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| import gradio as gr | |
| from Bio import PDB | |
| import requests | |
| import os | |
| import pandas as pd | |
| # Function to format PDB headers with bullet points and HTML styling | |
| def format_pdb_headers(headers, indent=0): | |
| ind_text = ' ' * indent | |
| output = "" | |
| for header, content in headers.items(): | |
| if isinstance(content, dict): | |
| output += f'<div style="font-weight: bold;">{ind_text}{header}:</div>' | |
| output += format_pdb_headers(content, indent + 4) | |
| elif isinstance(content, list): | |
| output += f'<div style="font-weight: bold;">{ind_text}{header}:</div>' | |
| for elem in content: | |
| output += f'<div>{ind_text}- {elem}</div>' | |
| else: | |
| output += f'<div>{ind_text}<strong>{header}:</strong> {content}</div>' | |
| return output | |
| # Function to download and parse the PDB file | |
| def fetch_and_parse_pdb(url): | |
| # Download the PDB file | |
| response = requests.get(url) | |
| if response.status_code != 200: | |
| return "Failed to download the PDB file. Please check the URL." | |
| # Save the file locally | |
| pdb_filename = url.split("/")[-1] | |
| with open(pdb_filename, 'wb') as f: | |
| f.write(response.content) | |
| # Parse the PDB file | |
| parser = PDB.PDBParser() | |
| structure = parser.get_structure(pdb_filename, pdb_filename) | |
| # Prepare header information | |
| headers = structure.header | |
| header_output = format_pdb_headers(headers) | |
| # Prepare components information | |
| components_info = [] | |
| for model in structure: | |
| for chain in model: | |
| for residue in chain: | |
| residue_info = { | |
| "Chain ID": chain.id, | |
| "Residue Name": residue.get_resname(), | |
| "Residue Number": residue.id[1], | |
| "Missing": residue.is_disordered() | |
| } | |
| components_info.append(residue_info) | |
| # Convert components info to DataFrame | |
| components_df = pd.DataFrame(components_info) | |
| # Clean up the downloaded file | |
| os.remove(pdb_filename) | |
| # Combine header output and components into one string with color coding | |
| full_output = f"<h3>Header Information:</h3>{header_output}<hr>" | |
| full_output += "<h3>Components Information:</h3>" | |
| for index, row in components_df.iterrows(): | |
| color = "#f9f9f9" if index % 2 == 0 else "#ffffff" | |
| full_output += f'<div style="background-color: {color}; padding: 5px;">' | |
| full_output += f'- <strong>Chain ID:</strong> {row["Chain ID"]} | ' | |
| full_output += f'<strong>Residue Name:</strong> {row["Residue Name"]} | ' | |
| full_output += f'<strong>Residue Number:</strong> {row["Residue Number"]} | ' | |
| full_output += f'<strong>Missing:</strong> {row["Missing"]}</div>' | |
| return full_output | |
| # Create Gradio interface with an informative title and description | |
| iface = gr.Interface( | |
| fn=fetch_and_parse_pdb, | |
| inputs=gr.Textbox(value="https://files.rcsb.org/download/1TUP.pdb", label="PDB File URL", elem_id="pdb-url"), | |
| outputs="html", # Change output to HTML for styled display | |
| title="PDB Metadata Explorer", | |
| description=( | |
| "This tool allows you to input the URL of a Protein Data Bank (PDB) file " | |
| "and retrieve its metadata." | |
| ) | |
| ) | |
| # Launch the interface | |
| iface.launch() | |