{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Building Workflow"
]
},
{
"attachments": {},
"cell_type": "markdown",
"metadata": {},
"source": [
"> ### In this tutorial we will cover:\n",
"> - the basic \"workflow\" of building a larger molecule in biobuild"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Building molecules is a straightforward task in biobuild. It involves always the same steps:\n",
"\n",
"```mermaid\n",
"\n",
"flowchart TB\n",
" node_1[\"identify suitable sub-structure A\"]\n",
" node_2[\"identify suitable sub-structure B\"]\n",
" node_3[\"identify what you want to build\"]\n",
" node_4[\"identify atom to connect to B\"]\n",
" node_5[\"identify atom to connect to A\"]\n",
" node_6[\"identify atom(s) to\\nremove when connecting to B\"]\n",
" node_7[\"identify atom(s) to\\nremove when connecting to A\"]\n",
" node_8((\"connect\"))\n",
" node_9(\"repeat\")\n",
" node_3 --> node_1\n",
" node_3 --> node_2\n",
" node_1 --> node_4\n",
" node_2 --> node_5\n",
" node_1 --> node_6\n",
" node_2 --> node_7\n",
" node_6 ---> node_8\n",
" node_4 ---> node_8\n",
" node_5 --> node_8\n",
" node_7 --> node_8\n",
" node_8 --> node_9\n",
"\n",
"```"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"As for steps 1 and 2, finding a structure to build and identifying subcomponents - that's on you, biobuild cannot help you there! As for steps 3 and 4, thats where biobuild can start to help you. How do you identify which atoms to connect and which to remove? Well, by looking at the structures, of course! \n",
"\n",
"If biobuild has a linkage already defined for your specific task, great! But most of the time we want to build custom molecules for which the CHARMM force field does not conveniently have a patch defined. So we need to define the linkage ourselves. We can do this by looking at the structure, checking out what the atoms we want to connect are called, and then define our linkage. We can either connect molecules using the `Molecule.attach` method where we can directly provide the information regarding atoms-to-connect and -remove, or we first set up a `Linkage` which can then use instead. \n",
"\n",
"The advantage of setting up a `Linkage` first is that we can then re-use the same linkage time and time again, without needing to keep filling in the information manually. We can even add custom linkages to the default settings to make them permanently available whenever we use biobuild (checkout the tutorials regarding built-in resources and setting defaults). "
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Working by example is usually best, so let us build the following molecule:"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
""
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"We can start by identifying the different components that we might want to work with. For example we can choose these:\n",
"\n",
""
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"With our components decided, we can start to build. The first step is getting the molecular structures we need. PubChem is sure to have the structures available, so we are not going to load any built-in structures."
]
},
{
"cell_type": "code",
"execution_count": 1,
"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": 2,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"Molecule(1,2,4a,8a-tetrahydronaphthalene)"
]
},
"execution_count": 2,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"import biobuild as bb\n",
"\n",
"# get the molecules we need\n",
"phenyl_methanol = bb.molecule(\"phenylmethanol\")\n",
"aldehyde = bb.molecule(\"butyraldehyde\")\n",
"amine = bb.molecule(\"methoxyethanamine\")\n",
"naphthalene = bb.molecule(\"1,2,4a,8a-tetrahydronaphthalene\")\n",
"\n",
"# because PubChem structures use a simple enumeration rather than hierarchical atom labelling\n",
"# we can (optionally) call `autolabel` to assign more descriptive atom labels which is useful for \n",
"# defining linkages\n",
"phenyl_methanol.autolabel()\n",
"aldehyde.autolabel()\n",
"amine.autolabel()\n",
"naphthalene.autolabel() "
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Now that our molecules are all ready, we can start building. We start by attaching the `phenyl_methanol` to the `aldehyde`. To do this, we first visualize both structures to identify the `atom ids` of the atoms we want to connect and remove in both cases."
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"data": {
"application/vnd.plotly.v1+json": {
"config": {
"plotlyServerURL": "https://plot.ly"
},
"data": [
{
"customdata": [
[
"O7",
1,
1,
"UNK",
"A"
]
],
"hovertemplate": "atom_element=O
x=%{x}
y=%{y}
z=%{z}
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,
"symbol": "circle"
},
"mode": "markers",
"name": "O",
"scene": "scene",
"showlegend": true,
"type": "scatter3d",
"x": [
2.7427
],
"y": [
0.0002
],
"z": [
-0.7083
]
},
{
"customdata": [
[
"C1",
2,
1,
"UNK",
"A"
],
[
"C7",
3,
1,
"UNK",
"A"
],
[
"C2",
4,
1,
"UNK",
"A"
],
[
"C6",
5,
1,
"UNK",
"A"
],
[
"C3",
6,
1,
"UNK",
"A"
],
[
"C5",
7,
1,
"UNK",
"A"
],
[
"C4",
8,
1,
"UNK",
"A"
]
],
"hovertemplate": "atom_element=C
x=%{x}
y=%{y}
z=%{z}
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,
"symbol": "circle"
},
"mode": "markers",
"name": "C",
"scene": "scene",
"showlegend": true,
"type": "scatter3d",
"x": [
0.5758,
2.0447,
-0.111,
-0.1111,
-1.4847,
-1.4848,
-2.1715
],
"y": [
-0.0002,
-0.0001,
1.2079,
-1.2082,
1.2081,
-1.2079,
0.0002
],
"z": [
0.272,
0.5309,
0.1508,
0.1507,
-0.0915,
-0.0917,
-0.2128
]
},
{
"customdata": [
[
"H71",
9,
1,
"UNK",
"A"
],
[
"H72",
10,
1,
"UNK",
"A"
],
[
"H2",
11,
1,
"UNK",
"A"
],
[
"H6",
12,
1,
"UNK",
"A"
],
[
"H3",
13,
1,
"UNK",
"A"
],
[
"H5",
14,
1,
"UNK",
"A"
],
[
"H4",
15,
1,
"UNK",
"A"
],
[
"HO7",
16,
1,
"UNK",
"A"
]
],
"hovertemplate": "atom_element=H
x=%{x}
y=%{y}
z=%{z}
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,
"symbol": "circle"
},
"mode": "markers",
"name": "H",
"scene": "scene",
"showlegend": true,
"type": "scatter3d",
"x": [
2.3502,
2.3501,
0.4133,
0.413,
-2.0194,
-2.0198,
-3.241,
2.3709
],
"y": [
0.8799,
-0.8828,
2.1555,
-2.1559,
2.1486,
-2.1484,
0.0003,
0.7034
],
"z": [
1.1071,
1.1025,
0.2415,
0.2413,
-0.1864,
-0.1868,
-0.4018,
-1.2677
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
2.7427,
2.0447
],
"y": [
0.0002,
-0.0001
],
"z": [
-0.7083,
0.5309
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
2.7427,
2.3709
],
"y": [
0.0002,
0.7034
],
"z": [
-0.7083,
-1.2677
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.5758,
2.0447
],
"y": [
-0.0002,
-0.0001
],
"z": [
0.272,
0.5309
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.5758,
-0.111
],
"y": [
-0.0002,
1.2079
],
"z": [
0.272,
0.1508
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.5758,
-0.1111
],
"y": [
-0.0002,
-1.2082
],
"z": [
0.272,
0.1507
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
2.0447,
2.3502
],
"y": [
-0.0001,
0.8799
],
"z": [
0.5309,
1.1071
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
2.0447,
2.3501
],
"y": [
-0.0001,
-0.8828
],
"z": [
0.5309,
1.1025
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.111,
-1.4847
],
"y": [
1.2079,
1.2081
],
"z": [
0.1508,
-0.0915
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.111,
0.4133
],
"y": [
1.2079,
2.1555
],
"z": [
0.1508,
0.2415
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.1111,
-1.4848
],
"y": [
-1.2082,
-1.2079
],
"z": [
0.1507,
-0.0917
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.1111,
0.413
],
"y": [
-1.2082,
-2.1559
],
"z": [
0.1507,
0.2413
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-1.4847,
-2.1715
],
"y": [
1.2081,
0.0002
],
"z": [
-0.0915,
-0.2128
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-1.4847,
-2.0194
],
"y": [
1.2081,
2.1486
],
"z": [
-0.0915,
-0.1864
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-1.4848,
-2.1715
],
"y": [
-1.2079,
0.0002
],
"z": [
-0.0917,
-0.2128
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-1.4848,
-2.0198
],
"y": [
-1.2079,
-2.1484
],
"z": [
-0.0917,
-0.1868
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-2.1715,
-3.241
],
"y": [
0.0002,
0.0003
],
"z": [
-0.2128,
-0.4018
]
}
],
"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": [
"# visulize the methanol\n",
"phenyl_methanol.show()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"From the inspection we can tell that the Oxygen is called `O7`, it is connected to `C7` and `HO7`. `C7` has two hydrogens called `H71` and `H72`. That's all we needed to know at this point. Next up is the aldehyde:"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"data": {
"application/vnd.plotly.v1+json": {
"config": {
"plotlyServerURL": "https://plot.ly"
},
"data": [
{
"customdata": [
[
"O1",
1,
1,
"UNK",
"A"
]
],
"hovertemplate": "atom_element=O
x=%{x}
y=%{y}
z=%{z}
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,
"symbol": "circle"
},
"mode": "markers",
"name": "O",
"scene": "scene",
"showlegend": true,
"type": "scatter3d",
"x": [
1.9015
],
"y": [
-0.6791
],
"z": [
-0.0023
]
},
{
"customdata": [
[
"C3",
2,
1,
"UNK",
"A"
],
[
"C2",
3,
1,
"UNK",
"A"
],
[
"C4",
4,
1,
"UNK",
"A"
],
[
"C1",
5,
1,
"UNK",
"A"
]
],
"hovertemplate": "atom_element=C
x=%{x}
y=%{y}
z=%{z}
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,
"symbol": "circle"
},
"mode": "markers",
"name": "C",
"scene": "scene",
"showlegend": true,
"type": "scatter3d",
"x": [
-0.9138,
-0.0353,
-2.3904,
1.438
],
"y": [
-0.4607,
0.7848,
-0.1013,
0.4562
],
"z": [
-0.0051,
-0.0105,
0.0069,
0.011
]
},
{
"customdata": [
[
"H31",
6,
1,
"UNK",
"A"
],
[
"H32",
7,
1,
"UNK",
"A"
],
[
"H21",
8,
1,
"UNK",
"A"
],
[
"H22",
9,
1,
"UNK",
"A"
],
[
"H41",
10,
1,
"UNK",
"A"
],
[
"H42",
11,
1,
"UNK",
"A"
],
[
"H43",
12,
1,
"UNK",
"A"
],
[
"H1",
13,
1,
"UNK",
"A"
]
],
"hovertemplate": "atom_element=H
x=%{x}
y=%{y}
z=%{z}
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,
"symbol": "circle"
},
"mode": "markers",
"name": "H",
"scene": "scene",
"showlegend": true,
"type": "scatter3d",
"x": [
-0.6968,
-0.6849,
-0.2273,
-0.2454,
-2.6582,
-3.0017,
-2.6451,
2.109
],
"y": [
-1.0749,
-1.0768,
1.3866,
1.4036,
0.4863,
-1.0092,
0.4818,
1.3323
],
"z": [
-0.8872,
0.8727,
-0.9052,
0.8687,
-0.877,
0.0092,
0.8977,
0.0337
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
1.9015,
1.438
],
"y": [
-0.6791,
0.4562
],
"z": [
-0.0023,
0.011
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.9138,
-0.0353
],
"y": [
-0.4607,
0.7848
],
"z": [
-0.0051,
-0.0105
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.9138,
-2.3904
],
"y": [
-0.4607,
-0.1013
],
"z": [
-0.0051,
0.0069
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.9138,
-0.6968
],
"y": [
-0.4607,
-1.0749
],
"z": [
-0.0051,
-0.8872
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.9138,
-0.6849
],
"y": [
-0.4607,
-1.0768
],
"z": [
-0.0051,
0.8727
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.0353,
1.438
],
"y": [
0.7848,
0.4562
],
"z": [
-0.0105,
0.011
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.0353,
-0.2273
],
"y": [
0.7848,
1.3866
],
"z": [
-0.0105,
-0.9052
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.0353,
-0.2454
],
"y": [
0.7848,
1.4036
],
"z": [
-0.0105,
0.8687
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-2.3904,
-2.6582
],
"y": [
-0.1013,
0.4863
],
"z": [
0.0069,
-0.877
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-2.3904,
-3.0017
],
"y": [
-0.1013,
-1.0092
],
"z": [
0.0069,
0.0092
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-2.3904,
-2.6451
],
"y": [
-0.1013,
0.4818
],
"z": [
0.0069,
0.8977
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
1.438,
2.109
],
"y": [
0.4562,
1.3323
],
"z": [
0.011,
0.0337
]
}
],
"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": [
"aldehyde.show()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"We can tell that the tail carbon is called `C4` with its hydrogen atoms `H41`, `H42`, `H43`. The carbon before that was called `C3` and it had hydrogens `H31` and `H32`. In fact, the labelling is quite intuitive, and that's thanks to `autolabel`. It uses a hierarchical ranking scheme to determine atom labels, starting with the highest ranked carbon and then iteratively labelling lesser carbons and hetero atoms. As a rule of thumb, start with the most connected carbon in a circular structure, that's `C1`, then try forming the longest possible chain of consequtive carbons. If you reach a dead-end find the next most connected carbon again and continue from there. Using this scheme, you won't even need to look at small structures like these to know their atom labelling."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Equipped with this information we can attach the aldehyde to the methanol like so:"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [
{
"data": {
"application/vnd.plotly.v1+json": {
"config": {
"plotlyServerURL": "https://plot.ly"
},
"data": [
{
"customdata": [
[
"O7",
1,
1,
"UNK",
"A"
],
[
"O1",
16,
2,
"UNK",
"A"
]
],
"hovertemplate": "atom_element=O
x=%{x}
y=%{y}
z=%{z}
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,
"symbol": "circle"
},
"mode": "markers",
"name": "O",
"scene": "scene",
"showlegend": true,
"type": "scatter3d",
"x": [
2.7427,
-0.3820124356293885
],
"y": [
0.0002,
0.5342381484331487
],
"z": [
-0.7083,
1.7301997102321232
]
},
{
"customdata": [
[
"C1",
2,
1,
"UNK",
"A"
],
[
"C7",
3,
1,
"UNK",
"A"
],
[
"C2",
4,
1,
"UNK",
"A"
],
[
"C6",
5,
1,
"UNK",
"A"
],
[
"C3",
6,
1,
"UNK",
"A"
],
[
"C5",
7,
1,
"UNK",
"A"
],
[
"C4",
8,
1,
"UNK",
"A"
],
[
"C3",
17,
2,
"UNK",
"A"
],
[
"C2",
18,
2,
"UNK",
"A"
],
[
"C4",
19,
2,
"UNK",
"A"
],
[
"C1",
20,
2,
"UNK",
"A"
]
],
"hovertemplate": "atom_element=C
x=%{x}
y=%{y}
z=%{z}
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,
"symbol": "circle"
},
"mode": "markers",
"name": "C",
"scene": "scene",
"showlegend": true,
"type": "scatter3d",
"x": [
0.5758,
2.0447,
-0.111,
-0.1111,
-1.4847,
-1.4848,
-2.1715,
2.3503762722289667,
1.8923314744202335,
3.8586433629188512,
0.40013594837585764
],
"y": [
-0.0002,
-0.0001,
1.2079,
-1.2082,
1.2081,
-1.2079,
0.0002,
0.8804077563387589,
0.7401379034385251,
1.0414415166538338,
0.5453861958743437
],
"z": [
0.272,
0.5309,
0.1508,
0.1507,
-0.0915,
-0.0917,
-0.2128,
1.107432465002719,
2.554353676253595,
1.013313225839526,
2.674675679453273
]
},
{
"customdata": [
[
"H72",
9,
1,
"UNK",
"A"
],
[
"H2",
10,
1,
"UNK",
"A"
],
[
"H6",
11,
1,
"UNK",
"A"
],
[
"H3",
12,
1,
"UNK",
"A"
],
[
"H5",
13,
1,
"UNK",
"A"
],
[
"H4",
14,
1,
"UNK",
"A"
],
[
"HO7",
15,
1,
"UNK",
"A"
],
[
"H31",
21,
2,
"UNK",
"A"
],
[
"H21",
22,
2,
"UNK",
"A"
],
[
"H22",
23,
2,
"UNK",
"A"
],
[
"H41",
24,
2,
"UNK",
"A"
],
[
"H42",
25,
2,
"UNK",
"A"
],
[
"H43",
26,
2,
"UNK",
"A"
],
[
"H1",
27,
2,
"UNK",
"A"
]
],
"hovertemplate": "atom_element=H
x=%{x}
y=%{y}
z=%{z}
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,
"symbol": "circle"
},
"mode": "markers",
"name": "H",
"scene": "scene",
"showlegend": true,
"type": "scatter3d",
"x": [
2.3501,
0.4133,
0.413,
-2.0194,
-2.0198,
-3.241,
2.3709,
1.863156179710383,
2.157069843289854,
2.374080823578091,
4.192101299647685,
4.164807239641435,
4.373174571005732,
0.030593432946712684
],
"y": [
-0.8828,
2.1555,
-2.1559,
2.1486,
-2.1484,
0.0003,
0.7034,
1.7463177571958557,
1.6337492907372808,
-0.12388783266035032,
1.9341749358852875,
1.1417005761356047,
0.17249754731538214,
0.41384549443482854
],
"z": [
1.1025,
0.2415,
0.2413,
-0.1864,
-0.1868,
-0.4018,
-1.2677,
0.6434847288708951,
3.129581991393111,
3.024912048769458,
1.5519250123981445,
-0.03272080399986213,
1.4359198444045824,
3.706394087331654
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
2.7427,
2.0447
],
"y": [
0.0002,
-0.0001
],
"z": [
-0.7083,
0.5309
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
2.7427,
2.3709
],
"y": [
0.0002,
0.7034
],
"z": [
-0.7083,
-1.2677
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.5758,
2.0447
],
"y": [
-0.0002,
-0.0001
],
"z": [
0.272,
0.5309
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.5758,
-0.111
],
"y": [
-0.0002,
1.2079
],
"z": [
0.272,
0.1508
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.5758,
-0.1111
],
"y": [
-0.0002,
-1.2082
],
"z": [
0.272,
0.1507
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
2.0447,
2.3501
],
"y": [
-0.0001,
-0.8828
],
"z": [
0.5309,
1.1025
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
2.0447,
2.3503762722289667
],
"y": [
-0.0001,
0.8804077563387589
],
"z": [
0.5309,
1.107432465002719
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.111,
-1.4847
],
"y": [
1.2079,
1.2081
],
"z": [
0.1508,
-0.0915
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.111,
0.4133
],
"y": [
1.2079,
2.1555
],
"z": [
0.1508,
0.2415
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.1111,
-1.4848
],
"y": [
-1.2082,
-1.2079
],
"z": [
0.1507,
-0.0917
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.1111,
0.413
],
"y": [
-1.2082,
-2.1559
],
"z": [
0.1507,
0.2413
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-1.4847,
-2.1715
],
"y": [
1.2081,
0.0002
],
"z": [
-0.0915,
-0.2128
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-1.4847,
-2.0194
],
"y": [
1.2081,
2.1486
],
"z": [
-0.0915,
-0.1864
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-1.4848,
-2.1715
],
"y": [
-1.2079,
0.0002
],
"z": [
-0.0917,
-0.2128
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-1.4848,
-2.0198
],
"y": [
-1.2079,
-2.1484
],
"z": [
-0.0917,
-0.1868
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-2.1715,
-3.241
],
"y": [
0.0002,
0.0003
],
"z": [
-0.2128,
-0.4018
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.3820124356293885,
0.40013594837585764
],
"y": [
0.5342381484331487,
0.5453861958743437
],
"z": [
1.7301997102321232,
2.674675679453273
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
2.3503762722289667,
1.8923314744202335
],
"y": [
0.8804077563387589,
0.7401379034385251
],
"z": [
1.107432465002719,
2.554353676253595
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
2.3503762722289667,
3.8586433629188512
],
"y": [
0.8804077563387589,
1.0414415166538338
],
"z": [
1.107432465002719,
1.013313225839526
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
2.3503762722289667,
1.863156179710383
],
"y": [
0.8804077563387589,
1.7463177571958557
],
"z": [
1.107432465002719,
0.6434847288708951
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
1.8923314744202335,
0.40013594837585764
],
"y": [
0.7401379034385251,
0.5453861958743437
],
"z": [
2.554353676253595,
2.674675679453273
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
1.8923314744202335,
2.157069843289854
],
"y": [
0.7401379034385251,
1.6337492907372808
],
"z": [
2.554353676253595,
3.129581991393111
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
1.8923314744202335,
2.374080823578091
],
"y": [
0.7401379034385251,
-0.12388783266035032
],
"z": [
2.554353676253595,
3.024912048769458
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
3.8586433629188512,
4.192101299647685
],
"y": [
1.0414415166538338,
1.9341749358852875
],
"z": [
1.013313225839526,
1.5519250123981445
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
3.8586433629188512,
4.164807239641435
],
"y": [
1.0414415166538338,
1.1417005761356047
],
"z": [
1.013313225839526,
-0.03272080399986213
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
3.8586433629188512,
4.373174571005732
],
"y": [
1.0414415166538338,
0.17249754731538214
],
"z": [
1.013313225839526,
1.4359198444045824
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.40013594837585764,
0.030593432946712684
],
"y": [
0.5453861958743437,
0.41384549443482854
],
"z": [
2.674675679453273,
3.706394087331654
]
}
],
"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": [
"# define a linkage for use with bb.connect\n",
"link1 = bb.linkage(atom1=\"C7\", # the atom in phenyl_methanol to connect\n",
" atom2=\"C3\", # the atom in aldehyde to connect\n",
" delete_in_target=[\"H71\"], # the atom in phenyl_methanol to delete\n",
" delete_in_source=[\"H32\"] # the atom in aldehyde to delete\n",
" )\n",
"\n",
"# now connect the molecules\n",
"mol = bb.connect(phenyl_methanol, aldehyde, link1)\n",
"\n",
"# visualize the result\n",
"mol.show()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Now we can go about attaching a second phenyl-methanol to the structure. This time by connecting it's oxygen `O7` to the `C1` of the aldehyde. We will use the method-syntax `Molecule.attach` this time, as opposed to the function `connect`. Assuming that we do not actually care much about which Hydrogen atom is getting replaced (i.e. we don't care about stereochemistry) or if there is only a single Hydrogen atom to replace anyway, we do not actually need to specify any atoms to delete. If we leave them blank, Biobuild will just look for the first Hydrogen it can find. "
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [
{
"data": {
"application/vnd.plotly.v1+json": {
"config": {
"plotlyServerURL": "https://plot.ly"
},
"data": [
{
"customdata": [
[
"O7",
1,
1,
"UNK",
"A"
],
[
"O1",
16,
2,
"UNK",
"A"
],
[
"O7",
27,
3,
"UNK",
"A"
]
],
"hovertemplate": "atom_element=O
x=%{x}
y=%{y}
z=%{z}
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,
"symbol": "circle"
},
"mode": "markers",
"name": "O",
"scene": "scene",
"showlegend": true,
"type": "scatter3d",
"x": [
2.7427,
-0.3820124356293885,
0.052576816664357956
],
"y": [
0.0002,
0.5342381484331487,
0.421670601407635
],
"z": [
-0.7083,
1.7301997102321232,
3.6450191150294557
]
},
{
"customdata": [
[
"C1",
2,
1,
"UNK",
"A"
],
[
"C7",
3,
1,
"UNK",
"A"
],
[
"C2",
4,
1,
"UNK",
"A"
],
[
"C6",
5,
1,
"UNK",
"A"
],
[
"C3",
6,
1,
"UNK",
"A"
],
[
"C5",
7,
1,
"UNK",
"A"
],
[
"C4",
8,
1,
"UNK",
"A"
],
[
"C3",
17,
2,
"UNK",
"A"
],
[
"C2",
18,
2,
"UNK",
"A"
],
[
"C4",
19,
2,
"UNK",
"A"
],
[
"C1",
20,
2,
"UNK",
"A"
],
[
"C1",
28,
3,
"UNK",
"A"
],
[
"C7",
29,
3,
"UNK",
"A"
],
[
"C2",
30,
3,
"UNK",
"A"
],
[
"C6",
31,
3,
"UNK",
"A"
],
[
"C3",
32,
3,
"UNK",
"A"
],
[
"C5",
33,
3,
"UNK",
"A"
],
[
"C4",
34,
3,
"UNK",
"A"
]
],
"hovertemplate": "atom_element=C
x=%{x}
y=%{y}
z=%{z}
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,
"symbol": "circle"
},
"mode": "markers",
"name": "C",
"scene": "scene",
"showlegend": true,
"type": "scatter3d",
"x": [
0.5758,
2.0447,
-0.111,
-0.1111,
-1.4847,
-1.4848,
-2.1715,
2.3503762722289667,
1.8923314744202335,
3.8586433629188512,
0.40013594837585764,
-1.3543904997273213,
-0.9640857331232335,
-2.3808998645276764,
-0.6927937431334183,
-2.7460044016172223,
-1.0579071178854595,
-2.084440180234212
],
"y": [
-0.0002,
-0.0001,
1.2079,
-1.2082,
1.2081,
-1.2079,
0.0002,
0.8804077563387589,
0.7401379034385251,
1.0414415166538338,
0.5453861958743437,
1.3540849083839732,
1.3877666509741302,
0.5103375708290909,
2.1659273292328125,
0.4785082936184537,
2.133957443600547,
1.2902717814626716
],
"z": [
0.272,
0.5309,
0.1508,
0.1507,
-0.0915,
-0.0917,
-0.2128,
1.107432465002719,
2.554353676253595,
1.013313225839526,
2.674675679453273,
5.320575855564202,
3.881401036655041,
5.745144159075217,
6.241993738706657,
7.091044078871958,
7.587905953522258,
8.01234921876258
]
},
{
"customdata": [
[
"H72",
9,
1,
"UNK",
"A"
],
[
"H2",
10,
1,
"UNK",
"A"
],
[
"H6",
11,
1,
"UNK",
"A"
],
[
"H3",
12,
1,
"UNK",
"A"
],
[
"H5",
13,
1,
"UNK",
"A"
],
[
"H4",
14,
1,
"UNK",
"A"
],
[
"HO7",
15,
1,
"UNK",
"A"
],
[
"H31",
21,
2,
"UNK",
"A"
],
[
"H21",
22,
2,
"UNK",
"A"
],
[
"H22",
23,
2,
"UNK",
"A"
],
[
"H41",
24,
2,
"UNK",
"A"
],
[
"H42",
25,
2,
"UNK",
"A"
],
[
"H43",
26,
2,
"UNK",
"A"
],
[
"H71",
35,
3,
"UNK",
"A"
],
[
"H72",
36,
3,
"UNK",
"A"
],
[
"H2",
37,
3,
"UNK",
"A"
],
[
"H6",
38,
3,
"UNK",
"A"
],
[
"H3",
39,
3,
"UNK",
"A"
],
[
"H5",
40,
3,
"UNK",
"A"
],
[
"H4",
41,
3,
"UNK",
"A"
]
],
"hovertemplate": "atom_element=H
x=%{x}
y=%{y}
z=%{z}
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,
"symbol": "circle"
},
"mode": "markers",
"name": "H",
"scene": "scene",
"showlegend": true,
"type": "scatter3d",
"x": [
2.3501,
0.4133,
0.413,
-2.0194,
-2.0198,
-3.241,
2.3709,
1.863156179710383,
2.157069843289854,
2.374080823578091,
4.192101299647685,
4.164807239641435,
4.373174571005732,
-1.8165300652445873,
-0.5821955407501225,
-2.902588091873367,
0.10971391282141474,
-3.5448145320804856,
-0.5424888014185122,
-2.368437500651611
],
"y": [
-0.8828,
2.1555,
-2.1559,
2.1486,
-2.1484,
0.0003,
0.7034,
1.7463177571958557,
1.6337492907372808,
-0.12388783266035032,
1.9341749358852875,
1.1417005761356047,
0.17249754731538214,
1.16828586669812,
2.372884442723782,
-0.12819885664161723,
2.8261087915160408,
-0.17873570026129681,
2.7655704771434273,
1.2652723072892869
],
"z": [
1.1025,
0.2415,
0.2413,
-0.1864,
-0.1868,
-0.4018,
-1.2677,
0.6434847288708951,
3.129581991393111,
3.024912048769458,
1.5519250123981445,
-0.03272080399986213,
1.4359198444045824,
3.229554784868805,
3.5935506808318873,
5.037206757716977,
5.92392714349198,
7.421775175048685,
8.305692965740462,
9.060333860008239
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
2.7427,
2.0447
],
"y": [
0.0002,
-0.0001
],
"z": [
-0.7083,
0.5309
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
2.7427,
2.3709
],
"y": [
0.0002,
0.7034
],
"z": [
-0.7083,
-1.2677
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.5758,
2.0447
],
"y": [
-0.0002,
-0.0001
],
"z": [
0.272,
0.5309
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.5758,
-0.111
],
"y": [
-0.0002,
1.2079
],
"z": [
0.272,
0.1508
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.5758,
-0.1111
],
"y": [
-0.0002,
-1.2082
],
"z": [
0.272,
0.1507
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
2.0447,
2.3501
],
"y": [
-0.0001,
-0.8828
],
"z": [
0.5309,
1.1025
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
2.0447,
2.3503762722289667
],
"y": [
-0.0001,
0.8804077563387589
],
"z": [
0.5309,
1.107432465002719
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.111,
-1.4847
],
"y": [
1.2079,
1.2081
],
"z": [
0.1508,
-0.0915
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.111,
0.4133
],
"y": [
1.2079,
2.1555
],
"z": [
0.1508,
0.2415
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.1111,
-1.4848
],
"y": [
-1.2082,
-1.2079
],
"z": [
0.1507,
-0.0917
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.1111,
0.413
],
"y": [
-1.2082,
-2.1559
],
"z": [
0.1507,
0.2413
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-1.4847,
-2.1715
],
"y": [
1.2081,
0.0002
],
"z": [
-0.0915,
-0.2128
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-1.4847,
-2.0194
],
"y": [
1.2081,
2.1486
],
"z": [
-0.0915,
-0.1864
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-1.4848,
-2.1715
],
"y": [
-1.2079,
0.0002
],
"z": [
-0.0917,
-0.2128
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-1.4848,
-2.0198
],
"y": [
-1.2079,
-2.1484
],
"z": [
-0.0917,
-0.1868
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-2.1715,
-3.241
],
"y": [
0.0002,
0.0003
],
"z": [
-0.2128,
-0.4018
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.3820124356293885,
0.40013594837585764
],
"y": [
0.5342381484331487,
0.5453861958743437
],
"z": [
1.7301997102321232,
2.674675679453273
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
2.3503762722289667,
1.8923314744202335
],
"y": [
0.8804077563387589,
0.7401379034385251
],
"z": [
1.107432465002719,
2.554353676253595
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
2.3503762722289667,
3.8586433629188512
],
"y": [
0.8804077563387589,
1.0414415166538338
],
"z": [
1.107432465002719,
1.013313225839526
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
2.3503762722289667,
1.863156179710383
],
"y": [
0.8804077563387589,
1.7463177571958557
],
"z": [
1.107432465002719,
0.6434847288708951
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
1.8923314744202335,
0.40013594837585764
],
"y": [
0.7401379034385251,
0.5453861958743437
],
"z": [
2.554353676253595,
2.674675679453273
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
1.8923314744202335,
2.157069843289854
],
"y": [
0.7401379034385251,
1.6337492907372808
],
"z": [
2.554353676253595,
3.129581991393111
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
1.8923314744202335,
2.374080823578091
],
"y": [
0.7401379034385251,
-0.12388783266035032
],
"z": [
2.554353676253595,
3.024912048769458
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
3.8586433629188512,
4.192101299647685
],
"y": [
1.0414415166538338,
1.9341749358852875
],
"z": [
1.013313225839526,
1.5519250123981445
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
3.8586433629188512,
4.164807239641435
],
"y": [
1.0414415166538338,
1.1417005761356047
],
"z": [
1.013313225839526,
-0.03272080399986213
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
3.8586433629188512,
4.373174571005732
],
"y": [
1.0414415166538338,
0.17249754731538214
],
"z": [
1.013313225839526,
1.4359198444045824
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.40013594837585764,
0.052576816664357956
],
"y": [
0.5453861958743437,
0.421670601407635
],
"z": [
2.674675679453273,
3.6450191150294557
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.052576816664357956,
-0.9640857331232335
],
"y": [
0.421670601407635,
1.3877666509741302
],
"z": [
3.6450191150294557,
3.881401036655041
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-1.3543904997273213,
-0.9640857331232335
],
"y": [
1.3540849083839732,
1.3877666509741302
],
"z": [
5.320575855564202,
3.881401036655041
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-1.3543904997273213,
-2.3808998645276764
],
"y": [
1.3540849083839732,
0.5103375708290909
],
"z": [
5.320575855564202,
5.745144159075217
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-1.3543904997273213,
-0.6927937431334183
],
"y": [
1.3540849083839732,
2.1659273292328125
],
"z": [
5.320575855564202,
6.241993738706657
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.9640857331232335,
-1.8165300652445873
],
"y": [
1.3877666509741302,
1.16828586669812
],
"z": [
3.881401036655041,
3.229554784868805
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.9640857331232335,
-0.5821955407501225
],
"y": [
1.3877666509741302,
2.372884442723782
],
"z": [
3.881401036655041,
3.5935506808318873
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-2.3808998645276764,
-2.7460044016172223
],
"y": [
0.5103375708290909,
0.4785082936184537
],
"z": [
5.745144159075217,
7.091044078871958
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-2.3808998645276764,
-2.902588091873367
],
"y": [
0.5103375708290909,
-0.12819885664161723
],
"z": [
5.745144159075217,
5.037206757716977
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.6927937431334183,
-1.0579071178854595
],
"y": [
2.1659273292328125,
2.133957443600547
],
"z": [
6.241993738706657,
7.587905953522258
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.6927937431334183,
0.10971391282141474
],
"y": [
2.1659273292328125,
2.8261087915160408
],
"z": [
6.241993738706657,
5.92392714349198
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-2.7460044016172223,
-2.084440180234212
],
"y": [
0.4785082936184537,
1.2902717814626716
],
"z": [
7.091044078871958,
8.01234921876258
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-2.7460044016172223,
-3.5448145320804856
],
"y": [
0.4785082936184537,
-0.17873570026129681
],
"z": [
7.091044078871958,
7.421775175048685
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-1.0579071178854595,
-2.084440180234212
],
"y": [
2.133957443600547,
1.2902717814626716
],
"z": [
7.587905953522258,
8.01234921876258
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-1.0579071178854595,
-0.5424888014185122
],
"y": [
2.133957443600547,
2.7655704771434273
],
"z": [
7.587905953522258,
8.305692965740462
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-2.084440180234212,
-2.368437500651611
],
"y": [
1.2902717814626716,
1.2652723072892869
],
"z": [
8.01234921876258,
9.060333860008239
]
}
],
"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": [
"# make a second linkage \n",
"# (this time without specifying atoms to delete)\n",
"link2 = bb.linkage(atom1=\"C1\",\n",
" atom2=\"O7\"\n",
")\n",
"# connect a second phenyl-methanol\n",
"mol.attach(phenyl_methanol, link2)\n",
"\n",
"# visualize the result\n",
"mol.show()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Now it's time for the amine to join the show. We can savely predict that the highest connected carbon is the one between the nitrogen and oxygen, so we can predict that the N will be called `N1` and the O `O1`. But let's look at the structure all the same to be sure:"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [
{
"data": {
"application/vnd.plotly.v1+json": {
"config": {
"plotlyServerURL": "https://plot.ly"
},
"data": [
{
"customdata": [
[
"O3",
1,
1,
"UNK",
"A"
]
],
"hovertemplate": "atom_element=O
x=%{x}
y=%{y}
z=%{z}
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,
"symbol": "circle"
},
"mode": "markers",
"name": "O",
"scene": "scene",
"showlegend": true,
"type": "scatter3d",
"x": [
-0.7484
],
"y": [
0.4868
],
"z": [
-0.3658
]
},
{
"customdata": [
[
"N1",
2,
1,
"UNK",
"A"
]
],
"hovertemplate": "atom_element=N
x=%{x}
y=%{y}
z=%{z}
atom_id=%{customdata[0]}
atom_serial=%{customdata[1]}
residue_serial=%{customdata[2]}
residue_name=%{customdata[3]}
chain_id=%{customdata[4]}",
"legendgroup": "N",
"marker": {
"color": "blue",
"opacity": 1,
"symbol": "circle"
},
"mode": "markers",
"name": "N",
"scene": "scene",
"showlegend": true,
"type": "scatter3d",
"x": [
0.7646
],
"y": [
-1.3729
],
"z": [
-0.1275
]
},
{
"customdata": [
[
"C1",
3,
1,
"UNK",
"A"
],
[
"C2",
4,
1,
"UNK",
"A"
],
[
"C3",
5,
1,
"UNK",
"A"
]
],
"hovertemplate": "atom_element=C
x=%{x}
y=%{y}
z=%{z}
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,
"symbol": "circle"
},
"mode": "markers",
"name": "C",
"scene": "scene",
"showlegend": true,
"type": "scatter3d",
"x": [
0.4001,
1.5587,
-1.9751
],
"y": [
-0.0289,
0.9149,
0.0002
],
"z": [
0.3163,
0.0132,
0.1637
]
},
{
"customdata": [
[
"H1",
6,
1,
"UNK",
"A"
],
[
"H21",
7,
1,
"UNK",
"A"
],
[
"H22",
8,
1,
"UNK",
"A"
],
[
"H23",
9,
1,
"UNK",
"A"
],
[
"HN11",
10,
1,
"UNK",
"A"
],
[
"HN12",
11,
1,
"UNK",
"A"
],
[
"H31",
12,
1,
"UNK",
"A"
],
[
"H32",
13,
1,
"UNK",
"A"
],
[
"H33",
14,
1,
"UNK",
"A"
]
],
"hovertemplate": "atom_element=H
x=%{x}
y=%{y}
z=%{z}
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,
"symbol": "circle"
},
"mode": "markers",
"name": "H",
"scene": "scene",
"showlegend": true,
"type": "scatter3d",
"x": [
0.2255,
1.7509,
2.4784,
1.3162,
-0.002,
0.8946,
-2.7945,
-2.0748,
-2.0484
],
"y": [
-0.0295,
0.9775,
0.5987,
1.9306,
-2.0158,
-1.3728,
0.4616,
0.2769,
-1.0849
],
"z": [
1.3987,
-1.0643,
0.5162,
0.3454,
0.0621,
-1.1383,
-0.3941,
1.2177,
0.0492
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.7484,
0.4001
],
"y": [
0.4868,
-0.0289
],
"z": [
-0.3658,
0.3163
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.7484,
-1.9751
],
"y": [
0.4868,
0.0002
],
"z": [
-0.3658,
0.1637
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.7646,
0.4001
],
"y": [
-1.3729,
-0.0289
],
"z": [
-0.1275,
0.3163
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.7646,
-0.002
],
"y": [
-1.3729,
-2.0158
],
"z": [
-0.1275,
0.0621
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.7646,
0.8946
],
"y": [
-1.3729,
-1.3728
],
"z": [
-0.1275,
-1.1383
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.4001,
1.5587
],
"y": [
-0.0289,
0.9149
],
"z": [
0.3163,
0.0132
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.4001,
0.2255
],
"y": [
-0.0289,
-0.0295
],
"z": [
0.3163,
1.3987
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
1.5587,
1.7509
],
"y": [
0.9149,
0.9775
],
"z": [
0.0132,
-1.0643
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
1.5587,
2.4784
],
"y": [
0.9149,
0.5987
],
"z": [
0.0132,
0.5162
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
1.5587,
1.3162
],
"y": [
0.9149,
1.9306
],
"z": [
0.0132,
0.3454
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-1.9751,
-2.7945
],
"y": [
0.0002,
0.4616
],
"z": [
0.1637,
-0.3941
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-1.9751,
-2.0748
],
"y": [
0.0002,
0.2769
],
"z": [
0.1637,
1.2177
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-1.9751,
-2.0484
],
"y": [
0.0002,
-1.0849
],
"z": [
0.1637,
0.0492
]
}
],
"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": [
"amine.show()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Phew, lucky we checked the structure. The oxygen was called `O3` because hetero atoms are labelled by the highest labelled neighbor. Nevertheless, we learned the next connection will need to be between `N1` in the amine and `C7` of the second phenyl-methanol in the molecule we are building.\n",
"\n",
"Since we are building \"from one end to the other\" we do not need to bother with speciying in which residue to search for the atoms to connect, because biobuild will by default use the latest residue for attaching new molecules. However, if we do find ourselves working with branched structures, we can always use the `at_residue` and `other_residue` arguments to specify which residues to use when attaching different molecules."
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [
{
"data": {
"application/vnd.plotly.v1+json": {
"config": {
"plotlyServerURL": "https://plot.ly"
},
"data": [
{
"customdata": [
[
"O7",
1,
1,
"UNK",
"A"
],
[
"O1",
16,
2,
"UNK",
"A"
],
[
"O7",
27,
3,
"UNK",
"A"
],
[
"O3",
41,
4,
"UNK",
"A"
]
],
"hovertemplate": "atom_element=O
x=%{x}
y=%{y}
z=%{z}
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,
"symbol": "circle"
},
"mode": "markers",
"name": "O",
"scene": "scene",
"showlegend": true,
"type": "scatter3d",
"x": [
2.7427,
-0.3820124356293885,
0.052576816664357956,
-1.10219617195545
],
"y": [
0.0002,
0.5342381484331487,
0.421670601407635,
4.247133027158526
],
"z": [
-0.7083,
1.7301997102321232,
3.6450191150294557,
2.2236513733913483
]
},
{
"customdata": [
[
"C1",
2,
1,
"UNK",
"A"
],
[
"C7",
3,
1,
"UNK",
"A"
],
[
"C2",
4,
1,
"UNK",
"A"
],
[
"C6",
5,
1,
"UNK",
"A"
],
[
"C3",
6,
1,
"UNK",
"A"
],
[
"C5",
7,
1,
"UNK",
"A"
],
[
"C4",
8,
1,
"UNK",
"A"
],
[
"C3",
17,
2,
"UNK",
"A"
],
[
"C2",
18,
2,
"UNK",
"A"
],
[
"C4",
19,
2,
"UNK",
"A"
],
[
"C1",
20,
2,
"UNK",
"A"
],
[
"C1",
28,
3,
"UNK",
"A"
],
[
"C7",
29,
3,
"UNK",
"A"
],
[
"C2",
30,
3,
"UNK",
"A"
],
[
"C6",
31,
3,
"UNK",
"A"
],
[
"C3",
32,
3,
"UNK",
"A"
],
[
"C5",
33,
3,
"UNK",
"A"
],
[
"C4",
34,
3,
"UNK",
"A"
],
[
"C1",
43,
4,
"UNK",
"A"
],
[
"C2",
44,
4,
"UNK",
"A"
],
[
"C3",
45,
4,
"UNK",
"A"
]
],
"hovertemplate": "atom_element=C
x=%{x}
y=%{y}
z=%{z}
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,
"symbol": "circle"
},
"mode": "markers",
"name": "C",
"scene": "scene",
"showlegend": true,
"type": "scatter3d",
"x": [
0.5758,
2.0447,
-0.111,
-0.1111,
-1.4847,
-1.4848,
-2.1715,
2.3503762722289667,
1.8923314744202335,
3.8586433629188512,
0.40013594837585764,
-1.3543904997273213,
-0.9640857331232335,
-2.3808998645276764,
-0.6927937431334183,
-2.7460044016172223,
-1.0579071178854595,
-2.084440180234212,
-1.3973557955054097,
-2.868912246378143,
0.06419086876858915
],
"y": [
-0.0002,
-0.0001,
1.2079,
-1.2082,
1.2081,
-1.2079,
0.0002,
0.8804077563387589,
0.7401379034385251,
1.0414415166538338,
0.5453861958743437,
1.3540849083839732,
1.3877666509741302,
0.5103375708290909,
2.1659273292328125,
0.4785082936184537,
2.133957443600547,
1.2902717814626716,
2.8746748426684583,
2.8077652507210527,
4.413257671176773
],
"z": [
0.272,
0.5309,
0.1508,
0.1507,
-0.0915,
-0.0917,
-0.2128,
1.107432465002719,
2.554353676253595,
1.013313225839526,
2.674675679453273,
5.320575855564202,
3.881401036655041,
5.745144159075217,
6.241993738706657,
7.091044078871958,
7.587905953522258,
8.01234921876258,
2.505606118788678,
2.8993404561283045,
1.4274814330640158
]
},
{
"customdata": [
[
"H72",
9,
1,
"UNK",
"A"
],
[
"H2",
10,
1,
"UNK",
"A"
],
[
"H6",
11,
1,
"UNK",
"A"
],
[
"H3",
12,
1,
"UNK",
"A"
],
[
"H5",
13,
1,
"UNK",
"A"
],
[
"H4",
14,
1,
"UNK",
"A"
],
[
"HO7",
15,
1,
"UNK",
"A"
],
[
"H31",
21,
2,
"UNK",
"A"
],
[
"H21",
22,
2,
"UNK",
"A"
],
[
"H22",
23,
2,
"UNK",
"A"
],
[
"H41",
24,
2,
"UNK",
"A"
],
[
"H42",
25,
2,
"UNK",
"A"
],
[
"H43",
26,
2,
"UNK",
"A"
],
[
"H71",
35,
3,
"UNK",
"A"
],
[
"H2",
36,
3,
"UNK",
"A"
],
[
"H6",
37,
3,
"UNK",
"A"
],
[
"H3",
38,
3,
"UNK",
"A"
],
[
"H5",
39,
3,
"UNK",
"A"
],
[
"H4",
40,
3,
"UNK",
"A"
],
[
"H1",
46,
4,
"UNK",
"A"
],
[
"H21",
47,
4,
"UNK",
"A"
],
[
"H22",
48,
4,
"UNK",
"A"
],
[
"H23",
49,
4,
"UNK",
"A"
],
[
"HN12",
50,
4,
"UNK",
"A"
],
[
"H31",
51,
4,
"UNK",
"A"
],
[
"H32",
52,
4,
"UNK",
"A"
],
[
"H33",
53,
4,
"UNK",
"A"
]
],
"hovertemplate": "atom_element=H
x=%{x}
y=%{y}
z=%{z}
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,
"symbol": "circle"
},
"mode": "markers",
"name": "H",
"scene": "scene",
"showlegend": true,
"type": "scatter3d",
"x": [
2.3501,
0.4133,
0.413,
-2.0194,
-2.0198,
-3.241,
2.3709,
1.863156179710383,
2.157069843289854,
2.374080823578091,
4.192101299647685,
4.164807239641435,
4.373174571005732,
-1.8165300652445873,
-2.902588091873367,
0.10971391282141474,
-3.5448145320804856,
-0.5424888014185122,
-2.368437500651611,
-1.2496527143516958,
-3.0757268893562846,
-3.182075085615842,
-3.495621097027113,
0.36141702816054355,
0.19955637109492108,
-0.05184781752645451,
0.9505357763986805
],
"y": [
-0.8828,
2.1555,
-2.1559,
2.1486,
-2.1484,
0.0003,
0.7034,
1.7463177571958557,
1.6337492907372808,
-0.12388783266035032,
1.9341749358852875,
1.1417005761356047,
0.17249754731538214,
1.16828586669812,
-0.12819885664161723,
2.8261087915160408,
-0.17873570026129681,
2.7655704771434273,
1.2652723072892869,
2.265983721485828,
3.4308129151653244,
1.7811186834786197,
3.1954035376288217,
2.192363544724671,
5.481751091069043,
3.904218646329364,
4.0401237756485155
],
"z": [
1.1025,
0.2415,
0.2413,
-0.1864,
-0.1868,
-0.4018,
-1.2677,
0.6434847288708951,
3.129581991393111,
3.024912048769458,
1.5519250123981445,
-0.03272080399986213,
1.4359198444045824,
3.229554784868805,
5.037206757716977,
5.92392714349198,
7.421775175048685,
8.305692965740462,
9.060333860008239,
1.6057426853660663,
3.7773525068886356,
3.1155935303027853,
2.0883027535265968,
3.285111133161488,
1.239212602858748,
0.4657989103647,
1.9481434642571058
]
},
{
"customdata": [
[
"N1",
42,
4,
"UNK",
"A"
]
],
"hovertemplate": "atom_element=N
x=%{x}
y=%{y}
z=%{z}
atom_id=%{customdata[0]}
atom_serial=%{customdata[1]}
residue_serial=%{customdata[2]}
residue_name=%{customdata[3]}
chain_id=%{customdata[4]}",
"legendgroup": "N",
"marker": {
"color": "blue",
"opacity": 1,
"symbol": "circle"
},
"mode": "markers",
"name": "N",
"scene": "scene",
"showlegend": true,
"type": "scatter3d",
"x": [
-0.5955792514946365
],
"y": [
2.338360037967217
],
"z": [
3.6036386746504836
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
2.7427,
2.0447
],
"y": [
0.0002,
-0.0001
],
"z": [
-0.7083,
0.5309
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
2.7427,
2.3709
],
"y": [
0.0002,
0.7034
],
"z": [
-0.7083,
-1.2677
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.5758,
2.0447
],
"y": [
-0.0002,
-0.0001
],
"z": [
0.272,
0.5309
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.5758,
-0.111
],
"y": [
-0.0002,
1.2079
],
"z": [
0.272,
0.1508
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.5758,
-0.1111
],
"y": [
-0.0002,
-1.2082
],
"z": [
0.272,
0.1507
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
2.0447,
2.3501
],
"y": [
-0.0001,
-0.8828
],
"z": [
0.5309,
1.1025
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
2.0447,
2.3503762722289667
],
"y": [
-0.0001,
0.8804077563387589
],
"z": [
0.5309,
1.107432465002719
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.111,
-1.4847
],
"y": [
1.2079,
1.2081
],
"z": [
0.1508,
-0.0915
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.111,
0.4133
],
"y": [
1.2079,
2.1555
],
"z": [
0.1508,
0.2415
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.1111,
-1.4848
],
"y": [
-1.2082,
-1.2079
],
"z": [
0.1507,
-0.0917
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.1111,
0.413
],
"y": [
-1.2082,
-2.1559
],
"z": [
0.1507,
0.2413
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-1.4847,
-2.1715
],
"y": [
1.2081,
0.0002
],
"z": [
-0.0915,
-0.2128
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-1.4847,
-2.0194
],
"y": [
1.2081,
2.1486
],
"z": [
-0.0915,
-0.1864
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-1.4848,
-2.1715
],
"y": [
-1.2079,
0.0002
],
"z": [
-0.0917,
-0.2128
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-1.4848,
-2.0198
],
"y": [
-1.2079,
-2.1484
],
"z": [
-0.0917,
-0.1868
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-2.1715,
-3.241
],
"y": [
0.0002,
0.0003
],
"z": [
-0.2128,
-0.4018
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.3820124356293885,
0.40013594837585764
],
"y": [
0.5342381484331487,
0.5453861958743437
],
"z": [
1.7301997102321232,
2.674675679453273
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
2.3503762722289667,
1.8923314744202335
],
"y": [
0.8804077563387589,
0.7401379034385251
],
"z": [
1.107432465002719,
2.554353676253595
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
2.3503762722289667,
3.8586433629188512
],
"y": [
0.8804077563387589,
1.0414415166538338
],
"z": [
1.107432465002719,
1.013313225839526
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
2.3503762722289667,
1.863156179710383
],
"y": [
0.8804077563387589,
1.7463177571958557
],
"z": [
1.107432465002719,
0.6434847288708951
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
1.8923314744202335,
0.40013594837585764
],
"y": [
0.7401379034385251,
0.5453861958743437
],
"z": [
2.554353676253595,
2.674675679453273
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
1.8923314744202335,
2.157069843289854
],
"y": [
0.7401379034385251,
1.6337492907372808
],
"z": [
2.554353676253595,
3.129581991393111
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
1.8923314744202335,
2.374080823578091
],
"y": [
0.7401379034385251,
-0.12388783266035032
],
"z": [
2.554353676253595,
3.024912048769458
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
3.8586433629188512,
4.192101299647685
],
"y": [
1.0414415166538338,
1.9341749358852875
],
"z": [
1.013313225839526,
1.5519250123981445
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
3.8586433629188512,
4.164807239641435
],
"y": [
1.0414415166538338,
1.1417005761356047
],
"z": [
1.013313225839526,
-0.03272080399986213
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
3.8586433629188512,
4.373174571005732
],
"y": [
1.0414415166538338,
0.17249754731538214
],
"z": [
1.013313225839526,
1.4359198444045824
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.40013594837585764,
0.052576816664357956
],
"y": [
0.5453861958743437,
0.421670601407635
],
"z": [
2.674675679453273,
3.6450191150294557
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.052576816664357956,
-0.9640857331232335
],
"y": [
0.421670601407635,
1.3877666509741302
],
"z": [
3.6450191150294557,
3.881401036655041
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-1.3543904997273213,
-0.9640857331232335
],
"y": [
1.3540849083839732,
1.3877666509741302
],
"z": [
5.320575855564202,
3.881401036655041
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-1.3543904997273213,
-2.3808998645276764
],
"y": [
1.3540849083839732,
0.5103375708290909
],
"z": [
5.320575855564202,
5.745144159075217
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-1.3543904997273213,
-0.6927937431334183
],
"y": [
1.3540849083839732,
2.1659273292328125
],
"z": [
5.320575855564202,
6.241993738706657
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.9640857331232335,
-1.8165300652445873
],
"y": [
1.3877666509741302,
1.16828586669812
],
"z": [
3.881401036655041,
3.229554784868805
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.9640857331232335,
-0.5955792514946365
],
"y": [
1.3877666509741302,
2.338360037967217
],
"z": [
3.881401036655041,
3.6036386746504836
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-2.3808998645276764,
-2.7460044016172223
],
"y": [
0.5103375708290909,
0.4785082936184537
],
"z": [
5.745144159075217,
7.091044078871958
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-2.3808998645276764,
-2.902588091873367
],
"y": [
0.5103375708290909,
-0.12819885664161723
],
"z": [
5.745144159075217,
5.037206757716977
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.6927937431334183,
-1.0579071178854595
],
"y": [
2.1659273292328125,
2.133957443600547
],
"z": [
6.241993738706657,
7.587905953522258
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.6927937431334183,
0.10971391282141474
],
"y": [
2.1659273292328125,
2.8261087915160408
],
"z": [
6.241993738706657,
5.92392714349198
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-2.7460044016172223,
-2.084440180234212
],
"y": [
0.4785082936184537,
1.2902717814626716
],
"z": [
7.091044078871958,
8.01234921876258
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-2.7460044016172223,
-3.5448145320804856
],
"y": [
0.4785082936184537,
-0.17873570026129681
],
"z": [
7.091044078871958,
7.421775175048685
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-1.0579071178854595,
-2.084440180234212
],
"y": [
2.133957443600547,
1.2902717814626716
],
"z": [
7.587905953522258,
8.01234921876258
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-1.0579071178854595,
-0.5424888014185122
],
"y": [
2.133957443600547,
2.7655704771434273
],
"z": [
7.587905953522258,
8.305692965740462
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-2.084440180234212,
-2.368437500651611
],
"y": [
1.2902717814626716,
1.2652723072892869
],
"z": [
8.01234921876258,
9.060333860008239
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-1.10219617195545,
-1.3973557955054097
],
"y": [
4.247133027158526,
2.8746748426684583
],
"z": [
2.2236513733913483,
2.505606118788678
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-1.10219617195545,
0.06419086876858915
],
"y": [
4.247133027158526,
4.413257671176773
],
"z": [
2.2236513733913483,
1.4274814330640158
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.5955792514946365,
-1.3973557955054097
],
"y": [
2.338360037967217,
2.8746748426684583
],
"z": [
3.6036386746504836,
2.505606118788678
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.5955792514946365,
0.36141702816054355
],
"y": [
2.338360037967217,
2.192363544724671
],
"z": [
3.6036386746504836,
3.285111133161488
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-1.3973557955054097,
-2.868912246378143
],
"y": [
2.8746748426684583,
2.8077652507210527
],
"z": [
2.505606118788678,
2.8993404561283045
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-1.3973557955054097,
-1.2496527143516958
],
"y": [
2.8746748426684583,
2.265983721485828
],
"z": [
2.505606118788678,
1.6057426853660663
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-2.868912246378143,
-3.0757268893562846
],
"y": [
2.8077652507210527,
3.4308129151653244
],
"z": [
2.8993404561283045,
3.7773525068886356
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-2.868912246378143,
-3.182075085615842
],
"y": [
2.8077652507210527,
1.7811186834786197
],
"z": [
2.8993404561283045,
3.1155935303027853
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-2.868912246378143,
-3.495621097027113
],
"y": [
2.8077652507210527,
3.1954035376288217
],
"z": [
2.8993404561283045,
2.0883027535265968
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.06419086876858915,
0.19955637109492108
],
"y": [
4.413257671176773,
5.481751091069043
],
"z": [
1.4274814330640158,
1.239212602858748
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.06419086876858915,
-0.05184781752645451
],
"y": [
4.413257671176773,
3.904218646329364
],
"z": [
1.4274814330640158,
0.4657989103647
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.06419086876858915,
0.9505357763986805
],
"y": [
4.413257671176773,
4.0401237756485155
],
"z": [
1.4274814330640158,
1.9481434642571058
]
}
],
"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": [
"# connect the amine to the molecule\n",
"# by now we understand these parameters\n",
"link3 = bb.linkage(\"C7\", \"N1\")\n",
"\n",
"# attach and visualize\n",
"mol.attach(amine, link3)\n",
"mol.show()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Almost there, the only thing left is the naphthalene. We know the drill by now, so let's just quickly visualize to find out what the carbon we want to connect is called."
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [
{
"data": {
"application/vnd.plotly.v1+json": {
"config": {
"plotlyServerURL": "https://plot.ly"
},
"data": [
{
"customdata": [
[
"C1",
1,
1,
"UNK",
"A"
],
[
"C2",
2,
1,
"UNK",
"A"
],
[
"C6",
3,
1,
"UNK",
"A"
],
[
"C5",
4,
1,
"UNK",
"A"
],
[
"C3",
5,
1,
"UNK",
"A"
],
[
"C7",
6,
1,
"UNK",
"A"
],
[
"C10",
7,
1,
"UNK",
"A"
],
[
"C4",
8,
1,
"UNK",
"A"
],
[
"C8",
9,
1,
"UNK",
"A"
],
[
"C9",
10,
1,
"UNK",
"A"
]
],
"hovertemplate": "atom_element=C
x=%{x}
y=%{y}
z=%{z}
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,
"symbol": "circle"
},
"mode": "markers",
"name": "C",
"scene": "scene",
"showlegend": true,
"type": "scatter3d",
"x": [
0.063,
-0.1026,
1.5407,
2.2092,
0.9058,
-0.8068,
-1.5021,
1.9202,
-1.9059,
-2.3215
],
"y": [
0.7481,
-0.8081,
1.1529,
0.5709,
-1.5075,
1.4683,
-1.2235,
-0.8868,
0.903,
-0.4172
],
"z": [
-0.8102,
-0.7729,
-0.6837,
0.5614,
0.1112,
0.1998,
-0.3707,
0.7279,
0.7182,
0.3189
]
},
{
"customdata": [
[
"H1",
11,
1,
"UNK",
"A"
],
[
"H2",
12,
1,
"UNK",
"A"
],
[
"H61",
13,
1,
"UNK",
"A"
],
[
"H62",
14,
1,
"UNK",
"A"
],
[
"H51",
15,
1,
"UNK",
"A"
],
[
"H52",
16,
1,
"UNK",
"A"
],
[
"H3",
17,
1,
"UNK",
"A"
],
[
"H7",
18,
1,
"UNK",
"A"
],
[
"H10",
19,
1,
"UNK",
"A"
],
[
"H4",
20,
1,
"UNK",
"A"
],
[
"H8",
21,
1,
"UNK",
"A"
],
[
"H9",
22,
1,
"UNK",
"A"
]
],
"hovertemplate": "atom_element=H
x=%{x}
y=%{y}
z=%{z}
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,
"symbol": "circle"
},
"mode": "markers",
"name": "H",
"scene": "scene",
"showlegend": true,
"type": "scatter3d",
"x": [
-0.2791,
0.0663,
1.6467,
2.0774,
1.8819,
3.2925,
0.7936,
-0.5502,
-1.8377,
2.582,
-2.5292,
-3.3128
],
"y": [
1.0982,
-1.1742,
2.2449,
0.7972,
1.105,
0.7162,
-2.5799,
2.4857,
-2.2218,
-1.4615,
1.4429,
-0.7484
],
"z": [
-1.7954,
-1.7951,
-0.6792,
-1.5741,
1.4608,
0.4793,
0.2553,
0.4807,
-0.6386,
1.3694,
1.4221,
0.6078
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.063,
-0.1026
],
"y": [
0.7481,
-0.8081
],
"z": [
-0.8102,
-0.7729
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.063,
1.5407
],
"y": [
0.7481,
1.1529
],
"z": [
-0.8102,
-0.6837
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.063,
-0.8068
],
"y": [
0.7481,
1.4683
],
"z": [
-0.8102,
0.1998
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.063,
-0.2791
],
"y": [
0.7481,
1.0982
],
"z": [
-0.8102,
-1.7954
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.1026,
0.9058
],
"y": [
-0.8081,
-1.5075
],
"z": [
-0.7729,
0.1112
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.1026,
-1.5021
],
"y": [
-0.8081,
-1.2235
],
"z": [
-0.7729,
-0.3707
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.1026,
0.0663
],
"y": [
-0.8081,
-1.1742
],
"z": [
-0.7729,
-1.7951
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
1.5407,
2.2092
],
"y": [
1.1529,
0.5709
],
"z": [
-0.6837,
0.5614
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
1.5407,
1.6467
],
"y": [
1.1529,
2.2449
],
"z": [
-0.6837,
-0.6792
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
1.5407,
2.0774
],
"y": [
1.1529,
0.7972
],
"z": [
-0.6837,
-1.5741
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
2.2092,
1.9202
],
"y": [
0.5709,
-0.8868
],
"z": [
0.5614,
0.7279
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
2.2092,
1.8819
],
"y": [
0.5709,
1.105
],
"z": [
0.5614,
1.4608
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
2.2092,
3.2925
],
"y": [
0.5709,
0.7162
],
"z": [
0.5614,
0.4793
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.9058,
1.9202
],
"y": [
-1.5075,
-0.8868
],
"z": [
0.1112,
0.7279
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.9058,
0.7936
],
"y": [
-1.5075,
-2.5799
],
"z": [
0.1112,
0.2553
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.8068,
-1.9059
],
"y": [
1.4683,
0.903
],
"z": [
0.1998,
0.7182
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.8068,
-0.5502
],
"y": [
1.4683,
2.4857
],
"z": [
0.1998,
0.4807
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-1.5021,
-2.3215
],
"y": [
-1.2235,
-0.4172
],
"z": [
-0.3707,
0.3189
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-1.5021,
-1.8377
],
"y": [
-1.2235,
-2.2218
],
"z": [
-0.3707,
-0.6386
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
1.9202,
2.582
],
"y": [
-0.8868,
-1.4615
],
"z": [
0.7279,
1.3694
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-1.9059,
-2.3215
],
"y": [
0.903,
-0.4172
],
"z": [
0.7182,
0.3189
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-1.9059,
-2.5292
],
"y": [
0.903,
1.4429
],
"z": [
0.7182,
1.4221
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-2.3215,
-3.3128
],
"y": [
-0.4172,
-0.7484
],
"z": [
0.3189,
0.6078
]
}
],
"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": [
"naphthalene.show()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"With the information that we are looking for `C6` and its hydrogens, we can finish our structure:"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [
{
"data": {
"application/vnd.plotly.v1+json": {
"config": {
"plotlyServerURL": "https://plot.ly"
},
"data": [
{
"customdata": [
[
"O7",
1,
1,
"UNK",
"A"
],
[
"O1",
16,
2,
"UNK",
"A"
],
[
"O7",
27,
3,
"UNK",
"A"
],
[
"O3",
41,
4,
"UNK",
"A"
]
],
"hovertemplate": "atom_element=O
x=%{x}
y=%{y}
z=%{z}
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,
"symbol": "circle"
},
"mode": "markers",
"name": "O",
"scene": "scene",
"showlegend": true,
"type": "scatter3d",
"x": [
2.4667057602678524,
-0.5993544079597652,
-0.15382410149959225,
-1.10219617195545
],
"y": [
0.0498501144262183,
0.5535815034775364,
0.2582020596200614,
4.247133027158526
],
"z": [
-1.1022711625191217,
1.4158303284167497,
3.308533779571458,
2.2236513733913483
]
},
{
"customdata": [
[
"C1",
2,
1,
"UNK",
"A"
],
[
"C7",
3,
1,
"UNK",
"A"
],
[
"C2",
4,
1,
"UNK",
"A"
],
[
"C6",
5,
1,
"UNK",
"A"
],
[
"C3",
6,
1,
"UNK",
"A"
],
[
"C5",
7,
1,
"UNK",
"A"
],
[
"C4",
8,
1,
"UNK",
"A"
],
[
"C3",
17,
2,
"UNK",
"A"
],
[
"C2",
18,
2,
"UNK",
"A"
],
[
"C4",
19,
2,
"UNK",
"A"
],
[
"C1",
20,
2,
"UNK",
"A"
],
[
"C1",
28,
3,
"UNK",
"A"
],
[
"C7",
29,
3,
"UNK",
"A"
],
[
"C2",
30,
3,
"UNK",
"A"
],
[
"C6",
31,
3,
"UNK",
"A"
],
[
"C3",
32,
3,
"UNK",
"A"
],
[
"C5",
33,
3,
"UNK",
"A"
],
[
"C4",
34,
3,
"UNK",
"A"
],
[
"C1",
43,
4,
"UNK",
"A"
],
[
"C2",
44,
4,
"UNK",
"A"
],
[
"C3",
45,
4,
"UNK",
"A"
],
[
"C1",
53,
5,
"UNK",
"A"
],
[
"C2",
54,
5,
"UNK",
"A"
],
[
"C6",
55,
5,
"UNK",
"A"
],
[
"C5",
56,
5,
"UNK",
"A"
],
[
"C3",
57,
5,
"UNK",
"A"
],
[
"C7",
58,
5,
"UNK",
"A"
],
[
"C10",
59,
5,
"UNK",
"A"
],
[
"C4",
60,
5,
"UNK",
"A"
],
[
"C8",
61,
5,
"UNK",
"A"
],
[
"C9",
62,
5,
"UNK",
"A"
]
],
"hovertemplate": "atom_element=C
x=%{x}
y=%{y}
z=%{z}
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,
"symbol": "circle"
},
"mode": "markers",
"name": "C",
"scene": "scene",
"showlegend": true,
"type": "scatter3d",
"x": [
0.3126525606562729,
1.7815522328213573,
-0.30533411819954764,
-0.44305301331474495,
-1.6790187869587725,
-1.8167329302901885,
-2.4346188318622546,
2.1423142668096413,
1.6907042423820315,
3.6563491167515423,
0.19104099358261412,
-1.4895164177484506,
-1.1115314226708142,
-2.5583639493044834,
-0.7740826627624255,
-2.9119658407064426,
-1.127701269892794,
-2.1965701269899647,
-1.4723750668265931,
-2.9415706661213434,
0.06419086876858915,
1.6704115013626706,
2.6205313150329435,
0.19989337707651678,
-0.2342638126311447,
2.014522231967489,
1.8775676542043402,
3.9551692286720286,
0.7491950483804148,
3.0221155350714337,
4.120807138454813
],
"y": [
0.08933263316239286,
-0.014303921829473515,
1.3398720102962447,
-1.0640628552236493,
1.4370987836817741,
-0.9667282785481541,
0.2837971942162518,
0.7967752568527462,
0.5626684820602113,
0.8803817980556864,
0.4424374012480973,
1.1255157827071043,
1.2567192657969595,
0.30821187060098415,
1.8197030602329989,
0.18518840508772216,
1.6965391669512417,
0.8793083326549296,
2.874681021906443,
2.857783473899638,
4.413257671176773,
5.844718475057669,
5.141695298051213,
5.48441121250036,
5.792502308761341,
4.973506782622986,
7.3433843250739645,
5.8472013804561,
5.2899178908636495,
7.921634358309114,
7.134057991635053
],
"z": [
-0.09482895377592876,
0.1424254404567714,
-0.1063624265586714,
-0.3055354625502364,
-0.3283948686767022,
-0.5276593151229398,
-0.5390945503996611,
0.7851718105899956,
2.221940429342761,
0.683346767356587,
2.3468713198667888,
5.074924676869857,
3.6380497973061394,
5.442985214747268,
6.050664327569663,
6.786708381671937,
7.3943882858597805,
7.7623296396148875,
2.395704356717751,
2.803332586707158,
1.4274814330640158,
1.5056103397884602,
0.4791582745350862,
1.238743888741511,
-0.19390319656242205,
-0.8963886510622272,
1.5857794007457566,
0.3611537950996877,
-1.2020451070017648,
1.1959582783496074,
0.6982715120885916
]
},
{
"customdata": [
[
"H72",
9,
1,
"UNK",
"A"
],
[
"H2",
10,
1,
"UNK",
"A"
],
[
"H6",
11,
1,
"UNK",
"A"
],
[
"H3",
12,
1,
"UNK",
"A"
],
[
"H5",
13,
1,
"UNK",
"A"
],
[
"H4",
14,
1,
"UNK",
"A"
],
[
"HO7",
15,
1,
"UNK",
"A"
],
[
"H31",
21,
2,
"UNK",
"A"
],
[
"H21",
22,
2,
"UNK",
"A"
],
[
"H22",
23,
2,
"UNK",
"A"
],
[
"H41",
24,
2,
"UNK",
"A"
],
[
"H42",
25,
2,
"UNK",
"A"
],
[
"H43",
26,
2,
"UNK",
"A"
],
[
"H71",
35,
3,
"UNK",
"A"
],
[
"H2",
36,
3,
"UNK",
"A"
],
[
"H6",
37,
3,
"UNK",
"A"
],
[
"H3",
38,
3,
"UNK",
"A"
],
[
"H5",
39,
3,
"UNK",
"A"
],
[
"H4",
40,
3,
"UNK",
"A"
],
[
"H1",
46,
4,
"UNK",
"A"
],
[
"H21",
47,
4,
"UNK",
"A"
],
[
"H22",
48,
4,
"UNK",
"A"
],
[
"H23",
49,
4,
"UNK",
"A"
],
[
"HN12",
50,
4,
"UNK",
"A"
],
[
"H32",
51,
4,
"UNK",
"A"
],
[
"H33",
52,
4,
"UNK",
"A"
],
[
"H1",
63,
5,
"UNK",
"A"
],
[
"H2",
64,
5,
"UNK",
"A"
],
[
"H61",
65,
5,
"UNK",
"A"
],
[
"H51",
66,
5,
"UNK",
"A"
],
[
"H52",
67,
5,
"UNK",
"A"
],
[
"H3",
68,
5,
"UNK",
"A"
],
[
"H7",
69,
5,
"UNK",
"A"
],
[
"H10",
70,
5,
"UNK",
"A"
],
[
"H4",
71,
5,
"UNK",
"A"
],
[
"H8",
72,
5,
"UNK",
"A"
],
[
"H9",
73,
5,
"UNK",
"A"
]
],
"hovertemplate": "atom_element=H
x=%{x}
y=%{y}
z=%{z}
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,
"symbol": "circle"
},
"mode": "markers",
"name": "H",
"scene": "scene",
"showlegend": true,
"type": "scatter3d",
"x": [
2.041561718695412,
0.27292172993905994,
0.027048241185559485,
-2.160153058820856,
-2.40530806246426,
-3.504113432695622,
2.1302981146307145,
1.7008479853575174,
2.0113307163537524,
2.1268786423582915,
4.045184824216871,
3.9578373620949603,
4.124517845448274,
-1.9812091890061918,
-3.1222358013048304,
0.061686606978976655,
-3.7437568733310704,
-0.5703902283326314,
-2.471623682175741,
-1.3680842386709395,
-3.1042630180798687,
-3.31064602211504,
-3.5528116561906917,
0.2519595758854295,
-0.05184781752645451,
0.9505357763986805,
1.9150768323738574,
2.817482948724505,
-0.4626517808854804,
-0.3688323969675731,
-1.2077577952180285,
2.6506753011637496,
1.0881514444482803,
4.798991121716275,
0.40339309135513224,
3.1609238895636937,
5.084981670199111
],
"y": [
-0.9571396762788134,
2.2458214194918362,
-2.0438619595536265,
2.410684670252219,
-1.864648919759131,
0.35946767817005576,
0.8167924380712381,
1.7241421877854288,
1.3891854815366478,
-0.3630664938990067,
1.7052196675976474,
1.049882968682121,
-0.04809887736175569,
1.1402072072064726,
-0.23910546208662525,
2.458057993012321,
-0.4515027667059093,
2.2365007944101083,
0.7832853066776577,
2.335527145640291,
3.416345868881275,
1.8358690753898859,
3.345922890603731,
2.0325950969746325,
3.904218646329364,
4.0401237756485155,
5.46017380341701,
4.131084764840773,
6.0046762886281755,
6.871310715761567,
5.322523508577383,
4.574557976507068,
7.959279470328645,
5.286045624160991,
5.164439065749729,
8.993390762418896,
7.617606206866266
],
"z": [
0.6349808357043045,
0.054692166892300775,
-0.30074112511799855,
-0.3379176786918484,
-0.692362368748375,
-0.712318499801796,
-1.5965213098725193,
0.4010765779284453,
2.865045120481715,
2.612855684981544,
1.2889201250676217,
-0.35508935541458087,
1.0256098486944045,
2.9824415202497,
4.692282202990008,
5.776771707091803,
7.07341097985568,
8.154424537513016,
8.808597473518727,
1.4467513542619979,
3.7325285291900023,
2.9386613483085946,
2.035925301154806,
3.0914197834368498,
0.4657989103647,
1.9481434642571058,
2.50685243404637,
0.8629885288798138,
1.9416510050967464,
-0.3330871650908569,
-0.3750682683747817,
-1.6835001632705424,
2.0069044983427693,
-0.03136307077500167,
-2.2240322160033976,
1.2827946818496438,
0.5870018581735374
]
},
{
"customdata": [
[
"N1",
42,
4,
"UNK",
"A"
]
],
"hovertemplate": "atom_element=N
x=%{x}
y=%{y}
z=%{z}
atom_id=%{customdata[0]}
atom_serial=%{customdata[1]}
residue_serial=%{customdata[2]}
residue_name=%{customdata[3]}
chain_id=%{customdata[4]}",
"legendgroup": "N",
"marker": {
"color": "blue",
"opacity": 1,
"symbol": "circle"
},
"mode": "markers",
"name": "N",
"scene": "scene",
"showlegend": true,
"type": "scatter3d",
"x": [
-0.6921173460214937
],
"y": [
2.2049738503146967
],
"z": [
3.434378936864302
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
2.4667057602678524,
1.7815522328213573
],
"y": [
0.0498501144262183,
-0.014303921829473515
],
"z": [
-1.1022711625191217,
0.1424254404567714
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
2.4667057602678524,
2.1302981146307145
],
"y": [
0.0498501144262183,
0.8167924380712381
],
"z": [
-1.1022711625191217,
-1.5965213098725193
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.3126525606562729,
1.7815522328213573
],
"y": [
0.08933263316239286,
-0.014303921829473515
],
"z": [
-0.09482895377592876,
0.1424254404567714
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.3126525606562729,
-0.30533411819954764
],
"y": [
0.08933263316239286,
1.3398720102962447
],
"z": [
-0.09482895377592876,
-0.1063624265586714
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.3126525606562729,
-0.44305301331474495
],
"y": [
0.08933263316239286,
-1.0640628552236493
],
"z": [
-0.09482895377592876,
-0.3055354625502364
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
1.7815522328213573,
2.041561718695412
],
"y": [
-0.014303921829473515,
-0.9571396762788134
],
"z": [
0.1424254404567714,
0.6349808357043045
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
1.7815522328213573,
2.1423142668096413
],
"y": [
-0.014303921829473515,
0.7967752568527462
],
"z": [
0.1424254404567714,
0.7851718105899956
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.30533411819954764,
-1.6790187869587725
],
"y": [
1.3398720102962447,
1.4370987836817741
],
"z": [
-0.1063624265586714,
-0.3283948686767022
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.30533411819954764,
0.27292172993905994
],
"y": [
1.3398720102962447,
2.2458214194918362
],
"z": [
-0.1063624265586714,
0.054692166892300775
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.44305301331474495,
-1.8167329302901885
],
"y": [
-1.0640628552236493,
-0.9667282785481541
],
"z": [
-0.3055354625502364,
-0.5276593151229398
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.44305301331474495,
0.027048241185559485
],
"y": [
-1.0640628552236493,
-2.0438619595536265
],
"z": [
-0.3055354625502364,
-0.30074112511799855
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-1.6790187869587725,
-2.4346188318622546
],
"y": [
1.4370987836817741,
0.2837971942162518
],
"z": [
-0.3283948686767022,
-0.5390945503996611
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-1.6790187869587725,
-2.160153058820856
],
"y": [
1.4370987836817741,
2.410684670252219
],
"z": [
-0.3283948686767022,
-0.3379176786918484
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-1.8167329302901885,
-2.4346188318622546
],
"y": [
-0.9667282785481541,
0.2837971942162518
],
"z": [
-0.5276593151229398,
-0.5390945503996611
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-1.8167329302901885,
-2.40530806246426
],
"y": [
-0.9667282785481541,
-1.864648919759131
],
"z": [
-0.5276593151229398,
-0.692362368748375
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-2.4346188318622546,
-3.504113432695622
],
"y": [
0.2837971942162518,
0.35946767817005576
],
"z": [
-0.5390945503996611,
-0.712318499801796
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.5993544079597652,
0.19104099358261412
],
"y": [
0.5535815034775364,
0.4424374012480973
],
"z": [
1.4158303284167497,
2.3468713198667888
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
2.1423142668096413,
1.6907042423820315
],
"y": [
0.7967752568527462,
0.5626684820602113
],
"z": [
0.7851718105899956,
2.221940429342761
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
2.1423142668096413,
3.6563491167515423
],
"y": [
0.7967752568527462,
0.8803817980556864
],
"z": [
0.7851718105899956,
0.683346767356587
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
2.1423142668096413,
1.7008479853575174
],
"y": [
0.7967752568527462,
1.7241421877854288
],
"z": [
0.7851718105899956,
0.4010765779284453
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
1.6907042423820315,
0.19104099358261412
],
"y": [
0.5626684820602113,
0.4424374012480973
],
"z": [
2.221940429342761,
2.3468713198667888
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
1.6907042423820315,
2.0113307163537524
],
"y": [
0.5626684820602113,
1.3891854815366478
],
"z": [
2.221940429342761,
2.865045120481715
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
1.6907042423820315,
2.1268786423582915
],
"y": [
0.5626684820602113,
-0.3630664938990067
],
"z": [
2.221940429342761,
2.612855684981544
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
3.6563491167515423,
4.045184824216871
],
"y": [
0.8803817980556864,
1.7052196675976474
],
"z": [
0.683346767356587,
1.2889201250676217
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
3.6563491167515423,
3.9578373620949603
],
"y": [
0.8803817980556864,
1.049882968682121
],
"z": [
0.683346767356587,
-0.35508935541458087
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
3.6563491167515423,
4.124517845448274
],
"y": [
0.8803817980556864,
-0.04809887736175569
],
"z": [
0.683346767356587,
1.0256098486944045
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.19104099358261412,
-0.15382410149959225
],
"y": [
0.4424374012480973,
0.2582020596200614
],
"z": [
2.3468713198667888,
3.308533779571458
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.15382410149959225,
-1.1115314226708142
],
"y": [
0.2582020596200614,
1.2567192657969595
],
"z": [
3.308533779571458,
3.6380497973061394
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-1.4895164177484506,
-1.1115314226708142
],
"y": [
1.1255157827071043,
1.2567192657969595
],
"z": [
5.074924676869857,
3.6380497973061394
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-1.4895164177484506,
-2.5583639493044834
],
"y": [
1.1255157827071043,
0.30821187060098415
],
"z": [
5.074924676869857,
5.442985214747268
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-1.4895164177484506,
-0.7740826627624255
],
"y": [
1.1255157827071043,
1.8197030602329989
],
"z": [
5.074924676869857,
6.050664327569663
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-1.1115314226708142,
-1.9812091890061918
],
"y": [
1.2567192657969595,
1.1402072072064726
],
"z": [
3.6380497973061394,
2.9824415202497
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-1.1115314226708142,
-0.6921173460214937
],
"y": [
1.2567192657969595,
2.2049738503146967
],
"z": [
3.6380497973061394,
3.434378936864302
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-2.5583639493044834,
-2.9119658407064426
],
"y": [
0.30821187060098415,
0.18518840508772216
],
"z": [
5.442985214747268,
6.786708381671937
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-2.5583639493044834,
-3.1222358013048304
],
"y": [
0.30821187060098415,
-0.23910546208662525
],
"z": [
5.442985214747268,
4.692282202990008
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.7740826627624255,
-1.127701269892794
],
"y": [
1.8197030602329989,
1.6965391669512417
],
"z": [
6.050664327569663,
7.3943882858597805
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.7740826627624255,
0.061686606978976655
],
"y": [
1.8197030602329989,
2.458057993012321
],
"z": [
6.050664327569663,
5.776771707091803
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-2.9119658407064426,
-2.1965701269899647
],
"y": [
0.18518840508772216,
0.8793083326549296
],
"z": [
6.786708381671937,
7.7623296396148875
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-2.9119658407064426,
-3.7437568733310704
],
"y": [
0.18518840508772216,
-0.4515027667059093
],
"z": [
6.786708381671937,
7.07341097985568
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-1.127701269892794,
-2.1965701269899647
],
"y": [
1.6965391669512417,
0.8793083326549296
],
"z": [
7.3943882858597805,
7.7623296396148875
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-1.127701269892794,
-0.5703902283326314
],
"y": [
1.6965391669512417,
2.2365007944101083
],
"z": [
7.3943882858597805,
8.154424537513016
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-2.1965701269899647,
-2.471623682175741
],
"y": [
0.8793083326549296,
0.7832853066776577
],
"z": [
7.7623296396148875,
8.808597473518727
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-1.10219617195545,
-1.4723750668265931
],
"y": [
4.247133027158526,
2.874681021906443
],
"z": [
2.2236513733913483,
2.395704356717751
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-1.10219617195545,
0.06419086876858915
],
"y": [
4.247133027158526,
4.413257671176773
],
"z": [
2.2236513733913483,
1.4274814330640158
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.6921173460214937,
-1.4723750668265931
],
"y": [
2.2049738503146967,
2.874681021906443
],
"z": [
3.434378936864302,
2.395704356717751
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.6921173460214937,
0.2519595758854295
],
"y": [
2.2049738503146967,
2.0325950969746325
],
"z": [
3.434378936864302,
3.0914197834368498
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-1.4723750668265931,
-2.9415706661213434
],
"y": [
2.874681021906443,
2.857783473899638
],
"z": [
2.395704356717751,
2.803332586707158
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-1.4723750668265931,
-1.3680842386709395
],
"y": [
2.874681021906443,
2.335527145640291
],
"z": [
2.395704356717751,
1.4467513542619979
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-2.9415706661213434,
-3.1042630180798687
],
"y": [
2.857783473899638,
3.416345868881275
],
"z": [
2.803332586707158,
3.7325285291900023
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-2.9415706661213434,
-3.31064602211504
],
"y": [
2.857783473899638,
1.8358690753898859
],
"z": [
2.803332586707158,
2.9386613483085946
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-2.9415706661213434,
-3.5528116561906917
],
"y": [
2.857783473899638,
3.345922890603731
],
"z": [
2.803332586707158,
2.035925301154806
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.06419086876858915,
-0.05184781752645451
],
"y": [
4.413257671176773,
3.904218646329364
],
"z": [
1.4274814330640158,
0.4657989103647
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.06419086876858915,
0.9505357763986805
],
"y": [
4.413257671176773,
4.0401237756485155
],
"z": [
1.4274814330640158,
1.9481434642571058
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.06419086876858915,
0.19989337707651678
],
"y": [
4.413257671176773,
5.48441121250036
],
"z": [
1.4274814330640158,
1.238743888741511
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
1.6704115013626706,
2.6205313150329435
],
"y": [
5.844718475057669,
5.141695298051213
],
"z": [
1.5056103397884602,
0.4791582745350862
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
1.6704115013626706,
0.19989337707651678
],
"y": [
5.844718475057669,
5.48441121250036
],
"z": [
1.5056103397884602,
1.238743888741511
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
1.6704115013626706,
1.8775676542043402
],
"y": [
5.844718475057669,
7.3433843250739645
],
"z": [
1.5056103397884602,
1.5857794007457566
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
1.6704115013626706,
1.9150768323738574
],
"y": [
5.844718475057669,
5.46017380341701
],
"z": [
1.5056103397884602,
2.50685243404637
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
2.6205313150329435,
2.014522231967489
],
"y": [
5.141695298051213,
4.973506782622986
],
"z": [
0.4791582745350862,
-0.8963886510622272
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
2.6205313150329435,
3.9551692286720286
],
"y": [
5.141695298051213,
5.8472013804561
],
"z": [
0.4791582745350862,
0.3611537950996877
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
2.6205313150329435,
2.817482948724505
],
"y": [
5.141695298051213,
4.131084764840773
],
"z": [
0.4791582745350862,
0.8629885288798138
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.19989337707651678,
-0.2342638126311447
],
"y": [
5.48441121250036,
5.792502308761341
],
"z": [
1.238743888741511,
-0.19390319656242205
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.19989337707651678,
-0.4626517808854804
],
"y": [
5.48441121250036,
6.0046762886281755
],
"z": [
1.238743888741511,
1.9416510050967464
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.2342638126311447,
0.7491950483804148
],
"y": [
5.792502308761341,
5.2899178908636495
],
"z": [
-0.19390319656242205,
-1.2020451070017648
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.2342638126311447,
-0.3688323969675731
],
"y": [
5.792502308761341,
6.871310715761567
],
"z": [
-0.19390319656242205,
-0.3330871650908569
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
-0.2342638126311447,
-1.2077577952180285
],
"y": [
5.792502308761341,
5.322523508577383
],
"z": [
-0.19390319656242205,
-0.3750682683747817
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
2.014522231967489,
0.7491950483804148
],
"y": [
4.973506782622986,
5.2899178908636495
],
"z": [
-0.8963886510622272,
-1.2020451070017648
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
2.014522231967489,
2.6506753011637496
],
"y": [
4.973506782622986,
4.574557976507068
],
"z": [
-0.8963886510622272,
-1.6835001632705424
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
1.8775676542043402,
3.0221155350714337
],
"y": [
7.3433843250739645,
7.921634358309114
],
"z": [
1.5857794007457566,
1.1959582783496074
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
1.8775676542043402,
1.0881514444482803
],
"y": [
7.3433843250739645,
7.959279470328645
],
"z": [
1.5857794007457566,
2.0069044983427693
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
3.9551692286720286,
4.120807138454813
],
"y": [
5.8472013804561,
7.134057991635053
],
"z": [
0.3611537950996877,
0.6982715120885916
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
3.9551692286720286,
4.798991121716275
],
"y": [
5.8472013804561,
5.286045624160991
],
"z": [
0.3611537950996877,
-0.03136307077500167
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
0.7491950483804148,
0.40339309135513224
],
"y": [
5.2899178908636495,
5.164439065749729
],
"z": [
-1.2020451070017648,
-2.2240322160033976
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
3.0221155350714337,
4.120807138454813
],
"y": [
7.921634358309114,
7.134057991635053
],
"z": [
1.1959582783496074,
0.6982715120885916
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
3.0221155350714337,
3.1609238895636937
],
"y": [
7.921634358309114,
8.993390762418896
],
"z": [
1.1959582783496074,
1.2827946818496438
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
4.120807138454813,
5.084981670199111
],
"y": [
7.134057991635053,
7.617606206866266
],
"z": [
0.6982715120885916,
0.5870018581735374
]
}
],
"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": [
"link4 = bb.linkage(\"C3\", \"C6\")\n",
"\n",
"# attach (using another whacky syntax) and visualize\n",
"final = mol % link4 + naphthalene\n",
"final.show()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Alrighty, that is the structure we just built! Admitedly, it looks a bit crammed. So, let's optimize the conformation a little. Optimizing conformations in biobuild is a topic all to its own, so go check out the tutorial on optimizing structures for a better introduction. Here is just some code that will optimize the little molecule we have:"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {},
"outputs": [
{
"data": {
"application/vnd.plotly.v1+json": {
"config": {
"plotlyServerURL": "https://plot.ly"
},
"data": [
{
"customdata": [
[
"O7",
1,
1,
"UNK",
"A"
],
[
"O1",
16,
2,
"UNK",
"A"
],
[
"O7",
27,
3,
"UNK",
"A"
],
[
"O3",
41,
4,
"UNK",
"A"
]
],
"hovertemplate": "atom_element=O
x=%{x}
y=%{y}
z=%{z}
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,
"symbol": "circle"
},
"mode": "markers",
"name": "O",
"scene": "scene",
"showlegend": true,
"type": "scatter3d",
"x": [
4.118178087351607,
3.820232896015799,
5.753808058147404,
3.921489105534512
],
"y": [
0.8769788207331339,
0.5358642489955203,
0.8757486509742243,
0.007157007082428279
],
"z": [
-5.745112708459128,
-3.545609332115606,
-3.4279729877304517,
0.25337705381189
]
},
{
"customdata": [
[
"C1",
2,
1,
"UNK",
"A"
],
[
"C7",
3,
1,
"UNK",
"A"
],
[
"C2",
4,
1,
"UNK",
"A"
],
[
"C6",
5,
1,
"UNK",
"A"
],
[
"C3",
6,
1,
"UNK",
"A"
],
[
"C5",
7,
1,
"UNK",
"A"
],
[
"C4",
8,
1,
"UNK",
"A"
],
[
"C3",
17,
2,
"UNK",
"A"
],
[
"C2",
18,
2,
"UNK",
"A"
],
[
"C4",
19,
2,
"UNK",
"A"
],
[
"C1",
20,
2,
"UNK",
"A"
],
[
"C1",
28,
3,
"UNK",
"A"
],
[
"C7",
29,
3,
"UNK",
"A"
],
[
"C2",
30,
3,
"UNK",
"A"
],
[
"C6",
31,
3,
"UNK",
"A"
],
[
"C3",
32,
3,
"UNK",
"A"
],
[
"C5",
33,
3,
"UNK",
"A"
],
[
"C4",
34,
3,
"UNK",
"A"
],
[
"C1",
43,
4,
"UNK",
"A"
],
[
"C2",
44,
4,
"UNK",
"A"
],
[
"C3",
45,
4,
"UNK",
"A"
],
[
"C1",
53,
5,
"UNK",
"A"
],
[
"C2",
54,
5,
"UNK",
"A"
],
[
"C6",
55,
5,
"UNK",
"A"
],
[
"C5",
56,
5,
"UNK",
"A"
],
[
"C3",
57,
5,
"UNK",
"A"
],
[
"C7",
58,
5,
"UNK",
"A"
],
[
"C10",
59,
5,
"UNK",
"A"
],
[
"C4",
60,
5,
"UNK",
"A"
],
[
"C8",
61,
5,
"UNK",
"A"
],
[
"C9",
62,
5,
"UNK",
"A"
]
],
"hovertemplate": "atom_element=C
x=%{x}
y=%{y}
z=%{z}
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,
"symbol": "circle"
},
"mode": "markers",
"name": "C",
"scene": "scene",
"showlegend": true,
"type": "scatter3d",
"x": [
5.484290726140651,
5.415940597850755,
4.353398971102852,
6.679019412808826,
4.417085421577411,
6.742636722826127,
5.611717986508108,
5.618375793658217,
5.450948226869103,
4.687604378603161,
4.991381127879431,
5.4751405290847,
5.392312818696337,
5.4179891878300745,
5.609367905364737,
5.495251410983014,
5.686525148375386,
5.62944811843548,
4.080397203776119,
2.7485267462496585,
4.0703344444242315,
4.4418981952833505,
3.0859332785077505,
4.81270390928659,
4.852798029268477,
2.844212689044748,
5.574800262689976,
2.9481123347554843,
3.6477789128551525,
5.348593233176091,
4.007330663978866
],
"y": [
1.0010555072038594,
0.5953155125860629,
1.5164117000876989,
0.8655583722022782,
1.8961063015283492,
1.2453756157404638,
1.7606253527018398,
-0.47459609265639346,
-0.8698628659739802,
-1.268154117279589,
0.28017054327746,
2.7729073683314693,
1.286651361643858,
3.54929038364126,
3.386552945522661,
4.939281231370799,
4.776572776370658,
5.552836287386774,
1.2055063635793068,
1.9461531895486424,
0.21805194200762346,
-0.8690531538532413,
-1.6495768817748941,
-0.49509747597600295,
-1.7050798755758447,
-2.532770030266034,
-1.5870351915691403,
-2.4700524187514366,
-2.5769637687822304,
-2.516438796361012,
-2.8611503543977457
],
"z": [
-7.687993325999813,
-6.254326786413183,
-8.32153979062873,
-8.39515185961056,
-9.662262381496346,
-9.735861089599382,
-10.369318452336678,
-6.130106320931334,
-4.667644749542132,
-7.032098645994321,
-3.8043520186960276,
-2.0209985496536613,
-2.1152274357598633,
-3.178518496665924,
-0.7755141390524434,
-3.090671970829174,
-0.6877578304455814,
-1.8452917971688783,
-0.5140642703926122,
-0.4636125751803022,
1.651701440895839,
3.472490217576176,
3.5245953480819305,
2.0281485497406426,
1.0952898711609307,
2.320766145458912,
4.177028917140024,
4.7898018650926115,
1.2498212461167233,
5.11583815186153,
5.512424273941399
]
},
{
"customdata": [
[
"H72",
9,
1,
"UNK",
"A"
],
[
"H2",
10,
1,
"UNK",
"A"
],
[
"H6",
11,
1,
"UNK",
"A"
],
[
"H3",
12,
1,
"UNK",
"A"
],
[
"H5",
13,
1,
"UNK",
"A"
],
[
"H4",
14,
1,
"UNK",
"A"
],
[
"HO7",
15,
1,
"UNK",
"A"
],
[
"H31",
21,
2,
"UNK",
"A"
],
[
"H21",
22,
2,
"UNK",
"A"
],
[
"H22",
23,
2,
"UNK",
"A"
],
[
"H41",
24,
2,
"UNK",
"A"
],
[
"H42",
25,
2,
"UNK",
"A"
],
[
"H43",
26,
2,
"UNK",
"A"
],
[
"H71",
35,
3,
"UNK",
"A"
],
[
"H2",
36,
3,
"UNK",
"A"
],
[
"H6",
37,
3,
"UNK",
"A"
],
[
"H3",
38,
3,
"UNK",
"A"
],
[
"H5",
39,
3,
"UNK",
"A"
],
[
"H4",
40,
3,
"UNK",
"A"
],
[
"H1",
46,
4,
"UNK",
"A"
],
[
"H21",
47,
4,
"UNK",
"A"
],
[
"H22",
48,
4,
"UNK",
"A"
],
[
"H23",
49,
4,
"UNK",
"A"
],
[
"HN12",
50,
4,
"UNK",
"A"
],
[
"H32",
51,
4,
"UNK",
"A"
],
[
"H33",
52,
4,
"UNK",
"A"
],
[
"H1",
63,
5,
"UNK",
"A"
],
[
"H2",
64,
5,
"UNK",
"A"
],
[
"H61",
65,
5,
"UNK",
"A"
],
[
"H51",
66,
5,
"UNK",
"A"
],
[
"H52",
67,
5,
"UNK",
"A"
],
[
"H3",
68,
5,
"UNK",
"A"
],
[
"H7",
69,
5,
"UNK",
"A"
],
[
"H10",
70,
5,
"UNK",
"A"
],
[
"H4",
71,
5,
"UNK",
"A"
],
[
"H8",
72,
5,
"UNK",
"A"
],
[
"H9",
73,
5,
"UNK",
"A"
]
],
"hovertemplate": "atom_element=H
x=%{x}
y=%{y}
z=%{z}
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,
"symbol": "circle"
},
"mode": "markers",
"name": "H",
"scene": "scene",
"showlegend": true,
"type": "scatter3d",
"x": [
6.152080306906299,
3.417397415750716,
7.56734721278136,
3.5368397723261724,
7.672983084827312,
5.661451574144692,
3.462120796375985,
6.655902232026921,
6.398765184656333,
4.707735531344284,
4.888913619231511,
4.825479041565505,
3.64023647076956,
6.062524536122155,
5.31167988485601,
5.653191600057221,
5.45023578236556,
5.790435066623585,
5.689259555362844,
4.850125889309804,
1.9362977550948122,
2.7911978861962323,
2.477364772556877,
4.427676379200855,
3.123499754163036,
4.428547477430437,
4.3065132871925975,
2.283007251955558,
5.778721124802753,
5.752634051113111,
4.909516530526894,
1.9645632633927148,
6.598010351407952,
1.9503172324102764,
3.4150394294056308,
6.172316908637534,
3.878826798936297
],
"y": [
1.1359152331277986,
1.6285243177873874,
0.4671453984380257,
2.297834667668709,
1.140537635921091,
2.0565641736580016,
0.5101604230338993,
-0.6382701469349878,
-1.2339699139769196,
-1.6688420127993038,
-2.341467542094767,
-0.9695894701680645,
-1.0949097381696034,
0.8014342287691963,
3.083046284378984,
2.792773133862573,
5.543841897301155,
5.2546811240509825,
6.635095091858845,
1.8420227868535148,
1.3349074724798902,
2.8904441097166,
2.1667952267095805,
-0.06523983532559063,
0.03811675311964002,
1.230199140853192,
0.07524527863231589,
-0.8994408472452311,
0.024013089008975808,
-2.3036814854892387,
-1.3492585471430654,
-3.172681356955812,
-1.3110035145443888,
-2.764456977122998,
-3.262753378311451,
-3.002822529562805,
-3.46276448291608
],
"z": [
-5.6501701172438255,
-7.780804560288682,
-7.912279948921735,
-10.155448215449901,
-10.286564189916195,
-11.413108682465257,
-6.36211103428108,
-6.445036064909193,
-4.257054440200144,
-4.571128936594146,
-6.956318096054709,
-8.076045540624595,
-6.764873664476756,
-1.3975107243827194,
-4.154416806944346,
0.13362252781805828,
-3.9917437462111476,
0.28199698226124004,
-1.7768101780629302,
-0.061913992753865,
-0.8741349123224924,
-1.0161823553022455,
0.574943083155111,
-2.0732499207515005,
2.1699160461684346,
1.8594672245407045,
4.020388800405682,
3.532010574661433,
1.9956645437164808,
1.2777171344740625,
0.06012535097714222,
2.3319818453557652,
3.9389139079015068,
5.104017634502682,
0.44031119410661157,
5.626112862738902,
6.4053853800575915
]
},
{
"customdata": [
[
"N1",
42,
4,
"UNK",
"A"
]
],
"hovertemplate": "atom_element=N
x=%{x}
y=%{y}
z=%{z}
atom_id=%{customdata[0]}
atom_serial=%{customdata[1]}
residue_serial=%{customdata[2]}
residue_name=%{customdata[3]}
chain_id=%{customdata[4]}",
"legendgroup": "N",
"marker": {
"color": "blue",
"opacity": 1,
"symbol": "circle"
},
"mode": "markers",
"name": "N",
"scene": "scene",
"showlegend": true,
"type": "scatter3d",
"x": [
4.414653687386504
],
"y": [
0.9409766942046631
],
"z": [
-1.9120812041902548
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
4.118178087351607,
5.415940597850755
],
"y": [
0.8769788207331339,
0.5953155125860629
],
"z": [
-5.745112708459128,
-6.254326786413183
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
4.118178087351607,
3.462120796375985
],
"y": [
0.8769788207331339,
0.5101604230338993
],
"z": [
-5.745112708459128,
-6.36211103428108
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
5.484290726140651,
5.415940597850755
],
"y": [
1.0010555072038594,
0.5953155125860629
],
"z": [
-7.687993325999813,
-6.254326786413183
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
5.484290726140651,
4.353398971102852
],
"y": [
1.0010555072038594,
1.5164117000876989
],
"z": [
-7.687993325999813,
-8.32153979062873
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
5.484290726140651,
6.679019412808826
],
"y": [
1.0010555072038594,
0.8655583722022782
],
"z": [
-7.687993325999813,
-8.39515185961056
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
5.415940597850755,
6.152080306906299
],
"y": [
0.5953155125860629,
1.1359152331277986
],
"z": [
-6.254326786413183,
-5.6501701172438255
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
5.415940597850755,
5.618375793658217
],
"y": [
0.5953155125860629,
-0.47459609265639346
],
"z": [
-6.254326786413183,
-6.130106320931334
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
4.353398971102852,
4.417085421577411
],
"y": [
1.5164117000876989,
1.8961063015283492
],
"z": [
-8.32153979062873,
-9.662262381496346
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
4.353398971102852,
3.417397415750716
],
"y": [
1.5164117000876989,
1.6285243177873874
],
"z": [
-8.32153979062873,
-7.780804560288682
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
6.679019412808826,
6.742636722826127
],
"y": [
0.8655583722022782,
1.2453756157404638
],
"z": [
-8.39515185961056,
-9.735861089599382
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
6.679019412808826,
7.56734721278136
],
"y": [
0.8655583722022782,
0.4671453984380257
],
"z": [
-8.39515185961056,
-7.912279948921735
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
4.417085421577411,
5.611717986508108
],
"y": [
1.8961063015283492,
1.7606253527018398
],
"z": [
-9.662262381496346,
-10.369318452336678
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
4.417085421577411,
3.5368397723261724
],
"y": [
1.8961063015283492,
2.297834667668709
],
"z": [
-9.662262381496346,
-10.155448215449901
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
6.742636722826127,
5.611717986508108
],
"y": [
1.2453756157404638,
1.7606253527018398
],
"z": [
-9.735861089599382,
-10.369318452336678
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
6.742636722826127,
7.672983084827312
],
"y": [
1.2453756157404638,
1.140537635921091
],
"z": [
-9.735861089599382,
-10.286564189916195
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
5.611717986508108,
5.661451574144692
],
"y": [
1.7606253527018398,
2.0565641736580016
],
"z": [
-10.369318452336678,
-11.413108682465257
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
3.820232896015799,
4.991381127879431
],
"y": [
0.5358642489955203,
0.28017054327746
],
"z": [
-3.545609332115606,
-3.8043520186960276
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
5.618375793658217,
5.450948226869103
],
"y": [
-0.47459609265639346,
-0.8698628659739802
],
"z": [
-6.130106320931334,
-4.667644749542132
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
5.618375793658217,
4.687604378603161
],
"y": [
-0.47459609265639346,
-1.268154117279589
],
"z": [
-6.130106320931334,
-7.032098645994321
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
5.618375793658217,
6.655902232026921
],
"y": [
-0.47459609265639346,
-0.6382701469349878
],
"z": [
-6.130106320931334,
-6.445036064909193
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
5.450948226869103,
4.991381127879431
],
"y": [
-0.8698628659739802,
0.28017054327746
],
"z": [
-4.667644749542132,
-3.8043520186960276
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
5.450948226869103,
6.398765184656333
],
"y": [
-0.8698628659739802,
-1.2339699139769196
],
"z": [
-4.667644749542132,
-4.257054440200144
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
5.450948226869103,
4.707735531344284
],
"y": [
-0.8698628659739802,
-1.6688420127993038
],
"z": [
-4.667644749542132,
-4.571128936594146
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
4.687604378603161,
4.888913619231511
],
"y": [
-1.268154117279589,
-2.341467542094767
],
"z": [
-7.032098645994321,
-6.956318096054709
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
4.687604378603161,
4.825479041565505
],
"y": [
-1.268154117279589,
-0.9695894701680645
],
"z": [
-7.032098645994321,
-8.076045540624595
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
4.687604378603161,
3.64023647076956
],
"y": [
-1.268154117279589,
-1.0949097381696034
],
"z": [
-7.032098645994321,
-6.764873664476756
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
4.991381127879431,
5.753808058147404
],
"y": [
0.28017054327746,
0.8757486509742243
],
"z": [
-3.8043520186960276,
-3.4279729877304517
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
5.753808058147404,
5.392312818696337
],
"y": [
0.8757486509742243,
1.286651361643858
],
"z": [
-3.4279729877304517,
-2.1152274357598633
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
5.4751405290847,
5.392312818696337
],
"y": [
2.7729073683314693,
1.286651361643858
],
"z": [
-2.0209985496536613,
-2.1152274357598633
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
5.4751405290847,
5.4179891878300745
],
"y": [
2.7729073683314693,
3.54929038364126
],
"z": [
-2.0209985496536613,
-3.178518496665924
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
5.4751405290847,
5.609367905364737
],
"y": [
2.7729073683314693,
3.386552945522661
],
"z": [
-2.0209985496536613,
-0.7755141390524434
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
5.392312818696337,
6.062524536122155
],
"y": [
1.286651361643858,
0.8014342287691963
],
"z": [
-2.1152274357598633,
-1.3975107243827194
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
5.392312818696337,
4.414653687386504
],
"y": [
1.286651361643858,
0.9409766942046631
],
"z": [
-2.1152274357598633,
-1.9120812041902548
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
5.4179891878300745,
5.495251410983014
],
"y": [
3.54929038364126,
4.939281231370799
],
"z": [
-3.178518496665924,
-3.090671970829174
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
5.4179891878300745,
5.31167988485601
],
"y": [
3.54929038364126,
3.083046284378984
],
"z": [
-3.178518496665924,
-4.154416806944346
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
5.609367905364737,
5.686525148375386
],
"y": [
3.386552945522661,
4.776572776370658
],
"z": [
-0.7755141390524434,
-0.6877578304455814
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
5.609367905364737,
5.653191600057221
],
"y": [
3.386552945522661,
2.792773133862573
],
"z": [
-0.7755141390524434,
0.13362252781805828
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
5.495251410983014,
5.62944811843548
],
"y": [
4.939281231370799,
5.552836287386774
],
"z": [
-3.090671970829174,
-1.8452917971688783
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
5.495251410983014,
5.45023578236556
],
"y": [
4.939281231370799,
5.543841897301155
],
"z": [
-3.090671970829174,
-3.9917437462111476
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
5.686525148375386,
5.62944811843548
],
"y": [
4.776572776370658,
5.552836287386774
],
"z": [
-0.6877578304455814,
-1.8452917971688783
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
5.686525148375386,
5.790435066623585
],
"y": [
4.776572776370658,
5.2546811240509825
],
"z": [
-0.6877578304455814,
0.28199698226124004
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
5.62944811843548,
5.689259555362844
],
"y": [
5.552836287386774,
6.635095091858845
],
"z": [
-1.8452917971688783,
-1.7768101780629302
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
3.921489105534512,
4.080397203776119
],
"y": [
0.007157007082428279,
1.2055063635793068
],
"z": [
0.25337705381189,
-0.5140642703926122
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
3.921489105534512,
4.0703344444242315
],
"y": [
0.007157007082428279,
0.21805194200762346
],
"z": [
0.25337705381189,
1.651701440895839
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
4.414653687386504,
4.080397203776119
],
"y": [
0.9409766942046631,
1.2055063635793068
],
"z": [
-1.9120812041902548,
-0.5140642703926122
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
4.414653687386504,
4.427676379200855
],
"y": [
0.9409766942046631,
-0.06523983532559063
],
"z": [
-1.9120812041902548,
-2.0732499207515005
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
4.080397203776119,
2.7485267462496585
],
"y": [
1.2055063635793068,
1.9461531895486424
],
"z": [
-0.5140642703926122,
-0.4636125751803022
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
4.080397203776119,
4.850125889309804
],
"y": [
1.2055063635793068,
1.8420227868535148
],
"z": [
-0.5140642703926122,
-0.061913992753865
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
2.7485267462496585,
1.9362977550948122
],
"y": [
1.9461531895486424,
1.3349074724798902
],
"z": [
-0.4636125751803022,
-0.8741349123224924
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
2.7485267462496585,
2.7911978861962323
],
"y": [
1.9461531895486424,
2.8904441097166
],
"z": [
-0.4636125751803022,
-1.0161823553022455
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
2.7485267462496585,
2.477364772556877
],
"y": [
1.9461531895486424,
2.1667952267095805
],
"z": [
-0.4636125751803022,
0.574943083155111
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
4.0703344444242315,
3.123499754163036
],
"y": [
0.21805194200762346,
0.03811675311964002
],
"z": [
1.651701440895839,
2.1699160461684346
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
4.0703344444242315,
4.428547477430437
],
"y": [
0.21805194200762346,
1.230199140853192
],
"z": [
1.651701440895839,
1.8594672245407045
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
4.0703344444242315,
4.81270390928659
],
"y": [
0.21805194200762346,
-0.49509747597600295
],
"z": [
1.651701440895839,
2.0281485497406426
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
4.4418981952833505,
3.0859332785077505
],
"y": [
-0.8690531538532413,
-1.6495768817748941
],
"z": [
3.472490217576176,
3.5245953480819305
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
4.4418981952833505,
4.81270390928659
],
"y": [
-0.8690531538532413,
-0.49509747597600295
],
"z": [
3.472490217576176,
2.0281485497406426
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
4.4418981952833505,
5.574800262689976
],
"y": [
-0.8690531538532413,
-1.5870351915691403
],
"z": [
3.472490217576176,
4.177028917140024
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
4.4418981952833505,
4.3065132871925975
],
"y": [
-0.8690531538532413,
0.07524527863231589
],
"z": [
3.472490217576176,
4.020388800405682
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
3.0859332785077505,
2.844212689044748
],
"y": [
-1.6495768817748941,
-2.532770030266034
],
"z": [
3.5245953480819305,
2.320766145458912
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
3.0859332785077505,
2.9481123347554843
],
"y": [
-1.6495768817748941,
-2.4700524187514366
],
"z": [
3.5245953480819305,
4.7898018650926115
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
3.0859332785077505,
2.283007251955558
],
"y": [
-1.6495768817748941,
-0.8994408472452311
],
"z": [
3.5245953480819305,
3.532010574661433
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
4.81270390928659,
4.852798029268477
],
"y": [
-0.49509747597600295,
-1.7050798755758447
],
"z": [
2.0281485497406426,
1.0952898711609307
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
4.81270390928659,
5.778721124802753
],
"y": [
-0.49509747597600295,
0.024013089008975808
],
"z": [
2.0281485497406426,
1.9956645437164808
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
4.852798029268477,
3.6477789128551525
],
"y": [
-1.7050798755758447,
-2.5769637687822304
],
"z": [
1.0952898711609307,
1.2498212461167233
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
4.852798029268477,
5.752634051113111
],
"y": [
-1.7050798755758447,
-2.3036814854892387
],
"z": [
1.0952898711609307,
1.2777171344740625
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
4.852798029268477,
4.909516530526894
],
"y": [
-1.7050798755758447,
-1.3492585471430654
],
"z": [
1.0952898711609307,
0.06012535097714222
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
2.844212689044748,
3.6477789128551525
],
"y": [
-2.532770030266034,
-2.5769637687822304
],
"z": [
2.320766145458912,
1.2498212461167233
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
2.844212689044748,
1.9645632633927148
],
"y": [
-2.532770030266034,
-3.172681356955812
],
"z": [
2.320766145458912,
2.3319818453557652
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
5.574800262689976,
5.348593233176091
],
"y": [
-1.5870351915691403,
-2.516438796361012
],
"z": [
4.177028917140024,
5.11583815186153
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
5.574800262689976,
6.598010351407952
],
"y": [
-1.5870351915691403,
-1.3110035145443888
],
"z": [
4.177028917140024,
3.9389139079015068
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
2.9481123347554843,
4.007330663978866
],
"y": [
-2.4700524187514366,
-2.8611503543977457
],
"z": [
4.7898018650926115,
5.512424273941399
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
2.9481123347554843,
1.9503172324102764
],
"y": [
-2.4700524187514366,
-2.764456977122998
],
"z": [
4.7898018650926115,
5.104017634502682
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
3.6477789128551525,
3.4150394294056308
],
"y": [
-2.5769637687822304,
-3.262753378311451
],
"z": [
1.2498212461167233,
0.44031119410661157
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
5.348593233176091,
4.007330663978866
],
"y": [
-2.516438796361012,
-2.8611503543977457
],
"z": [
5.11583815186153,
5.512424273941399
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
5.348593233176091,
6.172316908637534
],
"y": [
-2.516438796361012,
-3.002822529562805
],
"z": [
5.11583815186153,
5.626112862738902
]
},
{
"hoverinfo": "skip",
"line": {
"color": "black",
"width": 1.44
},
"mode": "lines",
"showlegend": false,
"type": "scatter3d",
"x": [
4.007330663978866,
3.878826798936297
],
"y": [
-2.8611503543977457,
-3.46276448291608
],
"z": [
5.512424273941399,
6.4053853800575915
]
}
],
"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": [
"from biobuild import optimizers\n",
"\n",
"graph = final.make_atom_graph()\n",
"\n",
"edges = graph.find_rotatable_edges(min_descendants=5, min_ancestors=5)\n",
"\n",
"env = optimizers.DistanceRotatron(graph, edges, pushback=4)\n",
"\n",
"final_optimized = bb.optimizers.optimize(final.copy(), env)\n",
"final_optimized.show()"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"That one looks a little better. Of course, since the structure is quite dense, there is a limit as to what we can achieve, but we can check if we have any clashes left in our final structure using:"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"clashes before: []\n",
"clashes after: []\n"
]
}
],
"source": [
"print(\"clashes before:\", final.find_clashes())\n",
"print(\"clashes after:\", final_optimized.find_clashes())"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"With that out of the way, we can think of what to do next with our molecule. Perhaps our project involves molecular docking simulations that require a PDB input. We can easily export our new molecule using the `to_pdb` method or the `write_pdb` function:"
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {},
"outputs": [],
"source": [
"bb.write_pdb(final_optimized, \"final_optimized.pdb\")"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"By the way, if we would like to see our molecule in 2D again, we can simply export it to `rdkit`, which has a native 2D rendering support:"
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {},
"outputs": [
{
"data": {
"image/png": "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",
"text/plain": [
""
]
},
"execution_count": 14,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# export to rdkit\n",
"rd_mol = final_optimized.to_rdkit()\n",
"\n",
"# remove the 3d coordinates\n",
"rd_mol.RemoveAllConformers()\n",
"\n",
"# show the image (automatically in a jupyter notebook)\n",
"rd_mol"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"With that we have reached the end of this little walkthrough to the basic work-routine of building structures in biobuild. As you hopefully agree, it is quite straightforward to use biobuild to create larger structures from small components. Of course, even though we have only used single-residue components in this tutorial, there is (in principle) no limit to what biobuild can connect. It becomes especially useful if you build parts of a molecule separately and then simply join them together. With that, good luck in your project using biobuild!"
]
}
],
"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": "3.11.2"
},
"orig_nbformat": 4
},
"nbformat": 4,
"nbformat_minor": 2
}