Crate molframe_pdb 

Reading and writing the legacy fixed-column structure format.

The format predates the archive’s current one and remains the most widely read structural format there is. It is also the most constrained: every field has a fixed width, and a structure large enough to overflow one cannot be written honestly. This crate reads what the archive contains — including the extended counting scheme that files past the field limits use — and refuses to write anything it would have to truncate.

Modules

fixed

Fixed-width PDB fields.

hybrid36

Hybrid-36 fixed-width integer coding.

Structs

MmtfEntityMetadata

Metadata for one MMTF entity entry.

MmtfGroupMetadata

Chemistry fields for one MMTF group dictionary entry.

MmtfMetadata

Source fields retained for faithful MMTF re-encoding.

PdbBatchSource

Incremental PDB rows over a seekable or resident byte source.

PdbHeaderRecord

One fixed-column metadata record exactly as deposited.

PdbHeaders

Every metadata record in archive order.

PdbOptions

How to write, and what to do about a structure that does not fit.

PdbReader

The reader for the legacy fixed-column format.

Enums

MmtfOptionalField

One optional top-level MMTF column.

PdbIdentifierNamespace

Identifier namespace projected into legacy PDB fields.

Constants

MMTF_METADATA_EXTENSION

Stable extension key for metadata required by lossless MMTF writing.

PDB_HEADERS_EXTENSION

Stable extension key for ordered legacy PDB metadata records.

Traits

PdbHeadersExt

Access to preserved legacy metadata.

Functions

read

Reads a structure from fixed-column text.

read_mmtf

Reads an MMTF MessagePack structure through all standard codecs.

read_pdbqt

Reads PDBQT coordinates with partial charge and AutoDock type annotations.

read_pqr

Reads PQR coordinates with partial charge and radius annotations.

write

Writes a structure, or explains why it cannot be written.

write_mmtf

Writes a deterministic standards-conforming MMTF MessagePack document.

write_mmtf_to

Streams deterministic MMTF MessagePack to a byte destination.

write_pdbqt

Writes a rigid PDBQT model, requiring charge and AutoDock type annotations.

write_pdbqt_to

Streams a rigid PDBQT model without retaining the complete text.

write_pqr

Writes PQR coordinates, requiring charge and radius annotations.

write_pqr_to

Streams PQR coordinates without retaining the complete text.

write_selected

Writes the parts of a structure a filter accepts.

write_selected_to

Streams selected PDB records without materialising the complete text.

write_to

Streams a complete PDB directly to a byte destination.