{
"cells": [
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
"# Adding Resources\n",
"\n",
"> ### In this tutorial we will cover:\n",
"> - how we can set custom default resources"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"If you checked out the tutorial on _built-in_ data resources you know that BuildAMol comes with a variety of molecular structures for the user to work with directly, such as compounds containing amino acids or sugars. These can be easily loaded using functions such as `load_sugars()`. However, what if we are working on a drug discovery project and would like to engineer small variations of a promising compound? We may have a structure of the compound itself but we don't want to keep re-loading them every time we open a new notebook to use buildamol. But we would like for it to be available by default. \n",
"\n",
"Luckily, BuildAMol allows us to set our own _defaults_ that can be loaded in every future session. We can add _custom linkages_ and _custom structures_ to the default CHARMM topology and PDBE Compounds, respecitively using functions `add_linkage` and `add_compound`. Here's how:"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Adding custom linkages\n",
"\n",
"You may know that you can refer to any registered linkage directly via its string identifier. For example, we can refer to a beta 1->4 glycosydic linkage by its id `14bb`. We do not need to get the linkage object first because BuildAMol will be able to interpret the id and search the linkage object automatically. To make a custom linkage available in such a way, we simply need to define it, give it an id (which is otherwise optional when creating a `Linkage` object). Then we call `add_linkage` with our new linkage and that's it!"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
" \n",
" "
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"import plotly\n",
"plotly.offline.init_notebook_mode()"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"[Linkage(SCK0),\n",
" Linkage(SCK1),\n",
" Linkage(LLLO),\n",
" Linkage(CERA),\n",
" Linkage(CERB),\n",
" Linkage(DAGA),\n",
" Linkage(DAGB),\n",
" Linkage(INS2A),\n",
" Linkage(INS2B),\n",
" Linkage(INS6A),\n",
" Linkage(INS6B),\n",
" Linkage(SGPA),\n",
" Linkage(TGPA),\n",
" Linkage(SGPB),\n",
" Linkage(TGPB),\n",
" Linkage(NGLA),\n",
" Linkage(11aa),\n",
" Linkage(11ab),\n",
" Linkage(11bb),\n",
" Linkage(12aa),\n",
" Linkage(12ab),\n",
" Linkage(12ba),\n",
" Linkage(12bb),\n",
" Linkage(13aa),\n",
" Linkage(13ab),\n",
" Linkage(13ba),\n",
" Linkage(13bb),\n",
" Linkage(14aa),\n",
" Linkage(14ab),\n",
" Linkage(14ba),\n",
" Linkage(14bb),\n",
" Linkage(16aa),\n",
" Linkage(16ab),\n",
" Linkage(16ba),\n",
" Linkage(SUCR),\n",
" Linkage(LCTL),\n",
" Linkage(AB15),\n",
" Linkage(SA23AB),\n",
" Linkage(LINK),\n",
" Linkage(my_14_glyco_link)]"
]
},
"execution_count": 12,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"import buildamol as bam\n",
"\n",
"# define a custom link\n",
"my_link = bam.linkage(atom1=\"C1\", atom2=\"O4\", delete_in_target=[\"O1\", \"HO1\"], delete_in_source=[\"HO4\"], id=\"my_14_glyco_link\")\n",
"\n",
"# now add the link to the default CHARMM topology\n",
"bam.add_linkage(my_link)\n",
"\n",
"# now we find it at the bottom of the list of 'out-of-the-box' available linkages\n",
"bam.available_linkages()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"So, now with our custom linkage added to the default resources, we can for instance make a glucose polymer using:"
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"/Users/noahhk/anaconda3/envs/glyco2/lib/python3.11/site-packages/plotly/express/_core.py:1985: FutureWarning:\n",
"\n",
"When grouping with a length-1 list-like, you will need to pass a length-1 tuple to get_group in a future version of pandas. Pass `(name,)` instead of `name` to silence this warning.\n",
"\n"
]
},
{
"data": {
"application/vnd.plotly.v1+json": {
"config": {
"plotlyServerURL": "https://plot.ly"
},
"data": [
{
"customdata": [
[
"C1",
1,
1,
"GLC",
"A"
],
[
"C2",
2,
1,
"GLC",
"A"
],
[
"C3",
3,
1,
"GLC",
"A"
],
[
"C4",
4,
1,
"GLC",
"A"
],
[
"C5",
5,
1,
"GLC",
"A"
],
[
"C6",
6,
1,
"GLC",
"A"
],
[
"C1",
23,
2,
"GLC",
"A"
],
[
"C2",
24,
2,
"GLC",
"A"
],
[
"C3",
25,
2,
"GLC",
"A"
],
[
"C4",
26,
2,
"GLC",
"A"
],
[
"C5",
27,
2,
"GLC",
"A"
],
[
"C6",
28,
2,
"GLC",
"A"
],
[
"C1",
44,
3,
"GLC",
"A"
],
[
"C2",
45,
3,
"GLC",
"A"
],
[
"C3",
46,
3,
"GLC",
"A"
],
[
"C4",
47,
3,
"GLC",
"A"
],
[
"C5",
48,
3,
"GLC",
"A"
],
[
"C6",
49,
3,
"GLC",
"A"
],
[
"C1",
65,
4,
"GLC",
"A"
],
[
"C2",
66,
4,
"GLC",
"A"
],
[
"C3",
67,
4,
"GLC",
"A"
],
[
"C4",
68,
4,
"GLC",
"A"
],
[
"C5",
69,
4,
"GLC",
"A"
],
[
"C6",
70,
4,
"GLC",
"A"
],
[
"C1",
86,
5,
"GLC",
"A"
],
[
"C2",
87,
5,
"GLC",
"A"
],
[
"C3",
88,
5,
"GLC",
"A"
],
[
"C4",
89,
5,
"GLC",
"A"
],
[
"C5",
90,
5,
"GLC",
"A"
],
[
"C6",
91,
5,
"GLC",
"A"
]
],
"hovertemplate": "atom_element=C
x=%{x}
y=%{y}
z=%{z}
__marker_size=%{marker.size}
atom_id=%{customdata[0]}
atom_serial=%{customdata[1]}
residue_serial=%{customdata[2]}
residue_name=%{customdata[3]}
chain_id=%{customdata[4]}",
"legendgroup": "C",
"marker": {
"color": "darkslategray",
"opacity": 1,
"size": [
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5
],
"sizemode": "area",
"sizeref": 0.0125,
"symbol": "circle"
},
"mode": "markers",
"name": "C",
"scene": "scene",
"showlegend": true,
"type": "scatter3d",
"x": [
8.00008872620539,
8.869329133567875,
10.2185745406163,
10.875138023496648,
9.928417969313866,
10.551911519131092,
4.279421777812658,
4.812962796533892,
6.286435627215825,
6.408932370490664,
5.813116823665707,
5.877799080086633,
3.12434093467413,
4.228261613535333,
5.058002102072048,
4.130010853019524,
3.0296989575155333,
2.06463280801794,
1.8948246970937017,
0.9917058174980087,
1.596245331307629,
3.0187120743880382,
3.8430339677713246,
5.247656818667664,
0.6746277818998989,
0.30286555903404166,
0.41961586392428973,
1.8419722397508378,
2.1545844264871477,
3.594148057016401
],
"y": [
4.653673895218352,
5.740008918186926,
5.794325294450755,
4.411759050387242,
3.376897710859161,
1.9848263017233854,
5.311486741288491,
6.590650092497606,
6.390200674824091,
5.173760659591837,
3.9499252492067383,
2.7440857155314995,
4.418818569786122,
5.478069371030477,
5.281130832923053,
5.350818090281997,
4.297524259757008,
4.400812939884572,
-0.10812378411966989,
1.1237068078103774,
2.1101276982522164,
2.465712914652844,
1.1824664662161186,
1.5238461511492376,
-4.53291084572971,
-3.9994455787413505,
-2.4716830099227023,
-2.0799027056243444,
-2.6880516468592615,
-2.350903258726991
],
"z": [
16.12226664493348,
16.760505105134815,
16.03643496845723,
16.09940300577887,
15.487798438302226,
15.60096638960935,
12.742624760495964,
13.392337083193768,
13.761645691537147,
14.684574853081418,
13.985641578405492,
14.924354114132047,
8.002715485076195,
8.051683585364204,
9.324647423770845,
10.541407847126123,
10.39593331605483,
11.578047005871252,
6.3200149488783754,
6.420118305980362,
7.424706183242854,
6.981222791549849,
6.858548553571687,
6.358640004480151,
8.281334410649556,
6.895600432366971,
6.896978701091941,
7.309217143391371,
8.678050765852038,
9.069715824336015
]
},
{
"customdata": [
[
"O2",
7,
1,
"GLC",
"A"
],
[
"O3",
8,
1,
"GLC",
"A"
],
[
"O4",
9,
1,
"GLC",
"A"
],
[
"O5",
10,
1,
"GLC",
"A"
],
[
"O6",
11,
1,
"GLC",
"A"
],
[
"O2",
29,
2,
"GLC",
"A"
],
[
"O3",
30,
2,
"GLC",
"A"
],
[
"O4",
31,
2,
"GLC",
"A"
],
[
"O5",
32,
2,
"GLC",
"A"
],
[
"O6",
33,
2,
"GLC",
"A"
],
[
"O2",
50,
3,
"GLC",
"A"
],
[
"O3",
51,
3,
"GLC",
"A"
],
[
"O4",
52,
3,
"GLC",
"A"
],
[
"O5",
53,
3,
"GLC",
"A"
],
[
"O6",
54,
3,
"GLC",
"A"
],
[
"O2",
71,
4,
"GLC",
"A"
],
[
"O3",
72,
4,
"GLC",
"A"
],
[
"O4",
73,
4,
"GLC",
"A"
],
[
"O5",
74,
4,
"GLC",
"A"
],
[
"O6",
75,
4,
"GLC",
"A"
],
[
"O1",
92,
5,
"GLC",
"A"
],
[
"O2",
93,
5,
"GLC",
"A"
],
[
"O3",
94,
5,
"GLC",
"A"
],
[
"O4",
95,
5,
"GLC",
"A"
],
[
"O5",
96,
5,
"GLC",
"A"
],
[
"O6",
97,
5,
"GLC",
"A"
]
],
"hovertemplate": "atom_element=O
x=%{x}
y=%{y}
z=%{z}
__marker_size=%{marker.size}
atom_id=%{customdata[0]}
atom_serial=%{customdata[1]}
residue_serial=%{customdata[2]}
residue_name=%{customdata[3]}
chain_id=%{customdata[4]}",
"legendgroup": "O",
"marker": {
"color": "red",
"opacity": 1,
"size": [
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5
],
"sizemode": "area",
"sizeref": 0.0125,
"symbol": "circle"
},
"mode": "markers",
"name": "O",
"scene": "scene",
"showlegend": true,
"type": "scatter3d",
"x": [
8.214204425734204,
11.064046819238435,
12.101016926204586,
8.682985026086307,
9.72400225349688,
4.6945201934631315,
6.772774325919608,
7.786951976022726,
4.451857630044419,
5.430390966373112,
5.071340018724094,
6.0448285257957695,
4.8817237427804185,
2.316913889323759,
1.10552780560133,
-0.3081007561085695,
0.7989314709575854,
3.6184712124039584,
3.2099326073320396,
6.053255601630695,
-0.24712076709293407,
-1.0397224949614254,
0.14586986766737442,
1.9420450814805592,
1.9974347508774162,
3.8495724064403465
],
"y": [
7.004526694524948,
6.754861682405801,
4.431856905739039,
3.399621242097724,
1.0347251668057145,
7.678176724562481,
7.552784147380224,
4.933968200731953,
4.214097636533385,
1.5761781745917136,
5.34231524071908,
6.310616629708775,
5.096662093965195,
4.5193667044800305,
3.343776684758924,
0.7280907425762873,
3.2951419367485717,
3.3291169052943403,
0.29706662536503947,
0.34336408390085615,
-4.028999323913058,
-4.375654817872916,
-1.970203780138926,
-0.6562943253271833,
-4.1065563625427295,
-2.817083246739686
],
"z": [
16.645455504913915,
16.672487225347943,
15.365193912872881,
16.18719419540373,
14.926866188374271,
12.473268438136474,
14.435359532483309,
14.977504099561163,
13.642188004314814,
14.232722018578858,
6.906162036545602,
9.416018117415575,
11.729927287818423,
9.177944245380484,
11.505047350465379,
6.862182554860344,
7.469959499746867,
7.949245789887564,
5.933333016936675,
6.355527161170869,
9.248680672651965,
6.583584526264871,
5.587170428240994,
7.383853635108437,
8.615422089995675,
10.396355044507732
]
},
{
"customdata": [
[
"H1",
12,
1,
"GLC",
"A"
],
[
"H2",
13,
1,
"GLC",
"A"
],
[
"H3",
14,
1,
"GLC",
"A"
],
[
"H4",
15,
1,
"GLC",
"A"
],
[
"H5",
16,
1,
"GLC",
"A"
],
[
"H61",
17,
1,
"GLC",
"A"
],
[
"H62",
18,
1,
"GLC",
"A"
],
[
"HO2",
19,
1,
"GLC",
"A"
],
[
"HO3",
20,
1,
"GLC",
"A"
],
[
"HO4",
21,
1,
"GLC",
"A"
],
[
"HO6",
22,
1,
"GLC",
"A"
],
[
"H1",
34,
2,
"GLC",
"A"
],
[
"H2",
35,
2,
"GLC",
"A"
],
[
"H3",
36,
2,
"GLC",
"A"
],
[
"H4",
37,
2,
"GLC",
"A"
],
[
"H5",
38,
2,
"GLC",
"A"
],
[
"H61",
39,
2,
"GLC",
"A"
],
[
"H62",
40,
2,
"GLC",
"A"
],
[
"HO2",
41,
2,
"GLC",
"A"
],
[
"HO3",
42,
2,
"GLC",
"A"
],
[
"HO6",
43,
2,
"GLC",
"A"
],
[
"H1",
55,
3,
"GLC",
"A"
],
[
"H2",
56,
3,
"GLC",
"A"
],
[
"H3",
57,
3,
"GLC",
"A"
],
[
"H4",
58,
3,
"GLC",
"A"
],
[
"H5",
59,
3,
"GLC",
"A"
],
[
"H61",
60,
3,
"GLC",
"A"
],
[
"H62",
61,
3,
"GLC",
"A"
],
[
"HO2",
62,
3,
"GLC",
"A"
],
[
"HO3",
63,
3,
"GLC",
"A"
],
[
"HO6",
64,
3,
"GLC",
"A"
],
[
"H1",
76,
4,
"GLC",
"A"
],
[
"H2",
77,
4,
"GLC",
"A"
],
[
"H3",
78,
4,
"GLC",
"A"
],
[
"H4",
79,
4,
"GLC",
"A"
],
[
"H5",
80,
4,
"GLC",
"A"
],
[
"H61",
81,
4,
"GLC",
"A"
],
[
"H62",
82,
4,
"GLC",
"A"
],
[
"HO2",
83,
4,
"GLC",
"A"
],
[
"HO3",
84,
4,
"GLC",
"A"
],
[
"HO6",
85,
4,
"GLC",
"A"
],
[
"H1",
98,
5,
"GLC",
"A"
],
[
"H2",
99,
5,
"GLC",
"A"
],
[
"H3",
100,
5,
"GLC",
"A"
],
[
"H4",
101,
5,
"GLC",
"A"
],
[
"H5",
102,
5,
"GLC",
"A"
],
[
"H61",
103,
5,
"GLC",
"A"
],
[
"H62",
104,
5,
"GLC",
"A"
],
[
"HO1",
105,
5,
"GLC",
"A"
],
[
"HO2",
106,
5,
"GLC",
"A"
],
[
"HO3",
107,
5,
"GLC",
"A"
],
[
"HO6",
108,
5,
"GLC",
"A"
]
],
"hovertemplate": "atom_element=H
x=%{x}
y=%{y}
z=%{z}
__marker_size=%{marker.size}
atom_id=%{customdata[0]}
atom_serial=%{customdata[1]}
residue_serial=%{customdata[2]}
residue_name=%{customdata[3]}
chain_id=%{customdata[4]}",
"legendgroup": "H",
"marker": {
"color": "lightgray",
"opacity": 1,
"size": [
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5,
5
],
"sizemode": "area",
"sizeref": 0.0125,
"symbol": "circle"
},
"mode": "markers",
"name": "H",
"scene": "scene",
"showlegend": true,
"type": "scatter3d",
"x": [
7.055020185426322,
9.030345697281339,
10.061391357681558,
11.076160189744037,
9.759102545167531,
11.541373371665681,
10.638338936309598,
7.3501890345449965,
10.705990045082007,
12.747767971305946,
10.058146293047937,
3.2195576570293287,
4.238279886557619,
6.868573801454046,
5.865893071048014,
6.381474961702765,
6.904601638874491,
5.23792058846046,
3.7868110099976233,
6.71871626249516,
5.443584565507713,
2.504290326081252,
3.7800502853489704,
5.546421889348567,
3.6792988428058155,
3.4781398263797385,
2.6218319204629648,
1.5500710906125033,
4.610516360958409,
6.663819440967799,
0.4595938246184854,
1.4916910136858579,
0.9152198419046713,
1.62589805959156,
2.983177902390366,
3.911715576062666,
5.697113576057102,
5.185826668702493,
-0.7496777205322704,
-0.11801809567642402,
6.958626718949353,
0.6348329725044726,
0.9813160307542244,
-0.29453055711324305,
2.5516638301853414,
1.4698744822586722,
3.738658673870412,
4.281955505839753,
-0.07231478626794718,
-1.1876858258093126,
-0.7378952755865401,
4.745713359358138
],
"y": [
4.581499716782729,
5.506781963277467,
6.076886339398849,
4.151431834094111,
3.6151934294878867,
1.9910829263869971,
1.7099031703867138,
7.041416944259252,
7.653542341232345,
5.070324946808429,
0.1283584160605189,
5.433716988135641,
6.809692953829707,
6.2213079431853195,
5.364014628584512,
3.736099819731116,
2.596844256770571,
2.9217379421572365,
7.859707148606053,
8.363311591168586,
0.7718135570035387,
4.5811645933424545,
6.472382533138391,
4.307123598086049,
6.342559646142245,
3.303088997554763,
4.320674079403297,
5.360895307820423,
5.45145055119542,
6.32923739933854,
3.347591692050206,
-0.7942283185432304,
1.6007372671884295,
1.65048565221338,
2.969415384256315,
0.6995772586088408,
2.267466050573238,
1.9238348535068364,
0.0994558139464744,
3.1423061749438843,
0.48510379927088654,
-5.622643124167124,
-4.415877879138565,
-2.0531446388898558,
-2.4581446113667913,
-2.2792872995256745,
-1.2717656900376768,
-2.834405748837942,
-4.326940417446038,
-5.331438731998715,
-2.1878399527249646,
-2.638088501350392
],
"z": [
16.661522930197606,
17.813732931254865,
14.995432229325221,
17.139511091092256,
14.436676924094964,
15.145047430772768,
16.651983313077235,
17.078757378049378,
16.675020983777937,
15.696604000518555,
14.958757785639042,
12.5169949481221,
14.293097749453484,
12.855652098130337,
15.611352467476248,
13.07924392139362,
15.257419360125475,
15.78846302065317,
12.192653500189573,
13.910039640755704,
14.768439752944731,
7.1204785489762354,
8.059295480290984,
9.293182874164467,
10.59896104190288,
10.378374944231972,
12.510807914213384,
11.544031042567909,
6.062737445695484,
8.672821297001974,
12.224022133007175,
5.574424712122652,
5.442262572058891,
8.412675770435978,
6.014255292232626,
7.834463431959619,
7.015872131218956,
5.346772883489668,
6.274422475408754,
7.737695791951123,
6.048309009018382,
8.273528356794627,
6.150014021138501,
7.606242066346666,
6.572144618325574,
9.42262648438145,
9.030795528091137,
8.37629296965092,
10.152422324813788,
6.568820982558592,
5.259402723987679,
10.711096642690464
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
8.00008872620539,
8.869329133567875
],
"y": [
4.653673895218352,
5.740008918186926
],
"z": [
16.12226664493348,
16.760505105134815
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
8.00008872620539,
8.682985026086307
],
"y": [
4.653673895218352,
3.399621242097724
],
"z": [
16.12226664493348,
16.18719419540373
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
8.00008872620539,
7.055020185426322
],
"y": [
4.653673895218352,
4.581499716782729
],
"z": [
16.12226664493348,
16.661522930197606
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
8.00008872620539,
7.786951976022726
],
"y": [
4.653673895218352,
4.933968200731953
],
"z": [
16.12226664493348,
14.977504099561163
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
8.869329133567875,
10.2185745406163
],
"y": [
5.740008918186926,
5.794325294450755
],
"z": [
16.760505105134815,
16.03643496845723
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
8.869329133567875,
8.214204425734204
],
"y": [
5.740008918186926,
7.004526694524948
],
"z": [
16.760505105134815,
16.645455504913915
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
8.869329133567875,
9.030345697281339
],
"y": [
5.740008918186926,
5.506781963277467
],
"z": [
16.760505105134815,
17.813732931254865
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
10.2185745406163,
10.875138023496648
],
"y": [
5.794325294450755,
4.411759050387242
],
"z": [
16.03643496845723,
16.09940300577887
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
10.2185745406163,
11.064046819238435
],
"y": [
5.794325294450755,
6.754861682405801
],
"z": [
16.03643496845723,
16.672487225347943
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
10.2185745406163,
10.061391357681558
],
"y": [
5.794325294450755,
6.076886339398849
],
"z": [
16.03643496845723,
14.995432229325221
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
10.875138023496648,
9.928417969313866
],
"y": [
4.411759050387242,
3.376897710859161
],
"z": [
16.09940300577887,
15.487798438302226
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
10.875138023496648,
12.101016926204586
],
"y": [
4.411759050387242,
4.431856905739039
],
"z": [
16.09940300577887,
15.365193912872881
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
10.875138023496648,
11.076160189744037
],
"y": [
4.411759050387242,
4.151431834094111
],
"z": [
16.09940300577887,
17.139511091092256
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
9.928417969313866,
10.551911519131092
],
"y": [
3.376897710859161,
1.9848263017233854
],
"z": [
15.487798438302226,
15.60096638960935
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
9.928417969313866,
8.682985026086307
],
"y": [
3.376897710859161,
3.399621242097724
],
"z": [
15.487798438302226,
16.18719419540373
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
9.928417969313866,
9.759102545167531
],
"y": [
3.376897710859161,
3.6151934294878867
],
"z": [
15.487798438302226,
14.436676924094964
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
10.551911519131092,
9.72400225349688
],
"y": [
1.9848263017233854,
1.0347251668057145
],
"z": [
15.60096638960935,
14.926866188374271
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
10.551911519131092,
11.541373371665681
],
"y": [
1.9848263017233854,
1.9910829263869971
],
"z": [
15.60096638960935,
15.145047430772768
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
10.551911519131092,
10.638338936309598
],
"y": [
1.9848263017233854,
1.7099031703867138
],
"z": [
15.60096638960935,
16.651983313077235
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
8.214204425734204,
7.3501890345449965
],
"y": [
7.004526694524948,
7.041416944259252
],
"z": [
16.645455504913915,
17.078757378049378
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
11.064046819238435,
10.705990045082007
],
"y": [
6.754861682405801,
7.653542341232345
],
"z": [
16.672487225347943,
16.675020983777937
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
12.101016926204586,
12.747767971305946
],
"y": [
4.431856905739039,
5.070324946808429
],
"z": [
15.365193912872881,
15.696604000518555
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
9.72400225349688,
10.058146293047937
],
"y": [
1.0347251668057145,
0.1283584160605189
],
"z": [
14.926866188374271,
14.958757785639042
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
4.279421777812658,
4.812962796533892
],
"y": [
5.311486741288491,
6.590650092497606
],
"z": [
12.742624760495964,
13.392337083193768
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
4.279421777812658,
4.451857630044419
],
"y": [
5.311486741288491,
4.214097636533385
],
"z": [
12.742624760495964,
13.642188004314814
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
4.279421777812658,
3.2195576570293287
],
"y": [
5.311486741288491,
5.433716988135641
],
"z": [
12.742624760495964,
12.5169949481221
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
4.279421777812658,
4.8817237427804185
],
"y": [
5.311486741288491,
5.096662093965195
],
"z": [
12.742624760495964,
11.729927287818423
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
4.812962796533892,
6.286435627215825
],
"y": [
6.590650092497606,
6.390200674824091
],
"z": [
13.392337083193768,
13.761645691537147
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
4.812962796533892,
4.6945201934631315
],
"y": [
6.590650092497606,
7.678176724562481
],
"z": [
13.392337083193768,
12.473268438136474
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
4.812962796533892,
4.238279886557619
],
"y": [
6.590650092497606,
6.809692953829707
],
"z": [
13.392337083193768,
14.293097749453484
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
6.286435627215825,
6.408932370490664
],
"y": [
6.390200674824091,
5.173760659591837
],
"z": [
13.761645691537147,
14.684574853081418
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
6.286435627215825,
6.772774325919608
],
"y": [
6.390200674824091,
7.552784147380224
],
"z": [
13.761645691537147,
14.435359532483309
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
6.286435627215825,
6.868573801454046
],
"y": [
6.390200674824091,
6.2213079431853195
],
"z": [
13.761645691537147,
12.855652098130337
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
6.408932370490664,
5.813116823665707
],
"y": [
5.173760659591837,
3.9499252492067383
],
"z": [
14.684574853081418,
13.985641578405492
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
6.408932370490664,
7.786951976022726
],
"y": [
5.173760659591837,
4.933968200731953
],
"z": [
14.684574853081418,
14.977504099561163
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
6.408932370490664,
5.865893071048014
],
"y": [
5.173760659591837,
5.364014628584512
],
"z": [
14.684574853081418,
15.611352467476248
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
5.813116823665707,
5.877799080086633
],
"y": [
3.9499252492067383,
2.7440857155314995
],
"z": [
13.985641578405492,
14.924354114132047
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
5.813116823665707,
4.451857630044419
],
"y": [
3.9499252492067383,
4.214097636533385
],
"z": [
13.985641578405492,
13.642188004314814
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
5.813116823665707,
6.381474961702765
],
"y": [
3.9499252492067383,
3.736099819731116
],
"z": [
13.985641578405492,
13.07924392139362
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
5.877799080086633,
5.430390966373112
],
"y": [
2.7440857155314995,
1.5761781745917136
],
"z": [
14.924354114132047,
14.232722018578858
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
5.877799080086633,
6.904601638874491
],
"y": [
2.7440857155314995,
2.596844256770571
],
"z": [
14.924354114132047,
15.257419360125475
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
5.877799080086633,
5.23792058846046
],
"y": [
2.7440857155314995,
2.9217379421572365
],
"z": [
14.924354114132047,
15.78846302065317
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
4.6945201934631315,
3.7868110099976233
],
"y": [
7.678176724562481,
7.859707148606053
],
"z": [
12.473268438136474,
12.192653500189573
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
6.772774325919608,
6.71871626249516
],
"y": [
7.552784147380224,
8.363311591168586
],
"z": [
14.435359532483309,
13.910039640755704
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
5.430390966373112,
5.443584565507713
],
"y": [
1.5761781745917136,
0.7718135570035387
],
"z": [
14.232722018578858,
14.768439752944731
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
3.12434093467413,
4.228261613535333
],
"y": [
4.418818569786122,
5.478069371030477
],
"z": [
8.002715485076195,
8.051683585364204
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
3.12434093467413,
2.316913889323759
],
"y": [
4.418818569786122,
4.5193667044800305
],
"z": [
8.002715485076195,
9.177944245380484
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
3.12434093467413,
2.504290326081252
],
"y": [
4.418818569786122,
4.5811645933424545
],
"z": [
8.002715485076195,
7.1204785489762354
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
3.12434093467413,
3.6184712124039584
],
"y": [
4.418818569786122,
3.3291169052943403
],
"z": [
8.002715485076195,
7.949245789887564
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
4.228261613535333,
5.058002102072048
],
"y": [
5.478069371030477,
5.281130832923053
],
"z": [
8.051683585364204,
9.324647423770845
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
4.228261613535333,
5.071340018724094
],
"y": [
5.478069371030477,
5.34231524071908
],
"z": [
8.051683585364204,
6.906162036545602
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
4.228261613535333,
3.7800502853489704
],
"y": [
5.478069371030477,
6.472382533138391
],
"z": [
8.051683585364204,
8.059295480290984
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
5.058002102072048,
4.130010853019524
],
"y": [
5.281130832923053,
5.350818090281997
],
"z": [
9.324647423770845,
10.541407847126123
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
5.058002102072048,
6.0448285257957695
],
"y": [
5.281130832923053,
6.310616629708775
],
"z": [
9.324647423770845,
9.416018117415575
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
5.058002102072048,
5.546421889348567
],
"y": [
5.281130832923053,
4.307123598086049
],
"z": [
9.324647423770845,
9.293182874164467
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
4.130010853019524,
3.0296989575155333
],
"y": [
5.350818090281997,
4.297524259757008
],
"z": [
10.541407847126123,
10.39593331605483
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
4.130010853019524,
4.8817237427804185
],
"y": [
5.350818090281997,
5.096662093965195
],
"z": [
10.541407847126123,
11.729927287818423
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
4.130010853019524,
3.6792988428058155
],
"y": [
5.350818090281997,
6.342559646142245
],
"z": [
10.541407847126123,
10.59896104190288
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
3.0296989575155333,
2.06463280801794
],
"y": [
4.297524259757008,
4.400812939884572
],
"z": [
10.39593331605483,
11.578047005871252
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
3.0296989575155333,
2.316913889323759
],
"y": [
4.297524259757008,
4.5193667044800305
],
"z": [
10.39593331605483,
9.177944245380484
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
3.0296989575155333,
3.4781398263797385
],
"y": [
4.297524259757008,
3.303088997554763
],
"z": [
10.39593331605483,
10.378374944231972
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
2.06463280801794,
1.10552780560133
],
"y": [
4.400812939884572,
3.343776684758924
],
"z": [
11.578047005871252,
11.505047350465379
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
2.06463280801794,
2.6218319204629648
],
"y": [
4.400812939884572,
4.320674079403297
],
"z": [
11.578047005871252,
12.510807914213384
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
2.06463280801794,
1.5500710906125033
],
"y": [
4.400812939884572,
5.360895307820423
],
"z": [
11.578047005871252,
11.544031042567909
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
5.071340018724094,
4.610516360958409
],
"y": [
5.34231524071908,
5.45145055119542
],
"z": [
6.906162036545602,
6.062737445695484
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
6.0448285257957695,
6.663819440967799
],
"y": [
6.310616629708775,
6.32923739933854
],
"z": [
9.416018117415575,
8.672821297001974
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
1.10552780560133,
0.4595938246184854
],
"y": [
3.343776684758924,
3.347591692050206
],
"z": [
11.505047350465379,
12.224022133007175
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
1.8948246970937017,
0.9917058174980087
],
"y": [
-0.10812378411966989,
1.1237068078103774
],
"z": [
6.3200149488783754,
6.420118305980362
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
1.8948246970937017,
3.2099326073320396
],
"y": [
-0.10812378411966989,
0.29706662536503947
],
"z": [
6.3200149488783754,
5.933333016936675
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
1.8948246970937017,
1.4916910136858579
],
"y": [
-0.10812378411966989,
-0.7942283185432304
],
"z": [
6.3200149488783754,
5.574424712122652
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
1.8948246970937017,
1.9420450814805592
],
"y": [
-0.10812378411966989,
-0.6562943253271833
],
"z": [
6.3200149488783754,
7.383853635108437
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.9917058174980087,
1.596245331307629
],
"y": [
1.1237068078103774,
2.1101276982522164
],
"z": [
6.420118305980362,
7.424706183242854
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.9917058174980087,
-0.3081007561085695
],
"y": [
1.1237068078103774,
0.7280907425762873
],
"z": [
6.420118305980362,
6.862182554860344
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.9917058174980087,
0.9152198419046713
],
"y": [
1.1237068078103774,
1.6007372671884295
],
"z": [
6.420118305980362,
5.442262572058891
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
1.596245331307629,
3.0187120743880382
],
"y": [
2.1101276982522164,
2.465712914652844
],
"z": [
7.424706183242854,
6.981222791549849
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
1.596245331307629,
0.7989314709575854
],
"y": [
2.1101276982522164,
3.2951419367485717
],
"z": [
7.424706183242854,
7.469959499746867
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
1.596245331307629,
1.62589805959156
],
"y": [
2.1101276982522164,
1.65048565221338
],
"z": [
7.424706183242854,
8.412675770435978
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
3.0187120743880382,
3.8430339677713246
],
"y": [
2.465712914652844,
1.1824664662161186
],
"z": [
6.981222791549849,
6.858548553571687
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
3.0187120743880382,
3.6184712124039584
],
"y": [
2.465712914652844,
3.3291169052943403
],
"z": [
6.981222791549849,
7.949245789887564
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
3.0187120743880382,
2.983177902390366
],
"y": [
2.465712914652844,
2.969415384256315
],
"z": [
6.981222791549849,
6.014255292232626
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
3.8430339677713246,
5.247656818667664
],
"y": [
1.1824664662161186,
1.5238461511492376
],
"z": [
6.858548553571687,
6.358640004480151
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
3.8430339677713246,
3.2099326073320396
],
"y": [
1.1824664662161186,
0.29706662536503947
],
"z": [
6.858548553571687,
5.933333016936675
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
3.8430339677713246,
3.911715576062666
],
"y": [
1.1824664662161186,
0.6995772586088408
],
"z": [
6.858548553571687,
7.834463431959619
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
5.247656818667664,
6.053255601630695
],
"y": [
1.5238461511492376,
0.34336408390085615
],
"z": [
6.358640004480151,
6.355527161170869
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
5.247656818667664,
5.697113576057102
],
"y": [
1.5238461511492376,
2.267466050573238
],
"z": [
6.358640004480151,
7.015872131218956
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
5.247656818667664,
5.185826668702493
],
"y": [
1.5238461511492376,
1.9238348535068364
],
"z": [
6.358640004480151,
5.346772883489668
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.3081007561085695,
-0.7496777205322704
],
"y": [
0.7280907425762873,
0.0994558139464744
],
"z": [
6.862182554860344,
6.274422475408754
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.7989314709575854,
-0.11801809567642402
],
"y": [
3.2951419367485717,
3.1423061749438843
],
"z": [
7.469959499746867,
7.737695791951123
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
6.053255601630695,
6.958626718949353
],
"y": [
0.34336408390085615,
0.48510379927088654
],
"z": [
6.355527161170869,
6.048309009018382
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.6746277818998989,
0.30286555903404166
],
"y": [
-4.53291084572971,
-3.9994455787413505
],
"z": [
8.281334410649556,
6.895600432366971
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.6746277818998989,
-0.24712076709293407
],
"y": [
-4.53291084572971,
-4.028999323913058
],
"z": [
8.281334410649556,
9.248680672651965
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.6746277818998989,
1.9974347508774162
],
"y": [
-4.53291084572971,
-4.1065563625427295
],
"z": [
8.281334410649556,
8.615422089995675
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.6746277818998989,
0.6348329725044726
],
"y": [
-4.53291084572971,
-5.622643124167124
],
"z": [
8.281334410649556,
8.273528356794627
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.30286555903404166,
0.41961586392428973
],
"y": [
-3.9994455787413505,
-2.4716830099227023
],
"z": [
6.895600432366971,
6.896978701091941
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.30286555903404166,
-1.0397224949614254
],
"y": [
-3.9994455787413505,
-4.375654817872916
],
"z": [
6.895600432366971,
6.583584526264871
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.30286555903404166,
0.9813160307542244
],
"y": [
-3.9994455787413505,
-4.415877879138565
],
"z": [
6.895600432366971,
6.150014021138501
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.41961586392428973,
1.8419722397508378
],
"y": [
-2.4716830099227023,
-2.0799027056243444
],
"z": [
6.896978701091941,
7.309217143391371
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.41961586392428973,
0.14586986766737442
],
"y": [
-2.4716830099227023,
-1.970203780138926
],
"z": [
6.896978701091941,
5.587170428240994
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.41961586392428973,
-0.29453055711324305
],
"y": [
-2.4716830099227023,
-2.0531446388898558
],
"z": [
6.896978701091941,
7.606242066346666
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
1.8419722397508378,
2.1545844264871477
],
"y": [
-2.0799027056243444,
-2.6880516468592615
],
"z": [
7.309217143391371,
8.678050765852038
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
1.8419722397508378,
1.9420450814805592
],
"y": [
-2.0799027056243444,
-0.6562943253271833
],
"z": [
7.309217143391371,
7.383853635108437
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
1.8419722397508378,
2.5516638301853414
],
"y": [
-2.0799027056243444,
-2.4581446113667913
],
"z": [
7.309217143391371,
6.572144618325574
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
2.1545844264871477,
3.594148057016401
],
"y": [
-2.6880516468592615,
-2.350903258726991
],
"z": [
8.678050765852038,
9.069715824336015
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
2.1545844264871477,
1.9974347508774162
],
"y": [
-2.6880516468592615,
-4.1065563625427295
],
"z": [
8.678050765852038,
8.615422089995675
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
2.1545844264871477,
1.4698744822586722
],
"y": [
-2.6880516468592615,
-2.2792872995256745
],
"z": [
8.678050765852038,
9.42262648438145
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
3.594148057016401,
3.8495724064403465
],
"y": [
-2.350903258726991,
-2.817083246739686
],
"z": [
9.069715824336015,
10.396355044507732
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
3.594148057016401,
3.738658673870412
],
"y": [
-2.350903258726991,
-1.2717656900376768
],
"z": [
9.069715824336015,
9.030795528091137
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
3.594148057016401,
4.281955505839753
],
"y": [
-2.350903258726991,
-2.834405748837942
],
"z": [
9.069715824336015,
8.37629296965092
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.24712076709293407,
-0.07231478626794718
],
"y": [
-4.028999323913058,
-4.326940417446038
],
"z": [
9.248680672651965,
10.152422324813788
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-1.0397224949614254,
-1.1876858258093126
],
"y": [
-4.375654817872916,
-5.331438731998715
],
"z": [
6.583584526264871,
6.568820982558592
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.14586986766737442,
-0.7378952755865401
],
"y": [
-1.970203780138926,
-2.1878399527249646
],
"z": [
5.587170428240994,
5.259402723987679
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
3.8495724064403465,
4.745713359358138
],
"y": [
-2.817083246739686,
-2.638088501350392
],
"z": [
10.396355044507732,
10.711096642690464
]
}
],
"layout": {
"scene": {
"xaxis": {
"showgrid": false,
"showline": false,
"showticklabels": false
},
"yaxis": {
"showgrid": false,
"showline": false,
"showticklabels": false
},
"zaxis": {
"showgrid": false,
"showline": false,
"showticklabels": false
}
},
"template": {
"data": {
"bar": [
{
"error_x": {
"color": "rgb(36,36,36)"
},
"error_y": {
"color": "rgb(36,36,36)"
},
"marker": {
"line": {
"color": "white",
"width": 0.5
},
"pattern": {
"fillmode": "overlay",
"size": 10,
"solidity": 0.2
}
},
"type": "bar"
}
],
"barpolar": [
{
"marker": {
"line": {
"color": "white",
"width": 0.5
},
"pattern": {
"fillmode": "overlay",
"size": 10,
"solidity": 0.2
}
},
"type": "barpolar"
}
],
"carpet": [
{
"aaxis": {
"endlinecolor": "rgb(36,36,36)",
"gridcolor": "white",
"linecolor": "white",
"minorgridcolor": "white",
"startlinecolor": "rgb(36,36,36)"
},
"baxis": {
"endlinecolor": "rgb(36,36,36)",
"gridcolor": "white",
"linecolor": "white",
"minorgridcolor": "white",
"startlinecolor": "rgb(36,36,36)"
},
"type": "carpet"
}
],
"choropleth": [
{
"colorbar": {
"outlinewidth": 1,
"tickcolor": "rgb(36,36,36)",
"ticks": "outside"
},
"type": "choropleth"
}
],
"contour": [
{
"colorbar": {
"outlinewidth": 1,
"tickcolor": "rgb(36,36,36)",
"ticks": "outside"
},
"colorscale": [
[
0,
"#440154"
],
[
0.1111111111111111,
"#482878"
],
[
0.2222222222222222,
"#3e4989"
],
[
0.3333333333333333,
"#31688e"
],
[
0.4444444444444444,
"#26828e"
],
[
0.5555555555555556,
"#1f9e89"
],
[
0.6666666666666666,
"#35b779"
],
[
0.7777777777777778,
"#6ece58"
],
[
0.8888888888888888,
"#b5de2b"
],
[
1,
"#fde725"
]
],
"type": "contour"
}
],
"contourcarpet": [
{
"colorbar": {
"outlinewidth": 1,
"tickcolor": "rgb(36,36,36)",
"ticks": "outside"
},
"type": "contourcarpet"
}
],
"heatmap": [
{
"colorbar": {
"outlinewidth": 1,
"tickcolor": "rgb(36,36,36)",
"ticks": "outside"
},
"colorscale": [
[
0,
"#440154"
],
[
0.1111111111111111,
"#482878"
],
[
0.2222222222222222,
"#3e4989"
],
[
0.3333333333333333,
"#31688e"
],
[
0.4444444444444444,
"#26828e"
],
[
0.5555555555555556,
"#1f9e89"
],
[
0.6666666666666666,
"#35b779"
],
[
0.7777777777777778,
"#6ece58"
],
[
0.8888888888888888,
"#b5de2b"
],
[
1,
"#fde725"
]
],
"type": "heatmap"
}
],
"heatmapgl": [
{
"colorbar": {
"outlinewidth": 1,
"tickcolor": "rgb(36,36,36)",
"ticks": "outside"
},
"colorscale": [
[
0,
"#440154"
],
[
0.1111111111111111,
"#482878"
],
[
0.2222222222222222,
"#3e4989"
],
[
0.3333333333333333,
"#31688e"
],
[
0.4444444444444444,
"#26828e"
],
[
0.5555555555555556,
"#1f9e89"
],
[
0.6666666666666666,
"#35b779"
],
[
0.7777777777777778,
"#6ece58"
],
[
0.8888888888888888,
"#b5de2b"
],
[
1,
"#fde725"
]
],
"type": "heatmapgl"
}
],
"histogram": [
{
"marker": {
"line": {
"color": "white",
"width": 0.6
}
},
"type": "histogram"
}
],
"histogram2d": [
{
"colorbar": {
"outlinewidth": 1,
"tickcolor": "rgb(36,36,36)",
"ticks": "outside"
},
"colorscale": [
[
0,
"#440154"
],
[
0.1111111111111111,
"#482878"
],
[
0.2222222222222222,
"#3e4989"
],
[
0.3333333333333333,
"#31688e"
],
[
0.4444444444444444,
"#26828e"
],
[
0.5555555555555556,
"#1f9e89"
],
[
0.6666666666666666,
"#35b779"
],
[
0.7777777777777778,
"#6ece58"
],
[
0.8888888888888888,
"#b5de2b"
],
[
1,
"#fde725"
]
],
"type": "histogram2d"
}
],
"histogram2dcontour": [
{
"colorbar": {
"outlinewidth": 1,
"tickcolor": "rgb(36,36,36)",
"ticks": "outside"
},
"colorscale": [
[
0,
"#440154"
],
[
0.1111111111111111,
"#482878"
],
[
0.2222222222222222,
"#3e4989"
],
[
0.3333333333333333,
"#31688e"
],
[
0.4444444444444444,
"#26828e"
],
[
0.5555555555555556,
"#1f9e89"
],
[
0.6666666666666666,
"#35b779"
],
[
0.7777777777777778,
"#6ece58"
],
[
0.8888888888888888,
"#b5de2b"
],
[
1,
"#fde725"
]
],
"type": "histogram2dcontour"
}
],
"mesh3d": [
{
"colorbar": {
"outlinewidth": 1,
"tickcolor": "rgb(36,36,36)",
"ticks": "outside"
},
"type": "mesh3d"
}
],
"parcoords": [
{
"line": {
"colorbar": {
"outlinewidth": 1,
"tickcolor": "rgb(36,36,36)",
"ticks": "outside"
}
},
"type": "parcoords"
}
],
"pie": [
{
"automargin": true,
"type": "pie"
}
],
"scatter": [
{
"fillpattern": {
"fillmode": "overlay",
"size": 10,
"solidity": 0.2
},
"type": "scatter"
}
],
"scatter3d": [
{
"line": {
"colorbar": {
"outlinewidth": 1,
"tickcolor": "rgb(36,36,36)",
"ticks": "outside"
}
},
"marker": {
"colorbar": {
"outlinewidth": 1,
"tickcolor": "rgb(36,36,36)",
"ticks": "outside"
}
},
"type": "scatter3d"
}
],
"scattercarpet": [
{
"marker": {
"colorbar": {
"outlinewidth": 1,
"tickcolor": "rgb(36,36,36)",
"ticks": "outside"
}
},
"type": "scattercarpet"
}
],
"scattergeo": [
{
"marker": {
"colorbar": {
"outlinewidth": 1,
"tickcolor": "rgb(36,36,36)",
"ticks": "outside"
}
},
"type": "scattergeo"
}
],
"scattergl": [
{
"marker": {
"colorbar": {
"outlinewidth": 1,
"tickcolor": "rgb(36,36,36)",
"ticks": "outside"
}
},
"type": "scattergl"
}
],
"scattermapbox": [
{
"marker": {
"colorbar": {
"outlinewidth": 1,
"tickcolor": "rgb(36,36,36)",
"ticks": "outside"
}
},
"type": "scattermapbox"
}
],
"scatterpolar": [
{
"marker": {
"colorbar": {
"outlinewidth": 1,
"tickcolor": "rgb(36,36,36)",
"ticks": "outside"
}
},
"type": "scatterpolar"
}
],
"scatterpolargl": [
{
"marker": {
"colorbar": {
"outlinewidth": 1,
"tickcolor": "rgb(36,36,36)",
"ticks": "outside"
}
},
"type": "scatterpolargl"
}
],
"scatterternary": [
{
"marker": {
"colorbar": {
"outlinewidth": 1,
"tickcolor": "rgb(36,36,36)",
"ticks": "outside"
}
},
"type": "scatterternary"
}
],
"surface": [
{
"colorbar": {
"outlinewidth": 1,
"tickcolor": "rgb(36,36,36)",
"ticks": "outside"
},
"colorscale": [
[
0,
"#440154"
],
[
0.1111111111111111,
"#482878"
],
[
0.2222222222222222,
"#3e4989"
],
[
0.3333333333333333,
"#31688e"
],
[
0.4444444444444444,
"#26828e"
],
[
0.5555555555555556,
"#1f9e89"
],
[
0.6666666666666666,
"#35b779"
],
[
0.7777777777777778,
"#6ece58"
],
[
0.8888888888888888,
"#b5de2b"
],
[
1,
"#fde725"
]
],
"type": "surface"
}
],
"table": [
{
"cells": {
"fill": {
"color": "rgb(237,237,237)"
},
"line": {
"color": "white"
}
},
"header": {
"fill": {
"color": "rgb(217,217,217)"
},
"line": {
"color": "white"
}
},
"type": "table"
}
]
},
"layout": {
"annotationdefaults": {
"arrowhead": 0,
"arrowwidth": 1
},
"autotypenumbers": "strict",
"coloraxis": {
"colorbar": {
"outlinewidth": 1,
"tickcolor": "rgb(36,36,36)",
"ticks": "outside"
}
},
"colorscale": {
"diverging": [
[
0,
"rgb(103,0,31)"
],
[
0.1,
"rgb(178,24,43)"
],
[
0.2,
"rgb(214,96,77)"
],
[
0.3,
"rgb(244,165,130)"
],
[
0.4,
"rgb(253,219,199)"
],
[
0.5,
"rgb(247,247,247)"
],
[
0.6,
"rgb(209,229,240)"
],
[
0.7,
"rgb(146,197,222)"
],
[
0.8,
"rgb(67,147,195)"
],
[
0.9,
"rgb(33,102,172)"
],
[
1,
"rgb(5,48,97)"
]
],
"sequential": [
[
0,
"#440154"
],
[
0.1111111111111111,
"#482878"
],
[
0.2222222222222222,
"#3e4989"
],
[
0.3333333333333333,
"#31688e"
],
[
0.4444444444444444,
"#26828e"
],
[
0.5555555555555556,
"#1f9e89"
],
[
0.6666666666666666,
"#35b779"
],
[
0.7777777777777778,
"#6ece58"
],
[
0.8888888888888888,
"#b5de2b"
],
[
1,
"#fde725"
]
],
"sequentialminus": [
[
0,
"#440154"
],
[
0.1111111111111111,
"#482878"
],
[
0.2222222222222222,
"#3e4989"
],
[
0.3333333333333333,
"#31688e"
],
[
0.4444444444444444,
"#26828e"
],
[
0.5555555555555556,
"#1f9e89"
],
[
0.6666666666666666,
"#35b779"
],
[
0.7777777777777778,
"#6ece58"
],
[
0.8888888888888888,
"#b5de2b"
],
[
1,
"#fde725"
]
]
},
"colorway": [
"#1F77B4",
"#FF7F0E",
"#2CA02C",
"#D62728",
"#9467BD",
"#8C564B",
"#E377C2",
"#7F7F7F",
"#BCBD22",
"#17BECF"
],
"font": {
"color": "rgb(36,36,36)"
},
"geo": {
"bgcolor": "white",
"lakecolor": "white",
"landcolor": "white",
"showlakes": true,
"showland": true,
"subunitcolor": "white"
},
"hoverlabel": {
"align": "left"
},
"hovermode": "closest",
"mapbox": {
"style": "light"
},
"paper_bgcolor": "white",
"plot_bgcolor": "white",
"polar": {
"angularaxis": {
"gridcolor": "rgb(232,232,232)",
"linecolor": "rgb(36,36,36)",
"showgrid": false,
"showline": true,
"ticks": "outside"
},
"bgcolor": "white",
"radialaxis": {
"gridcolor": "rgb(232,232,232)",
"linecolor": "rgb(36,36,36)",
"showgrid": false,
"showline": true,
"ticks": "outside"
}
},
"scene": {
"xaxis": {
"backgroundcolor": "white",
"gridcolor": "rgb(232,232,232)",
"gridwidth": 2,
"linecolor": "rgb(36,36,36)",
"showbackground": true,
"showgrid": false,
"showline": true,
"ticks": "outside",
"zeroline": false,
"zerolinecolor": "rgb(36,36,36)"
},
"yaxis": {
"backgroundcolor": "white",
"gridcolor": "rgb(232,232,232)",
"gridwidth": 2,
"linecolor": "rgb(36,36,36)",
"showbackground": true,
"showgrid": false,
"showline": true,
"ticks": "outside",
"zeroline": false,
"zerolinecolor": "rgb(36,36,36)"
},
"zaxis": {
"backgroundcolor": "white",
"gridcolor": "rgb(232,232,232)",
"gridwidth": 2,
"linecolor": "rgb(36,36,36)",
"showbackground": true,
"showgrid": false,
"showline": true,
"ticks": "outside",
"zeroline": false,
"zerolinecolor": "rgb(36,36,36)"
}
},
"shapedefaults": {
"fillcolor": "black",
"line": {
"width": 0
},
"opacity": 0.3
},
"ternary": {
"aaxis": {
"gridcolor": "rgb(232,232,232)",
"linecolor": "rgb(36,36,36)",
"showgrid": false,
"showline": true,
"ticks": "outside"
},
"baxis": {
"gridcolor": "rgb(232,232,232)",
"linecolor": "rgb(36,36,36)",
"showgrid": false,
"showline": true,
"ticks": "outside"
},
"bgcolor": "white",
"caxis": {
"gridcolor": "rgb(232,232,232)",
"linecolor": "rgb(36,36,36)",
"showgrid": false,
"showline": true,
"ticks": "outside"
}
},
"title": {
"x": 0.05
},
"xaxis": {
"automargin": true,
"gridcolor": "rgb(232,232,232)",
"linecolor": "rgb(36,36,36)",
"showgrid": false,
"showline": true,
"ticks": "outside",
"title": {
"standoff": 15
},
"zeroline": false,
"zerolinecolor": "rgb(36,36,36)"
},
"yaxis": {
"automargin": true,
"gridcolor": "rgb(232,232,232)",
"linecolor": "rgb(36,36,36)",
"showgrid": false,
"showline": true,
"ticks": "outside",
"title": {
"standoff": 15
},
"zeroline": false,
"zerolinecolor": "rgb(36,36,36)"
}
}
}
}
},
"text/html": [
""
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"bam.load_sugars()\n",
"\n",
"glc = bam.molecule(\"GLC\")\n",
"\n",
"# connect using only the string identifier\n",
"# instead of the actual Linkage object\n",
"new = bam.polymerize(glc, 5, \"my_14_glyco_link\")\n",
"new.show()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"If we close the notebook, we will have lost `\"my_14_glyco_link\"` however. In order to ensure it is available in all future sessions, we can call `add_linkage` with the additional argument `overwrite=True`. This will permanently save the modified CHARMM topology as the new default."
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {},
"outputs": [],
"source": [
"# now the linkage is available even the next time we open a new notebook or restart the kernel\n",
"# bam.add_linkage(my_link, overwrite=True)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Adding custom structures\n",
"\n",
"While it is true that BuildAMol does not load sugar-compounds and the like automatically, it does actually load a default PDBE compounds instance (it just happens to be empty be default). It can be populated with anything we want, however, using the `add_compound` function. The function expects a molecule, alongside with some additional metadata such as identifiers and name synonyms by which the molecule can be found. The logic is identical to `add_linkage` and we can make the additions permanent using the `overwrite=True` argument when calling `add_compound`. "
]
},
{
"cell_type": "code",
"execution_count": 15,
"metadata": {},
"outputs": [],
"source": [
"# first we need to make sure the molecule has a good id\n",
"# the id can be anything, but it needs to be unique\n",
"new.id = \"my_sugar\"\n",
"\n",
"# now let's add our small sugar compound to the PDBE compounds\n",
"# we provide as metadata only two names for the compound (more options are available)\n",
"bam.add_compound(new, names=[\"my first sugar\", \"glucose-mannose\"])"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Now we can check if `\"my_sugar\"` is available as a compound using `bam.has_compound`:"
]
},
{
"cell_type": "code",
"execution_count": 16,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"(True, True)"
]
},
"execution_count": 16,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# the has_compound function accepts both the \n",
"# registered id as well as any of the name synonyms or identifiers\n",
"bam.has_compound(\"my_sugar\"), bam.has_compound(\"my first sugar\")"
]
},
{
"cell_type": "code",
"execution_count": 17,
"metadata": {},
"outputs": [],
"source": [
"# again we can make the compound available for the next time we open a new notebook or restart the kernel\n",
"# by using the overwrite=True option\n",
"bam.add_compound(new, names=[\"my first sugar\", \"glucose-mannose\"], overwrite=True)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"> #### Warning\n",
"> Using the `add_compound` function using `overwrite=True` can lead to an unwanted consequence: all other loaded compounds are automatically also added to the default compounds! That means, since we called `load_sugars` before, now the default loaded compounds will include not only our `my_sugar` molecule but also all the sugars that we loaded before! To prevent this from happening it would be better first to create a new instance of `PDBECompounds`, add the compound there. Then use the `save_as_default_compounds` function to permanently set the defaults in this way."
]
},
{
"cell_type": "code",
"execution_count": 18,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"['my_sugar']"
]
},
"execution_count": 18,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# make a new empty PDBECompounds object\n",
"new_compounds = bam.PDBECompounds()\n",
"\n",
"# now we can add our compound to the new object\n",
"new_compounds.add(new, type=\"CUSTOM-MOLECULES\", names=[\"my first sugar\", \"glucose-mannose\"])\n",
"\n",
"# check what compounds are now available in the new object\n",
"new_compounds.ids"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Now we can save this object as the future default using `save_as_default_compounds`, without saving the 1000-something sugar compounds that are currently also loaded."
]
},
{
"cell_type": "code",
"execution_count": 19,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"1069"
]
},
"execution_count": 19,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# save as defaults\n",
"bam.save_as_default_compounds(new_compounds)\n",
"\n",
"# print the number of currently loaded compounds\n",
"len(bam.get_default_compounds())"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"What if we have multiple compounds already added to our defaults which we would like to keep? The easiest way to handle this kind of scenario is using `subset_compounds_by_types` in order to get a new `PDBECompounds` object that only contains compounds of interest. For instance, if we always set the type of our custom molecules to be `CUSTOM-MOLECULES`, then we can always get our custom defaults using `subset_compounds_by_types(\"CUSTOM-MOLECULES\")`, add any new compound to this database, and use `save_as_default_compounds` to make sure we have our molecules available in the future. \n",
"\n",
"All this will leave the currently loaded default compounds of 1000-sugars and our custom molecules completely unaffected. "
]
},
{
"cell_type": "code",
"execution_count": 20,
"metadata": {},
"outputs": [],
"source": [
"# get all custom compounds we may have already added in the past\n",
"my_compounds = bam.subset_compounds_by_types(\"CUSTOM-MOLECULES\")\n",
"\n",
"# now add the new compounds to the existing ones\n",
"my_compounds.add(new, type=\"CUSTOM-MOLECULES\", names=[\"my first sugar\", \"glucose-mannose\"])\n",
"\n",
"# (if we have not already done so) also add it to the current defaults (just don't use overwrite=True)\n",
"bam.add_compound(new, type=\"CUSTOM-MOLECULES\", names=[\"my first sugar\", \"glucose-mannose\"])\n",
"\n",
"# now save the new compounds as defaults\n",
"bam.save_as_default_compounds(my_compounds)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Handling updates\n",
"\n",
"Setting defaults like this will overwrite some files in your local BuildAMol package directory. Since BuildAMol comes with these same files when you install it, every update would overwrite your custom defaults again. To make sure your custom settings are not simply lost, be sure to call `export_custom_resources` before updating. This will export your CHARMM Topology and PDBECompounds database to external files in some directory of your choice. After the update you can use `import_custom_resources` to point to these files and re-set your precious settings (again `import_custom_resources` can be used transiently or permanently, depending on whether or not we use `overwrite=True` or not).\n",
"\n",
"> #### Note\n",
"> These functions will use the currently loaded default compounds."
]
},
{
"cell_type": "code",
"execution_count": 22,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"(True, True)"
]
},
"execution_count": 22,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# export the custom defaults we just made\n",
"# to the current directory\n",
"bam.export_custom_resources(\"./files\")\n",
"\n",
"# now we can load the custom resources from the current directory\n",
"bam.import_custom_resources(\"./files\")\n",
"\n",
"# and again check for our custom glycan\n",
"bam.has_compound(\"my_sugar\"), bam.has_compound(\"my first sugar\")"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"### Restoring BuildAMol defaults\n",
"\n",
"Made a mistake and now your compounds are messed up? You can always call `restore_default_compounds` or `restore_default_topology` to get the previous settings back. This will restore your settings to BuildAMol factory defaults, i.e. an empty component library! Make sure to first export any compounds you would like to keep using `subset_compounds_by_types` or more thoroughly using `export_compounds` and later use the `PDBECompounds.merge` method to create a custom library to your liking. "
]
}
],
"metadata": {
"kernelspec": {
"display_name": "glyco2",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.0"
},
"orig_nbformat": 4
},
"nbformat": 4,
"nbformat_minor": 2
}