1. Searching for Structures
Find PDB entries using various search criteria:
Text Search: Search by protein name, keywords, or descriptions
```python
from rcsbapi.search import TextQuery
query = TextQuery("hemoglobin")
results = list(query())
print(f"Found {len(results)} structures")
```
Attribute Search: Query specific properties (organism, resolution, method, etc.)
```python
from rcsbapi.search import AttributeQuery
from rcsbapi.search.attrs import rcsb_entity_source_organism
# Find human protein structures
query = AttributeQuery(
attribute=rcsb_entity_source_organism.scientific_name,
operator="exact_match",
value="Homo sapiens"
)
results = list(query())
```
Sequence Similarity: Find structures similar to a given sequence
```python
from rcsbapi.search import SequenceQuery
query = SequenceQuery(
value="MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEKMSKDGKKKKKKSKTKCVIM",
evalue_cutoff=0.1,
identity_cutoff=0.9
)
results = list(query())
```
Structure Similarity: Find structures with similar 3D geometry
```python
from rcsbapi.search import StructSimilarityQuery
query = StructSimilarityQuery(
structure_search_type="entry",
entry_id="4HHB" # Hemoglobin
)
results = list(query())
```
Combining Queries: Use logical operators to build complex searches
```python
from rcsbapi.search import TextQuery, AttributeQuery
from rcsbapi.search.attrs import rcsb_entry_info
# High-resolution human proteins
query1 = AttributeQuery(
attribute=rcsb_entity_source_organism.scientific_name,
operator="exact_match",
value="Homo sapiens"
)
query2 = AttributeQuery(
attribute=rcsb_entry_info.resolution_combined,
operator="less",
value=2.0
)
combined_query = query1 & query2 # AND operation
results = list(combined_query())
```
2. Retrieving Structure Data
Access detailed information about specific PDB entries:
Basic Entry Information:
```python
from rcsbapi.data import Schema, fetch
# Get entry-level data
entry_data = fetch("4HHB", schema=Schema.ENTRY)
print(entry_data["struct"]["title"])
print(entry_data["exptl"][0]["method"])
```
Polymer Entity Information:
```python
# Get protein/nucleic acid information
entity_data = fetch("4HHB_1", schema=Schema.POLYMER_ENTITY)
print(entity_data["entity_poly"]["pdbx_seq_one_letter_code"])
```
Using GraphQL for Flexible Queries:
```python
from rcsbapi.data import fetch
# Custom GraphQL query
query = """
{
entry(entry_id: "4HHB") {
struct {
title
}
exptl {
method
}
rcsb_entry_info {
resolution_combined
deposited_atom_count
}
}
}
"""
data = fetch(query_type="graphql", query=query)
```
3. Downloading Structure Files
Retrieve coordinate files in various formats:
Download Methods:
- PDB format (legacy text format):
https://files.rcsb.org/download/{PDB_ID}.pdb - mmCIF format (modern standard):
https://files.rcsb.org/download/{PDB_ID}.cif - BinaryCIF (compressed binary): Use ModelServer API for efficient access
- Biological assembly:
https://files.rcsb.org/download/{PDB_ID}.pdb1 (for assembly 1)
Example Download:
```python
import requests
pdb_id = "4HHB"
# Download PDB format
pdb_url = f"https://files.rcsb.org/download/{pdb_id}.pdb"
response = requests.get(pdb_url)
with open(f"{pdb_id}.pdb", "w") as f:
f.write(response.text)
# Download mmCIF format
cif_url = f"https://files.rcsb.org/download/{pdb_id}.cif"
response = requests.get(cif_url)
with open(f"{pdb_id}.cif", "w") as f:
f.write(response.text)
```
4. Working with Structure Data
Common operations with retrieved structures:
Parse and Analyze Coordinates:
Use BioPython or other structural biology libraries to work with downloaded files:
```python
from Bio.PDB import PDBParser
parser = PDBParser()
structure = parser.get_structure("protein", "4HHB.pdb")
# Iterate through atoms
for model in structure:
for chain in model:
for residue in chain:
for atom in residue:
print(atom.get_coord())
```
Extract Metadata:
```python
from rcsbapi.data import fetch, Schema
# Get experimental details
data = fetch("4HHB", schema=Schema.ENTRY)
resolution = data.get("rcsb_entry_info", {}).get("resolution_combined")
method = data.get("exptl", [{}])[0].get("method")
deposition_date = data.get("rcsb_accession_info", {}).get("deposit_date")
print(f"Resolution: {resolution} Γ
")
print(f"Method: {method}")
print(f"Deposited: {deposition_date}")
```
5. Batch Operations
Process multiple structures efficiently:
```python
from rcsbapi.data import fetch, Schema
pdb_ids = ["4HHB", "1MBN", "1GZX"] # Hemoglobin, myoglobin, etc.
results = {}
for pdb_id in pdb_ids:
try:
data = fetch(pdb_id, schema=Schema.ENTRY)
results[pdb_id] = {
"title": data["struct"]["title"],
"resolution": data.get("rcsb_entry_info", {}).get("resolution_combined"),
"organism": data.get("rcsb_entity_source_organism", [{}])[0].get("scientific_name")
}
except Exception as e:
print(f"Error fetching {pdb_id}: {e}")
# Display results
for pdb_id, info in results.items():
print(f"\n{pdb_id}: {info['title']}")
print(f" Resolution: {info['resolution']} Γ
")
print(f" Organism: {info['organism']}")
```
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