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Finished the view molecules example
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‎16_viewing_molecules.ipynb‎

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"Reading molecules from '['data/dioxin.pdb']'\n",
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"Rendering the molecules...\n"
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" If you're reading this message in the Jupyter Notebook or JupyterLab Notebook, it may mean\n",
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"outputs": [],
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"source": [
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"from BioSimSpace import viewMolecules\n",
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"v = viewMolecules(\"data/dioxin.pdb\")"
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" Widgets Documentation</a> for setup instructions.\n",
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" If you're reading this message in the Jupyter Notebook or JupyterLab Notebook, it may mean\n",
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" that the widgets JavaScript is still loading. If this message persists, it\n",
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" Widgets Documentation</a> for setup instructions.\n",
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"Tab(children=(Box(children=(Box(children=(Box(children=(Label(value='step'), IntSlider(value=1, min=-100)), layout=Layout(display='flex', flex_flow='row', justify_content='space-between')), Box(children=(Label(value='delay'), IntSlider(value=100, max=1000, min=10)), layout=Layout(display='flex', flex_flow='row', justify_content='space-between')), Box(children=(Label(value='background'), ColorPicker(value='white')), layout=Layout(display='flex', flex_flow='row', justify_content='space-between')), Box(children=(Label(value='camera'), Dropdown(options=('perspective', 'orthographic'), value='perspective')), layout=Layout(display='flex', flex_flow='row', justify_content='space-between')), Box(children=(Label(value=''), HBox(children=(ToggleButton(value=False, description='Smoothing', tooltip='smoothing trajectory'), Button(description=' Center', icon='bullseye', style=ButtonStyle()), Button(description=' Screenshot', icon='camera', style=ButtonStyle()), Button(description='qtconsole', style=ButtonStyle(), tooltip='pop up qtconsole')), layout=Layout(flex='1 1 auto', width='auto'))), layout=Layout(display='flex', flex_flow='row', justify_content='space-between'))), layout=Layout(align_items='stretch', display='flex', flex_flow='column', width='100%')),)), Box(), Box(), Box(), Box(), Box()), layout=Layout(align_items='stretch', align_self='center'), _titles={'1': 'Representation', '4': 'Extra', '2': 'Preference', '0': 'General', '3': 'Theme', '5': 'Help'})"
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"outputs": [],
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"source": [
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"v.system()"
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]
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Reading molecules from '['data/complex.pdb']'\n",
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"Rendering the molecules...\n"
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]
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" If you're reading this message in the Jupyter Notebook or JupyterLab Notebook, it may mean\n",
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" that the widgets JavaScript is still loading. If this message persists, it\n",
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" likely means that the widgets JavaScript library is either not installed or\n",
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" not enabled. See the <a href=\"https://ipywidgets.readthedocs.io/en/stable/user_install.html\">Jupyter\n",
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" Widgets Documentation</a> for setup instructions.\n",
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"</p>\n",
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"text/html": [
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"<p>Failed to display Jupyter Widget of type <code>Tab</code>.</p>\n",
273-
"<p>\n",
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" If you're reading this message in the Jupyter Notebook or JupyterLab Notebook, it may mean\n",
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" that the widgets JavaScript is still loading. If this message persists, it\n",
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" likely means that the widgets JavaScript library is either not installed or\n",
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" not enabled. See the <a href=\"https://ipywidgets.readthedocs.io/en/stable/user_install.html\">Jupyter\n",
278-
" Widgets Documentation</a> for setup instructions.\n",
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"Tab(children=(Box(children=(Box(children=(Box(children=(Label(value='step'), IntSlider(value=1, min=-100)), layout=Layout(display='flex', flex_flow='row', justify_content='space-between')), Box(children=(Label(value='delay'), IntSlider(value=100, max=1000, min=10)), layout=Layout(display='flex', flex_flow='row', justify_content='space-between')), Box(children=(Label(value='background'), ColorPicker(value='white')), layout=Layout(display='flex', flex_flow='row', justify_content='space-between')), Box(children=(Label(value='camera'), Dropdown(options=('perspective', 'orthographic'), value='perspective')), layout=Layout(display='flex', flex_flow='row', justify_content='space-between')), Box(children=(Label(value=''), HBox(children=(ToggleButton(value=False, description='Smoothing', tooltip='smoothing trajectory'), Button(description=' Center', icon='bullseye', style=ButtonStyle()), Button(description=' Screenshot', icon='camera', style=ButtonStyle()), Button(description='qtconsole', style=ButtonStyle(), tooltip='pop up qtconsole')), layout=Layout(flex='1 1 auto', width='auto'))), layout=Layout(display='flex', flex_flow='row', justify_content='space-between'))), layout=Layout(align_items='stretch', display='flex', flex_flow='column', width='100%')),)), Box(), Box(), Box(), Box(), Box()), layout=Layout(align_items='stretch', align_self='center'), _titles={'1': 'Representation', '4': 'Extra', '2': 'Preference', '0': 'General', '3': 'Theme', '5': 'Help'})"
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},
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"output_type": "display_data"
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}
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],
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"outputs": [],
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"source": [
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"v = viewMolecules(\"data/complex.pdb\")"
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]
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"\n",
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"![Select ligand](images/view_ligand.jpeg)\n",
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"\n",
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"The selection box can be used to select proteins (\"protein\"), everything (\"*\") or residues by name (e.g. \"LIG\") or number (e.g. \"35\"). Play around creating different selections and representations. For example, create a \"tube\" representation of the protein and a \"licorice\" representation of all alanine residues. Note - you can control the opacity (level of transparency) of a representation by selecting the representation in the drop down box and changing the \"opacity\" slider in the \"Parameters\" tab - see below.\n",
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"The selection box can be used to select proteins (\"protein\"), water (\"water\"), everything (\"*\") or residues by name (e.g. \"LIG\") or number (e.g. \"35\"). Play around creating different selections and representations. For example, create a \"point\" representation for water, a \"tube\" representation of the protein and a \"licorice\" representation of all alanine residues. Note - you can control the opacity (level of transparency) of a representation by selecting the representation in the drop down box and changing the \"opacity\" slider in the \"Parameters\" tab - see below. You can also change things like the colour scheme of the representation in this \"Parameters\" tab\n",
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"\n",
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"![Opacity](images/view_opacity.jpeg)"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# Viewing individual molecules\n",
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"\n",
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"The view object returned by BioSimSpace can be used to view specific molecules from the file. To do this, use the `molecules` function. This takes a list of indicies of the molecules you want to view. For example, to view the first molecule (molecule at index 0) type;"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": []
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"source": [
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"v.molecules([0])"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"while to view molecules 100-1000 use the below code (noting that you may need to add a \"ball and stick\" represntation in case nglview automatically hides the water molecules)."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"v.molecules( range(100,1000) )"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# Loading more complex files\n",
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"\n",
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"BioSimSpace provides reader and writers for a variety of molecular file formats. Some of these split the molecular data over multiple files, e.g. a topology and coordinate file. To view these, pass all of the necessary files to `viewMolecules` in a list, e.g."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"v = viewMolecules([\"data/ala.top\",\"data/ala.crd\"])"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"This can be combined with molecule selection, e.g. to load and view only molecules 0-4 in the file pass the indicies of the molecules you want to view as a second argument to `viewMolecule`, e.g."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"v = viewMolecules([\"data/ala.top\",\"data/ala.crd\"], [0,1,2,3,4])"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"(in reality, all molecules are loaded, but only molecules specified by the indicies are viewed. You can still use `v.system()` to view all molecules)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"v.system()"
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]
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}
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],
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"metadata": {

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