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--- ## Neurotransmitter Synthesis This repository contains scripts to simulate the synthesis of neurotransmitters from amino acids using RDKit. It includes the biochemical pathways for creating neurotransmitters such as serotonin from tryptophan. ### Features - Simulate the conversion of tryptophan to serotonin. - Generate and save molecular structure images at each step. - Easily extendable to other neurotransmitter synthesis pathways. ### Setup and Usage 1. Clone the repository:    ```sh    git clone https://github.com/AdwikParashar /NeurotransmitterSynthesis.git    cd NeurotransmitterSynthesis    ``` 2. Install the required packages:    ```sh    pip install -r requirements.txt    ``` 3. Run the script to simulate serotonin synthesis:    ```sh    python Serotonin_synthesis.py    ``` ### Requirements - RDKit - Pillow The script generates images of the molecules at each step and saves the...
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---


## Neurotransmitter Synthesis


This repository contains scripts to simulate the synthesis of neurotransmitters from amino acids using RDKit. It includes the biochemical pathways for creating neurotransmitters such as serotonin from tryptophan.


### Features

- Simulate the conversion of tryptophan to serotonin.

- Generate and save molecular structure images at each step.

- Easily extendable to other neurotransmitter synthesis pathways.


### Setup and Usage

1. Clone the repository:

   ```sh

   git clone https://github.com/AdwikParashar



/NeurotransmitterSynthesis.git

   cd NeurotransmitterSynthesis

   ```


2. Install the required packages:

   ```sh

   pip install -r requirements.txt

   ```


3. Run the script to simulate serotonin synthesis:

   ```sh

   python Serotonin_synthesis.py

   ```


### Requirements

- RDKit

- Pillow


The script generates images of the molecules at each step and saves them in the current directory.


---


Tryptophan







Serotonin



Code Starts From Here, can be run thrugh pycharm through bio_sim Conda Enivironment


 from rdkit import Chem

from rdkit.Chem import AllChem

from rdkit.Chem import Draw

import os


# Define a function to display a molecule and save it to a file

def display_and_save_molecule(mol, filename, title):

    if mol is not None:

        img = Draw.MolToImage(mol)

        img.save(filename)

        print(f"{title} molecule created and saved as {filename}.")

    else:

        print(f"Failed to create {title} molecule.")


# Define the SMILES string for tryptophan

tryptophan_smiles = "N[C@@H](C(O)=O)Cc1c[nH]c2ccccc12"


# Step 1: Create the molecule object for tryptophan

tryptophan = Chem.MolFromSmiles(tryptophan_smiles)

display_and_save_molecule(tryptophan, "tryptophan.png", "Tryptophan")


# Step 2: Manually simulate the hydroxylation of Tryptophan to 5-HTP

htp_smiles = "N[C@@H](C(O)=O)Cc1c[nH]c2ccc(O)cc12"

htp = Chem.MolFromSmiles(htp_smiles)

display_and_save_molecule(htp, "5-htp.png", "5-HTP")


# Step 3: Decarboxylation of 5-HTP to Serotonin

if htp is not None:

    # Define the decarboxylation reaction (removes the carboxyl group)

    decarboxylation_reaction = AllChem.ReactionFromSmarts('[C:1](C(=O)O)[C:2]>>[C:1][C:2]')


    # Apply the decarboxylation reaction to 5-HTP

    products = decarboxylation_reaction.RunReactants((htp,))

    if products:

        serotonin = products[0][0]  # Get the first product

        serotonin.UpdatePropertyCache()  # Ensure the molecule properties are up-to-date

        display_and_save_molecule(serotonin, "serotonin.png", "Serotonin")

    else:

        print("Decarboxylation reaction failed.")

else:

    print("Skipping decarboxylation step due to failed hydroxylation.")


# Check the current working directory

print("Current working directory:", os.getcwd())


# Verify that the images are saved in the current working directory

print("Files in current directory:", os.listdir(os.getcwd()))


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