Create app.py

app.py

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+from e_smiles import *
+import gradio as gr
+from rdkit import Chem
+from rdkit.Chem import Draw
+import os
+
+def remove_atom_mapping_and_isotopes(smiles):
+    mol = Chem.MolFromSmiles(smiles)
+    
+    if mol is None:
+        raise ValueError("Invalid SMILES string")
+    
+    for atom in mol.GetAtoms():
+        atom.SetIsotope(0)
+        atom.SetAtomMapNum(0)
+    
+    clean_smiles = Chem.MolToSmiles(Chem.RemoveHs(mol))
+    return clean_smiles
+
+def get_bondtype_and_convert2string(mol, atom1_idx, atom2_idx):
+    atom1_idx = int(atom1_idx)
+    atom2_idx = int(atom2_idx)
+    bond = mol.GetBondBetweenAtoms(atom1_idx - 1, atom2_idx - 1)
+    if bond is None:
+        raise ValueError("Atoms are not bonded")
+    
+    if bond.GetBondType() == Chem.BondType.SINGLE:
+        return '1.0'
+    elif bond.GetBondType() == Chem.BondType.DOUBLE:
+        return '2.0'
+    elif bond.GetBondType() == Chem.BondType.TRIPLE:
+        return '3.0'
+    else:
+        raise ValueError("Unsupported bond type")
+    
+def main_interface(smiles):
+    img, mapped_smiles, secondary_inputs_visible1, secondary_inputs_visible2, error = process_smiles(smiles)
+    return img, mapped_smiles, gr.update(visible=True), secondary_inputs_visible2, error
+
+def process_smiles(smiles):
+    try:
+        smiles = remove_atom_mapping_and_isotopes(smiles)
+        mol = Chem.MolFromSmiles(smiles)
+        if mol:
+            Chem.Kekulize(mol, clearAromaticFlags=True)
+            for atom in mol.GetAtoms():
+                atom.SetAtomMapNum(atom.GetIdx() + 1)
+
+            mapped_smiles = Chem.MolToSmiles(mol, canonical=False, kekuleSmiles=True)
+        else:
+            raise ValueError("Invalid SMILES string")
+
+        mol = Chem.MolFromSmiles(mapped_smiles)
+        img = Draw.MolToImage(mol, size=(450, 450))
+        return img, mapped_smiles, gr.update(visible=True), gr.update(visible=True), gr.update(visible=False)  
+    except Exception as e:
+        return None, None, gr.update(visible=False), gr.update(visible=False), gr.update(visible=True, value=str(e))
+
+def process_bond_operation(smiles, atom1_idx, atom2_idx, operation):
+    try:
+        mol = Chem.MolFromSmiles(smiles)
+        if mol is None:
+            raise ValueError("Invalid SMILES string")
+        
+        if atom1_idx > atom2_idx: 
+            atom1_idx, atom2_idx = atom2_idx, atom1_idx
+
+        first = str(atom1_idx)
+        second = str(atom2_idx)
+        third = get_bondtype_and_convert2string(mol, atom1_idx, atom2_idx)
+        
+        if operation == "break this bond":
+            prompt = [first + ':' + second + ':' + third + ':' + '0.0']
+        elif operation == "change this bond to single bond":
+            prompt = [first + ':' + second + ':' + third + ':' + '1.0']
+        elif operation == "change this bond to double bond":
+            prompt = [first + ':' + second + ':' + third + ':' + '2.0']
+        elif operation == "change this bond to triple bond":
+            prompt = [first + ':' + second + ':' + third + ':' + '3.0']
+        else:
+            raise ValueError("Unsupported operation")
+        
+        prompt = get_b_smiles_check([smiles, prompt, [], [], [], [], []])
+
+        return prompt, gr.update(visible=False)  
+    except Exception as e:
+        return None, gr.update(visible=True, value=str(e))
+
+def retrosynthesis(reactant, prompt):
+    # 1. generate src file
+    with open('tmp_data/src.txt', 'w') as f:
+        f.write(" ".join(prompt))
+
+    # 2. inference
+    os.system('bash infer.sh')
+
+
+    # 3. readout reactseq
+    with open('./tmp_data/tgt.txt', 'r') as f:
+        lines = f.readlines()
+
+    reactseq_list = []
+    for line in lines:
+        line = line.replace(" ", "").rstrip("\n")
+        reactseq_list.append(reactant + ">>>" + line)
+
+    # 4. merge reactseq
+    reactant_smiles = []
+    for seq in reactseq_list:
+        reactant_smiles.append(merge_smiles_with_mapping(seq))
+
+    # 5. draw reactants
+    reactants = []
+    reactant_images = []
+    for smiles in reactant_smiles:
+        mol = Chem.MolFromSmiles(smiles)
+        reactants.append(smiles)
+        reactant_images.append(Draw.MolToImage(mol, size=(600, 600)))
+
+    return reactants, reactant_images
+
+def secondary_interface(smiles, atom1_idx, atom2_idx, operation):
+    try:
+        prompt, error = process_bond_operation(smiles, atom1_idx, atom2_idx, operation)
+        
+        if prompt:
+            reactant_smiles, reactant_images = retrosynthesis(smiles, prompt)
+            output_components = [gr.update(value=prompt, visible=True)]  # prompt_output
+
+            # Add the reactant SMILES and images
+            for i in range(len(reactant_smiles)):
+                output_components.append(gr.update(value=reactant_smiles[i], visible=True))
+                output_components.append(gr.update(value=reactant_images[i], visible=True))
+
+            # Fill remaining hidden outputs
+            for j in range(len(reactant_smiles), 10):
+                output_components.append(gr.update(visible=False))
+                output_components.append(gr.update(visible=False))
+
+            output_components.append(gr.update(visible=False))  # error_output
+            return output_components
+        
+        else:
+            return [gr.update(visible=False)] * 21 + [error]  # Assuming 10 pairs of outputs + prompt_output + error_output
+    
+    except Exception as e:
+        return [gr.update(visible=False)] * 21 + [gr.update(visible=True, value=str(e))]
+
+def clear_interface():
+    return (
+        gr.update(value=None),  # img_output
+        gr.update(value=None),  # smiles_output
+        gr.update(visible=False),  # secondary_inputs
+        gr.update(visible=False),  # secondary_inputs
+        gr.update(visible=False, value=None),  # error_output
+        gr.update(value=None, visible=False),  # prompt_output
+    ) + (  # Reactant SMILES and Images
+        tuple(gr.update(value=None, visible=False) for _ in range(20))
+    )
+
+# 示例数据
+examples = [
+    ["N#CC1=CC=C(C(N2N=CN=C2)C(O)CC3=CC=C(F)C=C3)C=C1", 7, 18, "break this bond"],
+    ["N#CC1=CC=C(C(N2N=CN=C2)C(O)CC3=CC=C(F)C=C3)C=C1", 8, 9, "change this bond to double bond"],
+    ["N#CC1=CC=C(C(N2N=CN=C2)C(O)CC3=CC=C(F)C=C3)C=C1", 1, 2, "change this bond to single bond"],
+]
+
+with gr.Blocks() as interface:
+    gr.Markdown("# ReactSeq")
+    gr.Markdown("Please input a SMILES string and two atom indices between the bond which you want to perform an operation.")
+    gr.Markdown("The operation can be one of the following: break this bond, change this bond to single bond, change this bond to double bond, change this bond to triple bond.")
+    gr.Markdown("The molecule image and SMILES with atom mapping will be displayed.")
+    gr.Markdown("After you input the operation, the prompt will be displayed.")
+    gr.Markdown("The reactants SMILES and images will be displayed after the retrosynthesis with **default** ranking.")
+    
+    smiles_input = gr.Textbox(placeholder="Please input your SMILES string", label="SMILES input")
+    submit_smiles_button = gr.Button("Submit SMILES")
+
+    gr.Markdown("The molecule image and SMILES with atom mapping:")
+    img_output = gr.Image(label="Molecule image")
+    smiles_output = gr.Textbox(label="SMILES with atom mapping", interactive=False)
+    
+    with gr.Row(visible=False) as secondary_inputs:
+        atom1_idx = gr.Number(label="The first atom index", minimum=1)
+        atom2_idx = gr.Number(label="The second atom index", minimum=2)
+        operation = gr.Dropdown(choices=["break this bond", "change this bond to single bond", "change this bond to double bond", "change this bond to triple bond"], label="Operation")
+        submit_operation_button = gr.Button("Submit Operation")
+    
+    prompt_output = gr.Textbox(label="Prompt", interactive=False, visible=False)
+    
+    result_row = []
+    for i in range(10):
+        result_row.append(gr.Textbox(label=f"Reactant {i+1} SMILES", interactive=False, visible=False))
+        result_row.append(gr.Image(label=f"Reactant {i+1} Image", visible=False))
+
+    error_output = gr.Textbox(label="Error Message", interactive=False, visible=False)
+    
+    # 添加清除按钮
+    clear_button = gr.Button("Clear")
+
+    submit_smiles_button.click(main_interface, inputs=[smiles_input], outputs=[img_output, smiles_output, secondary_inputs, secondary_inputs, error_output])
+    submit_operation_button.click(
+        secondary_interface, 
+        inputs=[smiles_output, atom1_idx, atom2_idx, operation], 
+        outputs=[prompt_output] + result_row + [error_output]
+    )
+    
+    # 清除按钮的事件处理
+    clear_button.click(
+        clear_interface, 
+        inputs=[], 
+        outputs=[img_output, smiles_output, secondary_inputs, secondary_inputs, error_output, prompt_output] + result_row
+    )
+
+    gr.Examples(examples=examples, inputs=[smiles_input, atom1_idx, atom2_idx, operation])
+
+interface.launch()
+
+
+