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 = [] reactant_smiles = [] for line in lines: line = line.replace(" ", "").rstrip("\n") reactseq_list.append(line) rxn = reactant + ">>>" + line # 4. merge reactseq reactant_smiles.append(merge_smiles_with_mapping(rxn)) # 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 reactseq_list, reactants, reactant_images prompt_output = gr.Textbox(label="Prompt", interactive=False, visible=True) def secondary_interface(smiles, atom1_idx, atom2_idx, operation, progress=gr.Progress()): try: prompt, error = process_bond_operation(smiles, atom1_idx, atom2_idx, operation) if prompt: reactseq_list, reactant_smiles, reactant_images = retrosynthesis(smiles, prompt) output_components = [gr.update(value=prompt)] for i in range(len(reactant_smiles)): if reactant_smiles[i] != "": output_components.append(gr.update(value=reactseq_list[i], visible=True)) output_components.append(gr.update(value=reactant_smiles[i], visible=True)) output_components.append(gr.update(value=reactant_images[i], visible=True)) else: output_components.append(gr.update(visible=False)) 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)] * 31 + [error] except Exception as e: return [gr.update(visible=False)] * 31 + [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=True), # prompt_output ) + ( # Reactant SMILES and Images tuple(gr.update(value=None, visible=False) for _ in range(30)) ) # 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, with the invalid ones deleted.") 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=1) 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=True) result_row = [] for i in range(10): result_row.append(gr.Textbox(label=f"Reactseq {i+1} ", interactive=False, visible=False)) 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) 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] ) 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()