diff --git "a/testing_py3Dmol.ipynb" "b/testing_py3Dmol.ipynb" new file mode 100644--- /dev/null +++ "b/testing_py3Dmol.ipynb" @@ -0,0 +1,382 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "id": "e1a8d51a", + "metadata": {}, + "outputs": [], + "source": [ + "import py3Dmol" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "id": "65c56235", + "metadata": {}, + "outputs": [], + "source": [ + "benz='''\n", + " RDKit 3D\n", + "\n", + " 6 6 0 0 0 0 0 0 0 0999 V2000\n", + " -0.9517 0.7811 -0.6622 C 0 0 0 0 0 0 0 0 0 0 0 0\n", + " 0.2847 1.3329 -0.3121 C 0 0 0 0 0 0 0 0 0 0 0 0\n", + " 1.2365 0.5518 0.3512 C 0 0 0 0 0 0 0 0 0 0 0 0\n", + " 0.9517 -0.7811 0.6644 C 0 0 0 0 0 0 0 0 0 0 0 0\n", + " -0.2847 -1.3329 0.3144 C 0 0 0 0 0 0 0 0 0 0 0 0\n", + " -1.2365 -0.5518 -0.3489 C 0 0 0 0 0 0 0 0 0 0 0 0\n", + " 1 2 2 0\n", + " 2 3 1 0\n", + " 3 4 2 0\n", + " 4 5 1 0\n", + " 5 6 2 0\n", + " 6 1 1 0\n", + "M END\n", + "$$$$'''" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "e8c69a5b", + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": 4, + "id": "e0e64ef1", + "metadata": {}, + "outputs": [ + { + "data": { + "application/3dmoljs_load.v0": "
\n

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n jupyter labextension install jupyterlab_3dmol

\n
\n", + "text/html": [ + "
\n", + "

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n", + " jupyter labextension install jupyterlab_3dmol

\n", + "
\n", + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/plain": [ + "" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "view = py3Dmol.view(query='pdb:1dc9',linked=False,viewergrid=(2,2))\n", + "view.setViewStyle({'style':'outline','color':'black','width':0.1})\n", + "view.setStyle({'cartoon':{'arrows':True, 'tubes':True, 'style':'oval', 'color':'white'}},viewer=(0,1))\n", + "view.setStyle({'stick':{'colorscheme':'greenCarbon'}},viewer=(1,0))\n", + "view.setStyle({'cartoon':{'color':'spectrum'}},viewer=(1,1))\n", + "view.removeAllModels(viewer=(0,0))\n", + "view.addModel(benz,'sdf',viewer=(0,0))\n", + "view.setStyle({'stick':{}},viewer=(0,0))\n", + "view.zoomTo(viewer=(0,0))\n", + "view.render()" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "id": "5c274e26", + "metadata": {}, + "outputs": [ + { + "data": { + "application/3dmoljs_load.v0": "
\n

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n jupyter labextension install jupyterlab_3dmol

\n
\n", + "text/html": [ + "
\n", + "

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n", + " jupyter labextension install jupyterlab_3dmol

\n", + "
\n", + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/plain": [ + "" + ] + }, + "execution_count": 10, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "view = py3Dmol.view(query='',linked=False,viewergrid=(2,2))\n", + "#view.setViewStyle({'style':'outline','color':'black','width':0.1})\n", + "#view.setStyle({'cartoon':{'arrows':True, 'tubes':True, 'style':'oval', 'color':'white'}},viewer=(0,1))\n", + "#view.setStyle({'stick':{'colorscheme':'greenCarbon'}},viewer=(1,0))\n", + "#view.setStyle({'cartoon':{'color':'spectrum'}},viewer=(1,1))\n", + "view.removeAllModels(viewer=(0,0))\n", + "view.addModel(benz,'sdf',viewer=(0,0))\n", + "view.addModel(benz,'sdf',viewer=(0,1))\n", + "view.addModel(benz,'sdf',viewer=(1,0))\n", + "view.addModel(benz,'sdf',viewer=(1,1))\n", + "view.setStyle({'stick':{}},viewer=(0,0))\n", + "view.setStyle({'stick':{}},viewer=(0,1))\n", + "view.setStyle({'stick':{}},viewer=(1,0))\n", + "view.setStyle({'stick':{}},viewer=(1,1))\n", + "view.zoomTo(viewer=(0,0))\n", + "view.render()" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "id": "c41ad7fc", + "metadata": {}, + "outputs": [], + "source": [ + "dens = open('dummy_struct_dens.cub', \"r\").read()" + ] + }, + { + "cell_type": "code", + "execution_count": 22, + "id": "4ff28831", + "metadata": {}, + "outputs": [ + { + "data": { + "application/3dmoljs_load.v0": "
\n

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n jupyter labextension install jupyterlab_3dmol

\n
\n", + "text/html": [ + "
\n", + "

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
\n", + " jupyter labextension install jupyterlab_3dmol

\n", + "
\n", + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "view = py3Dmol.view()#,style={'stick':{'colorscheme':'cyanCarbon'}})\n", + "view.addVolumetricData(dens, \"cube\", {'isoval': 0.01, 'color': \"red\", 'opacity': 0.75})\n", + "view.show()" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "id": "218a79e3", + "metadata": {}, + "outputs": [], + "source": [ + "py3Dmol.view?" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "d7687d67", + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "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": "3.10.13" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +}