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requirements.txt

@@ -1,5 +1,158 @@
-# RDKit dependencies
-rdkit
-gradio==4.44.1
-huggingface_hub==0.19.4
-cirpy
+import gradio as gr
+from rdkit import Chem
+from rdkit.Chem import Descriptors, Draw, AllChem
+import cirpy
+import py3Dmol
+
+
+def _mol_from_smiles(smiles: str):
+    mol = Chem.MolFromSmiles(smiles)
+    if mol is None:
+        raise gr.Error("Invalid SMILES string.")
+    return mol
+
+
+def smiles_to_canonical(smiles: str) -> str:
+    mol = _mol_from_smiles(smiles)
+    return Chem.MolToSmiles(mol)
+
+
+def molecular_weight(smiles: str) -> float:
+    mol = _mol_from_smiles(smiles)
+    return float(Descriptors.MolWt(mol))
+
+
+def logp(smiles: str) -> float:
+    mol = _mol_from_smiles(smiles)
+    return float(Descriptors.MolLogP(mol))
+
+
+def tpsa(smiles: str) -> float:
+    mol = _mol_from_smiles(smiles)
+    return float(Descriptors.TPSA(mol))
+
+
+def mol_image(smiles: str):
+    mol = _mol_from_smiles(smiles)
+    return Draw.MolToImage(mol)
+
+
+def name_to_smiles(name: str) -> str:
+    """Convert chemical name to SMILES using Chemical Identifier Resolver (CIR)"""
+    try:
+        smiles = cirpy.resolve(name, 'smiles')
+        if smiles is None:
+            raise gr.Error(f"Could not find SMILES for chemical name: {name}")
+        return smiles
+    except Exception as e:
+        raise gr.Error(f"Error converting name to SMILES: {str(e)}")
+
+
+def name_to_3d_molecule(name: str) -> str:
+    """Convert chemical name to 3D molecule visualization"""
+    try:
+        # Convert name to SMILES
+        smiles = cirpy.resolve(name, 'smiles')
+        if smiles is None:
+            raise gr.Error(f"Could not find SMILES for chemical name: {name}")
+
+        # Create molecule from SMILES
+        mol = Chem.MolFromSmiles(smiles)
+        if mol is None:
+            raise gr.Error(f"Could not create molecule from SMILES: {smiles}")
+
+        # Add hydrogens for better 3D structure
+        mol = Chem.AddHs(mol)
+
+        # Generate 3D coordinates
+        success = AllChem.EmbedMolecule(mol, AllChem.ETKDG())
+        if success == -1:
+            raise gr.Error(f"Could not generate 3D coordinates for: {name}")
+
+        # Optimize geometry
+        AllChem.MMFFOptimizeMolecule(mol)
+
+        # Convert to PDB format for py3Dmol
+        pdb_block = Chem.MolToPDBBlock(mol)
+
+        # Create 3D viewer
+        viewer = py3Dmol.view(width=400, height=400)
+        viewer.addModel(pdb_block, 'pdb')
+        viewer.setStyle({'stick': {}})
+        viewer.zoomTo()
+
+        # Return HTML representation
+        return viewer._repr_html_()
+
+    except Exception as e:
+        raise gr.Error(f"Error creating 3D molecule: {str(e)}")
+
+
+smiles_interface = gr.Interface(
+    fn=smiles_to_canonical,
+    inputs=gr.Textbox(label="SMILES"),
+    outputs=gr.Textbox(label="Canonical SMILES"),
+    api_name="smiles_to_mol",
+    description="Convert an input SMILES string to its canonical form.",
+)
+
+name_interface = gr.Interface(
+    fn=name_to_smiles,
+    inputs=gr.Textbox(label="Chemical Name", placeholder="e.g., aspirin, caffeine, benzene"),
+    outputs=gr.Textbox(label="SMILES"),
+    api_name="name_to_smiles",
+    description="Convert a chemical name to SMILES notation.",
+    examples=[["aspirin"], ["caffeine"], ["benzene"], ["ethanol"]],
+)
+
+mw_interface = gr.Interface(
+    fn=molecular_weight,
+    inputs=gr.Textbox(label="SMILES"),
+    outputs=gr.Number(label="Molecular Weight (g/mol)"),
+    api_name="molecular_weight",
+    description="Compute the molecular weight from a SMILES string.",
+)
+
+logp_interface = gr.Interface(
+    fn=logp,
+    inputs=gr.Textbox(label="SMILES"),
+    outputs=gr.Number(label="logP"),
+    api_name="logp",
+    description="Calculate the octanol/water partition coefficient (logP).",
+)
+
+tpsa_interface = gr.Interface(
+    fn=tpsa,
+    inputs=gr.Textbox(label="SMILES"),
+    outputs=gr.Number(label="TPSA"),
+    api_name="tpsa",
+    description="Calculate the topological polar surface area (TPSA).",
+)
+
+molecule_3d_interface = gr.Interface(
+    fn=name_to_3d_molecule,
+    inputs=gr.Textbox(label="Chemical Name", placeholder="e.g., benzene, aspirin, caffeine"),
+    outputs=gr.HTML(label="3D Molecule Viewer"),
+    api_name="name_to_3d_molecule",
+    description="Convert a chemical name to an interactive 3D molecule visualization.",
+    examples=[["benzene"], ["aspirin"], ["caffeine"], ["ethanol"]],
+)
+
+
+demo = gr.TabbedInterface(
+    [name_interface, molecule_3d_interface, smiles_interface, mw_interface, logp_interface, tpsa_interface],
+    [
+        "Name to SMILES",
+        "3D Molecule Viewer",
+        "SMILES to Canonical",
+        "Molecular Weight",
+        "LogP",
+        "TPSA",
+    ],
+    title="RDKit API",
+    css=".gradio-container {max-width: 800px; margin: auto;}",
+)
+
+
+if __name__ == "__main__":
+    demo.queue().launch(server_name="0.0.0.0", server_port=7860)