bioexplorer/pythonsdk/notebooks/molecular_systems/BioExplorer_enzyme_reaction.ipynb

{
    "cells": [
        {
            "cell_type": "markdown",
            "metadata": {},
            "source": [
                "# Blue Brain BioExplorer\n",
                "\n",
                "![](../bioexplorer_banner.png)"
            ]
        },
        {
            "cell_type": "markdown",
            "metadata": {},
            "source": [
                "## Simplest script to create a visualization of an enzyme reaction"
            ]
        },
        {
            "cell_type": "code",
            "execution_count": null,
            "metadata": {},
            "outputs": [],
            "source": [
                "from bioexplorer import BioExplorer, Protein, EnzymeReaction, MolecularSystemAnimationParams, \\\n",
                "                        Volume, Vector3, Quaternion\n",
                "import os\n",
                "\n",
                "be = BioExplorer('localhost:5000')\n",
                "core = be.core_api()\n",
                "status = be.reset_scene()"
            ]
        },
        {
            "cell_type": "code",
            "execution_count": null,
            "metadata": {},
            "outputs": [],
            "source": [
                "representation=be.REPRESENTATION_ATOMS_AND_STICKS\n",
                "atom_radius_multiplier=1.0\n",
                "draft = True\n",
                "generate_movie = False\n",
                "\n",
                "# Resources\n",
                "resource_folder = os.path.abspath('../../tests/test_files')\n",
                "pdb_folder = os.path.join(resource_folder, 'pdb')\n",
                "metabolites_folder = os.path.join(pdb_folder, 'metabolites')\n",
                "enzymes_folder = os.path.join(pdb_folder, 'enzymes')\n",
                "mesh_folder = os.path.join(resource_folder, 'obj')\n",
                "\n",
                "pdb_glucose = os.path.join(metabolites_folder, '5793.pdb')\n",
                "pdb_atp = os.path.join(metabolites_folder, '59.pdb')\n",
                "pdb_g6p = os.path.join(metabolites_folder, '439284.pdb')\n",
                "pdb_adp = os.path.join(metabolites_folder, '6022.pdb')\n",
                "pdb_hexokinase = os.path.join(enzymes_folder, '1bdg.pdb')\n",
                "\n",
                "be.set_general_settings(logging_level=3, mesh_folder=mesh_folder)\n",
                "\n",
                "scene_size = Vector3(200.0, 200.0, 200.0)\n",
                "nb_occurences = 200\n",
                "seed = 5"
            ]
        },
        {
            "cell_type": "code",
            "execution_count": null,
            "metadata": {},
            "outputs": [],
            "source": [
                "def add_molecule(\n",
                "        seed, position_seed, name, pdb_file, nb_occurence,\n",
                "        representation=be.REPRESENTATION_ATOMS_AND_STICKS, rotation=Quaternion()):\n",
                "    protein = Protein(\n",
                "        name=name,\n",
                "        source=pdb_file,\n",
                "        load_bonds=True, load_hydrogen=True, load_non_polymer_chemicals=True,\n",
                "        occurrences=nb_occurence, animation_params=MolecularSystemAnimationParams(seed, position_seed, 25.0, seed, 0.025),\n",
                "        rotation=rotation\n",
                "    )\n",
                "    volume = Volume(\n",
                "        name=name + 's',\n",
                "        shape=be.ASSEMBLY_SHAPE_CUBE, shape_params=scene_size,\n",
                "        protein=protein)\n",
                "    be.add_volume(\n",
                "        volume=volume,\n",
                "        atom_radius_multiplier=atom_radius_multiplier, representation=representation)\n",
                "    return protein\n",
                "\n",
                "# Substrates\n",
                "substrates = list()\n",
                "substrates.append(\n",
                "    add_molecule(seed, 6, 'Glucose', pdb_glucose, nb_occurences))\n",
                "substrates.append(\n",
                "    add_molecule(seed, 7, 'ATP', pdb_atp, nb_occurences))\n",
                "\n",
                "# Product\n",
                "products = list()\n",
                "products.append(\n",
                "    add_molecule(seed, 8, 'G6P', pdb_g6p, nb_occurences))\n",
                "products.append(\n",
                "    add_molecule(seed, 9, 'ADP', pdb_adp, nb_occurences))\n",
                "\n",
                "# Hexokinase\n",
                "enzyme = add_molecule(\n",
                "    seed, 0, 'Hexokinase', pdb_hexokinase, nb_occurences, \n",
                "    be.REPRESENTATION_ATOMS_AND_STICKS, Quaternion(0.707, 0.707, 0.0, 0.0)\n",
                ")\n",
                "\n",
                "# Enzyme reaction\n",
                "enzyme_reaction = EnzymeReaction(\n",
                "    assembly_name='Hexokinase',\n",
                "    name='Hexokinase',\n",
                "    enzyme=enzyme,\n",
                "    substrates=substrates,\n",
                "    products=products)\n",
                "\n",
                "# Add the reaction to the scene\n",
                "status = be.add_enzyme_reaction(enzyme_reaction)"
            ]
        },
        {
            "cell_type": "markdown",
            "metadata": {},
            "source": [
                "## Rendering settings"
            ]
        },
        {
            "cell_type": "code",
            "execution_count": null,
            "metadata": {},
            "outputs": [],
            "source": [
                "status = be.core_api().set_renderer(\n",
                "    background_color=[96 / 255, 125 / 255, 139 / 255],\n",
                "    current='advanced',\n",
                "    samples_per_pixel=1, subsampling=4, max_accum_frames=16)\n",
                "params = status = be.core_api().AdvancedRendererParams()\n",
                "params.gi_samples = 2\n",
                "params.gi_strength = 0.2\n",
                "params.gi_ray_length = 5\n",
                "params.shadow_intensity = 1.0\n",
                "params.soft_shadow_strength = 1.0\n",
                "params.fog_start = 1500\n",
                "params.fog_thickness = 1500\n",
                "params.max_ray_depth = 1\n",
                "status = be.core_api().set_renderer_params(params)"
            ]
        },
        {
            "cell_type": "markdown",
            "metadata": {},
            "source": [
                "## Materials"
            ]
        },
        {
            "cell_type": "code",
            "execution_count": null,
            "metadata": {},
            "outputs": [],
            "source": [
                "status = be.set_protein_color_scheme(\n",
                "    assembly_name='ATPs', name='ATP',\n",
                "    color_scheme=be.COLOR_SCHEME_ATOMS,\n",
                "    palette_name='Blues', palette_size=2)\n",
                "\n",
                "status = be.set_protein_color_scheme(\n",
                "    assembly_name='Glucoses', name='Glucose',\n",
                "    color_scheme=be.COLOR_SCHEME_ATOMS,\n",
                "    palette_name='Blues', palette_size=2)\n",
                "\n",
                "\n",
                "status = be.set_protein_color_scheme(\n",
                "    assembly_name='ADPs', name='ADP',\n",
                "    color_scheme=be.COLOR_SCHEME_ATOMS,\n",
                "    palette_name='Set1', palette_size=3)\n",
                "\n",
                "status = be.set_protein_color_scheme(\n",
                "    assembly_name='G6Ps', name='G6P',\n",
                "    color_scheme=be.COLOR_SCHEME_ATOMS,\n",
                "    palette_name='Set1', palette_size=3)\n",
                "\n",
                "status = be.set_protein_color_scheme(\n",
                "    assembly_name='Hexokinases', name='Hexokinase',\n",
                "    color_scheme=be.COLOR_SCHEME_CHAINS,\n",
                "    palette_name='Reds', palette_size=2)\n",
                "be.core_api().set_renderer()"
            ]
        },
        {
            "cell_type": "markdown",
            "metadata": {},
            "source": [
                "## Movie"
            ]
        },
        {
            "cell_type": "code",
            "execution_count": null,
            "metadata": {},
            "outputs": [],
            "source": [
                "from bioexplorer import MovieMaker\n",
                "mm = MovieMaker(be)"
            ]
        },
        {
            "cell_type": "code",
            "execution_count": null,
            "metadata": {},
            "outputs": [],
            "source": [
                "if draft:\n",
                "    instance_id = 2\n",
                "    key_frames = [\n",
                "        {\n",
                "            'apertureRadius': 0.0,\n",
                "            'direction': [-0.4228059199334163, 0.13956182704765893, -0.8954092084071824],\n",
                "            'focalDistance': 1000000.0,\n",
                "            'origin': [-76.94388312721057, 27.008762696107365, 101.90818416814368],\n",
                "            'up': [0.03825535069708487, 0.9899381257456357, 0.13623155045091803]\n",
                "        }, \n",
                "        {\n",
                "            'apertureRadius': 0.0,\n",
                "            'direction': [-0.2931756929393873, -0.19137884221190335, -0.9367081465553406],\n",
                "            'focalDistance': 1000000.0,\n",
                "            'origin': [-80.78751362339919, 32.810933007328735, 98.7370846157903],\n",
                "            'up': [-0.04288359642471887, 0.9814064493156495, -0.18708922577030282]\n",
                "        }\n",
                "    ]\n",
                "else:\n",
                "    instance_id = 25\n",
                "    key_frames = [\n",
                "        {\n",
                "            'apertureRadius': 0.0,\n",
                "            'direction': [-0.813281188551245, -0.09740833983733163, -0.5736595886750337],\n",
                "            'focalDistance': 1000000.0,\n",
                "            'origin': [11.06562396175978, -42.45183472913227, 71.07319024762178],\n",
                "            'up': [-0.26548353789130863, 0.9394084115205614, 0.2168647677081957]\n",
                "        }, \n",
                "        {\n",
                "            'apertureRadius': 0.0,\n",
                "            'direction': [-0.06265926430929034, -0.21184739821321946, -0.975292005743156],\n",
                "            'focalDistance': 1000000.0,\n",
                "            'origin': [-3.900908980540925, -40.62438454349056, 76.12253643837245],\n",
                "            'up': [0.09475544149237422, 0.9715352310065103, -0.21711909455575734]\n",
                "        }\n",
                "    ]    "
            ]
        },
        {
            "cell_type": "code",
            "execution_count": null,
            "metadata": {},
            "outputs": [],
            "source": [
                "from tqdm import tqdm\n",
                "\n",
                "nb_frames = 360\n",
                "output_folder = '/tmp'\n",
                "if draft:\n",
                "    image_size=[960, 540]\n",
                "else:\n",
                "    image_size=[3840, 2160]\n",
                "\n",
                "mm.build_camera_path(key_frames, nb_frames, 1)\n",
                "\n",
                "if generate_movie:\n",
                "    for frame in tqdm(range(nb_frames)):\n",
                "        mm.set_current_frame(frame)\n",
                "        for instance in range(nb_occurences):\n",
                "            progress = float(frame + instance) / float(nb_frames)\n",
                "            be.set_enzyme_reaction_progress(\n",
                "                enzyme_reaction, instance_id=instance, progress=progress)\n",
                "        mm.create_snapshot(\n",
                "            renderer='advanced',\n",
                "            path=os.path.join(output_folder, 'bio_explorer'), base_name='%05d' % frame,\n",
                "            size=image_size, samples_per_pixel=64)\n",
                "        mm.create_snapshot(\n",
                "            renderer='depth',\n",
                "            path=os.path.join(output_folder, 'depth'), base_name='%05d' % frame,\n",
                "            size=image_size, samples_per_pixel=1)\n",
                "else:\n",
                "    be.core_api().set_renderer(\n",
                "        current='basic',\n",
                "        samples_per_pixel=1, subsampling=1, max_accum_frames=1)\n",
                "    model_id = core.scene.models[len(core.scene.models)-1]['id']\n",
                "    import time\n",
                "    for frame in tqdm(range(nb_frames)):\n",
                "        mm.set_current_frame(frame)\n",
                "        progress = float(frame) / float(nb_frames)\n",
                "        for instance in range(nb_occurences):\n",
                "            progress = float(frame + instance) / float(nb_frames)\n",
                "            be.set_enzyme_reaction_progress(\n",
                "                enzyme_reaction, instance_id=instance, progress=progress)\n",
                "        be.core_api().set_renderer()\n",
                "        time.sleep(0.1)"
            ]
        }
    ],
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