Skip to content

nerd nmr_add_kinetics

nerd nmr_add_kinetics fits NMR-based adduction kinetics (k_add) for reactions registered via nmr_create. It relies on trace files (peak and DMS traces) staged in the database and records results in nmr_fit_runs/nmr_fit_params.

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

If --db is omitted, the CLI uses <run.output_dir>/nerd.sqlite.

Configuration Layout

run:
  label: nmr_add_demo
  output_dir: examples
  backend: local

nmr_add_kinetics:
  search_roots:
    - ../../test_data
  plugin: ode_lsq_ntp_add
  plugin_options:
    k_add_init: 0.002
    k_deg_init: 0.001
  fit_params:
    S_factor: 1.0
  species:
    - ATP_C8

Key Fields

Field Description
search_roots Directories to resolve trace files if trace_files.path is relative.
plugin Registered NMR fit engine (defaults to ode_lsq_ntp_add).
plugin_options Passed to the engine constructor (e.g., initial guesses).
fit_params Forwarded to the plugin’s fit call (e.g., scaling factors).
species One or more trace species to fit (e.g., ATP_C8). If omitted, defaults to substrate or ntp_probe.

Optional filters:

  • reaction_ids: explicit list of reactions to fit.
  • substrates: restrict to specific substrates (e.g., ATP, CTP).
  • buffer, construct, temperature, etc., can be enforced via custom pre-filters (deprecated in favor of species/substrate lists).

Prerequisites

  1. Run nerd nmr_create with trace_files entries: yaml trace_files: peak_trace: path: nmr_ntp_adduction_data/ATP_peak_percentages/20_1_peak8.csv species: ATP_C8 dms_trace: path: nmr_ntp_adduction_data/ATP_peak_percentages/20_1_peakDMS.csv species: ATP_DMS
  2. Ensure constructs, buffers, and sequencing runs are already in the database (nerd create).

Outputs

  • New rows in nmr_fit_runs capturing plugin name, model, species, and run metadata.
  • Associated parameters in nmr_fit_params (k_value, k_error, r2, chisq, plus plugin diagnostics).
  • JSON artifacts under <output_dir>/<label>/nmr_add_kinetics_latest/results/ describing each reaction fit.

Examples

# Fit ATP C8 adduction kinetics
nerd nmr_add_kinetics --config examples/nmr_fit_add/configs/fit_add.yaml                       --db examples/nerd.sqlite

# Run with multiple species (C8 + DMS)
nerd nmr_add_kinetics --config configs/fit_add_multi.yaml --db nerd.sqlite

After the fits complete, downstream tasks (e.g., tempgrad_fit with data_source: nmr) can consume the stored rates for Arrhenius analysis.