`nerd nmr_create`

nerd nmr_create registers NMR reactions and their trace files in the database, enabling downstream kinetics tasks (nmr_deg_kinetics, nmr_add_kinetics). You can inline reactions in YAML or point to CSV sheets.

nerd nmr_create --config PATH/TO/config.yaml --db PATH/TO/nerd.sqlite

If --db is omitted, <run.output_dir>/nerd.sqlite is used.

Configuration Layout

run:
  label: nmr_create_deg
  output_dir: examples

nmr_create:
  search_roots:
    - ../../test_data
  reactions:
    - reaction_type: deg
      temperature: 25
      replicate: 1
      probe: dms
      probe_conc: 0.01585
      buffer: Schwalbe_bistris
      substrate: none
      substrate_conc: 0
      num_scans: 64
      time_per_read: 5
      total_kinetic_reads: 96
      total_kinetic_time: 28800
      nmr_machine: A600
      trace_files:
        decay_trace: nmr_degradation_data/dms_schwalbe_25C_rep1.csv

Key Fields

Field	Description
`search_roots`	Extra directories to resolve trace file paths.
`reactions`	List (or CSV filename) describing each NMR reaction to ingest.
`trace_files`	Mapping of trace roles (e.g., `decay_trace`, `peak_trace`, `dms_trace`) to file paths. Can be `{path, species}` for adduction traces.

Optional: kinetic_data_dir, mnova_analysis_dir, raw_fid_dir for bookkeeping.

CSV Mode

If reactions is a string (e.g., reactions: nmr_degradation_samples.csv), NERD loads that CSV. Headers should match the YAML fields above. Use search_roots so relative trace paths resolve correctly.

Outputs

Rows in nmr_reactions (temperature, replicate, buffer, construct association).
Trace metadata in nmr_trace_files for each role/path/species.
Run artifacts and logs under <output_dir>/<label>/nmr_create_latest/.

Examples

# Import degradation reactions from CSV
nerd nmr_create --config examples/nmr_create/nmr_create_deg.yaml --db nerd.sqlite

# Inline adduction entries
nerd nmr_create --config configs/nmr_create_add.yaml --db nerd.sqlite

After nmr_create, run nmr_deg_kinetics or nmr_add_kinetics to fit the registered reactions.