R: A Comprehensive Interface for Accessing the Protein Data Bank

# A Comprehensive Interface for Accessing the Protein Data Bank

## 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