ethanholz.com / sonic-pdb-parser
A high performance Protein Databank parser written in Zig.
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README.md

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