Details on Database of Molecular Structures

Details on Database of Molecular Structures

Database Construction.

I stored SMILES structures for each class in a MongoDB collection. Each document needed a SMILES_string and identifier field. There were no constraints on other fields. I created the MongoDB collection as


A simple way to extend identifier is to abstract it to a dictionary


One retrieves the compounds that belong to compound_class x with db[collection].find({"compound_class":"x"},{"_id":False}).

I stored the compounds in CSV files, with the following headers

Name Synonym ID Relation Rarget
Psilocin 4-HO-DMT   metabolite via dephosphorylation psilocybin
Psilocin 4-PO-DMT   metabolite via dephosphorylation psilacetin
psilocybin 4-HO-DMT   parent compound of psilocybin