- Standardize spacing and formatting in various files for consistency - Remove unnecessary blank lines and adjust line breaks for better readability - Ensure consistent use of comments and code structure across the project
- Use pdbtbx for PDB/mmCIF parsing (re-exported) - Keep custom XYZ reader/writer (simple format) - Add PdbTrajectoryWriter for multi-MODEL output - Remove redundant custom PDB reader/writer
- PDB reader: parse ATOM/HETATM records - PDB writer: write ATOM, MODEL/ENDMDL, CRYST1 - XYZ reader/writer: simple coordinate format - Force field module placeholder Update todo.md: mark completed items
