Crate molframe_cif 

Reading and writing PDBx/mmCIF.

The format the archive actually distributes, and the one every other structural format is now defined against. Reading it happens in two steps that are deliberately separate: a document that preserves what the file said, and a structure that says what it means. Keeping them apart is what lets a file survive a round trip through categories this library has no interpretation for.

Re-exports

pub use document::Category;

pub use document::CifValue;

pub use document::Column;

pub use document::DataBlock;

pub use document::Document;

pub use write::CanonicalAtomRow;

pub use write::CanonicalProjection;

pub use write::CanonicalValue;

pub use write::canonical_projection;

Modules

document

Lossless, order-preserving CIF document model.

lexer

CIF lexical analysis.

Structs

CanonicalAtomRow

One allocation-free atom-site row over a borrowed model snapshot.

CanonicalProjection

A validated semantic projection that can be consumed without text or a DOM.

CifReader

The reader for PDBx/mmCIF.

CifWriteOptions

Decisions that cannot be recovered from a lowered structure.

MmcifBatchSource

Incremental mmCIF coordinate rows.

Rows

The rows of one category, as a cursor a caller can walk.

SmallCifAtom

One crystallographic atom site from core CIF.

SmallCifBond

One geometric bond record with resolved atom indices.

SmallCifOptions

Explicit decisions for lowering a small-molecule CIF.

SmallCifStructure

One core-CIF crystal model.

Enums

CanonicalValue

A typed canonical value with CIF’s two distinct missing-value states.

CifWriteError

A missing or invalid value that prevents canonical output.

CifWriteToError

A canonical projection or output-stream failure.

PdbmlError

Malformed or unsupported PDBML framing.

PdbmlReadError

Failure either in XML conversion or existing mmCIF semantic lowering.

SmallCifDialect

Dictionary dialect used to resolve core-CIF item names.

SmallCifError

Invalid core-CIF small-molecule model.

Functions

canonical_projection

Validates and borrows the canonical structure projection.

lower

Builds a structure from the first block of a document.

lower_small_cif

Lowers the first core-CIF data block to a small-molecule crystal model. Current DDL2 category/item names are used. Legacy DDL1 tags require lower_small_cif_with_options and SmallCifOptions::ddl1.

lower_small_cif_with_options

Lowers the first core-CIF block under an explicit dictionary dialect.

parse

Reads a document.

parse_pdbml_document

Parses PDBML/XML into the same lossless document used by mmCIF. Unknown categories and items are retained in source order.

quote_text

Quotes arbitrary text without changing its value when reparsed.

read

Reads a structure.

read_pdbml

Parses and semantically lowers PDBML through the existing mmCIF lowering.

read_with_document

Reads both the lossless document and its normalised structure in one parse.

render_value

Renders a typed value as one CIF token or text field.

split_tag

Splits an item name into its category and its item.

write_canonical

Writes a structure using only identifiers retained in the structure.

write_canonical_to

Streams canonical mmCIF directly to a byte destination.

write_canonical_with_options

Writes a structure with explicit choices for identities not retained by the graph.

write_pdbml

Writes one lossless document as PDBML/XML.

write_preserving

Writes a document back out, preserving what it held.

write_preserving_to

Streams a document while preserving its retained category/value order.

write_quoted

Appends arbitrary text as one CIF token or text field without a temporary allocation.

Type Aliases

ParseResult

A document and everything that was wrong with the file it came from.