A Comprehensive Interface for Accessing the Protein Data Bank

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Documentation for package ‘rPDBapi’ version 3.0.1

• DESCRIPTION file
• User guides, package vignettes and other documentation
• Package NEWS
• Package README

Help Pages

add_property	Add or Merge Properties for RCSB PDB Data Fetching
as_rpdb_assembly	Convert Data to an rPDBapi Assembly Object
as_rpdb_chemical_component	Convert Data to an rPDBapi Chemical Component Object
as_rpdb_entry	Convert Data to an rPDBapi Entry Object
as_rpdb_polymer_entity	Convert Data to an rPDBapi Polymer Entity Object
as_rpdb_structure	Convert Data to an rPDBapi Structure Object
autoresolve_sequence_type	Automatically Determine the Sequence Type
build_assembly_id	Build an Assembly Identifier
build_entity_id	Build an Entity Identifier
build_entry_id	Build an Entry Identifier
build_instance_id	Build an Instance Identifier
cache_info	Inspect rPDBapi Cache Contents
ChemicalOperator	Create a Chemical Search Operator for SMILES/InChI Descriptors
clear_rpdbapi_cache	Clear rPDBapi Cache Directory
ComparisonOperator	Create a Comparison Search Operator
ContainsPhraseOperator	Create a Contains Phrase Search Operator
ContainsWordsOperator	Create a Contains Words Search Operator
data_fetcher	Fetch RCSB PDB Data Based on Specified Criteria
data_fetcher_batch	Batch Fetch RCSB PDB Data with Optional Retry and Cache
DefaultOperator	Create a Default Search Operator
describe_chemical	Describe Chemical Compound from RCSB PDB
ExactMatchOperator	Create an Exact Match Search Operator
ExistsOperator	Create an Existence Search Operator
extract_calpha_coordinates	Extract C-alpha Coordinates
extract_ligand_table	Extract Ligand Table
extract_taxonomy_table	Extract Taxonomy Table
fetch_data	Fetch Data from RCSB PDB Using a JSON Query
find_papers	Search for and Retrieve Paper Titles from PDB
find_results	Retrieve Specific Fields for Search Results from RCSB PDB
generate_json_query	Generate a JSON Query for RCSB PDB Data Retrieval
get_fasta_from_rcsb_entry	Retrieve FASTA Sequence from PDB Entry or Specific Chain
get_info	Retrieve Information for a Given PDB ID
get_pdb_api_url	Generate a PDB API URL
get_pdb_file	Download and Process PDB Files from the RCSB Database
handle_api_errors	Handle API Errors
infer_id_type	Infer RCSB Identifier Type
infer_search_service	Infer the Appropriate Search Service for RCSB PDB Queries
InOperator	Create an Inclusion Search Operator
join_structure_sequence	Join Structure and Sequence Summaries
list_rcsb_fields	List Known RCSB Fields by Data Type
parse_fasta_text_to_list	Helper Function: Parse FASTA Text to List Grouped by Header
parse_rcsb_id	Parse an RCSB Identifier
parse_response	Parse API Response
perform_search	Perform a Search in the RCSB PDB
QueryGroup	Create a Grouped Query Object for RCSB PDB Searches
QueryNode	Create a Query Node for RCSB PDB Searches
query_search	Search Query Function
RangeOperator	Create a Range Search Operator
RequestOptions	Define Request Options for RCSB PDB Search Queries
return_data_as_dataframe	Convert RCSB PDB Response Data into a Dataframe
ScoredResult	Create a Scored Result Object for PDB Searches
search_graphql	Perform a GraphQL Query to RCSB PDB
search_rcsb_fields	Search Known RCSB Fields by Pattern
send_api_request	Send API Request to a Specified URL
SeqMotifOperator	Create a Sequence Motif Operator for RCSB PDB Searches
SequenceOperator	Create a Sequence Operator for Sequence-Based Searches
StructureOperator	Create a Structure Operator for Structure-Based Searches
summarize_assemblies	Summarize Assembly-Level Data
summarize_entries	Summarize Entry-Level Data
validate_properties	Validate Property Specification Against Known Field Registry
walk_nested_dict	Recursively Walk Through a Nested Dictionary