Sonic PDB Parser

A WIP sonic-speed PDB parser written in Zig. This project contains two modules (sonic and sonic-fasta) for importing into other Zig projects. Furthermore, there are two binaries, one for parsing and benchmarking PDB parsing (sonic-pdb-parser) and another for converting PDB files to FASTA files (pdb2fasta).

Usage - sonic-pdb-parser

sonic-pdb-parser -r <runs> -f <file> -o <output>

• -r -> specifies the number of times to run test, if r = 1, this will print the parsed file
• -f -> specifies the file you want to parse
• -o -> specifies the CSV you want to output to
• --json -> if r = 1, print the output as JSON

Usage - pdb2fasta

pdb2fasta -f <file>.pdb -o <out>.fasta

• -f -> specifies the file you want to convert
• -o -> specifies the output FASTA file

Goals

• Be able to completely parse the wwPDB 3.3 spec
• Provide WASM and/or C bindings
• Integrate FASTA conversion (BETA)

References

pdb2fasta