diff --git a/bioexplorer/pythonsdk/notebooks/animation/BioExplorer_spike.ipynb b/bioexplorer/pythonsdk/notebooks/animation/BioExplorer_spike.ipynb index eda38fb0d..a0509384d 100644 --- a/bioexplorer/pythonsdk/notebooks/animation/BioExplorer_spike.ipynb +++ b/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", diff --git a/bioexplorer/pythonsdk/notebooks/animation/BioExplorer_virus_entering_cell.ipynb b/bioexplorer/pythonsdk/notebooks/animation/BioExplorer_virus_entering_cell.ipynb index 00f3e0435..c04308629 100644 --- a/bioexplorer/pythonsdk/notebooks/animation/BioExplorer_virus_entering_cell.ipynb +++ b/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", diff --git a/bioexplorer/pythonsdk/notebooks/animation/BioExplorer_virus_fusion.ipynb b/bioexplorer/pythonsdk/notebooks/animation/BioExplorer_virus_fusion.ipynb index 267bde16a..6b589510b 100644 --- a/bioexplorer/pythonsdk/notebooks/animation/BioExplorer_virus_fusion.ipynb +++ b/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", diff --git a/bioexplorer/pythonsdk/notebooks/assemblies/BioExplorer_ACE2_Receptor.ipynb b/bioexplorer/pythonsdk/notebooks/assemblies/BioExplorer_ACE2_Receptor.ipynb index 2bc0f1c10..ee0d6acad 100644 --- a/bioexplorer/pythonsdk/notebooks/assemblies/BioExplorer_ACE2_Receptor.ipynb +++ b/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", diff --git a/bioexplorer/pythonsdk/notebooks/assemblies/BioExplorer_E_protein.ipynb b/bioexplorer/pythonsdk/notebooks/assemblies/BioExplorer_E_protein.ipynb index 308342ffe..b9d678f21 100644 --- a/bioexplorer/pythonsdk/notebooks/assemblies/BioExplorer_E_protein.ipynb +++ b/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", diff --git a/bioexplorer/pythonsdk/notebooks/assemblies/BioExplorer_M_protein.ipynb b/bioexplorer/pythonsdk/notebooks/assemblies/BioExplorer_M_protein.ipynb index 92f6a42bb..57174d79c 100644 --- a/bioexplorer/pythonsdk/notebooks/assemblies/BioExplorer_M_protein.ipynb +++ b/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", diff --git a/bioexplorer/pythonsdk/notebooks/assemblies/BioExplorer_full_scene.ipynb b/bioexplorer/pythonsdk/notebooks/assemblies/BioExplorer_full_scene.ipynb index 0ca252a1c..2bbd35e0e 100644 --- a/bioexplorer/pythonsdk/notebooks/assemblies/BioExplorer_full_scene.ipynb +++ b/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", diff --git a/bioexplorer/pythonsdk/notebooks/assemblies/BioExplorer_spike.ipynb b/bioexplorer/pythonsdk/notebooks/assemblies/BioExplorer_spike.ipynb index dd262bc0f..0b9f09b51 100644 --- a/bioexplorer/pythonsdk/notebooks/assemblies/BioExplorer_spike.ipynb +++ b/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", diff --git a/bioexplorer/pythonsdk/notebooks/assemblies/BioExplorer_spike_and_ACE2_receptor.ipynb b/bioexplorer/pythonsdk/notebooks/assemblies/BioExplorer_spike_and_ACE2_receptor.ipynb index 937eefdfc..fdb4e37ea 100644 --- a/bioexplorer/pythonsdk/notebooks/assemblies/BioExplorer_spike_and_ACE2_receptor.ipynb +++ b/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", diff --git a/bioexplorer/pythonsdk/notebooks/scenarios/high_glucose/BioExplorer_high_glucose_scenario.ipynb b/bioexplorer/pythonsdk/notebooks/scenarios/high_glucose/BioExplorer_high_glucose_scenario.ipynb index ff02fa359..f92ec6b14 100644 --- a/bioexplorer/pythonsdk/notebooks/scenarios/high_glucose/BioExplorer_high_glucose_scenario.ipynb +++ b/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", diff --git a/bioexplorer/pythonsdk/notebooks/scenarios/low_glucose/BioExplorer_low_glucose_scenario.ipynb b/bioexplorer/pythonsdk/notebooks/scenarios/low_glucose/BioExplorer_low_glucose_scenario.ipynb index 1ad4c82c4..a40065ebb 100644 --- a/bioexplorer/pythonsdk/notebooks/scenarios/low_glucose/BioExplorer_low_glucose_scenario.ipynb +++ b/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", diff --git a/bioexplorer/pythonsdk/notebooks/utils/BioExplorer_drop_virus_on_receptor.ipynb b/bioexplorer/pythonsdk/notebooks/utils/BioExplorer_drop_virus_on_receptor.ipynb index 52cabd42d..4fb8115b8 100644 --- a/bioexplorer/pythonsdk/notebooks/utils/BioExplorer_drop_virus_on_receptor.ipynb +++ b/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",