Merab099/3D_Structures

1import streamlit as st2from rdkit import Chem3from rdkit.Chem import AllChem4from rdkit.Chem.rdForceFieldHelpers import MMFFOptimizeMolecule5import py3Dmol6import io7 8# --- Helper Functions ---9 10@st.cache_data11def generate_3d_mol(smiles):12    """13    Generates a 3D conformation of a molecule from a SMILES string14    using RDKit and returns its SDF string representation.15    """16    try:17        # Convert SMILES to RDKit molecule object18        mol = Chem.MolFromSmiles(smiles)19        if mol is None:20            return None, "Invalid SMILES string. Please check your input."21 22        # Add explicit hydrogens, crucial for proper 3D geometry23        mol = Chem.AddHs(mol)24 25        # Generate initial 3D coordinates using the ETKDGv2 algorithm26        # This is a good general-purpose conformer generator.27        AllChem.EmbedMolecule(mol, AllChem.ETKDGv2())28 29        # Optimize the geometry using the MMFF94 force field30        # This helps in obtaining a more stable and chemically reasonable conformation.31        MMFFOptimizeMolecule(mol)32 33        # Convert the RDKit molecule to an SDF (Structure-Data File) block string.34        # SDF is a common format for storing molecular structures and properties.35        sdf_string = Chem.MolToMolBlock(mol)36        return sdf_string, None37    except Exception as e:38        # Catch any errors during 3D generation and return an error message39        return None, f"Error generating 3D structure: {e}"40 41# --- Streamlit Application Layout ---42 43def main():44    """45    Main function to define the Streamlit application interface.46    """47    st.set_page_config(layout="centered", page_title="3D Molecule Viewer")48 49    st.title("🧪 3D Molecule Structure Viewer")50    st.markdown(51        """52        Enter a SMILES string (Simplified Molecular Input Line Entry System)53        to visualize its 3D molecular structure interactively.54        """55    )56 57    # Input field for SMILES string with a default example (Ethanol)58    smiles_input = st.text_input("SMILES String:", "CCO", help="e.g., CCO for Ethanol, CC(=O)Oc1ccccc1C(=O)O for Aspirin")59 60    # Button to trigger 3D structure generation61    if st.button("Generate 3D Structure"):62        if smiles_input:63            # Call the cached function to generate the 3D molecule data64            sdf_data, error = generate_3d_mol(smiles_input)65 66            if sdf_data:67                st.subheader(f"3D Structure for: `{smiles_input}`")68 69                # Create a py3Dmol viewer instance70                # Set width and height for the viewer71                view = py3Dmol.view(width=800, height=600)72 73                # Add the molecule model to the viewer using the SDF data74                view.addModel(sdf_data, 'sdf')75 76                # Apply a style to the molecule: 'stick' for bonds, 'sphere' for atoms77                view.setStyle({'stick': {}, 'sphere': {'radius': 0.3}})78 79                # Zoom to fit the molecule within the viewer80                view.zoomTo()81 82                # Optional: Make the molecule spin for better visualization83                view.spin(True)84 85                # Embed the py3Dmol viewer into the Streamlit app using st.components.v1.html86                # scrolling=False prevents scrollbars within the viewer itself87                st.components.v1.html(view.to_html(), width=800, height=600, scrolling=False)88            else:89                # Display any error messages from the 3D generation process90                st.error(error)91        else:92            st.warning("Please enter a SMILES string to generate a 3D structure.")93 94    st.markdown("---")95    st.markdown("### How it works:")96    st.markdown(97        """98        This application uses:99        - **Streamlit** for the interactive web interface.100        - **RDKit** (a cheminformatics library) to convert SMILES strings into 3D molecular coordinates and optimize their geometry.101        - **py3Dmol** to render and display the interactive 3D molecular structures in your browser.102        """103    )104    st.markdown("Built with ❤️ for chemistry enthusiasts.")105 106if __name__ == "__main__":107    main()