#!/usr/bin/env python
# coding: utf-8

# ## One-bin Association/Dissociation reaction `A + B <-> C`
# ### with 1st-order kinetics for each species, taken to equilibrium
# 
# Diffusion not applicable (just 1 bin)
# 
# See also the experiment _"reactions_single_compartment/react_3"_  

# ### TAGS :  "reactions 1D", "basic"

# In[1]:


LAST_REVISED = "June 6, 2025"
LIFE123_VERSION = "1.0.0rc6"        # Library version this experiment is based on


# In[2]:


#import set_path                    # Using MyBinder?  Uncomment this before running the next cell!


# In[3]:


#import sys, os
#os.getcwd()
#sys.path.append("C:/some_path/my_env_or_install")   # CHANGE to the folder containing your venv or libraries installation!
# NOTE: If any of the imports below can't find a module, uncomment the lines above, or try:  import set_path

from experiments.get_notebook_info import get_notebook_basename

from life123 import ChemData, BioSim1D, check_version

from life123 import GraphicLog


# In[4]:


check_version(LIFE123_VERSION)


# In[ ]:





# In[5]:


# Initialize the HTML logging
log_file = get_notebook_basename() + ".log.htm"    # Use the notebook base filename for the log file

# Set up the use of some specified graphic (Vue) components
GraphicLog.config(filename=log_file,
                  components=["vue_cytoscape_2"],
                  extra_js="https://cdnjs.cloudflare.com/ajax/libs/cytoscape/3.21.2/cytoscape.umd.js")


# In[6]:


# Initialize the system.  NOTE: Diffusion not applicable (using just 1 bin)
chem_data = ChemData(names=["A", "B", "C"], plot_colors=['red', 'darkorange', 'green'])

bio = BioSim1D(n_bins=1, chem_data=chem_data)

bio.set_uniform_concentration(chem_index=0, conc=10.)
bio.set_uniform_concentration(chem_index=1, conc=50.)
bio.set_uniform_concentration(chem_index=2, conc=20.)

bio.describe_state()


# In[7]:


# Specify the reaction
reactions = bio.get_reactions()

# Reaction A + B <-> C , with 1st-order kinetics for each species
reactions.add_reaction(reactants=["A" , "B"], products="C",
                       forward_rate=5., reverse_rate=2.)

reactions.describe_reactions()


# In[8]:


# Send the plot of the reaction network to the HTML log file
reactions.plot_reaction_network("vue_cytoscape_2")


# In[ ]:





# In[9]:


# Let's enable history - by default for all chemicals and all bins
bio.enable_history(take_snapshot=True, caption="Initial state")


# In[10]:


bio.get_bin_history(bin_address=0)


# In[ ]:





# In[ ]:





# ### <a name="sec_2_first_step"></a>First step

# In[11]:


# First step
bio.react(time_step=0.002, n_steps=1)
bio.describe_state()


# In[12]:


bio.get_bin_history(bin_address=0)


# In[ ]:





# ### <a name="sec_2"></a>Numerous more steps

# In[13]:


# Numerous more steps
bio.react(time_step=0.002, n_steps=29)

bio.describe_state()


# ### <a name="sec_2_equilibrium"></a>Equilibrium

# Consistent with the 5/2 ratio of forward/reverse rates (and the 1st order reactions),
# the systems settles in the following equilibrium:  
# [A] = 0.29487831 , [B] = 40.29487831 , [C] = 29.70512169

# In[14]:


# Verify that the reaction has reached equilibrium
bio.get_reaction_handler().is_in_equilibrium(rxn_index=0, conc=bio.bin_snapshot(bin_address = 0))


# In[15]:


bio.get_bin_history(bin_address=0)


# ## Note: `A` (now largely depleted) is largely the limiting reagent

# ## Plots of changes of concentration with time

# In[17]:


bio.plot_history_single_bin(bin_address=0, 
                            title_prefix="Reaction  `A + B <-> C`")


# ## For more in-depth analysis of this reaction, including variable time steps, see the experiment _"reactions_single_compartment/react_3"_ 

# In[ ]: