Architecture

In SDFEater, there are four main architecture modules, including CLI controller, input file parser, additional data adder, and output generators. In the first module, SDFEater reacts to parameters selected by the user. The second module is responsible for parsing the entire compound, including atoms, bonds, and compound properties in the key-value form. The parser can also add extra information that is not present in the SDF file (third module). For instance, the given atoms may be enriched with data from the table of chemical elements. Additional atoms data is stored in a JSON file and can be edited to add another information. SDF files containing information about molecules sometimes include compound identifiers from different databases. SDFEater can replace these identifiers with full URLs to the other databases and datasets. The GitHub repository contains ready-to-use JAR files and sample SDF files.