From a9b0781ceda923bde971d9d6a28f1d890c03969d Mon Sep 17 00:00:00 2001
From: Evan De la Garza <edelagarza2002@gmail.com>
Date: Sun, 3 Mar 2024 17:11:53 -0600
Subject: [PATCH] extracted concentrations and reaction rates from evolving
 conditions

---
 src/box_model.py | 28 +++++++++++++++++++++++++++-
 1 file changed, 27 insertions(+), 1 deletion(-)

diff --git a/src/box_model.py b/src/box_model.py
index f403143d..e89c4f5e 100644
--- a/src/box_model.py
+++ b/src/box_model.py
@@ -10,6 +10,7 @@
 from music_box_model_options import BoxModelOptions
 from music_box_conditions import Conditions
 from music_box_species_concentration import SpeciesConcentration
+from music_box_reaction_rate import ReactionRate
 
 class BoxModel:
     """
@@ -398,7 +399,32 @@ def readFromJson(self, path_to_json):
             for i in range(1, len(evol_from_json)):
                 time.append(evol_from_json[i][0])
 
-                # TODO: Add species concentrations and reaction rates
+                if 'ENV.pressure.Pa' in headers:
+                    pressure = float(evol_from_json[i][headers.index('ENV.pressure.Pa')]) / 101325
+
+                if 'ENV.temperature.K' in headers:
+                    temperature = float(evol_from_json[i][headers.index('ENV.temperature.K')])
+
+                # TODO: make sure species concentrations and reaction rates handle all cases
+                concentrations = []
+                concentration_headers = list(filter(lambda x: 'molm-3' in x, headers))
+                for j in range(len(concentration_headers)):
+                    match = filter(lambda x: x.name == concentration_headers[j].split('.')[1], species_from_json)
+                    species = next(match, None)
+
+                    concentration = float(evol_from_json[i][headers.index(concentration_headers[j])])
+                    concentrations.append(SpeciesConcentration(species, concentration))
+
+                rates = []
+                rate_headers = list(filter(lambda x: 's-1' in x, headers))
+                for k in range(len(rate_headers)):
+                    match = filter(lambda x: x.name == rate_headers[k].split('.')[1], reactions)
+                    reaction = next(match, None)
+
+                    rate = float(evol_from_json[i][headers.index(rate_headers[k])])
+                    rates.append(ReactionRate(reaction, rate))
+
+                conditions.append(Conditions(pressure, temperature, concentrations, rates))    
 
 # for testing purposes
 def __main__():