Module io

Expand description

Getting bytes in, recognising what they are, and the contract readers meet.

Structs§

BatchContinuity: Whether hierarchy rows continue across adjacent batches.
ByteWindow: One stable view into a source.
InputBuffer: Bytes to read, however they were obtained.
Limits: Ceilings that turn hostile input into diagnostics rather than exhaustion.
OutputOptions: Working-memory policy for incremental output.
OutputSink: A deterministic compressed or plain output stream.
ReadOptions: What a read should and should not bother doing.
SelectAll: A filter that writes everything.
SpillWindowedFile: A bounded source backed by an immutable, automatically deleted spill file.
StructureAtomRecord: One atom row accepted by StructureBatchBuilder.
StructureBatch: Bounded structure rows in a format-neutral layout.
StructureBatchBuffer: Finished structural columns whose backing allocations can be recycled.
StructureBatchBuilder: Incremental builder that interns each distinct identifier once per batch.
StructureBatchPool: One reusable columnar batch owned by a structural source.
TextOutput: Adapts a byte writer for allocation-free std::fmt::Write formatting.
WindowedFile: A seekable file read through one reusable, budget-charged window.

AmbiguousResidueBoundaryPolicy: Policy for adjacent mmCIF atom groups whose residue identifiers are identical.
CategoryFilter: Which optional categories (mmCIF/BinaryCIF) or records (PDB) a read keeps.
Compression: How a stream of bytes was compressed.
ContinuityLevel: Deepest hierarchy level that continues across one batch boundary.
Format: A format molframe can read or write.
InputDigest: Whether a read records a digest of the bytes it parsed.
InputKind: The storage that backs an input byte slice.
MissingElementPolicy: Policy for atom rows whose format-specific element field is absent or invalid.
OccupancyPolicy: Policy for atoms whose recorded occupancy lies outside zero to one.
ParseMode: How much irregularity a read tolerates, and what it does about it.
Perception: Whether a read infers bonds, components and secondary structure afterwards.
StructureBatchError: Failure shared by bounded structural batch readers and collectors.
WindowedSourceFile: A seekable bounded source, with compressed input spooled only when the execution context explicitly permits temporary storage.

DEFAULT_OUTPUT_MEMORY_LIMIT_BYTES: Default ceiling for format-owned output workspace.
REQUIRED_CIF_CATEGORIES: mmCIF/BinaryCIF categories every structure read needs, whatever the filter.
REQUIRED_PDB_RECORDS: PDB records every structure read needs, whatever the filter.

Reader: A reader for one format.
Select: Which parts of a structure a write should include.
SourceBytes: Random-access bytes exposed through bounded, borrow-stable windows.

collect_structure: Materialises a bounded snapshot from a structural batch source.
write_output: Writes existing bytes through the bounded incremental sink.

ReadResult: A structure and everything that was wrong with the file it came from.