StressME-DynamicME/config_stressME.yaml at master · SBRG/StressME-DynamicME · GitHub

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project_root: /app  # for Docker compatibility
project_results_folder: run_stressme_results
project_name: 'demo' # change to your own run

model_file: FoldME_Ali_keff.pickle

# Simulation parameters
temperature: 37
pH: 7.0
ROS: 1.0
unmodeled_protein_fraction: 0.1

# Keff updates (dictionary)
updated_dxr_keff:
  DXPRIi_FWD_DXPREDISOM-CPLX_mod_cobalt2: 88.72


# ROS substrate dictionary (optional, can add more species)
ros_substrate_dict:
  h2o2_c: 5e-08
  o2s_c: 2e-10
  # h2o2_e: 1.5e-06
  # o2s_e: 0
  # pq2_c: 0.0


exchange_bounds:
  EX_glc__D_e: 0     # Glucose (closed)
  EX_ac_e: -1000    # Acetate (open)
  EX_malt_e: 0            # Maltose (closed)
  EX_lcts_e: 0            # Lactose (closed)
  EX_gal_e: 0             # Galactose (closed)
  EX_fru_e: 0             # Fructose (closed)
  EX_sbt__D_e: 0          # Sorbitol (closed)
  EX_man_e: 0             # Mannose (closed)
  EX_arab__L_e: 0         # Arabinose (closed)
  EX_glyc_e: 0            # Glycerol (closed)
  EX_xyl__D_e: 0          # Xylose (closed)
  EX_rib__D_e: 0          # Ribose (closed)
  EX_pyr_e: 0             # Pyruvate (closed)
  EX_succ_e: 0            # Succinate (closed)
  EX_fum_e: 0             # Fumarate (closed)
  EX_mal__L_e: 0          # L-Malate (closed)
  EX_mal__D_e: 0          # D-Malate (closed)
  EX_akg_e: 0             # α-Ketoglutarate (closed)
  EX_cit_e: 0             # Citrate (closed)

# Simulation options
warm_start: true
basis_file: basis.npy
mu_precision: 1e-4

# Output
output_prefix: StressME_heatevolved