Crate molframe_pdb

Expand description

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§

Biomolecule: One biological assembly, from REMARK 350.
Biomt: One rigid operation of a biological assembly, from BIOMT1..3.
BiomtGroup: Operations applied to a set of chains.
Link: A covalent link declared by LINK.
MissingResidue: A residue the model leaves out, from REMARK 465.
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.
Mtrix: One non-crystallographic operator, from MTRIX1..3.
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.
ResidueId: A residue named the way connectivity records name it.
SeqRes: The residue sequence one chain declares in its SEQRES records.
SsBond: A disulfide bond declared by SSBOND.

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§

pdbqt_loss: One aggregated finding per kind of loss a rigid PDBQT write incurs.
pqr_loss: One aggregated finding per kind of loss a PQR write incurs.
projection_loss: One aggregated finding per kind of loss, with a count and the first example.
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.