Molecule databases

Molchanica includes support for molecule databases using Apache Parquet. To get started, click the "Mol DBs" button in the UI.

Included Human Metabolome and ChEBI databases

Two default parquet databases are included with Molchanica: Human Metabolome Database, and Chemical Entities of Biological Interest . These can be viewed along with custom databases in this Datbases window, but cannot be edited. Molecules from ChEBI are automatically selected when searching using the Query button.

Warning: These databases currently contain 2D structures only.

Your own databases

You can add molecules from a SDF or Mol2 file (Including multi-molecule SDFs), or add all molecules in a folder using the window.

Screening

When screening (For example, from pharmacophores or alignment), we optionally create databases: This is much faster than loading molecule files into memory each time a screening is run.