NEWS

RBMRB 3.0.0

This is a major release that modernises the package, upgrades the API endpoint, and adds all features from PyBMRB 3.0.

The BMRB API endpoint has moved from the deprecated webapi.bmrb.wisc.edu/v2 to the current api.bmrb.io/v2. All network calls now target the new endpoint automatically.
HTTP requests migrated from httr (archived) to httr2 (>= 1.0.0).
JSON parsing migrated from rjson to jsonlite for better null handling and consistent behaviour across platforms.
Entry data is now fetched with ?format=zlib compression, matching PyBMRB/pynmrstar behaviour, and decompressed with memDecompress().
The old get_data() function is replaced by get_cs_data().
The old hist_cs() function is replaced by cs_hist().
Plotting now uses plotly for fully interactive spectra instead of static ggplot2 images.

cs_from_bmrb() — fetch per-entry chemical shifts from BMRB as a nested list (dataset → chain → seq_id → atom → ppm value).
cs_from_file() — parse local NMR-STAR .str files using a pure-R NMR-STAR 3 parser (no external C library required).
cs_table() — flat data.frame form of per-entry chemical shifts.
cs_to_df(), cs_peek(), cs_summary() — data inspection helpers.

get_cs_data() — database-wide chemical shift query with filtering by pH, temperature, ambiguity code, and outlier removal.
get_2d_cs_data() — paired 2D chemical shift data for two atoms in the same residue.
get_cs_from_bmrb_db() — raw BMRB search results (no filtering).

n15hsqc() — simulate an interactive 1H-15N HSQC spectrum.
c13hsqc() — simulate an interactive 1H-13C HSQC spectrum.
tocsy() — simulate an interactive 1H-1H TOCSY spectrum.
generic_2d() — any two-atom 2D correlation with optional sequence-walk tracing.
create_n15hsqc_peaklist(), create_c13hsqc_peaklist(), create_tocsy_peaklist(), create_2d_peaklist() — build peak lists without plotting.
export_peak_list() — export peak lists to CSV or Sparky format.
All spectrum functions support multi-dataset overlay, draw-trace between matched residues, and external peak-list overlay.

cs_hist() — interactive 1D chemical shift distribution as histogram, box plot, or violin plot.
cs_hist2d() — 2D correlation heat-map or contour plot.
conditional_cs_hist() — distribution conditioned on known chemical shifts of other atoms in the same residue.

bmrb_test() — three-step connectivity self-test.
bmrb_debug_entry() — diagnostic for entry fetch failures.
bmrb_search() — BMRB instant search.
bmrb_pdb_ids() / bmrb_from_pdb() — cross-reference PDB IDs.
bmrb_citation() — retrieve entry citations in BibTeX/text/JSON-LD.
bmrb_upload_entry() — upload a local NMR-STAR file for temporary BMRB-hosted access (7-day token).
filter_cs_outliers(), cs_stats() — chemical shift statistics.
standard_amino_acids(), standard_nucleic_acids() — residue code reference vectors.

Fixed silent data loss when API returns JSON null values in loop rows — unlist() was dropping nulls; replaced with vapply().
Fixed chemical shift search endpoint parser to use "columns" key (not "tags") matching the current BMRB API response format.
Fixed plain JSON entry response unwrapping for {"entry_id": VALUE} wrapper structure returned by the non-zlib endpoint.