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requirements.txt

@@ -1,161 +1,7 @@
-import gradio as gr
-from rdkit import Chem
-from rdkit.Chem import Descriptors, Draw, AllChem
-import cirpy
-import py3Dmol
-
-
-# RDKit API with multiple endpoints
-
-
-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)
+# RDKit dependencies
+rdkit
+gradio==4.44.1
+huggingface_hub==0.19.4
+cirpy
+py3Dmol
+# Updated for 3D molecule viewer