Changelog¶

Changelog¶

All notable changes to this project are documented in this file. The format follows Keep a Changelog.

[Unreleased]¶

[1.7.1] - 2026-07-15¶

Added¶

mmCIF REMARK.350 (biological assembly) records now expose header_label, the raw label asym_id list, alongside the existing header (author chains, mapped via the chainmap). This preserves the full per-chain (label) detail — including glycan/ligand chains — that the deduplicated author-chain list collapses.

[1.7.0] - 2026-07-14¶

Added¶

Substantially expanded PDBx/mmCIF parsing: coverage grew from 6 to 16 record types (reading 22 of a typical file’s ~73 categories). New mmCIF-mapped records: HEADER, TITLE, EXPDTA, KEYWDS, CRYST1, SEQRES, HELIX, SHEET (complete — ranges, sense, numStrands, H-bond registration), and COMPND/SOURCE (as native per-entity records). Metal coordination (metalc) now folds into LINK. Every mapping is validated against the legacy PDB parse.
mmCIF↔PDB correspondence test suite revived and extended (atoms, links, ssbonds, seqadv, missing residues, assembly, metadata, seqres, helix, sheet, entities, metal coordination).
mmCIF coverage summary logged at parse time: how many of a file’s categories pidibble reads, with the unmapped ones listed at DEBUG level.
docs/mmcif_coverage.md: PDB vs PDBx/mmCIF coverage audit and roadmap.
Reusable declarative mmCIF mapspec directives: merge, join (multi-key match: conditions with nested residue dicts), groupby/collect/lengths, as_list, value_maps, list-aware allcaps, and multi-value signal_value.

Changed¶

mmCIF gen_dict refactored onto the py-mmcif higher-level API (selectIndices, getRowAttributeDict) instead of positional getValue loops; verified byte-for-byte identical output on existing records.
A mapped-but-absent mmCIF category now emits no records (previously produced a spurious empty {'tables': {}} record).

Removed¶

Dead MMCIFDict class and resolve() stub in mmcif_parse.py.

[1.6.0] - 2026-07-14¶

Added¶

NonconformanceRegistry: PDB-format deviations (e.g. a charge column that cannot be coerced to its declared type, or a record exceeding 80 bytes) are now aggregated by type — keyed by (record_key, field, kind) — rather than logged per instance. At the end of a parse, PDBParser emits a single INFO summary line per type with a count and one exemplar, replacing what could be tens of thousands of repeated warnings. The registry is available programmatically as PDBParser.nonconformances (.types(), len(), bool()).

Changed¶

Per-instance field/record parse-error messages demoted from WARNING to DEBUG; the INFO type-summary is the default-visible output, with full per-instance detail available by setting the logger to DEBUG.

[1.5.4] - 2026-07-14¶

Fixed¶

ATOM/HETATM/ANISOU charge field retyped from Float to String. The PDB charge column (79–80) is a formatted string (e.g. 1-, 2+), never a plain float, so every populated charge previously failed float() and emitted a spurious “Could not parse field charge” warning while discarding the value. Charges are now captured correctly (e.g. 1-).
Off-by-one in StringParser.report_record_error() highlight: the error display dropped the character at the field’s first column and coloured a window shifted one column to the right of the offending field. The highlight now wraps exactly the columns given by the field’s byte range.

[1.5.3] - 2026-05-03¶

Fixed¶

PDBParser(PDBcode=...) legacy parameter silently swallowed by **kwargs; restored via explicit mapping to source_id/source_db='rcsb'
Eight bare except: clauses narrowed to specific exception types throughout
Bitwise &= used as logical AND in BaseRecord.empty() replaced with all()
str2int_sig raised IndexError on empty-string input; added guard before index access
!= None / == None comparisons replaced with is not None / is None throughout
type(x) == T identity comparisons replaced with isinstance(x, T) throughout
elif type(p) == list: in parse_tokens() was unreachable; corrected to isinstance(p, PDBRecordList)
Mutable default arguments hold={} and hold=[] in gather_token and header_check replaced with None

Changed¶

Global hex-tripped flag in hex.py replaced with AtomSerialParser callable class; each PDBParser instance owns its own state, eliminating thread-safety hazard and cross-parse contamination
mappers default argument changed from a mutable dict literal to None; default built inside __init__
Resource YAML files now loaded via importlib.resources.files() instead of os.path.dirname(resources.__file__), ensuring correct behavior inside wheels and zip archives
resources/__init__.py removed; resources/ is now a plain data directory, not a sub-package
MANIFEST.in removed; hatchling auto-discovers package data from git-tracked files
PEP 8 spacing applied throughout all source files
parse_embedded() refactored: triggered/capturing boolean pair replaced with explicit _EmbedState enum (SEARCHING, PRE_CAPTURE, CAPTURING); setup phase extracted into _setup_embed_context()

Added¶

CHANGELOG.md with full release history
scripts/release.sh for automated version rotation, tagging, and push
[test] optional dependency group in pyproject.toml

[1.5.2] - 2025-09-16¶

Added¶

Capability to download structures from OPM and split DUM residues into a separate PDB file

[1.5.1] - 2025-09-15¶

Fixed¶

Minor fixes following 1.5.0

[1.5.0] - 2025-09-15¶

Added¶

Initial OPM support

[1.4.2] - 2025-08-11¶

Changed¶

Updated AlphaFold interface to current API

[1.4.1] - 2025-08-07¶

Fixed¶

Parsing bug in PDBRecordList

[1.4.0] - 2025-07-29¶

Added¶

PDBRecordList and PDBRecordDict classes

[1.3.3] - 2025-07-29¶

Fixed¶

Bugs where missing records were incorrectly assumed present during mmCIF parsing

[1.3.2] - 2025-07-25¶

Added¶

filepath parameter in PDBParser() for transparent reading of local files

[1.3.1] - 2025-07-25¶

Fixed¶

Minor fixes following 1.3.0

[1.3.0] - 2025-07-16¶

Changed¶

Streamlined class attribute usage throughout
Full API documentation published

[1.2.3] - 2025-03-06¶

Fixed¶

Negative residue sequence numbers now parsed correctly

[1.2.2] - 2025-03-04¶

Fixed¶

Minor fixes following 1.2.1

[1.2.1] - 2024-10-01¶

Fixed¶

Hexadecimal serial number parsing issues (again)

[1.2.0] - 2024-09-08¶

Fixed¶

Hexadecimal serial number parsing issues

[1.1.9] - 2024-08-08¶

Fixed¶

nan values and * filler characters in numeric fields now handled gracefully

[1.1.8] - 2024-07-15¶

Added¶

Unstructured REMARK records (e.g. from PACKMOL output) parsed as REMARK.-1

[1.1.6] - 2024-07-11¶

Fixed¶

Hexadecimal atom serial detection when no a-f characters are present, based on value exceeding 99999

[1.1.5] - 2024-07-11¶

Fixed¶

Hex-or-integer detection now restricted to atom serial number fields only

[1.1.4] - 2024-07-11¶

Added¶

Hexadecimal atom serial number support for files with more than 99999 atoms

[1.1.3] - 2024-03-21¶

Added¶

Ability to group records into models for multi-model PDB entries

[1.1.2] - 2024-02-28¶

Added¶

Ability to fetch structures from the AlphaFold database

[1.1.1] - 2023-09-19¶

Added¶

Version detection via importlib.metadata

[1.0.9.1] - 2023-08-28¶

Added¶

Limited mmCIF parsing: ATOM, HETATM, SSBOND, LINK, SEQADV, REMARK 350, and REMARK 465 records

[1.0.8] - 2023-08-23¶

Fixed¶

Variations in how symmetry operation matrices are represented in PDB files

[1.0.7.7] - 2023-08-22¶

Changed¶

Cleaned up logging throughout

[1.0.7.6] - 2023-08-22¶

Fixed¶

Leading whitespace in resName field of Residue10 record sometimes ignored

[1.0.7.5] - 2023-08-18¶

Added¶

Support for four-letter residue names

[1.0.7.4] - 2023-08-04¶

Added¶

Logging functionality

[1.0.7.3] - 2023-08-03¶

Changed¶

Improved parsing of BIOMT transforms

[1.0.7.2] - 2023-08-03¶

Added¶

Documentation stub on ReadTheDocs

[1.0.7.1] - 2023-08-03¶

Added¶

Support for split BIOMT tables and REMARK 280, 375, 650, and 700

[1.0.7] - 2023-08-01¶

Added¶

Pretty-print support for parsed records

[1.0] - 2023-07-01¶

Added¶

Initial release