/dbs_ETL

Search for experimental data for organic molecules.

Primary LanguagePython

DBS script - Collect reference data for force-field optimization.

  • DBS stands for DataBase System. It is data based of experimental data maitained by tge CSMS group.
  • Search for identifier (name, InChIKey, CAS registry number) in PubChem given smiles strings.
  • Search for themodynamic, dielectric, transport and solvation data of organic molecules in an in-house database of experimental data of organic compounds.
  • For every molecule, plot all available data and let the user select the reference data points.
  • Write selected data to csv file.

J. Chem. Theory Comput., 16, 7525-​7555 (2020).

The five main options of this script are:

  1. Get identifiers

    • Given list of SMILES strings, search for identifiers in PubChem.

      If a file with CID (id) and smiles from pubchem is given, then the CID is used directly to retrieve the molecule from pubchem.

      If an empty file is given, then the smiles is used to search for the molecule in the database.

      In both cases RDKit is used to canonicalize the smiles strings.

  2. Write identifiers to csv file

    • Write matched identifiers (name, smiles, standardInChiKey, CAS registry number and molecular foruma) to csv file.

  3. Search for all availabe reference data in database

    • Search for reference data in the tables.
    • The tables are saved in tmp/ directory.
    • The output matched data is saved in data/ directory.

  4. Select data points

    • Plot all available data for each property and each molecule so that the user can select the data points that will be used as reference data for force-field optimization.

  5. Plot data

    • For each molecule and each property save plot with all available data and simulated results if input file with simulated values is given.