03 Jun 2020 (Last Modified 03 Jun 2022)

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

{"compound_class":[],
 "SMILES_string":"",
 "identifier":""}

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

{
	"type":"@identifier",
	"value":"",
	"format":""
}

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