Merge pull request #133 from favreau/master

Notebooks cleanup

Author: Cyrille Favreau

bioexplorer/pythonsdk/notebooks/animation/BioExplorer_spike.ipynb

@@ -22,7 +22,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from bioexplorer import BioExplorer, AnimationParams, MovieMaker, Protein, Sugars, Quaternion\n",
+    "from bioexplorer import BioExplorer, AnimationParams, MovieMaker, Protein, Sugar, Quaternion\n",
     "uri = 'localhost:5000'\n",
     "be = BioExplorer(uri)\n",
     "core = be.core_api()\n",
@@ -106,7 +106,7 @@
     "    '''High-mannose'''\n",
     "    indices = [61, 122, 234, 603, 709, 717, 801, 1074]\n",
     "\n",
-    "    high_mannose_glycans = Sugars(\n",
+    "    high_mannose_glycans = Sugar(\n",
     "        rotation=Quaternion(0.707, 0.0, 0.0, 0.707),\n",
     "        assembly_name=name, name=be.NAME_GLYCAN_HIGH_MANNOSE, \n",
     "        protein_name=name, source=high_mannose_paths[0], \n",
@@ -123,7 +123,7 @@
     "\n",
     "    for index in [323, 325]:\n",
     "        o_glycan_name = name + '_' + be.NAME_GLYCAN_O_GLYCAN + '_' + str(index)\n",
-    "        o_glycan = Sugars(\n",
+    "        o_glycan = Sugar(\n",
     "            assembly_name=name, name=o_glycan_name, source=o_glycan_paths[0],\n",
     "            protein_name=protein_name, site_indices=[index],\n",
     "            representation=glycan_representation,\n",
@@ -136,7 +136,7 @@
     "    if open_spike:\n",
     "        indices = [17, 74, 149, 165, 282, 331, 343, 657, 1098, 1134, 1158, 1173, 1194]\n",
     "\n",
-    "    complex_glycans = Sugars(\n",
+    "    complex_glycans = Sugar(\n",
     "        rotation=Quaternion(0.0, 0.0, 0.0, 1.0),\n",
     "        assembly_name=name, name=be.NAME_GLYCAN_COMPLEX, \n",
     "        protein_name=name, source=complex_paths[0], \n",

bioexplorer/pythonsdk/notebooks/animation/BioExplorer_virus_entering_cell.ipynb

@@ -25,7 +25,7 @@
    "outputs": [],
    "source": [
     "from bioexplorer import BioExplorer, Protein, Surfactant, Membrane, Volume, \\\n",
-    "                        Cell, Sugars, AnimationParams, Vector2, Vector3, Quaternion, MovieMaker\n",
+    "                        Cell, Sugar, AnimationParams, Vector2, Vector3, Quaternion, MovieMaker\n",
     "import glob\n",
     "\n",
     "url = 'localhost:5000'\n",
@@ -226,7 +226,7 @@
     "                   [739, Quaternion(0.707, 0.0, 0.707, 0.0)]]\n",
     "        for index in indices:\n",
     "            o_glycan_name = name + '_' + be.NAME_GLYCAN_O_GLYCAN + '_' + str(index[0])\n",
-    "            o_glycan = Sugars(\n",
+    "            o_glycan = Sugar(\n",
     "                assembly_name=name, name=o_glycan_name, \n",
     "                source=o_glycan_paths[0],\n",
     "                protein_name=name + '_' + be.NAME_RECEPTOR, \n",

bioexplorer/pythonsdk/notebooks/animation/BioExplorer_virus_fusion.ipynb

@@ -22,7 +22,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from bioexplorer import BioExplorer, Protein, Membrane, Cell, Sugars, \\\n",
+    "from bioexplorer import BioExplorer, Protein, Membrane, Cell, Sugar, \\\n",
     "                        AnimationParams, Vector2, Vector3, Quaternion, MovieMaker\n",
     "be = BioExplorer('localhost:5000')\n",
     "core = be.core_api()\n",
@@ -151,7 +151,7 @@
     "               [739, Quaternion(0.707, 0.0, 0.707, 0.0)]]\n",
     "    for index in indices:\n",
     "        o_glycan_name = name + '_' + be.NAME_GLYCAN_O_GLYCAN + '_' + str(index[0])\n",
-    "        o_glycan = Sugars(\n",
+    "        o_glycan = Sugar(\n",
     "            assembly_name=name, name=o_glycan_name, \n",
     "            source=o_glycan_paths[0],\n",
     "            protein_name=name + '_' + be.NAME_RECEPTOR, \n",

bioexplorer/pythonsdk/notebooks/assemblies/BioExplorer_ACE2_Receptor.ipynb

@@ -22,7 +22,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from bioexplorer import BioExplorer, Protein, Sugars, Quaternion, MovieMaker\n",
+    "from bioexplorer import BioExplorer, Protein, Sugar, Quaternion, MovieMaker\n",
     "import os\n",
     "\n",
     "be = BioExplorer('localhost:5000')\n",
@@ -231,7 +231,7 @@
    "outputs": [],
    "source": [
     "glycan_name = name + '_Complex'\n",
-    "glycans = Sugars(\n",
+    "glycans = Sugar(\n",
     "    rotation=Quaternion(0.707, 0.0, 0.0, 0.707),\n",
     "    assembly_name=name, name=glycan_name, protein_name=name,\n",
     "    source=os.path.join(complex_folder, '36.pdb'),\n",

bioexplorer/pythonsdk/notebooks/assemblies/BioExplorer_E_protein.ipynb

@@ -22,7 +22,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from bioexplorer import BioExplorer, Protein, Sugars, Quaternion\n",
+    "from bioexplorer import BioExplorer, Protein, Sugar, Quaternion\n",
     "be = BioExplorer('localhost:5000')\n",
     "be.reset_scene()\n",
     "print(be.version())\n",
@@ -136,7 +136,7 @@
    "outputs": [],
    "source": [
     "indices = [48, 66]\n",
-    "complex_glycans = Sugars(\n",
+    "complex_glycans = Sugar(\n",
     "    rotation=Quaternion(0.707, 0.0, 0.0, 0.707),\n",
     "    assembly_name=name, name=be.NAME_GLYCAN_COMPLEX, \n",
     "    protein_name=name, source=complex_paths[0], \n",

bioexplorer/pythonsdk/notebooks/assemblies/BioExplorer_M_protein.ipynb

@@ -22,7 +22,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from bioexplorer import BioExplorer, Protein, Sugars, Quaternion\n",
+    "from bioexplorer import BioExplorer, Protein, Sugar, Quaternion\n",
     "be = BioExplorer('localhost:5000')\n",
     "be.reset_scene()\n",
     "print(be.version())\n",
@@ -117,7 +117,7 @@
    "outputs": [],
    "source": [
     "indices = [5]\n",
-    "high_mannose_glycans = Sugars(\n",
+    "high_mannose_glycans = Sugar(\n",
     "    rotation=Quaternion(0.707, 0.0, 0.0, 0.707),\n",
     "    assembly_name=name, name=be.NAME_GLYCAN_HIGH_MANNOSE, \n",
     "    protein_name=name, source=high_mannose_paths[0], \n",

bioexplorer/pythonsdk/notebooks/assemblies/BioExplorer_full_scene.ipynb

@@ -18,7 +18,7 @@
    "outputs": [],
    "source": [
     "from bioexplorer import BioExplorer, Protein, Surfactant, Membrane, Volume, \\\n",
-    "                        Cell, Sugars, Vector2, Vector3, Quaternion, AnimationParams\n",
+    "                        Cell, Sugar, Vector2, Vector3, Quaternion, AnimationParams\n",
     "import nglview\n",
     "\n",
     "be = BioExplorer('localhost:5000')"
@@ -239,7 +239,7 @@
     "           [739, Quaternion(0.707, 0.0, 0.707, 0.0)]]\n",
     "for index in indices:\n",
     "    o_glycan_name = name + '_' + be.NAME_GLYCAN_O_GLYCAN + '_' + str(index[0])\n",
-    "    o_glycan = Sugars(\n",
+    "    o_glycan = Sugar(\n",
     "        assembly_name=name, name=o_glycan_name, \n",
     "        source=o_glycan_paths[0],\n",
     "        protein_name=name + '_' + be.NAME_RECEPTOR, \n",

bioexplorer/pythonsdk/notebooks/assemblies/BioExplorer_spike.ipynb

@@ -21,7 +21,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from bioexplorer import BioExplorer, Protein, Sugars, Quaternion, MovieMaker\n",
+    "from bioexplorer import BioExplorer, Protein, Sugar, Quaternion, MovieMaker\n",
     "be = BioExplorer()\n",
     "core = be.core_api()\n",
     "print(be.version())\n",
@@ -145,7 +145,7 @@
    "source": [
     "indices = [61, 122, 234, 603, 709, 717, 801, 1074]\n",
     "\n",
-    "high_mannose_glycans = Sugars(\n",
+    "high_mannose_glycans = Sugar(\n",
     "    rotation=Quaternion(0.707, 0.0, 0.0, 0.707),\n",
     "    assembly_name=name, name=be.NAME_GLYCAN_HIGH_MANNOSE, \n",
     "    protein_name=name, source=high_mannose_paths[0], \n",
@@ -176,7 +176,7 @@
     "    \n",
     "for index in [323, 325]:\n",
     "    o_glycan_name = name + '_' + be.NAME_GLYCAN_O_GLYCAN + '_' + str(index)\n",
-    "    o_glycan = Sugars(\n",
+    "    o_glycan = Sugar(\n",
     "        assembly_name=name, name=o_glycan_name, source=o_glycan_paths[0],\n",
     "        protein_name=protein_name, site_indices=[index],\n",
     "        representation=glycan_representation)\n",
@@ -201,7 +201,7 @@
     "if open_spike:\n",
     "    indices = [17, 74, 149, 165, 282, 331, 343, 657, 1098, 1134, 1158, 1173, 1194]\n",
     "\n",
-    "complex_glycans = Sugars(\n",
+    "complex_glycans = Sugar(\n",
     "    rotation=Quaternion(0.0, 0.0, 0.0, 1.0),\n",
     "    assembly_name=name, name=be.NAME_GLYCAN_COMPLEX, \n",
     "    protein_name=name, source=complex_paths[0], \n",
@@ -439,7 +439,7 @@
     "\n",
     "indices = [modified_aa_index]\n",
     "glycan_variant_name = be.NAME_GLYCAN_COMPLEX + '_variant'\n",
-    "complex_glycans = Sugars(\n",
+    "complex_glycans = Sugar(\n",
     "    assembly_name=name, name=glycan_variant_name,\n",
     "    protein_name=name, source=complex_paths[0], \n",
     "    site_indices=indices,\n",

bioexplorer/pythonsdk/notebooks/assemblies/BioExplorer_spike_and_ACE2_receptor.ipynb

@@ -14,7 +14,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from bioexplorer import BioExplorer, Protein, Membrane, Cell, Sugars, \\\n",
+    "from bioexplorer import BioExplorer, Protein, Membrane, Cell, Sugar, \\\n",
     "                        AnimationParams, Vector2, Vector3, Quaternion, MovieMaker\n",
     "\n",
     "be = BioExplorer('localhost:5000')\n",
@@ -208,7 +208,7 @@
     "           [730, Quaternion(0.0, 0.707, 0.0, 0.707)]]\n",
     "for index in indices:\n",
     "    o_glycan_name = name + '_' + be.NAME_GLYCAN_O_GLYCAN + '_' + str(index[0])\n",
-    "    o_glycan = Sugars(\n",
+    "    o_glycan = Sugar(\n",
     "        assembly_name=name, name=o_glycan_name, \n",
     "        source=o_glycan_paths[0],\n",
     "        protein_name=name + '_' + be.NAME_RECEPTOR, \n",

bioexplorer/pythonsdk/notebooks/scenarios/high_glucose/BioExplorer_high_glucose_scenario.ipynb

@@ -30,7 +30,7 @@
             },
             "outputs": [],
             "source": [
-                "from bioexplorer import BioExplorer, Protein, Surfactant, Membrane, Cell, Sugars, \\\n",
+                "from bioexplorer import BioExplorer, Protein, Surfactant, Membrane, Cell, Sugar, \\\n",
                 "                        Volume, AnimationParams, Vector2, Vector3, Quaternion\n",
                 "import nglview\n",
                 "\n",
@@ -305,7 +305,7 @@
                 "                   [730, Quaternion(0.707, 0.0, 0.707, 0.0)]]\n",
                 "        for index in indices:\n",
                 "            o_glycan_name = name + '_' + be.NAME_GLYCAN_O_GLYCAN + '_' + str(index[0])\n",
-                "            o_glycan = Sugars(\n",
+                "            o_glycan = Sugar(\n",
                 "                assembly_name=name, name=o_glycan_name, source=o_glycan_paths[0],\n",
                 "                protein_name=name + '_' + be.NAME_RECEPTOR, representation=glycan_representation,\n",
                 "                chain_ids=[2, 4], site_indices=[index[0]], rotation=index[1])\n",
@@ -437,7 +437,7 @@
                 "def add_glucose_to_surfactant_head(name):\n",
                 "    for index in [321, 323]:\n",
                 "        glucose_name = name + '_' + be.NAME_GLUCOSE + '_' + str(index)\n",
-                "        glucose = Sugars(\n",
+                "        glucose = Sugar(\n",
                 "            assembly_name=name, name=glucose_name, source=glucose_path,\n",
                 "            protein_name=name + '_' + be.NAME_SURFACTANT_HEAD, \n",
                 "            representation=glycan_representation, site_indices=[index])\n",

bioexplorer/pythonsdk/notebooks/scenarios/low_glucose/BioExplorer_low_glucose_scenario.ipynb

@@ -30,7 +30,7 @@
             },
             "outputs": [],
             "source": [
-                "from bioexplorer import BioExplorer, Protein, Surfactant, Membrane, Cell, Sugars, \\\n",
+                "from bioexplorer import BioExplorer, Protein, Surfactant, Membrane, Cell, Sugar, \\\n",
                 "                        Volume, AnimationParams, Vector2, Vector3, Quaternion\n",
                 "import nglview\n",
                 "\n",
@@ -318,7 +318,7 @@
                 "                   [730, Quaternion(0.707, 0.0, 0.707, 0.0)]]\n",
                 "        for index in indices:\n",
                 "            o_glycan_name = name + '_' + be.NAME_GLYCAN_O_GLYCAN + '_' + str(index[0])\n",
-                "            o_glycan = Sugars(\n",
+                "            o_glycan = Sugar(\n",
                 "                assembly_name=name, name=o_glycan_name, source=o_glycan_paths[0],\n",
                 "                protein_name=name + '_' + be.NAME_RECEPTOR, representation=glycan_representation,\n",
                 "                chain_ids=[2, 4], site_indices=[index[0]], rotation=index[1])\n",

bioexplorer/pythonsdk/notebooks/utils/BioExplorer_drop_virus_on_receptor.ipynb

@@ -30,7 +30,7 @@
             },
             "outputs": [],
             "source": [
-                "from bioexplorer import BioExplorer, MovieMaker, Protein, ParametricMembrane, Cell, Sugars, \\\n",
+                "from bioexplorer import BioExplorer, MovieMaker, Protein, ParametricMembrane, Cell, Sugar, \\\n",
                 "                        Vector2, Vector3, Quaternion\n",
                 "\n",
                 "hostname = 'localhost:5000'\n",
@@ -201,7 +201,7 @@
                 "                   [730, Quaternion(0.707, 0.0, 0.707, 0.0)]]\n",
                 "        for index in indices:\n",
                 "            o_glycan_name = name + '_' + be.NAME_GLYCAN_O_GLYCAN + '_' + str(index[0])\n",
-                "            o_glycan = Sugars(\n",
+                "            o_glycan = Sugar(\n",
                 "                assembly_name=name, name=o_glycan_name, source=o_glycan_paths[0],\n",
                 "                protein_name=name + '_' + be.NAME_RECEPTOR, representation=glycan_representation,\n",
                 "                chain_ids=[2, 4], site_indices=[index[0]], rotation=index[1])\n",