23-3 Salt strip in ChEMBL structure pipeline

{"nbformat":4,"nbformat_minor":0,"metadata":{"colab":{"name":"23-3 Salt strip in ChEMBL structure pipeline","provenance":[],"collapsed_sections":[],"authorship_tag":"ABX9TyNM3sTUJ3VY55X9ZD6874rs"},"kernelspec":{"name":"python3","display_name":"Python 3"}},"cells":[{"cell_type":"code","metadata":{"id":"bnn2EnPK1XCu"},"source":["# Salt strip in ChEMBL structure pipeline\n","# author: Gressling, T\n","# license: MIT License # code: github.com/gressling/examples\n","# activity: single example # index: 23-3 \n","# requires RDKit to work"],"execution_count":null,"outputs":[]},{"cell_type":"code","metadata":{"id":"zSSeepVQ1hFy"},"source":["o_molblock = \"\"\"\n"," Marvin 10310613082D\n"," 6 6 0 0 0 0 999 V2000\n"," 0.7145 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"," 0.0000 -0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"," 0.7145 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"," 0.0000 0.8250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"," -0.7145 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"," -0.7145 0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n"," 2 1 2 0 0 0 0\n"," 3 1 1 0 0 0 0\n"," 4 3 2 0 0 0 0\n"," 5 2 1 0 0 0 0\n"," 6 4 1 0 0 0 0\n"," 5 6 2 0 0 0 0\n","M END\"\"\""],"execution_count":null,"outputs":[]},{"cell_type":"code","metadata":{"id":"11uBTBXs1qTI"},"source":["from chembl_structure_pipeline import standardizer\n","std_molblock = standardizer.standardize_molblock(o_molblock)"],"execution_count":null,"outputs":[]},{"cell_type":"code","metadata":{"id":"hukE3xeT1sQ_"},"source":["# Get the parent molecule\n","parent_molblock, _ = standardizer.get_parent_molblock(o_molblock)"],"execution_count":null,"outputs":[]},{"cell_type":"code","metadata":{"id":"XnY44qG61tfH"},"source":["# Check the molecule\n","from chembl_structure_pipeline import checker\n","issues = checker.check_molblock(o_molblock)"],"execution_count":null,"outputs":[]}]}