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update example notebook
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@Jhsmit
Jhsmit committed Feb 26, 2024
1 parent d299d22 commit c1857a3
Showing 1 changed file with 146 additions and 98 deletions.
244 changes: 146 additions & 98 deletions example.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -2,149 +2,97 @@
"cells": [
{
"cell_type": "code",
"execution_count": 2,
"execution_count": 1,
"metadata": {},
"outputs": [
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "e372fdbd91934f4b973c43d1c7a1eb5a",
"model_id": "898f20dddae440c8aa41c8197975bef7",
"version_major": 2,
"version_minor": 0
},
"text/plain": [
"PDBeMolstar(molecule_id='1onf')"
"PDBeMolstar(bg_color='#111111', hide_water=True, lighting='metallic', loading_overlay=True, molecule_id='1qyn'…"
]
},
"execution_count": 2,
"execution_count": 1,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"from ipymolstar import PDBeMolstar\n",
"import pathlib\n",
"import anywidget\n",
"import traitlets\n",
"\n",
"c = PDBeMolstar(molecule_id='1onf')\n",
"c"
"view = PDBeMolstar(molecule_id='1qyn', theme='dark', \n",
" hide_water=True, visual_style='cartoon',\n",
" lighting='metallic',hide_expand_icon=False,hide_controls_icon=False,\n",
" hide_controls=False, sequence_panel=True, pdbe_link=False, \n",
" loading_overlay=True, expanded=False,\n",
" )\n",
"\n",
"view"
]
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 4,
"metadata": {},
"outputs": [],
"source": [
"\t\tmoleculeId: model.get('molecule_id')"
"data = [{\n",
" 'entity_id': '1',\n",
" 'struct_asym_id': 'A',\n",
" 'start_residue_number': 10,\n",
" 'end_residue_number': 15\n",
"}]\n",
"\n",
"view.focus(data)"
]
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 3,
"metadata": {},
"outputs": [],
"source": []
"source": [
"data_dict = {\n",
" 'data': [{\n",
" 'entity_id': '1',\n",
" 'struct_asym_id': 'A',\n",
" 'start_residue_number': 10,\n",
" 'end_residue_number': 15\n",
" }]\n",
"}\n",
"\n",
"view.highlight(data_dict)"
]
},
{
"cell_type": "code",
"execution_count": 90,
"execution_count": 4,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"@import url('https://www.ebi.ac.uk/pdbe/pdb-component-library/css/pdbe-molstar-light-3.1.3.css');\n",
"\n"
]
},
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "c52928444c8840f1b178d284843f787c",
"version_major": 2,
"version_minor": 0
},
"text/plain": [
"PDBeMolstar(custom_data={'url': 'http://localhost:8888/files/assets/1qyn.pdb?_xsrf=2%7Cc1810e12%7C8a144937b5ea…"
]
},
"execution_count": 90,
"metadata": {},
"output_type": "execute_result"
}
],
"outputs": [],
"source": [
"import pathlib\n",
"\n",
"import anywidget\n",
"import traitlets\n",
"from pathlib import Path\n",
"\n",
"\n",
"__file__ = Path().resolve() / 'src' / 'ipymolstar' / 'script.py'\n",
"\n",
"custom_data = { \"url\": \"http://localhost:8888/files/assets/1qyn.pdb?_xsrf=2%7Cc1810e12%7C8a144937b5ea77b35b1a4a393c7ee119%7C1707130076\", \"format\": \"pdb\" }\n",
"\n",
"class PDBeMolstar(anywidget.AnyWidget):\n",
" _esm = pathlib.Path(__file__).parent / \"widget.js\"\n",
" _css = pathlib.Path(__file__).parent / \"widget.css\"\n",
" value = traitlets.Int(0).tag(sync=True)\n",
"\n",
" molecule_id = traitlets.Unicode().tag(sync=True)\n",
" custom_data = traitlets.Dict().tag(sync=True)\n",
"\n",
" bg_color = traitlets.Unicode(\"#F7F7F7\").tag(sync=True)\n",
"\n",
" spin = traitlets.Bool(False).tag(sync=True)\n",
"\n",
" hide_polymer = traitlets.Bool(False).tag(sync=True)\n",
" hide_water = traitlets.Bool(False).tag(sync=True)\n",
" hide_heteroatoms = traitlets.Bool(False).tag(sync=True)\n",
" hide_carbs = traitlets.Bool(False).tag(sync=True)\n",
" hide_non_standard = traitlets.Bool(False).tag(sync=True)\n",
" hide_coarse = traitlets.Bool(False).tag(sync=True)\n",
"\n",
" _select = traitlets.Dict().tag(sync=True)\n",
"\n",
" # def __init__(self, *args, **kwargs):\n",
" # print(self._css)\n",
" # _css = (pathlib.Path(__file__).parent / \"widget.css\").read_text()\n",
" # super().__init__(*args, _css=_css, **kwargs)\n",
" \n",
" def color(self, data, non_selected_color=None):\n",
" \"\"\"\n",
" Alias for PDBE Molstar's `select` method.\n",
"\n",
" See https://github.com/molstar/pdbe-molstar/wiki/3.-Helper-Methods for parameter\n",
" details\n",
" \"\"\"\n",
"\n",
" self._select = {\"data\": data, \"nonSelectedColor\": non_selected_color}\n",
"\n",
"\n",
"view = PDBeMolstar(custom_data=custom_data, hide_water=True)\n",
"view"
"view.clear_highlight()"
]
},
{
"cell_type": "code",
"execution_count": 85,
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"data = [{\n",
" 'start_residue_number': 10,\n",
" 'end_residue_number': 150,\n",
" 'start_residue_number': 0,\n",
" 'end_residue_number': 200,\n",
" 'struct_asym_id': 'A',\n",
" 'color': {'r': 255, 'g': 215, 'b': 0},\n",
" 'color': {'r': 100, 'g': 150, 'b': 120},\n",
" 'focus': False,\n",
" },\n",
" {\n",
" 'start_residue_number': 30,\n",
" 'end_residue_number': 200,\n",
" 'end_residue_number': 190,\n",
" 'struct_asym_id': 'B',\n",
" 'color': {'r': 213, 'g': 52, 'b': 235},\n",
" 'focus': False,\n",
Expand All @@ -155,7 +103,93 @@
},
{
"cell_type": "code",
"execution_count": 41,
"execution_count": 5,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'1.28.0'"
]
},
"execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"import solara\n",
"solara.__version__"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [],
"source": [
"view.visual_style='cartoon'"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'molecular-surface'"
]
},
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"view.visual_style"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'plastic'"
]
},
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"view.lighting "
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [],
"source": [
"view.lighting = 'metallic'"
]
},
{
"cell_type": "code",
"execution_count": 17,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -164,11 +198,25 @@
},
{
"cell_type": "code",
"execution_count": 79,
"execution_count": 27,
"metadata": {},
"outputs": [],
"source": [
"view.spin = True"
"view.spin = False"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"data = [{\n",
" 'entity_id': '1',\n",
" 'struct_asym_id': 'A',\n",
" 'start_residue_number': 10,\n",
" 'end_residue_number': 15\n",
"}]\n"
]
},
{
Expand All @@ -188,7 +236,7 @@
}
],
"source": [
"view.spin"
"view.spin = True"
]
},
{
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