Changelog

Changelog

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

[Unreleased]

[1.8.0] - 2026-07-22

Added

  • PDB writing: parsed structures can be serialized back to conformant fixed-column PDB. PDBParser.write_PDB() assembles a document in canonical section order, reconstructs the coordinate section (ATOM with interleaved ANISOU and chain-terminating TER cards, then HETATM), and regenerates the MASTER/END bookkeeping records from the emitted content. The record-level engine (pidibble.pdbwrite.PDBWriter) is the inverse of the parser, driven by the same field specs plus optional per-field writer hints ({prec, just}) carried as a third element in the YAML field definitions.

  • Coverage spans all four writable record families: single-line records (types 1/3, plus TER), continuation records (type 2 — TITLE, COMPND, SOURCE, KEYWDS, AUTHOR, …), and determinant-group records (type 4 — SEQRES, HETNAM, HETSYN, FORMUL, SITE, and the multi-line REVDAT), re-wrapped/chunked across numbered continuation lines. REMARK and JRNL (type 6) are re-emitted verbatim from the source lines.

  • A full parse -> write -> re-parse round-trip preserves every parsed record type and all field values on 4ZMJ (60 keys) and 4TVP (64 keys, incl. SITE); the regenerated MASTER matches the original entry’s byte-for-byte, and the coordinate/SEQRES/HETNAM/FORMUL/KEYWDS/TITLE records re-serialize byte-exactly.

  • Hexadecimal serial numbers for structures with more than 99999 atoms (e.g. large solvated systems): HexSerialEncoder is the exact inverse of the parser’s AtomSerialParser, switching to hex once a serial passes 99999 and staying hex thereafter — including small CONECT back-references, which the parser reads as hex once tripped. Serials round-trip up to the 5-column hybrid-hex ceiling (0xFFFFF = 1 048 575 atoms).

  • CHARMM read/write dialect (PDBParser(dialect='charmm'), write_PDB(dialect='charmm')), for coordinate PDBs that must stay column-congruent with a CHARMM/psfgen PSF. It widens resName to 6 columns for CHARMM/glycan names (e.g. BGLCNA, ANE5AC) and writes the authoritative segID column (73-76) that psfgen coordpdb depends on, while pinning x/y/z at columns 31-54 regardless of resName width — designing out the wide-resName coordinate-column drift that scrambles fixed-column readers. Parser and writer share one column model (charmm_formats/ResidueCharmm in the YAML) so they are exact inverses; the default 'standard' dialect remains strict wwPDB. A parse -> write -> parse round-trip on a glycan structure with a populated segID column is the identity for every coordinate field.

Changed

  • Field specs may now carry an optional third element with writer formatting hints; parsing ignores it (the byte-range unpacking is now width-tolerant), so the change is fully backward-compatible.

Not yet supported

  • Re-serialization of REMARK/JRNL from the parsed model (they are passed through from the source instead, so they are omitted when the input was mmCIF), and multi-model coordinate sections.

[1.7.2] - 2026-07-21

Added

  • Continuous-integration workflow (tests.yaml) running the unit tests on Python 3.10–3.12 and the documentation doctests on every push and pull request. Previously tests ran only on tagged releases.

  • README now documents PDBx/mmCIF parsing (with a worked example) and carries version, Python-versions, license, tests, docs, and downloads badges.

Changed

  • Documentation overhauled from a single quickstart page into a multi-page User Guide — loading structures, the parsed data model, working with records, biological assemblies and symmetry, PDBx/mmCIF, large structures, nonconformant files, and advanced/customization — plus a supported-record-types coverage table. Numerous example corrections; every doctest is now validated (sphinx -b doctest), with NORMALIZE_WHITESPACE enabled so pretty-printed output validates on content rather than incidental spacing. The docs landing page is retitled from “Welcome to Pidibble’s documentation!” to “pidibble”.

[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