Package rPDBapi updated to version 3.0.0 with previous version 2.1.2 dated 2025-10-29

Fri, 06 Mar 2026 19:02:00 CDT

Title: A Comprehensive Interface for Accessing the Protein Data Bank
Description: Streamlines the interaction with the 'RCSB' Protein Data Bank ('PDB') <https://www.rcsb.org/>. This interface offers an intuitive and powerful tool for searching and retrieving a diverse range of data types from the 'PDB'. It includes advanced functionalities like BLAST and sequence motif queries. Built upon the existing XML-based API of the 'PDB', it simplifies the creation of custom requests, thereby enhancing usability and flexibility for researchers.
Author: Selcuk Korkmaz [aut, cre] , Bilge Eren Yamasan [aut]
Maintainer: Selcuk Korkmaz <selcukorkmaz@gmail.com>

Diff between rPDBapi versions 2.1.2 dated 2025-10-29 and 3.0.0 dated 2026-03-06

 DESCRIPTION                                                     |   18 -
 LICENSE                                                         |only
 MD5                                                             |  133 +++++---
 NAMESPACE                                                       |   30 +
 NEWS.md                                                         |only
 R/00_globals.R                                                  |   10
 R/01_contracts.R                                                |only
 R/99_global_variables.R                                         |only
 R/add_property.R                                                |   30 +
 R/analysis_helpers.R                                            |only
 R/batch_cache_api.R                                             |only
 R/data_fetcher.R                                                |   60 +++
 R/describe_chemical.R                                           |   34 +-
 R/fetch_data.R                                                  |   52 ---
 R/find_papers.R                                                 |   15
 R/find_results.R                                                |   19 +
 R/generate_json_query.R                                         |    3
 R/get_fasta_from_rcsb_entry.R                                   |   41 ++
 R/get_info.R                                                    |   27 +
 R/get_pdb_file.R                                                |  126 +++++--
 R/handle_api_errors.R                                           |   13
 R/id_helpers.R                                                  |only
 R/internal_cache_retry.R                                        |only
 R/internal_fetch.R                                              |only
 R/internal_http.R                                               |only
 R/internal_query.R                                              |only
 R/internal_schema.R                                             |only
 R/internal_search.R                                             |only
 R/object_model.R                                                |only
 R/parse_response.R                                              |   15
 R/perform_search.R                                              |  114 ++----
 R/query_search.R                                                |  165 ++++------
 R/return_data_as_dataframe.R                                    |   21 -
 R/schema_helpers.R                                              |only
 R/search_client.R                                               |   22 -
 R/search_graphql.R                                              |   22 +
 R/send_api_request.R                                            |   24 -
 README.md                                                       |   44 ++
 build                                                           |only
 inst/doc                                                        |only
 man/as_rpdb_assembly.Rd                                         |only
 man/as_rpdb_chemical_component.Rd                               |only
 man/as_rpdb_entry.Rd                                            |only
 man/as_rpdb_polymer_entity.Rd                                   |only
 man/as_rpdb_structure.Rd                                        |only
 man/build_assembly_id.Rd                                        |only
 man/build_entity_id.Rd                                          |only
 man/build_entry_id.Rd                                           |only
 man/build_instance_id.Rd                                        |only
 man/cache_info.Rd                                               |only
 man/clear_rpdbapi_cache.Rd                                      |only
 man/data_fetcher.Rd                                             |    4
 man/data_fetcher_batch.Rd                                       |only
 man/extract_calpha_coordinates.Rd                               |only
 man/extract_ligand_table.Rd                                     |only
 man/extract_taxonomy_table.Rd                                   |only
 man/fetch_data.Rd                                               |    6
 man/get_pdb_file.Rd                                             |   40 +-
 man/infer_id_type.Rd                                            |only
 man/join_structure_sequence.Rd                                  |only
 man/list_rcsb_fields.Rd                                         |only
 man/parse_rcsb_id.Rd                                            |only
 man/perform_search.Rd                                           |    4
 man/query_search.Rd                                             |    5
 man/search_rcsb_fields.Rd                                       |only
 man/summarize_assemblies.Rd                                     |only
 man/summarize_entries.Rd                                        |only
 man/validate_properties.Rd                                      |only
 tests/testthat/helper_live.R                                    |only
 tests/testthat/test_QueryNode.R                                 |   16
 tests/testthat/test_add_property.R                              |only
 tests/testthat/test_api_contracts.R                             |only
 tests/testthat/test_citation_field_compatibility.R              |only
 tests/testthat/test_data_fetcher.R                              |   18 +
 tests/testthat/test_fetch_data.R                                |only
 tests/testthat/test_find_results.R                              |    2
 tests/testthat/test_get_fasta_from_rcsb_entry.R                 |    2
 tests/testthat/test_get_info.R                                  |    1
 tests/testthat/test_get_pdb_file.R                              |    1
 tests/testthat/test_get_pdb_file_structfact.R                   |only
 tests/testthat/test_group_query_serialization.R                 |only
 tests/testthat/test_infer_search_service.R                      |only
 tests/testthat/test_milestone1_additional_export_contracts.R    |only
 tests/testthat/test_milestone1_backward_compatibility_exports.R |only
 tests/testthat/test_milestone2_internal_modules.R               |only
 tests/testthat/test_milestone3_error_contracts.R                |only
 tests/testthat/test_milestone4_identifier_system.R              |only
 tests/testthat/test_milestone5_schema_layer.R                   |only
 tests/testthat/test_milestone6_batch_cache.R                    |only
 tests/testthat/test_milestone7_object_model_analysis_helpers.R  |only
 tests/testthat/test_perform_search.R                            |    1
 tests/testthat/test_perform_search_return_type.R                |only
 tests/testthat/test_query_search.R                              |    1
 tests/testthat/test_query_search_scan_params.R                  |only
 tests/testthat/test_request_encoding.R                          |only
 tests/testthat/test_return_data_as_dataframe.R                  |only
 vignettes                                                       |only
 97 files changed, 765 insertions(+), 374 deletions(-)

More information about rPDBapi at CRAN