\n",
- " 330,\n",
- " 333,\n",
- " 335,\n",
- " 336,\n",
- " 338,\n",
- " 339,\n",
- " 343,\n",
- " 345,\n",
- " 346,\n",
- " 347,\n",
- " 348,\n",
- " 351,\n",
- " 353,\n",
- " 354,\n",
- " 355,\n",
- " 358,\n",
- " 360,\n",
- " 361,\n",
- " 363,\n",
- " 366,\n",
- " 368,\n",
- " 370,\n",
- " 373,\n",
- " 375,\n",
- " 376,\n",
- " 377,\n",
- " 378,\n",
- " 382,\n",
- " 384,\n",
- " 387,\n",
- " 389,\n",
- " 390,\n",
- " 391,\n",
- " 393,\n",
- " 398,\n",
- " 400,\n",
- " 401,\n",
- " 402,\n",
- " 403,\n",
- " 406,\n",
- " 408,\n",
- " 410,\n",
- " 413,\n",
- " 415,\n",
- " 416,\n",
- " 421,\n",
- " 423,\n",
- " 424,\n",
- " 425,\n",
- " 428,\n",
- " 430,\n",
- " 431,\n",
- " 432,\n",
- " 433,\n",
- " 437,\n",
- " 439,\n",
- " 440,\n",
- " 441,\n",
- " 442,\n",
- " 443,\n",
- " 444,\n",
- " 445,\n",
- " 448,\n",
- " 450,\n",
- " 451,\n",
- " 452,\n",
- " 457,\n",
- " 459,\n",
- " 460,\n",
- " 461,\n",
- " 462,\n",
- " 465,\n",
- " 467,\n",
- " 470,\n",
- " 472,\n",
- " 475,\n",
- " 477,\n",
- " 478,\n",
- " 479,\n",
- " 484,\n",
- " 486,\n",
- " 487,\n",
- " 492,\n",
- " 494,\n",
- " 497,\n",
- " 499,\n",
- " 500,\n",
- " 501,\n",
- " 502,\n",
- " 505,\n",
- " 507,\n",
- " 509,\n",
- " 512,\n",
- " 514,\n",
- " 515,\n",
- " 516,\n",
- " 518,\n",
- " 523,\n",
- " 525,\n",
- " 529,\n",
- " 533,\n",
- " 535,\n",
- " 538,\n",
- " 540,\n",
- " 541,\n",
- " 542,\n",
- " 543,\n",
- " 544,\n",
- " 545,\n",
- " 546,\n",
- " 549,\n",
- " 551,\n",
- " 553,\n",
- " 556,\n",
- " 560,\n",
- " 562,\n",
- " 563,\n",
- " 564,\n",
- " 569,\n",
- " 571,\n",
- " 572,\n",
- " 573,\n",
- " 576,\n",
- " 578,\n",
- " 582,\n",
- " 584,\n",
- " 585,\n",
- " 586,\n",
- " 587,\n",
- " 590,\n",
- " 592,\n",
- " 593,\n",
- " 594,\n",
- " 599,\n",
- " 601,\n",
- " 602,\n",
- " 603,\n",
- " 604,\n",
- " 607,\n",
- " 609,\n",
- " 610,\n",
- " 611,\n",
- " 612,\n",
- " 615,\n",
- " 617,\n",
- " 618,\n",
- " 619,\n",
- " 620,\n",
- " 624,\n",
- " 626,\n",
- " 627,\n",
- " 632,\n",
- " 634,\n",
- " 635,\n",
- " 636,\n",
- " 637,\n",
- " 638,\n",
- " 639,\n",
- " 640,\n",
- " 644,\n",
- " 648,\n",
- " 650,\n",
- " 651,\n",
- " 652,\n",
- " 653,\n",
- " 656,\n",
- " 658,\n",
- " 662,\n",
- " 664,\n",
- " 665,\n",
- " 666,\n",
- " 667,\n",
- " 669,\n",
- " 670,\n",
- " 671,\n",
- " 672,\n",
- " 673,\n",
- " 676,\n",
- " 678,\n",
- " 679,\n",
- " 680,\n",
- " 683,\n",
- " 685,\n",
- " 686,\n",
- " 687,\n",
- " 690,\n",
- " 692,\n",
- " 693,\n",
- " 694,\n",
- " 695,\n",
- " 698,\n",
- " 702,\n",
- " 704,\n",
- " 705,\n",
- " 707,\n",
- " 708,\n",
- " 712,\n",
- " 714,\n",
- " 718,\n",
- " 720,\n",
- " 721,\n",
- " 722,\n",
- " 727,\n",
- " 729,\n",
- " 730,\n",
- " 731,\n",
- " 733,\n",
- " 738,\n",
- " 740,\n",
- " 741,\n",
- " 742,\n",
- " 744,\n",
- " 749,\n",
- " 751,\n",
- " 752,\n",
- " 753,\n",
- " 754,\n",
- " 757,\n",
- " 759,\n",
- " 760,\n",
- " 761,\n",
- " 762,\n",
- " 763,\n",
- " 764,\n",
- " 765,\n",
- " 769,\n",
- " 771,\n",
- " 772,\n",
- " 773,\n",
- " 774,\n",
- " 775,\n",
- " 776,\n",
- " 777,\n",
- " 781,\n",
- " 785,\n",
- " 787,\n",
- " 788,\n",
- " 789,\n",
- " 794,\n",
- " 796,\n",
- " 798,\n",
- " 801,\n",
- " 803,\n",
- " 804,\n",
- " 809,\n",
- " 811,\n",
- " 812,\n",
- " 813,\n",
- " 818,\n",
- " 820,\n",
- " 821,\n",
- " 822,\n",
- " 823,\n",
- " 826,\n",
- " 828,\n",
- " 829,\n",
- " 830,\n",
- " 833,\n",
- " 835,\n",
- " 838,\n",
- " 840,\n",
- " 841,\n",
- " 842,\n",
- " 847,\n",
- " 849,\n",
- " 850,\n",
- " 851,\n",
- " 852,\n",
- " 856,\n",
- " 858,\n",
- " 859,\n",
- " 860,\n",
- " 863,\n",
- " 865,\n",
- " 868,\n",
- " 870,\n",
- " 871,\n",
- " 872,\n",
- " 877,\n",
- " 879,\n",
- " 882,\n",
- " 884,\n",
- " 888,\n",
- " 890,\n",
- " 893,\n",
- " 895,\n",
- " 898,\n",
- " 902,\n",
- " 904,\n",
- " 905,\n",
- " 906,\n",
- " 907,\n",
- " 908,\n",
- " 909,\n",
- " 910,\n",
- " 913,\n",
- " 915,\n",
- " 916,\n",
- " 918,\n",
- " 919,\n",
- " 923,\n",
- " 925,\n",
- " 926,\n",
- " 927,\n",
- " 930,\n",
- " 932,\n",
- " 933,\n",
- " 934,\n",
- " 935,\n",
- " 938,\n",
- " 940,\n",
- " 941,\n",
- " 942,\n",
- " 945,\n",
- " 947,\n",
- " 951,\n",
- " 953,\n",
- " 954,\n",
- " 955,\n",
- " 958,\n",
- " 962,\n",
- " 964,\n",
- " 965,\n",
- " 966,\n",
- " 971,\n",
- " 973,\n",
- " 975,\n",
- " 978,\n",
- " 980,\n",
- " 981,\n",
- " 986,\n",
- " 988,\n",
- " 989,\n",
- " 990,\n",
- " 995,\n",
- " 997,\n",
- " 998,\n",
- " 999,\n",
- " 1004,\n",
- " 1006,\n",
- " 1007,\n",
- " 1008,\n",
- " 1010,\n",
- " 1015,\n",
- " 1017,\n",
- " 1018,\n",
- " 1019,\n",
- " 1024,\n",
- " 1026,\n",
- " 1029,\n",
- " 1033,\n",
- " 1035,\n",
- " 1036,\n",
- " 1037,\n",
- " 1039,\n",
- " 1044,\n",
- " 1046,\n",
- " 1048,\n",
- " 1051,\n",
- " 1053,\n",
- " 1056,\n",
- " 1058,\n",
- " 1061,\n",
- " 1063,\n",
- " 1064,\n",
- " 1065,\n",
- " 1068,\n",
- " 1070,\n",
- " 1071,\n",
- " 1072,\n",
- " 1075,\n",
- " 1077,\n",
- " 1078,\n",
- " 1079,\n",
- " 1080,\n",
- " 1083,\n",
- " 1085,\n",
- " 1087,\n",
- " 1090,\n",
- " 1092,\n",
- " 1093,\n",
- " 1094,\n",
- " 1099,\n",
- " 1101,\n",
- " 1102,\n",
- " 1103,\n",
- " 1104,\n",
- " 1107,\n",
- " 1109,\n",
- " 1112,\n",
- " 1114,\n",
- " 1117,\n",
- " 1119,\n",
- " 1120,\n",
- " 1121,\n",
- " 1124,\n",
- " 1126,\n",
- " 1129,\n",
- " 1131,\n",
- " 1132,\n",
- " 1133,\n",
- " 1138,\n",
- " 1140,\n",
- " 1141,\n",
- " 1142,\n",
- " 1143,\n",
- " 1147,\n",
- " 1149,\n",
- " 1150,\n",
- " 1151,\n",
- " 1152,\n",
- " 1155,\n",
- " 1157,\n",
- " 1161,\n",
- " 1163,\n",
- " 1164,\n",
- " 1165,\n",
- " 1166,\n",
- " 1170,\n",
- " 1172,\n",
- " 1173,\n",
- " 1174,\n",
- " 1179,\n",
- " 1181,\n",
- " 1184,\n",
- " 1186,\n",
- " 1187,\n",
- " 1188,\n",
- " 1189,\n",
- " 1191,\n",
- " 1192,\n",
- " 1193,\n",
- " 1194,\n",
- " 1195,\n",
- " 1198,\n",
- " 1200,\n",
- " 1204,\n",
- " 1206,\n",
- " 1207,\n",
- " 1208,\n",
- " 1210,\n",
- " 1215,\n",
- " 1217,\n",
- " 1218,\n",
- " 1219,\n",
- " 1222,\n",
- " 1224,\n",
- " 1225,\n",
- " 1226,\n",
- " 1229,\n",
- " 1231,\n",
- " 1232,\n",
- " 1233,\n",
- " 1234,\n",
- " 1237,\n",
- " 1239,\n",
- " 1242,\n",
- " 1244,\n",
- " 1245,\n",
- " 1246,\n",
- " 1247,\n",
- " 1248,\n",
- " 1249,\n",
- " 1250,\n",
- " 1254,\n",
- " 1256,\n",
- " 1257,\n",
- " 1258,\n",
- " 1263,\n",
- " 1265,\n",
- " 1266,\n",
- " 1267,\n",
- " 1270,\n",
- " 1272,\n",
- " 1273,\n",
- " 1274,\n",
- " 1277,\n",
- " 1279,\n",
- " 1280,\n",
- " 1281,\n",
- " 1282,\n",
- " 1284,\n",
- " 1285,\n",
- " 1286,\n",
- " 1287,\n",
- " 1288,\n",
- " 1291,\n",
- " 1293,\n",
- " 1296,\n",
- " 1298,\n",
- " 1299,\n",
- " 1300,\n",
- " 1301,\n",
- " 1304,\n",
- " 1308,\n",
- " 1310,\n",
- " 1312,\n",
- " 1315,\n",
- " 1319,\n",
- " 1321,\n",
- " 1322,\n",
- " 1323,\n",
- " 1324,\n",
- " 1328,\n",
- " 1330,\n",
- " 1331,\n",
- " 1332,\n",
- " 1335,\n",
- " 1337,\n",
- " 1340,\n",
- " 1342,\n",
- " 1344,\n",
- " 1347,\n",
- " 1349,\n",
- " 1350,\n",
- " 1351,\n",
- " 1354,\n",
- " 1356,\n",
- " 1357,\n",
- " 1358,\n",
- " 1363,\n",
- " 1365,\n",
- " 1366,\n",
- " 1367,\n",
- " 1372,\n",
- " 1374,\n",
- " 1377,\n",
- " 1379,\n",
- " 1380,\n",
- " 1381,\n",
- " 1386,\n",
- " 1388,\n",
- " 1389,\n",
- " 1390,\n",
- " 1395,\n",
- " 1397,\n",
- " 1398,\n",
- " 1399,\n",
- " 1402,\n",
- " 1404,\n",
- " 1405,\n",
- " 1407,\n",
- " 1408,\n",
- " 1412,\n",
- " 1414,\n",
- " 1415,\n",
- " 1416,\n",
- " 1421,\n",
- " 1423,\n",
- " 1424,\n",
- " 1425,\n",
- " 1426,\n",
- " 1429,\n",
- " 1431,\n",
- " 1432,\n",
- " 1433,\n",
- " 1434,\n",
- " 1437,\n",
- " 1439,\n",
- " 1440,\n",
- " 1441,\n",
- " 1443,\n",
- " 1448,\n",
- " 1450,\n",
- " 1451,\n",
- " 1452,\n",
- " 1454,\n",
- " 1459,\n",
- " 1461,\n",
- " 1462,\n",
- " 1463,\n",
- " 1464,\n",
- " 1466,\n",
- " 1467,\n",
- " 1468,\n",
- " 1469,\n",
- " 1470,\n",
- " 1473,\n",
- " 1475,\n",
- " 1476,\n",
- " 1477,\n",
- " 1480,\n",
- " 1482,\n",
- " 1483,\n",
- " 1484,\n",
- " 1486,\n",
- " 1491,\n",
- " 1493,\n",
- " 1497,\n",
- " 1499,\n",
- " 1500,\n",
- " 1501,\n",
- " 1502,\n",
- " 1506,\n",
- " 1508,\n",
- " 1509,\n",
- " 1510,\n",
- " 1511,\n",
- " 1514,\n",
- " 1518,\n",
- " 1520,\n",
- " 1522,\n",
- " 1525,\n",
- " 1527,\n",
- " 1528,\n",
- " 1533,\n",
- " 1535,\n",
- " 1536,\n",
- " 1537,\n",
- " 1538,\n",
- " 1541,\n",
- " 1543,\n",
- " 1546,\n",
- " 1548,\n",
- " 1551,\n",
- " 1553,\n",
- " 1554,\n",
- " 1555,\n",
- " 1560,\n",
- " 1562,\n",
- " 1563,\n",
- " 1564,\n",
- " 1565,\n",
- " 1568,\n",
- " 1570,\n",
- " 1571,\n",
- " 1572,\n",
- " 1574,\n",
- " 1579,\n",
- " 1581,\n",
- " 1582,\n",
- " 1583,\n",
- " 1584,\n",
- " 1587,\n",
- " 1589,\n",
- " 1590,\n",
- " 1591,\n",
- " 1592,\n",
- " 1595,\n",
- " 1597,\n",
- " 1598,\n",
- " 1599,\n",
- " 1600,\n",
- " 1601,\n",
- " 1602,\n",
- " 1603,\n",
- " 1607,\n",
- " 1611,\n",
- " 1615,\n",
- " 1617,\n",
- " 1621,\n",
- " 1623,\n",
- " 1624,\n",
- " 1625,\n",
- " 1628,\n",
- " 1630,\n",
- " 1632,\n",
- " 1635,\n",
- " 1637,\n",
- " 1640,\n",
- " 1642,\n",
- " 1643,\n",
- " 1644,\n",
- " 1645,\n",
- " 1649,\n",
- " 1651,\n",
- " 1652,\n",
- " 1657,\n",
- " 1659,\n",
- " 1662,\n",
- " 1664,\n",
- " 1665,\n",
- " 1666,\n",
- " 1668,\n",
- " 1673,\n",
- " 1675,\n",
- " 1677,\n",
- " 1680,\n",
- " 1682,\n",
- " 1683,\n",
- " 1684,\n",
- " 1685,\n",
- " 1688,\n",
- " 1690,\n",
- " 1691,\n",
- " 1692,\n",
- " 1693,\n",
- " 1694,\n",
- " 1695,\n",
- " 1696,\n",
- " 1700,\n",
- " 1702,\n",
- " 1703,\n",
- " 1704,\n",
- " 1709,\n",
- " 1711,\n",
- " 1712,\n",
- " 1714,\n",
- " 1717,\n",
- " 1719,\n",
- " 1720,\n",
- " 1721,\n",
- " 1723,\n",
- " 1728,\n",
- " 1730,\n",
- " 1731,\n",
- " 1736,\n",
- " 1738,\n",
- " 1739,\n",
- " 1740,\n",
- " 1741,\n",
- " 1744,\n",
- " 1746,\n",
- " 1747,\n",
- " 1752,\n",
- " 1756,\n",
- " 1758,\n",
- " 1759,\n",
- " 1760,\n",
- " 1761,\n",
- " 1762,\n",
- " 1763,\n",
- " 1764,\n",
- " 1767,\n",
- " 1769,\n",
- " 1770,\n",
- " 1771,\n",
- " 1772,\n",
- " 1775,\n",
- " 1777,\n",
- " 1778,\n",
- " 1779,\n",
- " 1782,\n",
- " 1786,\n",
- " 1790,\n",
- " 1792,\n",
- " 1795,\n",
- " 1797,\n",
- " 1801,\n",
- " 1803,\n",
- " 1804,\n",
- " 1805,\n",
- " 1806,\n",
- " 1809,\n",
- " 1811,\n",
- " 1812,\n",
- " 1813,\n",
- " 1814,\n",
- " 1818,\n",
- " 1820,\n",
- " 1821,\n",
- " 1822,\n",
- " 1825,\n",
- " 1827,\n",
- " 1828,\n",
- " 1829,\n",
- " 1834,\n",
- " 1836,\n",
- " 1837,\n",
- " 1838,\n",
- " 1839,\n",
- " 1840,\n",
- " 1841,\n",
- " 1842,\n",
- " 1845,\n",
- " 1847,\n",
- " 1848,\n",
- " 1849,\n",
- " 1852,\n",
- " 1854,\n",
- " 1855,\n",
- " 1856,\n",
- " 1861,\n",
- " 1863,\n",
- " 1864,\n",
- " 1865,\n",
- " 1866,\n",
- " 1869,\n",
- " 1871,\n",
- " 1872,\n",
- " 1873,\n",
- " 1874,\n",
- " 1877,\n",
- " 1879,\n",
- " 1880,\n",
- " 1881,\n",
- " 1886,\n",
- " 1888,\n",
- " 1891,\n",
- " 1893,\n",
- " 1895,\n",
- " 1898,\n",
- " 1900,\n",
- " 1901,\n",
- " 1902,\n",
- " 1903,\n",
- " 1908,\n",
- " 1910,\n",
- " 1914,\n",
- " 1916,\n",
- " 1917,\n",
- " 1918,\n",
- " 1919,\n",
- " 1923,\n",
- " 1925,\n",
- " 1926,\n",
- " 1927,\n",
- " 1930,\n",
- " 1932,\n",
- " 1933,\n",
- " 1934,\n",
- " 1939,\n",
- " 1941,\n",
- " 1942,\n",
- " 1943,\n",
- " 1946,\n",
- " 1948,\n",
- " 1949,\n",
- " 1950,\n",
- " 1951,\n",
- " 1954,\n",
- " 1956,\n",
- " 1959,\n",
- " 1961,\n",
- " 1964,\n",
- " 1966,\n",
- " 1969,\n",
- " 1971,\n",
- " 1972,\n",
- " 1977,\n",
- " 1979,\n",
- " 1980,\n",
- " ...]"
- ]
- },
- "execution_count": 7,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
+ "outputs": [],
"source": [
"# Atoms of type C not named CA\n",
"msm.select(molecular_system, 'atom_type==\"C\" and not atom_name==\"CA\"')"
@@ -2390,1020 +334,9 @@
},
{
"cell_type": "code",
- "execution_count": 8,
+ "execution_count": null,
"metadata": {},
- "outputs": [
- {
- "data": {
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- " 231,\n",
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- " 236,\n",
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- " 256,\n",
- " 257,\n",
- " 260,\n",
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- " 267,\n",
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- " 270,\n",
- " 271,\n",
- " 272,\n",
- " 273,\n",
- " 276,\n",
- " 278,\n",
- " 279,\n",
- " 282,\n",
- " 284,\n",
- " 285,\n",
- " 286,\n",
- " 289,\n",
- " 291,\n",
- " 292,\n",
- " 293,\n",
- " 296,\n",
- " 298,\n",
- " 301,\n",
- " 303,\n",
- " 304,\n",
- " 305,\n",
- " 308,\n",
- " 310,\n",
- " 311,\n",
- " 312,\n",
- " 315,\n",
- " 317,\n",
- " 318,\n",
- " 319,\n",
- " 320,\n",
- " 321,\n",
- " 322,\n",
- " 323,\n",
- " 326,\n",
- " 328,\n",
- " 329,\n",
- " 330,\n",
- " 331,\n",
- " 334,\n",
- " 336,\n",
- " 337,\n",
- " 338,\n",
- " 339,\n",
- " 340,\n",
- " 341,\n",
- " 344,\n",
- " 346,\n",
- " 347,\n",
- " 348,\n",
- " 349,\n",
- " 352,\n",
- " 354,\n",
- " 355,\n",
- " 356,\n",
- " 359,\n",
- " 361,\n",
- " 362,\n",
- " 363,\n",
- " 364,\n",
- " 367,\n",
- " 369,\n",
- " 370,\n",
- " 371,\n",
- " 374,\n",
- " 376,\n",
- " 377,\n",
- " 378,\n",
- " 379,\n",
- " 380,\n",
- " 383,\n",
- " 385,\n",
- " 388,\n",
- " 390,\n",
- " 391,\n",
- " 392,\n",
- " 393,\n",
- " 394,\n",
- " 395,\n",
- " 396,\n",
- " 399,\n",
- " 401,\n",
- " 402,\n",
- " 403,\n",
- " 404,\n",
- " 407,\n",
- " 409,\n",
- " 410,\n",
- " 411,\n",
- " 414,\n",
- " 416,\n",
- " 417,\n",
- " 418,\n",
- " 419,\n",
- " 422,\n",
- " 424,\n",
- " 425,\n",
- " 426,\n",
- " 429,\n",
- " 431,\n",
- " 432,\n",
- " 433,\n",
- " 434,\n",
- " 435,\n",
- " 438,\n",
- " 440,\n",
- " 441,\n",
- " 442,\n",
- " 443,\n",
- " 444,\n",
- " 445,\n",
- " 446,\n",
- " 449,\n",
- " 451,\n",
- " 452,\n",
- " 453,\n",
- " 454,\n",
- " 455,\n",
- " 458,\n",
- " 460,\n",
- " 461,\n",
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- " 558,\n",
- " 561,\n",
- " 563,\n",
- " 564,\n",
- " 565,\n",
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- " 567,\n",
- " 570,\n",
- " 572,\n",
- " 573,\n",
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- " 612,\n",
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- " 616,\n",
- " 618,\n",
- " 619,\n",
- " 620,\n",
- " 621,\n",
- " 622,\n",
- " 625,\n",
- " 627,\n",
- " 628,\n",
- " 629,\n",
- " 630,\n",
- " 633,\n",
- " 635,\n",
- " 636,\n",
- " 637,\n",
- " 638,\n",
- " 639,\n",
- " 640,\n",
- " 641,\n",
- " 642,\n",
- " 645,\n",
- " 646,\n",
- " 649,\n",
- " 651,\n",
- " 652,\n",
- " 653,\n",
- " 654,\n",
- " 657,\n",
- " 659,\n",
- " 660,\n",
- " 663,\n",
- " 665,\n",
- " 666,\n",
- " 667,\n",
- " 668,\n",
- " 669,\n",
- " 670,\n",
- " 671,\n",
- " 672,\n",
- " 673,\n",
- " 674,\n",
- " 677,\n",
- " 679,\n",
- " 680,\n",
- " 681,\n",
- " 684,\n",
- " 686,\n",
- " 687,\n",
- " 688,\n",
- " 691,\n",
- " 693,\n",
- " 694,\n",
- " 695,\n",
- " 696,\n",
- " 699,\n",
- " 700,\n",
- " 703,\n",
- " 705,\n",
- " 706,\n",
- " 707,\n",
- " 708,\n",
- " 709,\n",
- " 710,\n",
- " 713,\n",
- " 715,\n",
- " 716,\n",
- " 719,\n",
- " 721,\n",
- " 722,\n",
- " 723,\n",
- " 724,\n",
- " 725,\n",
- " 728,\n",
- " 730,\n",
- " 731,\n",
- " 732,\n",
- " 733,\n",
- " 734,\n",
- " 735,\n",
- " 736,\n",
- " 739,\n",
- " 741,\n",
- " 742,\n",
- " 743,\n",
- " 744,\n",
- " 745,\n",
- " 746,\n",
- " 747,\n",
- " 750,\n",
- " 752,\n",
- " 753,\n",
- " 754,\n",
- " 755,\n",
- " 758,\n",
- " 760,\n",
- " 761,\n",
- " 762,\n",
- " 763,\n",
- " 764,\n",
- " 765,\n",
- " 766,\n",
- " 767,\n",
- " 770,\n",
- " 772,\n",
- " 773,\n",
- " 774,\n",
- " 775,\n",
- " 776,\n",
- " 777,\n",
- " 778,\n",
- " 779,\n",
- " 782,\n",
- " 783,\n",
- " 786,\n",
- " 788,\n",
- " 789,\n",
- " 790,\n",
- " 791,\n",
- " 792,\n",
- " 795,\n",
- " 797,\n",
- " 798,\n",
- " 799,\n",
- " 802,\n",
- " 804,\n",
- " 805,\n",
- " 806,\n",
- " 807,\n",
- " 810,\n",
- " 812,\n",
- " 813,\n",
- " 814,\n",
- " 815,\n",
- " 816,\n",
- " 819,\n",
- " 821,\n",
- " 822,\n",
- " 823,\n",
- " 824,\n",
- " 827,\n",
- " 829,\n",
- " 830,\n",
- " 831,\n",
- " 834,\n",
- " 836,\n",
- " 839,\n",
- " 841,\n",
- " 842,\n",
- " 843,\n",
- " 844,\n",
- " 845,\n",
- " 848,\n",
- " 850,\n",
- " 851,\n",
- " 852,\n",
- " 853,\n",
- " 854,\n",
- " 857,\n",
- " 859,\n",
- " 860,\n",
- " 861,\n",
- " 864,\n",
- " 866,\n",
- " 869,\n",
- " 871,\n",
- " 872,\n",
- " 873,\n",
- " 874,\n",
- " 875,\n",
- " 878,\n",
- " 880,\n",
- " 883,\n",
- " 885,\n",
- " 886,\n",
- " 889,\n",
- " 891,\n",
- " 894,\n",
- " 896,\n",
- " 899,\n",
- " 900,\n",
- " 903,\n",
- " 905,\n",
- " 906,\n",
- " 907,\n",
- " 908,\n",
- " 909,\n",
- " 910,\n",
- " 911,\n",
- " 914,\n",
- " 916,\n",
- " 917,\n",
- " 918,\n",
- " 919,\n",
- " 920,\n",
- " 921,\n",
- " 924,\n",
- " 926,\n",
- " 927,\n",
- " 928,\n",
- " 931,\n",
- " 933,\n",
- " 934,\n",
- " 935,\n",
- " 936,\n",
- " 939,\n",
- " 941,\n",
- " 942,\n",
- " 943,\n",
- " 946,\n",
- " 948,\n",
- " 949,\n",
- " 952,\n",
- " 954,\n",
- " 955,\n",
- " 956,\n",
- " 959,\n",
- " 960,\n",
- " 963,\n",
- " 965,\n",
- " 966,\n",
- " 967,\n",
- " 968,\n",
- " 969,\n",
- " 972,\n",
- " 974,\n",
- " 975,\n",
- " 976,\n",
- " 979,\n",
- " 981,\n",
- " 982,\n",
- " 983,\n",
- " 984,\n",
- " 987,\n",
- " 989,\n",
- " 990,\n",
- " 991,\n",
- " 992,\n",
- " 993,\n",
- " 996,\n",
- " 998,\n",
- " 999,\n",
- " 1000,\n",
- " 1001,\n",
- " 1002,\n",
- " 1005,\n",
- " 1007,\n",
- " 1008,\n",
- " 1009,\n",
- " 1010,\n",
- " 1011,\n",
- " 1012,\n",
- " 1013,\n",
- " 1016,\n",
- " 1018,\n",
- " 1019,\n",
- " 1020,\n",
- " 1021,\n",
- " 1022,\n",
- " 1025,\n",
- " 1027,\n",
- " 1030,\n",
- " 1031,\n",
- " 1034,\n",
- " 1036,\n",
- " 1037,\n",
- " 1038,\n",
- " 1039,\n",
- " 1040,\n",
- " 1041,\n",
- " 1042,\n",
- " 1045,\n",
- " 1047,\n",
- " 1048,\n",
- " 1049,\n",
- " 1052,\n",
- " 1054,\n",
- " 1057,\n",
- " 1059,\n",
- " 1062,\n",
- " 1064,\n",
- " 1065,\n",
- " 1066,\n",
- " 1069,\n",
- " 1071,\n",
- " 1072,\n",
- " 1073,\n",
- " 1076,\n",
- " 1078,\n",
- " 1079,\n",
- " 1080,\n",
- " 1081,\n",
- " 1084,\n",
- " 1086,\n",
- " 1087,\n",
- " 1088,\n",
- " 1091,\n",
- " 1093,\n",
- " 1094,\n",
- " 1095,\n",
- " 1096,\n",
- " 1097,\n",
- " 1100,\n",
- " 1102,\n",
- " 1103,\n",
- " 1104,\n",
- " 1105,\n",
- " 1108,\n",
- " 1110,\n",
- " 1113,\n",
- " 1115,\n",
- " 1118,\n",
- " 1120,\n",
- " 1121,\n",
- " 1122,\n",
- " 1125,\n",
- " 1127,\n",
- " 1130,\n",
- " 1132,\n",
- " 1133,\n",
- " 1134,\n",
- " 1135,\n",
- " 1136,\n",
- " 1139,\n",
- " 1141,\n",
- " 1142,\n",
- " 1143,\n",
- " 1144,\n",
- " 1145,\n",
- " 1148,\n",
- " 1150,\n",
- " 1151,\n",
- " 1152,\n",
- " 1153,\n",
- " 1156,\n",
- " 1158,\n",
- " 1159,\n",
- " 1162,\n",
- " 1164,\n",
- " 1165,\n",
- " 1166,\n",
- " 1167,\n",
- " 1168,\n",
- " 1171,\n",
- " 1173,\n",
- " 1174,\n",
- " 1175,\n",
- " 1176,\n",
- " 1177,\n",
- " 1180,\n",
- " 1182,\n",
- " 1185,\n",
- " 1187,\n",
- " 1188,\n",
- " 1189,\n",
- " 1190,\n",
- " 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",
- "execution_count": 31,
+ "execution_count": null,
"metadata": {
"tags": [
"scroll-output"
]
},
- "outputs": [
- {
- "data": {
- "text/plain": [
- "[0,\n",
- " 9,\n",
- " 16,\n",
- " 25,\n",
- " 32,\n",
- " 40,\n",
- " 45,\n",
- " 50,\n",
- " 55,\n",
- " 63,\n",
- " 77,\n",
- " 86,\n",
- " 92,\n",
- " 100,\n",
- " 104,\n",
- " 110,\n",
- " 119,\n",
- " 125,\n",
- " 133,\n",
- " 141,\n",
- " 148,\n",
- " 155,\n",
- " 163,\n",
- " 171,\n",
- " 180,\n",
- " 187,\n",
- " 195,\n",
- " 203,\n",
- " 208,\n",
- " 213,\n",
- " 220,\n",
- " 231,\n",
- " 239,\n",
- " 249,\n",
- " 257,\n",
- " 264,\n",
- " 273,\n",
- " 279,\n",
- " 286,\n",
- " 293,\n",
- " 298,\n",
- " 305,\n",
- " 312,\n",
- " 323,\n",
- " 331,\n",
- " 341,\n",
- " 349,\n",
- " 356,\n",
- " 364,\n",
- " 371,\n",
- " 380,\n",
- " 385,\n",
- " 396,\n",
- " 404,\n",
- " 411,\n",
- " 419,\n",
- " 426,\n",
- " 435,\n",
- " 446,\n",
- " 455,\n",
- " 463,\n",
- " 468,\n",
- " 473,\n",
- " 482,\n",
- " 490,\n",
- " 495,\n",
- " 503,\n",
- " 510,\n",
- " 521,\n",
- " 527,\n",
- " 531,\n",
- " 536,\n",
- " 547,\n",
- " 554,\n",
- " 558,\n",
- " 567,\n",
- " 574,\n",
- " 580,\n",
- " 588,\n",
- " 597,\n",
- " 605,\n",
- " 613,\n",
- " 622,\n",
- " 630,\n",
- " 642,\n",
- " 646,\n",
- " 654,\n",
- " 660,\n",
- " 674,\n",
- " 681,\n",
- " 688,\n",
- " 696,\n",
- " 700,\n",
- " 710,\n",
- " 716,\n",
- " 725,\n",
- " 736,\n",
- " 747,\n",
- " 755,\n",
- " 767,\n",
- " 779,\n",
- " 783,\n",
- " 792,\n",
- " 799,\n",
- " 807,\n",
- " 816,\n",
- " 824,\n",
- " 831,\n",
- " 836,\n",
- " 845,\n",
- " 854,\n",
- " 861,\n",
- " 866,\n",
- " 875,\n",
- " 880,\n",
- " 886,\n",
- " 891,\n",
- " 896,\n",
- " 900,\n",
- " 911,\n",
- " 921,\n",
- " 928,\n",
- " 936,\n",
- " 943,\n",
- " 949,\n",
- " 956,\n",
- " 960,\n",
- " 969,\n",
- " 976,\n",
- " 984,\n",
- " 993,\n",
- " 1002,\n",
- " 1013,\n",
- " 1022,\n",
- " 1027,\n",
- " 1031,\n",
- " 1042,\n",
- " 1049,\n",
- " 1054,\n",
- " 1059,\n",
- " 1066,\n",
- " 1073,\n",
- " 1081,\n",
- " 1088,\n",
- " 1097,\n",
- " 1105,\n",
- " 1110,\n",
- " 1115,\n",
- " 1122,\n",
- " 1127,\n",
- " 1136,\n",
- " 1145,\n",
- " 1153,\n",
- " 1159,\n",
- " 1168,\n",
- " 1177,\n",
- " 1182,\n",
- " 1196,\n",
- " 1202,\n",
- " 1213,\n",
- " 1220,\n",
- " 1227,\n",
- " 1235,\n",
- " 1240,\n",
- " 1252,\n",
- " 1261,\n",
- " 1268,\n",
- " 1275,\n",
- " 1289,\n",
- " 1294,\n",
- " 1302,\n",
- " 1306,\n",
- " 1313,\n",
- " 1317,\n",
- " 1326,\n",
- " 1333,\n",
- " 1338,\n",
- " 1345,\n",
- " 1352,\n",
- " 1361,\n",
- " 1370,\n",
- " 1375,\n",
- " 1384,\n",
- " 1393,\n",
- " 1400,\n",
- " 1410,\n",
- " 1419,\n",
- " 1427,\n",
- " 1435,\n",
- " 1446,\n",
- " 1457,\n",
- " 1471,\n",
- " 1478,\n",
- " 1489,\n",
- " 1495,\n",
- " 1504,\n",
- " 1512,\n",
- " 1516,\n",
- " 1523,\n",
- " 1531,\n",
- " 1539,\n",
- " 1544,\n",
- " 1549,\n",
- " 1558,\n",
- " 1566,\n",
- " 1577,\n",
- " 1585,\n",
- " 1593,\n",
- " 1605,\n",
- " 1609,\n",
- " 1613,\n",
- " 1619,\n",
- " 1626,\n",
- " 1633,\n",
- " 1638,\n",
- " 1647,\n",
- " 1655,\n",
- " 1660,\n",
- " 1671,\n",
- " 1678,\n",
- " 1686,\n",
- " 1698,\n",
- " 1707,\n",
- " 1715,\n",
- " 1726,\n",
- " 1734,\n",
- " 1742,\n",
- " 1750,\n",
- " 1754,\n",
- " 1765,\n",
- " 1773,\n",
- " 1780,\n",
- " 1784,\n",
- " 1788,\n",
- " 1793,\n",
- " 1799,\n",
- " 1807,\n",
- " 1816,\n",
- " 1823,\n",
- " 1832,\n",
- " 1843,\n",
- " 1850,\n",
- " 1859,\n",
- " 1867,\n",
- " 1875,\n",
- " 1884,\n",
- " 1889,\n",
- " 1896,\n",
- " 1906,\n",
- " 1912,\n",
- " 1921,\n",
- " 1928,\n",
- " 1937,\n",
- " 1944,\n",
- " 1952,\n",
- " 1957,\n",
- " 1962,\n",
- " 1967,\n",
- " 1975,\n",
- " 1989,\n",
- " 1998,\n",
- " 2004,\n",
- " 2012,\n",
- " 2016,\n",
- " 2022,\n",
- " 2031,\n",
- " 2037,\n",
- " 2045,\n",
- " 2053,\n",
- " 2060,\n",
- " 2067,\n",
- " 2075,\n",
- " 2083,\n",
- " 2092,\n",
- " 2099,\n",
- " 2107,\n",
- " 2115,\n",
- " 2120,\n",
- " 2125,\n",
- " 2132,\n",
- " 2143,\n",
- " 2151,\n",
- " 2161,\n",
- " 2169,\n",
- " 2176,\n",
- " 2185,\n",
- " 2191,\n",
- " 2198,\n",
- " 2205,\n",
- " 2210,\n",
- " 2217,\n",
- " 2224,\n",
- " 2235,\n",
- " 2243,\n",
- " 2253,\n",
- " 2261,\n",
- " 2268,\n",
- " 2276,\n",
- " 2283,\n",
- " 2292,\n",
- " 2297,\n",
- " 2308,\n",
- " 2316,\n",
- " 2323,\n",
- " 2331,\n",
- " 2338,\n",
- " 2347,\n",
- " 2358,\n",
- " 2367,\n",
- " 2375,\n",
- " 2380,\n",
- " 2385,\n",
- " 2394,\n",
- " 2402,\n",
- " 2407,\n",
- " 2415,\n",
- " 2422,\n",
- " 2433,\n",
- " 2439,\n",
- " 2443,\n",
- " 2448,\n",
- " 2459,\n",
- " 2466,\n",
- " 2470,\n",
- " 2479,\n",
- " 2486,\n",
- " 2492,\n",
- " 2500,\n",
- " 2509,\n",
- " 2517,\n",
- " 2525,\n",
- " 2534,\n",
- " 2542,\n",
- " 2554,\n",
- " 2558,\n",
- " 2566,\n",
- " 2572,\n",
- " 2586,\n",
- " 2593,\n",
- " 2600,\n",
- " 2608,\n",
- " 2612,\n",
- " 2622,\n",
- " 2628,\n",
- " 2637,\n",
- " 2648,\n",
- " 2659,\n",
- " 2667,\n",
- " 2679,\n",
- " 2691,\n",
- " 2695,\n",
- " 2704,\n",
- " 2711,\n",
- " 2719,\n",
- " 2728,\n",
- " 2736,\n",
- " 2743,\n",
- " 2748,\n",
- " 2757,\n",
- " 2766,\n",
- " 2773,\n",
- " 2778,\n",
- " 2787,\n",
- " 2792,\n",
- " 2798,\n",
- " 2803,\n",
- " 2808,\n",
- " 2812,\n",
- " 2823,\n",
- " 2833,\n",
- " 2840,\n",
- " 2848,\n",
- " 2855,\n",
- " 2861,\n",
- " 2868,\n",
- " 2872,\n",
- " 2881,\n",
- " 2888,\n",
- " 2896,\n",
- " 2905,\n",
- " 2914,\n",
- " 2925,\n",
- " 2934,\n",
- " 2939,\n",
- " 2943,\n",
- " 2954,\n",
- " 2961,\n",
- " 2966,\n",
- " 2971,\n",
- " 2978,\n",
- " 2985,\n",
- " 2993,\n",
- " 3000,\n",
- " 3009,\n",
- " 3017,\n",
- " 3022,\n",
- " 3027,\n",
- " 3034,\n",
- " 3039,\n",
- " 3048,\n",
- " 3057,\n",
- " 3065,\n",
- " 3071,\n",
- " 3080,\n",
- " 3089,\n",
- " 3094,\n",
- " 3108,\n",
- " 3114,\n",
- " 3125,\n",
- " 3132,\n",
- " 3139,\n",
- " 3147,\n",
- " 3152,\n",
- " 3164,\n",
- " 3173,\n",
- " 3180,\n",
- " 3187,\n",
- " 3201,\n",
- " 3206,\n",
- " 3214,\n",
- " 3218,\n",
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- " 3808]"
- ]
- },
- "execution_count": 31,
- "metadata": {},
- "output_type": "execute_result"
- }
- ],
+ "outputs": [],
"source": [
"msm.select(molecular_system, 'atom_name==\"N\" bonded to atom_type==\"C\"')"
]
},
{
"cell_type": "code",
- "execution_count": 32,
+ "execution_count": null,
"metadata": {
"tags": [
"scroll-output"
]
},
- "outputs": [
- {
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- " 1894,\n",
- " 1899,\n",
- " 1905]"
- ]
- },
- "execution_count": 32,
- "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",
- " form | \n",
- " n_atoms | \n",
- " n_groups | \n",
- " n_components | \n",
- " n_chains | \n",
- " n_molecules | \n",
- " n_entities | \n",
- " n_peptides | \n",
- " n_structures | \n",
- "
\n",
- " \n",
- " \n",
- " \n",
- " molsysmt.MolSys | \n",
- " 304 | \n",
- " 20 | \n",
- " 1 | \n",
- " 1 | \n",
- " 1 | \n",
- " 1 | \n",
- " 1 | \n",
- " 38 | \n",
- "
\n",
- " \n",
- "
\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": {