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Changelog

v1.7.2 (2026-04-28)

  • Set maximum possible value for DATA_API_BATCH_ID_SIZE to be 1000
  • Use typing.get_type_hints in config.py instead of annotations (Issue #86)
  • Update README.md

v1.7.1 (2026-03-30)

  • Fix issue with retry_backoff usage in rcsbapi.sequence module
  • Move "Custom Configuration" readthedocs page to its own section
  • Update search API schema fetching to include timeout (20 seconds) and more informative logging message (Issue #90)
  • Various other logging updates

v1.7.0 (2026-03-16)

  • When working in Jupyter environments with Python 3.14+, execution of Data API queries (DataQuery) must be explicitly awaited (see details)
    • This addresses an issue with the async behavior of Jupyter environments due to the kernel already having an active asyncio event loop running, coupled with changes to asyncio in Python 3.14 (Issue #98)
    • This change does not impact code run in standard Python scripts (of any Python version); it only affects code run in Jupyter that uses Python 3.14 or greater
  • Updates to documentation and notebooks
  • Add GitHub issue form templates
  • Update search schemas: 1.53.0 -> 1.55.0
  • Update data schemas:
    • entry schema 9.1.0 -> 9.1.1
    • polymer_entity schema 10.1.0 -> 10.1.1
    • polymer_entity_instance schema 10.1.0 -> 10.1.2
    • nonpolymer_entity_instance schema 10.1.0 -> 10.1.2

v1.6.0 (2026-03-10)

  • Updated parameters for newly released embeddings-based structure similarity search (StructSimilarityQuery)
    • Added number_of_candidates, ptmscore_cutoff, and similarity_type parameters
    • operator parameter is deprecated
  • Fixed attrs.get_attribute_details() helper method
  • Documentation fixes

v1.5.0 (2025-11-20)

  • Updates to StructSimilarityQuery in rcsbapi.search:
    • Add support for specifying assembly_id or asym_id for input file/URL-based structure similarity searches
    • Deprecate structure_input_type argument (to be removed in version 2.0.0)
  • Updates to StructMotifQuery in rcsbapi.search:
    • Deprecate url argumemt in favor of file_url (to be removed in version 2.0.0)
    • Deprecate file_extension argumemt in favor of file_format (to be removed in version 2.0.0)
  • Update Search API schema URL in const.py to use "https" (related to Issue #90)
  • Remove "fallback" mechanism to local schema files and replace with explicit error messages (i.e., likely network connection issues or API service unavailability)
  • Move package version and metadata from __init__.py to pyproject.toml
  • Adjust project build pipelines:
    • Include wheels when publishing to PyPI
    • Use hatch instead of setuptools for building

v1.4.2 (2025-10-10)

  • Fix issue with annotations evaluation during config setting override, arising in Python 3.14 (Issue #86)
  • Add testing support for Python 3.14
  • Update search schemas: 1.52.1 -> 1.53.0
  • Update data schemas:
    • entry schema 9.0.4 -> 9.1.0
    • polymer_entity schema 10.0.5 -> 10.1.0
    • branched_entity schema 10.0.0 -> 10.1.0
    • nonpolymer_entity schema 10.0.0 -> 10.1.0
    • polymer_entity_instance schema 10.0.4 -> 10.1.0
    • branched_entity_instance schema 9.0.0 -> 9.1.0
    • nonpolymer_entity_instance schema 10.0.1 -> 10.1.0
    • assembly schema 9.0.0 -> 9.1.0
    • chem_comp schema 7.1.4 -> 7.2.0
    • drugbank schema 1.3.2 -> 1.4.0

v1.4.1 (2025-10-07)

  • Switch from using setup.py to pyproject.toml (Issue #67)
  • End support for Python 3.8 (due to PEP 639)
  • Fix and improve formatting of several warning messages

v1.4.0 (2025-08-19)

  • Switch from using requests to httpx (Issue #33)
  • Add asynchronous request support for Data API (rcsbapi.data) to speed up requests (see config settings)
  • Add retry support for Search API (rcsbapi.search), Data API (rcsbapi.data), Model Server API (rcsbapi.model), and Sequence Coordinate API (rcsbapi.sequence) requests (see config settings)
  • Adjust and add default settings to rcsbapi.config configuration (see config settings)
  • Stop overriding logging configuration within package—this should be done by client applications (Issue #52)
  • Fixed bug associated with typing observed for Python 3.8

v1.3.0 (2025-07-23)

  • Add support for Model Server API via new module rcsbapi.model. Use this to fetch structure/coordinate data from PDB entries and ligands as well as mmCIF metadata. (PR #73)
  • Fixed bug with rcsbapi.data Data API module, in which requesting multiple data items with redundant target field names was causing them to be overwritten in the final constructed query (PR #74)
  • Added Azure testing support for Windows (PR #75)
  • Add model server API schema: 0.9.12
  • Update search schemas: 1.50.1 -> 1.52.1
  • Update data schemas:
    • polymer_entity_instance schema 10.0.3 -> 10.0.4

v1.2.0 (2025-07-11)

  • Add support for Sequence Coordinates API via new module rcsbapi.sequence. Use this to fetch alignments between sequences from different databases as well as sequence-level annotations integrated from external resources and RCSB PDB. (PRs #46, #68)
    • Documentation and Jupyter notebook provided
    • Generalized pre-existing Data API module GraphQL schema and query generation code to be re-used by both rcsbapi.data and rcsbapi.sequence modules (no impact to user)
  • Add NestedAttributeQuery to Search API rcsbapi.search module to support restricted/pair-wise grouping of nested attributes and prevent them from being automatically flattened down to the same group level as adjacent terminal nodes. Warning messages have been added to notify users of the need to make use of this for any nested attributes being included in search queries. (PR #66; Issue #49)
  • Change rcsbapi.search Search API requests to use POST instead of GET, to handle very large query bodies that would otherwise generate massive URL lengths
  • Add custom User-Agent to API request headers ("User-Agent": "py-rcsb-api/__version__ (+https://github.com/rcsb/py-rcsb-api)")
  • Add sequence-coordinates API schema (GraphQL; no version)
  • Update search schemas: 1.49.0 -> 1.50.1
  • Update data schemas:
    • entry schema 9.0.4 -> 9.0.4
    • polymer_entity schema 10.0.5 -> 10.0.5

v1.1.4 (2025-07-09)

  • Fix: Patch schema parsing for search attributes - delete duplicate chemical attributes from structure attribute schema (following update to RCSB.org schemas in July 2025, in which chemical attributes are now merged into structure attribute schema). (Issue #70)

v1.1.3 (2025-05-05)

  • Fix: Update regex pattern for instances in const.py to support suffixes longer than one character (e.g., "1S5L.AA")

v1.1.2 (2025-03-20)

  • Update how dataclass attributes are created in const.py

v1.1.1 (2025-03-13)

  • Add missing dependency for building documentation
  • Add docstrings

v1.1.0 (2025-03-12)

  • Add ALL_STRUCTURES object, allowing Data API queries for all PDB structures and chemical components
  • Add progress_bar and batch_size parameters to Data API package's .exec
  • Add group function to Search API package to enforce nested grouping
  • Update README with new citation information
  • Update search schemas: 1.48.0 -> 1.49.0
  • Update data schemas:
    • entry schema 9.0.3 -> 9.0.4
    • polymer_entity_instance schema 10.0.2 -> 10.0.3
    • nonpolymer_entity_instance schema 10.0.0 -> 10.0.1

v1.0.1 (2025-01-17)

  • Add import to const.py for compatibility with Python 3.8
  • Update search schemas: 1.47.7 -> 1.48.0

v1.0.0 (2024-11-6)

  • Release version 1.0.0 of package
  • Update search schemas: 1.47.6 -> 1.47.7
  • Update data schemas:
    • entry schema 9.0.2 -> 9.0.3
    • chem_comp schema 7.1.3 -> 7.1.4
  • Update documentation

v0.5.0 (2024-10-28)

  • Separate out package-wide settings into immutable constants (const.py) and configurable parameters (config.py)
  • Renamed rcsb_attributes -> search_attributes
  • Automatically capitalize input_ids
  • Added dev_tools directory and updated update_schema.py
  • Search API chemical_schema and structure_schema at v1.47.6
  • Update documentation

v0.4.0 (2024-10-15)

  • Merge rcsbsearchapi package into package as separate rcsbapi.search module
    • Renamed several classes and methods in this process:
      • SequenceQuery -> SeqSimilarityQuery
      • StructureMotifResidue -> StructMotifResidue
      • Range -> FacetRange
      • rcsb_query_editor_url -> get_editor_link
      • rcsb_query_builder_url -> get_query_builder_link
  • Renamed several files and classes to prevent overlap with future developments:
    • data/query.py -> data/data_query.py
    • data/schema.py -> data/schema_query.py
    • Query() Data API class -> DataQuery()
    • Schema() Data API class -> DataSchema()
    • search/search.py -> search/search_query.py
    • search/schema.py -> search/search_schema.py
  • Automatically change singular "input_type" to plural when possible
  • Add warning message if fully qualified field path not provided
  • Update documentation

v0.3.0 (2024-08-23)

  • Falls back to local schema file when fetch fails
  • Supports dot separated field names for requesting data
  • get_unique_fields deleted and replaced with find_paths
  • find_field_names changed to return only field names, no descriptions
  • Executing queries called with .exec()
  • Updates to documentation
  • See PR #31 for full details
  • Updated data_api_schema.json and added all schema files on https://data.rcsb.org/#data-schema

v0.2.0 (2024-07-25)

  • Updates to Query methods
  • Added GraphQL query validation
  • Updates to documentation

v0.1.0 (2024-07-22)

  • First release!
  • Provides Pythonic interface for interacting with RCSB.org Data API
  • Automated Data API schema parsing via Schema.py
  • Enables query building and execution via Query.py
  • Documentation and example notebooks
  • See PR #23 for full details