ss-main: added depedency

Global-Chem · Apr 5, 2022 · 579e939 · 579e939
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diff --git a/example_notebooks/cheminformatics/GlobalChemExtensions_Demonstration (1).ipynb b/example_notebooks/cheminformatics/GlobalChemExtensions_Demonstration (1).ipynb
@@ -0,0 +1,83 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {
+    "id": "PY-f8bB8jpqi"
+   },
+   "outputs": [],
+   "source": [
+    "# Environment Setup\n",
+    "\n",
+    "!rm -rf global-chem\n",
+    "!git clone -q https://github.com/Sulstice/global-chem\n",
+    "\n",
+    "!pip install -q global-chem-extensions --upgrade"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {
+    "id": "NoYEtzDf1jYF"
+   },
+   "outputs": [],
+   "source": [
+    "# Header\n",
+    "\n",
+    "from global_chem import GlobalChem\n",
+    "from global_chem_extensions import GlobalChemExtensions\n",
+    "\n",
+    "gc = GlobalChem()\n",
+    "gce = GlobalChemExtensions()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "id": "o6q50QS4DEq_",
+    "colab": {
+     "base_uri": "https://localhost:8080/"
+    },
+    "outputId": "d06d1fb9-4545-4728-97e7-800c3a8fec62"
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "['NC(CCCCNC(N)=N)C(NC(CO)C(NC(C(C)([H])O)C(NC(CCC(O)=O)C(NC(CC1=CC=CC=C1)C(NC([H])C(NC(CC1=CNC=N1)C(NC(C(CC)([H])C)C(NC(CCCCN)C(NC(CC(C)C)C(NC(C)C(NC(CC(O)=O)C(NC(C2CCCN2)C(NC(CCC(N)=O)C(NCC(O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O)=O']\n",
+      "['RSTEFGHIKLADPQ', None]\n"
+     ]
+    }
+   ],
+   "source": [
+    "# Amino Acids\n",
+    "\n",
+    "amino_acid_test = ['RSTEFGHIKLADPQ']\n",
+    "smiles = gce.amino_acids_to_smiles(amino_acid_test)\n",
+    "print (smiles)\n",
+    "\n",
+    "amino_acid = gce.smiles_to_amino_acids(smiles)\n",
+    "print (amino_acid)"
+   ]
+  }
+ ],
+ "metadata": {
+  "colab": {
+   "name": "GlobalChemExtensions_Demonstration.ipynb",
+   "provenance": []
+  },
+  "kernelspec": {
+   "name": "python3",
+   "display_name": "Python 3"
+  },
+  "language_info": {
+   "name": "python"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 0
+}
diff --git a/example_notebooks/cheminformatics/GlobalChemExtensions_Demonstration (2).ipynb b/example_notebooks/cheminformatics/GlobalChemExtensions_Demonstration (2).ipynb
@@ -0,0 +1,93 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {
+    "id": "PY-f8bB8jpqi"
+   },
+   "outputs": [],
+   "source": [
+    "# Environment Setup\n",
+    "\n",
+    "!rm -rf global-chem\n",
+    "!git clone -q https://github.com/Sulstice/global-chem\n",
+    "\n",
+    "!pip install -q global-chem-extensions --upgrade"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {
+    "id": "NoYEtzDf1jYF"
+   },
+   "outputs": [],
+   "source": [
+    "# Header\n",
+    "\n",
+    "from global_chem import GlobalChem\n",
+    "from global_chem_extensions import GlobalChemExtensions\n",
+    "\n",
+    "gc = GlobalChem()\n",
+    "gce = GlobalChemExtensions()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "id": "XWGLAGE8TLyH",
+    "colab": {
+     "base_uri": "https://localhost:8080/"
+    },
+    "outputId": "33435a75-cc5d-455d-ebd2-706910030c43"
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Method: 'generate' Time: 0.98 seconds\n",
+      "[b'CCC(N)CC1=CC(=C(OC)C(=C1)OC)OC', b'COC1=CC(=CC(=C1OCC=C)OC)CCN', b'COC1=CC(=C(OC)C=C1CC(C)N)SC', b'CCSC1=C(OC)C=C(CC(C)N)C(=C1)OC', b'COC1=CC(=C(OC)C=C1CC(C)N)SC(C)C', b'COC1=CC(=C(OC)C=C1CC(C)N)SC2=CC=CC=C2', b'CCCSC1=C(OC)C=C(CC(C)N)C(=C1)OC', b'CCC(N)CC1=CC(=C(C)C=C1OC)OC', b'CCOC1=CC(=CC(=C1OCC)OC)CCN', b'CCCCOC1=C(OC)C=C(CCN)C=C1OC', b'CNC(C)CC1=CC(=C(C)C=C1OC)OC', b'CSC1=C(C)C=C(SC)C(=C1)CC(C)N', b'COC(CN)C1=CC(=C(Br)C=C1OC)OC', b'COC(CN)C1=CC(=C(C)C=C1OC)OC', b'COC(CN)C1=CC(=C(C)C=C1OC)OC', b'CC1=C(O)C=C(C(O)CN)C(=C1)Br', b'COC(CN)C1=CC(=C(OC)C(=C1)OC)OC', b'COC1=C(Br)C(=CC(=C1)CC(C)N)OC', b'CC(N)CC1=C(Br)C=C2OCOC2=C1', b'[CH3:20][O:13][C:6]1=[CH:5][C:4](=[C:3]([O:16][CH3:11])[CH:2]=[C:1]1[Br:12])[CH2:8][CH2:9][NH2:10]', b'COC1=C(OCC2=CC=CC=C2)C(=CC(=C1)CC(C)N)OC', b'COC1=CC(=C(OC)C=C1Cl)CCN', b'[CH3:20][O:13][C:6]1=[CH:5][C:4](=[C:3]([O:16][CH3:11])[CH:2]=[C:1]1[CH3:12])[CH2:8][CH2:9][NH2:10]', b'CCC1=CC(=C(CCN)C=C1OC)OC', b'CCOC1=C(OC)C=C(CC(C)N)C=C1OC', 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b'COC1=C(CC(C)N)C=C2OC(C)CC2=C1', b'COC1=C(CC(C)N)C=C2OC(C)(C)CC2=C1', b'CC(CC1=CC=C2OCOC2=C1)N(C)O', b'COC1=C2CCCC2=C(OC)C(=C1)CC(C)N', b'COC1=C2CCCCC2=C(OC)C(=C1)CC(C)N', b'COC1=C2C3CCC(C3)C2=C(OC)C(=C1)CC(C)N', b'COC1=CC(=C(OC)C(=C1C)C)CC(C)N', b'COC1=CC(=C(OC)C2=C1C=CC=C2)CC(C)N', b'', b'CCCSC1=CC(=C(CCNO)C=C1OC)OC', b'CCC(C)SC1=CC(=C(CCNO)C=C1OC)OC', b'COC1=CC(=C(OC)C=C1I)CC(C)N(C)C', b'COC1=C(OC)C(=C(CCN)C=C1)OC', b'COC1=CC(=CC(=C1OC(C)C)OC)CCN', b'CCOC1=CC(=C(OC)C=C1C)CC(C)N', b'CCC(N)CC1=CC=C2OCOC2=C1', b'COC1=C2OCOC2=CC(=C1)CCN', b'C[O:7][C:2]1=[CH:1][C:6](=[CH:5][C:4](=[C:3]1[O:9]C)[O:20]C)[CH2:10][CH2:11][NH2:12]', b'CC(CC1=CC=C(C=C1)OC)N', b'CNC(C)CC1=C(C)C=C2OCOC2=C1', b'COC1=CC(=CC(=C1OCC(C)=C)OC)CCN', b'CC(N)CC1=CC=C2OCOC2=C1', b'CC(CC1=CC=C2OCOC2=C1)NCC=C', b'CCCCNC(C)CC1=CC=C2OCOC2=C1', b'CC(CC1=CC=C2OCOC2=C1)NCC3=CC=CC=C3', b'CC(CC1=CC=C2OCOC2=C1)NCC3CC3', b'CC(CC1=CC=C2OCOC2=C1)N(C)C', b'CCNC(C)CC1=CC=C2OCOC2=C1', b'CC(CC1=CC=C2OCOC2=C1)NCCO', b'CC(C)NC(C)CC1=CC=C2OCOC2=C1', b'CNC(C)CC1=CC=C2OCOC2=C1', b'CNC(C)CC1=CC=C2OCCOC2=C1', b'CONC(C)CC1=CC=C2OCOC2=C1', b'COCCNC(C)CC1=CC=C2OCOC2=C1', b'CNC(C)(C)CC1=CC=C2OCOC2=C1', b'CC(CC1=CC=C2OCOC2=C1)NO', b'NCCC1=CC=C2OCOC2=C1', b'CC(C)(N)CC1=CC=C2OCOC2=C1', b'CC(CC1=CC=C2OCOC2=C1)NCC#C', b'CCCNC(C)CC1=CC=C2OCOC2=C1', b'CCOC1=CC(=CC(=C1OC)OC)CCN', b'COC1=C2OCCOC2=CC(=C1)CCN', b'CCOC1=CC(=C(OC)C=C1OCC)CC(C)N', b'CCOC1=CC(=C(CC(C)N)C=C1OC)OC', b'CCOC1=CC=C(CCN)C=C1OC', b'COC1=CC(=C(CC(C)N)C=C1Br)OC', b'COC1=C(CC(C)N)C=C(SC)C(=C1)OC', b'CNC(C)CC1=C(OC)C=CC(=C1)OC', b'CNC(C)CC1=C(OC)C=C(Br)C(=C1)OC', b'CCC(CC1=CC=C2OCOC2=C1)NC', b'CCCC(CC1=CC=C2OCOC2=C1)NC', b'CNC(C)CC1=CC=C(OC)C=C1', b'CNC(C)CC1=C(OC)C=C2OCOC2=C1', b'COC1=C2OCOC2=CC(=C1)CC(C)N', b'COC1=C(CC(C)N)C=C2OCOC2=C1', b'COC1=C2OCOC2=CC=C1CC(C)N', b'COC1=CC=C(CC(C)N)C2=C1OCO2', b'CCOC1=CC(=C(OC)C=C1OC)CC(C)N', b'CCCOC1=CC(=CC(=C1OC)OC)CCN', b'COc1cc(OC)c(cc1OCCC)CC(C)N', b'COC1=CC(=C(SC)C=C1OC)CC(C)N', b'CCCOC1=C(OC)C=C(CCN)C=C1OC', b'COC1=CC(=CC(=C1OCCCC2=CC=CC=C2)OC)CCN', b'NCCC1=CC=CC=C1', b'COC1=CC(=CC(=C1OCC=C)OC)CCN', b'CCOC1=CC(=CC(=C1OC)OCC)CCN', b'COC1=C(OC)C(=C(OC)C(=C1)CC(C)N)OC', b'[CH3:16][CH2:15][O:14][C:8]1=[C:1]([S:10][CH2:11][CH3:17])[CH:2]=[C:3]([CH2:5][CH2:6][NH2:7])[CH:4]=[C:9]1[O:12][CH3:13]', b'CCOC1=CC(=CC(=C1SCC)OC)CCN', b'CCOC1=CC(=CC(=C1OCC)SC)CCN', b'CCCCSC1=C(OC)C=C(CCN)C=C1OC', b'CCOC1=C(OC)C=C(CCN)C=C1SC', b'[CH3:16][CH2:11][S:10][C:8]1=[C:1]([O:12][CH3:13])[CH:2]=[C:3]([CH2:5][CH2:6][NH2:7])[CH:4]=[C:9]1[O:14][CH3:15]', b'COC1=C(OC)C(=C(CCN)C=C1)SC', b'COC1=C(SC)C(=C(CCN)C=C1)OC', b'COC1=C(CCN)C=CC(=C1OC)SC', b'COC1=CC(=CC(=C1OC)SC)CCN', b'COC1=CC(=CC(=C1SC)OC)CCN', b'COC1=CC(=CC(=C1OC)OC)CC(C)N', b'COC1=C(CC(C)N)C=C(OC)C(=C1)OC', b'COC1=C(OC)C(=C(CC(C)N)C=C1)OC', b'COC1=CC(=C(OC)C(=C1)OC)CC(C)N', b'COC1=CC=C(OC)C(=C1CC(C)N)OC', b'COC1=CC(=C(CC(C)N)C(=C1)OC)OC', b'CCSC1=CC(=CC(=C1OC)OC)CCN', b'CCOC1=CC(=CC(=C1SC)OC)CCN', b'CCOC1=CC(=CC(=C1OC)SC)CCN', b'CSC1=C2OCOC2=CC=C1CC(C)N', b'COC1=C(CC(C)N)C=C2OCSC2=C1', b'COC1=C(CCN)C=C(OC)C(=C1)OC', b'CCC1=CC(=C(CC(C)N)C=C1OC)SC', b'CCC1=CC(=C(CC(C)N)C=C1SC)OC', b'COC1=CC(=C(SC)C=C1C)CC(C)N', b'COC1=C(CC(C)N)C=C(SC)C(=C1)C', b'COC1=C(CC(C)N)C=C(C(=C1)C)[S](C)=O', b'CCCSC1=C(OC)C=C(CCN)C=C1OC', b'CCOC1=CC(=CC(=C1OCC)OCC)CCN', b'CCOC1=C(OC)C(=CC(=C1)CCN)SCC', b'CCOC1=CC(=CC(=C1SC)OCC)CCN', b'CCOC1=C(OCC)C(=CC(=C1)CCN)SCC', b'CCOC1=CC(=CC(=C1SCC)OCC)CCN']\n"
+     ]
+    }
+   ],
+   "source": [
+    "# PDF Generation & Parsing\n",
+    "\n",
+    "gc.build_global_chem_network(print_output=False, debugger=False)\n",
+    "smiles_list = list(gc.get_node_smiles('pihkal').values())\n",
+    "\n",
+    "gce.smiles_to_pdf(\n",
+    "    smiles=smiles_list,\n",
+    "    labels = [],\n",
+    "    file_name = 'molecules.pdf',\n",
+    "    include_failed_smiles = True,\n",
+    "    title = 'MY MOLECULES',\n",
+    ")\n",
+    "\n",
+    "molecules = gce.pdf_to_smiles(\n",
+    "    'molecules.pdf',\n",
+    ")\n",
+    "\n",
+    "print (molecules)\n"
+   ]
+  }
+ ],
+ "metadata": {
+  "colab": {
+   "name": "GlobalChemExtensions_Demonstration.ipynb",
+   "provenance": []
+  },
+  "kernelspec": {
+   "name": "python3",
+   "display_name": "Python 3"
+  },
+  "language_info": {
+   "name": "python"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 0
+}
diff --git a/example_notebooks/cheminformatics/GlobalChemExtensions_Demonstration.ipynb b/example_notebooks/cheminformatics/GlobalChemExtensions_Demonstration.ipynb
@@ -0,0 +1,91 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {
+    "id": "PY-f8bB8jpqi"
+   },
+   "outputs": [],
+   "source": [
+    "# Environment Setup\n",
+    "\n",
+    "!rm -rf global-chem\n",
+    "!git clone -q https://github.com/Sulstice/global-chem\n",
+    "\n",
+    "!pip install -q global-chem-extensions --upgrade"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {
+    "id": "NoYEtzDf1jYF"
+   },
+   "outputs": [],
+   "source": [
+    "# Header\n",
+    "\n",
+    "from global_chem import GlobalChem\n",
+    "from global_chem_extensions import GlobalChemExtensions\n",
+    "\n",
+    "gc = GlobalChem()\n",
+    "gce = GlobalChemExtensions()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {
+    "colab": {
+     "base_uri": "https://localhost:8080/"
+    },
+    "id": "IMm6kQvpSIQr",
+    "outputId": "ba25b01c-496e-4cec-b552-275ccbb42cf0"
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Percantage of Accepted SMILES: 100.0\n"
+     ]
+    }
+   ],
+   "source": [
+    "# Check the Validity of the SMILES\n",
+    "\n",
+    "smiles_list = gc.get_all_smiles()\n",
+    "\n",
+    "sucesses, failures = gce.verify_smiles(\n",
+    "    smiles_list,\n",
+    "    rdkit=False, \n",
+    "    partial_smiles=False,\n",
+    "    return_failures=True,\n",
+    "    pysmiles=False,\n",
+    "    molvs=False,\n",
+    "    deepsmiles=False,\n",
+    "    selfies=True\n",
+    ")\n",
+    "\n",
+    "total = len(sucesses) + len(failures)\n",
+    "print (\"Percantage of Accepted SMILES: %s\" % ((len(sucesses) / total) * 100))"
+   ]
+  }
+ ],
+ "metadata": {
+  "colab": {
+   "name": "GlobalChemExtensions_Demonstration.ipynb",
+   "provenance": []
+  },
+  "kernelspec": {
+   "name": "python3",
+   "display_name": "Python 3"
+  },
+  "language_info": {
+   "name": "python"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 0
+}
diff --git a/example_notebooks/development_operations/GlobalChemExtensions_Demonstration (1).ipynb b/example_notebooks/development_operations/GlobalChemExtensions_Demonstration (1).ipynb
@@ -0,0 +1,109 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {
+    "id": "PY-f8bB8jpqi"
+   },
+   "outputs": [],
+   "source": [
+    "# Environment Setup\n",
+    "\n",
+    "!rm -rf global-chem\n",
+    "!git clone -q https://github.com/Sulstice/global-chem\n",
+    "\n",
+    "!pip install -q global-chem-extensions --upgrade"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {
+    "id": "NoYEtzDf1jYF"
+   },
+   "outputs": [],
+   "source": [
+    "# Header\n",
+    "\n",
+    "from global_chem import GlobalChem\n",
+    "from global_chem_extensions import GlobalChemExtensions\n",
+    "\n",
+    "gc = GlobalChem()\n",
+    "gce = GlobalChemExtensions()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "colab": {
+     "base_uri": "https://localhost:8080/"
+    },
+    "id": "UWRGdx8zStAL",
+    "outputId": "f916b146-4f1d-4dc1-86fc-d1121719d965"
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      " Zinc 15\n",
+      " Zinc 20\n",
+      " PubChem\n",
+      " NIST Chemistry Webhook\n",
+      " Chem Exper\n",
+      " NMR Shift Database\n",
+      " Drug Bank\n",
+      " Binding Database\n",
+      " Spectral Database for Organic Compounds\n",
+      " Sider\n",
+      " ChemSpider\n",
+      " Stitch\n",
+      " CardPred\n",
+      " Comparative Toxicogenomics Database\n",
+      " AMED Cardiotoxicity Database\n",
+      " Tox21\n",
+      " Drug Safety Analysis System\n",
+      " OpenFDA\n",
+      " Metabolites Biological Role\n",
+      " MetaboAnalyst\n",
+      " Adverse Drug Reaction Classification System\n",
+      " Metabolism and Transport Database\n",
+      " Ecology Toxicity \n",
+      " Human and Environment Risk Assessment \n",
+      " International Toxicity Information for Risk Assesments\n",
+      " Japan Exisiting Database\n",
+      " National Pesticide Center\n",
+      " Pesticide Info\n",
+      " Kyoto Encyclopedia of Genes and Genomes\n",
+      " Hetereocycles\n",
+      " Chemical Resolver\n",
+      " LookChem\n",
+      " Lipid Maps\n"
+     ]
+    }
+   ],
+   "source": [
+    "# Database Monitoring\n",
+    "\n",
+    "GlobalChemExtensions.check_status_on_open_source_databases()"
+   ]
+  }
+ ],
+ "metadata": {
+  "colab": {
+   "name": "GlobalChemExtensions_Demonstration.ipynb",
+   "provenance": []
+  },
+  "kernelspec": {
+   "name": "python3",
+   "display_name": "Python 3"
+  },
+  "language_info": {
+   "name": "python"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 0
+}