Upload app.py

app.py

@@ -62,15 +62,33 @@ class PDBSearchAssistant:
             Organism: none
             Similarity: 100
 
-            Query: "Find human insulin structures with X-ray better than 2.5Å resolution"
+            Query: "human insulin"
             Protein: insulin
-            Resolution: 2.5
+            Resolution: none
             Sequence: none
             PDB_ID: none
-            Method: X-RAY
+            Method: none
             Organism: Homo sapiens
             Similarity: none
 
+            Query: "Spike protein"
+            Protein: Spike protein
+            Resolution: none
+            Sequence: none
+            PDB_ID: none
+            Method: none
+            Organism: none
+            Similarity: none
+            
+            Query: "Human hemoglobin C resolution better than 2.5Å"
+            Protein: hemoglobin C
+            Resolution: 2.5
+            Sequence: none
+            PDB_ID: none
+            Method: none
+            Organism: Homo sapiens
+            Similarity: none    
+            
             Query: "Find structures containing sequence with similarity 90% MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRN"
             Protein: none
             Resolution: none
@@ -191,9 +209,37 @@ class PDBSearchAssistant:
                     has_resolution_query = True
                     print(f"Extracted resolution from query: {resolution_limit}Å")
 
+            # Add protein name extraction from response pairs
+            protein_name = None
+            if 'protein' in response_pairs:
+                protein_name = response_pairs['protein']
+                print(f"Extracted protein name: {protein_name}")
+            
             # Build queries list
             queries = []
             
+            # Add protein name query if specified
+            if protein_name:
+                print(f"Adding protein name filter: {protein_name}")
+                try:
+                    protein_query = AttributeQuery(
+                        attribute="struct.title",
+                        operator="contains_words",
+                        value=protein_name
+                    )
+                    queries.append(protein_query)
+                    
+                    protein_entity_query = AttributeQuery(
+                        attribute="rcsb_entity_container_identifiers.entity_names.value",
+                        operator="contains_words",
+                        value=protein_name
+                    )
+                    queries.append(protein_entity_query)
+                    
+                    print(f"Created protein queries successfully: {protein_query}, {protein_entity_query}")
+                except Exception as e:
+                    print(f"Error creating protein queries: {str(e)}")
+                
             # Add sequence query if present
             query_words = query.split()
             for word in query_words:
@@ -264,74 +310,93 @@ class PDBSearchAssistant:
                 )
                 queries.append(organism_query)
             
-            # Combine queries with AND operator
+            # Combine queries with improved error handling
             if queries:
-                final_query = queries[0]
-                for q in queries[1:]:
-                    final_query = final_query & q
-                
-                print("Final query:", final_query)
-                
-                # Execute search
-                session = final_query.exec()
-                results = []
-                
-                # Process results with additional information
-                # search_engine = ProteinSearchEngine()
-                
                 try:
-                    for entry in session:
-                        try:
-                            # PDB ID 추출 방식 개선
-                            if isinstance(entry, dict):
-                                pdb_id = entry.get('identifier')
-                            elif hasattr(entry, 'identifier'):
-                                pdb_id = entry.identifier
-                            else:
-                                pdb_id = str(entry)
-                            
-                            pdb_id = pdb_id.upper()  # PDB ID는 항상 대문자
-                            
-                            if not pdb_id or len(pdb_id) != 4:  # PDB ID는 항상 4자리
-                                continue
+                    if protein_name and len(queries) >= 2:
+                        print("Combining protein queries with OR")
+                        protein_queries = queries[0] | queries[1]
+                        print("Successfully combined protein queries")
+                        
+                        if len(queries) > 2:
+                            print("Combining with additional queries using AND")
+                            final_query = protein_queries
+                            for q in queries[2:]:
+                                final_query = final_query & q
+                        else:
+                            final_query = protein_queries
+                    else:
+                        final_query = queries[0]
+                        for q in queries[1:]:
+                            final_query = final_query & q
+                    
+                    print("Final query:", final_query)
+                    
+                    # Execute search
+                    session = final_query.exec()
+                    results = []
+                    
+                    # Process results with additional information
+                    # search_engine = ProteinSearchEngine()
+                    
+                    try:
+                        for entry in session:
+                            try:
+                                # PDB ID 추출 방식 개선
+                                if isinstance(entry, dict):
+                                    pdb_id = entry.get('identifier')
+                                elif hasattr(entry, 'identifier'):
+                                    pdb_id = entry.identifier
+                                else:
+                                    pdb_id = str(entry)
                                 
-                            # RCSB PDB REST API를 직접 사용하여 구조 정보 가져오기
-                            structure_url = f"https://data.rcsb.org/rest/v1/core/entry/{pdb_id}"
-                            response = requests.get(structure_url)
-                            
-                            if response.status_code != 200:
-                                continue
+                                pdb_id = pdb_id.upper()  # PDB ID는 항상 대문자
                                 
-                            structure_data = response.json()
-                            # 결과 구성
-                            result = {
-                                'PDB ID': pdb_id,
-                                'Title': structure_data.get('struct', {}).get('title', 'N/A'),
-                                '# of total residues': structure_data.get('refine_hist', [{}])[0].get('pdbx_number_residues_total', 'N/A'),
-                                '# of atoms of protein': structure_data.get('refine_hist', [{}])[0].get('pdbx_number_atoms_protein', 'N/A'),
-                                'Resolution': f"{structure_data.get('rcsb_entry_info', {}).get('resolution_combined', [0.0])[0]:.2f}Å",
-                                'Method': structure_data.get('exptl', [{}])[0].get('method', 'Unknown'),
-                                'Release Date': structure_data.get('rcsb_accession_info', {}).get('initial_release_date', 'N/A')
+                                if not pdb_id or len(pdb_id) != 4:  # PDB ID는 항상 4자리
+                                    continue
+                                    
+                                # RCSB PDB REST API를 직접 사용하여 구조 정보 가져오기
+                                structure_url = f"https://data.rcsb.org/rest/v1/core/entry/{pdb_id}"
+                                response = requests.get(structure_url)
                                 
+                                if response.status_code != 200:
+                                    continue
+                                    
+                                structure_data = response.json()
+                                # 결과 구성
+                                result = {
+                                    'PDB ID': pdb_id,
+                                    'Title': structure_data.get('struct', {}).get('title', 'N/A'),
+                                    '# of total residues': structure_data.get('refine_hist', [{}])[0].get('pdbx_number_residues_total', 'N/A'),
+                                    '# of atoms of protein': structure_data.get('refine_hist', [{}])[0].get('pdbx_number_atoms_protein', 'N/A'),
+                                    'Resolution': f"{structure_data.get('rcsb_entry_info', {}).get('resolution_combined', [0.0])[0]:.2f}Å",
+                                    'Method': structure_data.get('exptl', [{}])[0].get('method', 'Unknown'),
+                                    'Release Date': structure_data.get('rcsb_accession_info', {}).get('initial_release_date', 'N/A')
+                                    
+                                    
+                                }
                                 
-                            }
-                            
-                            results.append(result)
-                            
-                            # Limit to top 10 results
-                            if len(results) >= 10:
-                                break
+                                results.append(result)
                                 
-                        except Exception as e:
-                            print(f"Error processing entry: {str(e)}")
-                            continue
-                            
-                except Exception as e:
-                    print(f"Error processing results: {str(e)}")
-                    print(f"Error type: {type(e)}")
+                                # Limit to top 10 results
+                                if len(results) >= 10:
+                                    break
+                                    
+                            except Exception as e:
+                                print(f"Error processing entry: {str(e)}")
+                                continue
+                                
+                    except Exception as e:
+                        print(f"Error processing results: {str(e)}")
+                        print(f"Error type: {type(e)}")
+                        
+                    print(f"Found {len(results)} structures")
+                    return results
                     
-                print(f"Found {len(results)} structures")
-                return results
+                except Exception as e:
+                    print(f"Error combining queries: {str(e)}")
+                    print(f"Query state: {queries}")
+                    return []
                 
             return []
             
@@ -954,7 +1019,7 @@ app_ui = ui.page_fluid(
                         ui.input_text_area(
                             "query", 
                             "", 
-                            value="Human insulin",
+                            value="",
                             width="100%",
                             resize="vertical"
                         ),
@@ -970,10 +1035,13 @@ app_ui = ui.page_fluid(
                             {"class": "example-box"},
                             ui.p("Example queries:"),
                             ui.tags.ul(
+                                ui.tags.li("Sequence of PDB ID 8ET6"),
+                                ui.tags.li("Spike protein"),
+                                ui.tags.li("Human insulin"),
                                 ui.tags.li("Human hemoglobin C resolution better than 2.5Å"),
                                 ui.tags.li("Find structures containing sequence with similarity 90% FVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGPGAGSLQPLALEGSLQKR"),
                                 ui.tags.li("Find structures with resolution better than 3 angstrom and sequence similarity 90% of FVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGPGAGSLQPLALEGSLQKR"),
-                                ui.tags.li("Sequence of PDB ID 8ET6")
+                               
                             )
                         )
                     )