Processors

Processors parse structure files on disk (PDB, mmCIF, SDF, …) into Awkward records during adapter ingestion. Summaries below are taken from each class docstring.

Parse mmCIF structure files into Awkward records.

class bioverse.processors.cif.CifProcessor

Bases: Processor

Parse mmCIF structure files into Awkward records.

Parse PDB structure files into Awkward records.

class bioverse.processors.pdb.PdbProcessor

Bases: Processor

Parse PDB structure files into Awkward records.

Walks a directory tree, reads .pdb / .pdb.gz files, and emits one record per structure with scene/frame/molecule/residue/atom fields. Subclass for dataset-specific filename or metadata conventions.

Parse XYZ coordinate files into Awkward records.

class bioverse.processors.xyz.XyzProcessor

Bases: Processor

Parse XYZ coordinate files into Awkward records.