Package: rPDBapi 3.0.1

Introduction | Installation and Setup | Why Access the PDB from R? | rPDBapi Capabilities | Package Feature Map | Core Concepts in the RCSB PDB API | Workflow 1: Simple Search for Kinase Structures | Workflow 2: Refine the Search with Structured Operators | Workflow 3: Retrieve Entry-Level Metadata | Workflow 4: Inspect the Raw API Payload and Convert It to Tidy Data | Workflow 4b: Batch Retrieval, Provenance, and Cache-Aware Access | Workflow 5: Retrieve Assembly-Level Data | Workflow 5b: Identifier-Aware Retrieval Patterns | Workflow 6: Retrieve Taxonomy and Chain-Level Biological Context | Workflow 7: Retrieve Detailed Entry Annotations | Workflow 8: Download Coordinates and Inspect Atomic Data | Workflow 8b: Working with the Rich Object Model | Workflow 9: Downstream Analysis in R | Workflow 10: Optional Visualization with r3dmol | Advanced Search Modalities | Sequence Search | Sequence Motif Search | Structure Similarity Search | Chemical Search | Complete Search Operator Reference | Query Search Variants and Scan Parameters | Complete Metadata Retrieval Surface | Building Property Lists Incrementally | Non-polymer and Chemical Component Data | Instance-Level Retrieval | Low-Level API Access and Parsing Helpers | Return Contracts and Error Handling | Appendix A: Export-by-Export Reference | Appendix B: Minimal Example Pattern for Every Export | Appendix C: Supported Identifier Levels and Typical Formats | Appendix D: Return Classes and Their Meaning | Appendix E: Error and Failure-Mode Guidance | Reproducible Research with rPDBapi | Summary | Session Information