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@dominiquesydow
Last active October 28, 2019 12:16
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NGLviewer: Attempt to add text labels to selection
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{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# NGL viewer - Add labels"
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "216f1874f5ad4447a03e4697edf231d3",
"version_major": 2,
"version_minor": 0
},
"text/plain": [
"_ColormakerRegistry()"
]
},
"metadata": {},
"output_type": "display_data"
},
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "86873e6202c743d0a71993acfff274f9",
"version_major": 2,
"version_minor": 0
},
"text/plain": [
"NGLWidget()"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"import nglview as nv\n",
"\n",
"pdb_id = '2g2i'\n",
"chain = 'A'\n",
"res_id = 229\n",
"\n",
"viewer = nv.show_pdbid(pdb_id, default=False)\n",
"viewer.clear()\n",
"viewer.add_cartoon(selection=f':{chain}', assembly='AU')\n",
"viewer.center(selection=f'{res_id}')\n",
"\n",
"viewer"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"label_kwargs = dict(labelType='text', showBackground=True, backgroundColor='black')"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [],
"source": [
"viewer.add_label(sele=f'@0', labelText=[f'First atom? ID 0'], **label_kwargs)\n",
"# Label shows up!"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [],
"source": [
"viewer.add_label(sele=f'@1', labelText=[f'Also first atom? ID 1'], **label_kwargs)\n",
"# Vertical mini-label without text shows up..."
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [],
"source": [
"viewer.remove_label()\n",
"viewer.remove_label()"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [],
"source": [
"viewer.add_label(sele=f'{res_id}:{chain}.CA', labelText=[f'Atom I am interested in'], **label_kwargs)\n",
"# Same vertical mini-label without text shows up..."
]
}
],
"metadata": {
"kernelspec": {
"display_name": "kinsim",
"language": "python",
"name": "kinsim"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.7"
}
},
"nbformat": 4,
"nbformat_minor": 4
}
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