Package: rPDBapi 2.1

Selcuk Korkmaz

rPDBapi: A Comprehensive Interface for Accessing the Protein Data Bank

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.

Authors:Selcuk Korkmaz [aut, cre], Bilge Eren Yamasan [aut]

rPDBapi_2.1.tar.gz
rPDBapi_2.1.tar.gz(r-4.5-noble)rPDBapi_2.1.tar.gz(r-4.4-noble)
rPDBapi_2.1.tgz(r-4.4-emscripten)rPDBapi_2.1.tgz(r-4.3-emscripten)
rPDBapi.pdf |rPDBapi.html✨
rPDBapi/json (API)

# Install 'rPDBapi' in R:
install.packages('rPDBapi', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

35 exports 0.49 score 44 dependencies 2 scripts 569 downloads

Last updated 11 days agofrom:c90e2f3a26. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 08 2024
R-4.5-linuxOKSep 08 2024

Exports:add_propertyautoresolve_sequence_typeChemicalOperatorComparisonOperatorContainsPhraseOperatorContainsWordsOperatordata_fetcherDefaultOperatordescribe_chemicalExactMatchOperatorExistsOperatorfind_papersfind_resultsgenerate_json_queryget_fasta_from_rcsb_entryget_infoget_pdb_api_urlget_pdb_filehandle_api_errorsinfer_search_serviceInOperatorparse_responseperform_searchquery_searchQueryGroupQueryNodeRangeOperatorRequestOptionsreturn_data_as_dataframeScoredResultsearch_graphqlsend_api_requestSeqMotifOperatorSequenceOperatorStructureOperator

Dependencies:askpassbio3dbriocallrclicrayoncurldescdiffobjdigestdplyrevaluatefansifsgenericsgluehttrjsonlitelifecyclemagrittrmimeopensslpillarpkgbuildpkgconfigpkgloadpraiseprocessxpspurrrR6Rcpprematch2rlangrprojrootsystestthattibbletidyselectutf8vctrswaldowithrxml2

Readme and manuals

Help Manual

Help pageTopics
Add or Merge Properties for RCSB PDB Data Fetchingadd_property
Automatically Determine the Sequence Typeautoresolve_sequence_type
Create a Chemical Search Operator for SMILES/InChI DescriptorsChemicalOperator
Create a Comparison Search OperatorComparisonOperator
Create a Contains Phrase Search OperatorContainsPhraseOperator
Create a Contains Words Search OperatorContainsWordsOperator
Fetch RCSB PDB Data Based on Specified Criteriadata_fetcher
Create a Default Search OperatorDefaultOperator
Describe Chemical Compound from RCSB PDBdescribe_chemical
Create an Exact Match Search OperatorExactMatchOperator
Create an Existence Search OperatorExistsOperator
Fetch Data from RCSB PDB Using a JSON Queryfetch_data
Search for and Retrieve Paper Titles from PDBfind_papers
Retrieve Specific Fields for Search Results from RCSB PDBfind_results
Generate a JSON Query for RCSB PDB Data Retrievalgenerate_json_query
Retrieve FASTA Sequence from PDB Entry or Specific Chainget_fasta_from_rcsb_entry
Retrieve Information for a Given PDB IDget_info
Generate a PDB API URLget_pdb_api_url
Download and Process PDB Files from the RCSB Databaseget_pdb_file
Handle API Errorshandle_api_errors
Infer the Appropriate Search Service for RCSB PDB Queriesinfer_search_service
Create an Inclusion Search OperatorInOperator
Helper Function: Parse FASTA Text to List Grouped by Headerparse_fasta_text_to_list
Parse API Responseparse_response
Perform a Search in the RCSB PDBperform_search
Search Query Functionquery_search
Create a Grouped Query Object for RCSB PDB SearchesQueryGroup
Create a Query Node for RCSB PDB SearchesQueryNode
Create a Range Search OperatorRangeOperator
Define Request Options for RCSB PDB Search QueriesRequestOptions
Convert RCSB PDB Response Data into a Dataframereturn_data_as_dataframe
Create a Scored Result Object for PDB SearchesScoredResult
Perform a GraphQL Query to RCSB PDBsearch_graphql
Send API Request to a Specified URLsend_api_request
Create a Sequence Motif Operator for RCSB PDB SearchesSeqMotifOperator
Create a Sequence Operator for Sequence-Based SearchesSequenceOperator
Create a Structure Operator for Structure-Based SearchesStructureOperator
Recursively Walk Through a Nested Dictionarywalk_nested_dict