add pdbl

app.py

@@ -7,7 +7,7 @@ from shiny import App, render, ui, reactive
 import pandas as pd
 import warnings
 import re
-from  UniprotKB_P_Sequence_RCSB_API_test import ProteinQuery, ProteinSearchEngine
+from  UniprotKB_P_Sequence_RCSB_API_test import ProteinSearchEngine
 import plotly.graph_objects as go
 from shinywidgets import output_widget, render_widget
 import requests
@@ -395,7 +395,31 @@ class PDBSearchAssistant:
             
             if not pdb_path or not os.path.exists(pdb_path):
                 print(f"Failed to download PDB file for {pdb_id}")
-                return []
+
+                structure_url = f"https://data.rcsb.org/rest/v1/core/entry/{pdb_id}"
+                response = requests.get(structure_url)
+                structure_data = response.json() if response.status_code == 200 else {}
+
+
+                sequence_url = f"https://data.rcsb.org/rest/v1/core/polymer_entity/{pdb_id}/1"
+                seq_response = requests.get(sequence_url)
+                seq_data = seq_response.json() if response.status_code == 200 else {}
+                sequence = seq_data.get('entity_poly', {}).get('pdbx_seq_one_letter_code', 'N/A')
+                
+                sequences = []
+
+                chain_info = {
+                            'chain_id': "A", # chain.id, 임의 설정 api 3개써서 가져오기는 가능
+                            'entity_id': '1',  # Default entity ID
+                            'description': structure_data.get('struct', {}).get('title', 'N/A'),
+                            'sequence': sequence,
+                            'length': len(sequence),
+                            'resolution': structure_data.get('rcsb_entry_info', {}).get('resolution_combined', [0.0])[0],
+                            'method': structure_data.get('exptl', [{}])[0].get('method', 'Unknown'),
+                            'release_date': structure_data.get('rcsb_accession_info', {}).get('initial_release_date', 'N/A')
+                        }
+                sequences.append(chain_info)
+                return sequences
             
             # Parse structure
             parser = PDB.PDBParser(QUIET=True)
@@ -488,27 +512,6 @@ class PDBSearchAssistant:
             print(f"Error processing query: {str(e)}")
             return {"type": "structure", "results": []}
 
-def pdbsummary(name):
-
-    search_engine = ProteinSearchEngine()
-
-    query = ProteinQuery(
-        name,
-        max_resolution= 5.0
-    )
-
-    results = search_engine.search(query)
-
-    answer = ""
-    for i, structure in enumerate(results, 1):
-        answer += f"\n{i}. PDB ID : {structure.pdb_id}\n"
-        answer += f"\nResolution : {structure.resolution:.2f} A \n"
-        answer += f"Method : {structure.method}\n Title : {structure.title}\n"
-        answer += f"Release Date : {structure.release_date}\n Sequence length: {len(structure.sequence)} aa\n"
-        answer += f"    Sequence:\n {structure.sequence}\n"
-
-    return answer
-
 def render_html(pdb_id):
     if pdb_id is None:
         return ""
@@ -1012,7 +1015,7 @@ app_ui = ui.page_fluid(
                             ui.tags.ul(
                                 ui.tags.li("Human hemoglobin C resolution better than 2.5Å"),
                                 ui.tags.li("Find structures containing sequence with similarity 90% MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYKNL"),
-                                ui.tags.li("Sequence of PDB ID 8ET6")
+                                ui.tags.li("Sequence of PDB ID 8ET6"),
                             )
                         )
                     )