Pdb Database

pip install requests
# Optional, for coordinate parsing:
pip install biopython

import requests

SEARCH = "https://search.rcsb.org/rcsbsearch/v2/query"
DATA   = "https://data.rcsb.org/graphql"

# 1. Search: human X-ray structures of "kinase" at resolution < 2.0 Å
payload = {
    "query": {
        "type": "group", "logical_operator": "and",
        "nodes": [
            {"type": "terminal", "service": "full_text",
             "parameters": {"value": "kinase"}},
            {"type": "terminal", "service": "text",
             "parameters": {"attribute": "rcsb_entity_source_organism.scientific_name",
                            "operator": "exact_match", "value": "Homo sapiens"}},
            {"type": "terminal", "service": "text",
             "parameters": {"attribute": "rcsb_entry_info.resolution_combined",
                            "operator": "less", "value": 2.0}},
        ],
    },
    "return_type": "entry",
    "request_options": {"paginate": {"rows": 10}},
}
r = requests.post(SEARCH, json=payload, timeout=30)
r.raise_for_status()
result = r.json()
pdb_ids = [hit["identifier"] for hit in result["result_set"]]
print(f"Total matches: {result['total_count']}, first batch: {pdb_ids}")

# 2. Fetch metadata for the first hit via GraphQL
gql = """{ entry(entry_id: "%s") {
  struct { title }
  exptl { method }
  rcsb_entry_info { resolution_combined deposited_atom_count polymer_entity_count }
} }""" % pdb_ids[0]
r2 = requests.post(DATA, json={"query": gql}, timeout=30)
entry = r2.json()["data"]["entry"]
print(entry["struct"]["title"])
print(f"Method: {entry['exptl'][0]['method']}, Resolution: {entry['rcsb_entry_info']['resolution_combined']} Å")

import requests
SEARCH = "https://search.rcsb.org/rcsbsearch/v2/query"

def text_search(keyword, rows=25):
    payload = {
        "query": {"type": "terminal", "service": "full_text",
                  "parameters": {"value": keyword}},
        "return_type": "entry",
        "request_options": {"paginate": {"rows": rows}},
    }
    r = requests.post(SEARCH, json=payload, timeout=30)
    r.raise_for_status()
    data = r.json()
    return [hit["identifier"] for hit in data["result_set"]], data["total_count"]

ids, total = text_search("hemoglobin")
print(f"Found {total} structures; first batch: {ids[:5]}")

import requests
SEARCH = "https://search.rcsb.org/rcsbsearch/v2/query"

def attribute_search(attribute, operator, value, return_type="entry", rows=25):
    payload = {
        "query": {"type": "terminal", "service": "text",
                  "parameters": {"attribute": attribute,
                                 "operator": operator,
                                 "value": value}},
        "return_type": return_type,
        "request_options": {"paginate": {"rows": rows}},
    }
    r = requests.post(SEARCH, json=payload, timeout=30)
    r.raise_for_status()
    return r.json()

# Human proteins
human = attribute_search("rcsb_entity_source_organism.scientific_name",
                          "exact_match", "Homo sapiens", rows=5)
print(f"Human structures: {human['total_count']}")

# X-ray only
xray = attribute_search("exptl.method", "exact_match", "X-RAY DIFFRACTION", rows=5)
print(f"X-ray structures: {xray['total_count']}")

# Resolution range: 1.5–2.5 Å
res = attribute_search(
    "rcsb_entry_info.resolution_combined", "range",
    {"from": 1.5, "to": 2.5, "include_lower": True, "include_upper": True},
    rows=5
)
print(f"1.5–2.5 Å: {res['total_count']}")

import requests
SEARCH = "https://search.rcsb.org/rcsbsearch/v2/query"

kras_seq = ("MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQ"
            "EEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPS"
            "RTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEKMSK")

payload = {
    "query": {
        "type": "terminal", "service": "sequence",
        "parameters": {
            "target": "pdb_protein_sequence",  # or "pdb_dna_sequence", "pdb_rna_sequence"
            "value": kras_seq,
            "evalue_cutoff": 0.1,
            "identity_cutoff": 0.9,
        },
    },
    "return_type": "polymer_entity",
    "request_options": {"paginate": {"rows": 10}},
}
r = requests.post(SEARCH, json=payload, timeout=30)
r.raise_for_status()
data = r.json()
print(f"KRAS-like hits: {data['total_count']}")
for hit in data["result_set"][:5]:
    print(f"  {hit['identifier']}  score={hit.get('score', 'n/a')}")

import requests
SEARCH = "https://search.rcsb.org/rcsbsearch/v2/query"

payload = {
    "query": {
        "type": "terminal", "service": "structure",
        "parameters": {
            "value": {"entry_id": "4HHB", "assembly_id": "1"},
            "operator": "strict_shape_match",  # or "relaxed_shape_match"
        },
    },
    "return_type": "polymer_entity",
    "request_options": {"paginate": {"rows": 10}},
}
r = requests.post(SEARCH, json=payload, timeout=30)
r.raise_for_status()
data = r.json()
print(f"Structurally similar to 4HHB: {data['total_count']}")
for hit in data["result_set"][:5]:
    print(f"  {hit['identifier']}  score={hit.get('score', 'n/a')}")

import requests
DATA = "https://data.rcsb.org/graphql"

# Entry-level metadata
gql = """{ entry(entry_id: "4HHB") {
  struct { title }
  exptl { method }
  rcsb_entry_info { resolution_combined deposited_atom_count polymer_entity_count nonpolymer_entity_count }
  rcsb_accession_info { deposit_date initial_release_date }
} }"""
r = requests.post(DATA, json={"query": gql}, timeout=30)
entry = r.json()["data"]["entry"]
print(f"Title       : {entry['struct']['title']}")
print(f"Method      : {entry['exptl'][0]['method']}")
print(f"Resolution  : {entry['rcsb_entry_info']['resolution_combined']} Å")
print(f"Atoms       : {entry['rcsb_entry_info']['deposited_atom_count']}")

# Polymer entity (sequence, organism, MW)
gql = """{ polymer_entity(entry_id: "4HHB", entity_id: "1") {
  entity_poly { pdbx_seq_one_letter_code }
  rcsb_polymer_entity { formula_weight }
  rcsb_entity_source_organism { scientific_name ncbi_taxonomy_id }
} }"""
r = requests.post(DATA, json={"query": gql}, timeout=30)
pe = r.json()["data"]["polymer_entity"]
print(f"Sequence (first 50): {pe['entity_poly']['pdbx_seq_one_letter_code'][:50]}")
print(f"Organism : {pe['rcsb_entity_source_organism'][0]['scientific_name']}")
print(f"MW       : {pe['rcsb_polymer_entity']['formula_weight']}")

# Batch: pull metadata for many entries in one request
gql = """{ entries(entry_ids: ["4HHB", "1A3N", "1HHB"]) {
  rcsb_id
  struct { title }
  exptl { method }
  rcsb_entry_info { resolution_combined }
} }"""
r = requests.post(DATA, json={"query": gql}, timeout=30)
for e in r.json()["data"]["entries"]:
    res = e["rcsb_entry_info"]["resolution_combined"]
    print(f"  {e['rcsb_id']}: {e['exptl'][0]['method']:<25} {res} Å  — {e['struct']['title'][:40]}")

import requests

def download_structure(pdb_id, fmt="cif", output_dir="."):
    """Download mmCIF / PDB / FASTA. URLs: .pdb, .cif, /fasta/entry/{ID}, .pdb1 (assembly)."""
    url = f"https://files.rcsb.org/download/{pdb_id}.{fmt}"
    r = requests.get(url, timeout=60)
    if r.status_code == 200:
        path = f"{output_dir}/{pdb_id}.{fmt}"
        # mmCIF / PDB are text; assemblies and biological units are also text
        with open(path, "w") as f:
            f.write(r.text)
        print(f"Downloaded {path}  ({len(r.text)/1024:.1f} KB)")
        return path
    print(f"HTTP {r.status_code} for {pdb_id}.{fmt}")
    return None

download_structure("4HHB", fmt="cif")
download_structure("4HHB", fmt="pdb")

# FASTA sequence for an entry
r = requests.get("https://www.rcsb.org/fasta/entry/4HHB", timeout=30)
r.raise_for_status()
print(r.text[:400])

import requests, datetime
SEARCH = "https://search.rcsb.org/rcsbsearch/v2/query"

# AND: high-resolution human structures
q_and = {
    "type": "group", "logical_operator": "and",
    "nodes": [
        {"type": "terminal", "service": "text",
         "parameters": {"attribute": "rcsb_entity_source_organism.scientific_name",
                        "operator": "exact_match", "value": "Homo sapiens"}},
        {"type": "terminal", "service": "text",
         "parameters": {"attribute": "rcsb_entry_info.resolution_combined",
                        "operator": "less", "value": 2.0}},
    ],
}

# OR: human or mouse
q_or = {
    "type": "group", "logical_operator": "or",
    "nodes": [
        {"type": "terminal", "service": "text",
         "parameters": {"attribute": "rcsb_entity_source_organism.scientific_name",
                        "operator": "exact_match", "value": "Homo sapiens"}},
        {"type": "terminal", "service": "text",
         "parameters": {"attribute": "rcsb_entity_source_organism.scientific_name",
                        "operator": "exact_match", "value": "Mus musculus"}},
    ],
}

# Combined: recent (last 30 days) + high-quality
one_month_ago = (datetime.date.today() - datetime.timedelta(days=30)).isoformat()
today = datetime.date.today().isoformat()
q_recent_hq = {
    "type": "group", "logical_operator": "and",
    "nodes": [
        {"type": "terminal", "service": "text",
         "parameters": {"attribute": "rcsb_entry_info.resolution_combined",
                        "operator": "less", "value": 2.0}},
        {"type": "terminal", "service": "text",
         "parameters": {"attribute": "refine.ls_R_factor_R_free",
                        "operator": "less", "value": 0.25}},
        {"type": "terminal", "service": "text",
         "parameters": {"attribute": "rcsb_accession_info.initial_release_date",
                        "operator": "range",
                        "value": {"from": one_month_ago, "to": today,
                                  "include_lower": True, "include_upper": True}}},
    ],
}

payload = {"query": q_recent_hq, "return_type": "entry",
           "request_options": {"paginate": {"rows": 5}}}
r = requests.post(SEARCH, json=payload, timeout=30)
print(f"Recent high-quality: {r.json()['total_count']} structures")

import requests, time
SEARCH = "https://search.rcsb.org/rcsbsearch/v2/query"

def search_all(query_node, return_type="entry", page=100, max_results=None, delay=0.3):
    """Paginate through every result; rate-limit between pages."""
    out, start = [], 0
    while True:
        payload = {"query": query_node, "return_type": return_type,
                   "request_options": {"paginate": {"start": start, "rows": page}}}
        r = requests.post(SEARCH, json=payload, timeout=30)
        r.raise_for_status()
        d = r.json()
        batch = [h["identifier"] for h in d.get("result_set", [])]
        if not batch:
            break
        out.extend(batch)
        if max_results and len(out) >= max_results:
            return out[:max_results]
        if len(batch) < page or len(out) >= d.get("total_count", 0):
            break
        start += page
        time.sleep(delay)
    return out

# Example: every insulin entry
ids = search_all(
    {"type": "terminal", "service": "full_text", "parameters": {"value": "insulin"}},
    max_results=300,
)
print(f"Insulin entries collected: {len(ids)}")

# Batch metadata fetch via GraphQL `entries(...)` to avoid one round-trip per ID
DATA = "https://data.rcsb.org/graphql"

def batch_metadata(pdb_ids, chunk=50):
    """Fetch (title, method, resolution) for many entries with one POST per chunk."""
    all_rows = []
    for i in range(0, len(pdb_ids), chunk):
        ids_arr = pdb_ids[i:i+chunk]
        ids_str = ", ".join(f'"{p}"' for p in ids_arr)
        gql = f"""{{ entries(entry_ids: [{ids_str}]) {{
            rcsb_id
            struct {{ title }}
            exptl {{ method }}
            rcsb_entry_info {{ resolution_combined }}
        }} }}"""
        r = requests.post(DATA, json={"query": gql}, timeout=60)
        r.raise_for_status()
        for e in r.json()["data"]["entries"]:
            res = e["rcsb_entry_info"]["resolution_combined"]
            all_rows.append({
                "pdb_id": e["rcsb_id"],
                "method": e["exptl"][0]["method"] if e["exptl"] else None,
                "resolution": res[0] if isinstance(res, list) and res else res,
                "title": e["struct"]["title"],
            })
    return all_rows

rows = batch_metadata(ids[:20])
for r in rows[:5]:
    print(f"  {r['pdb_id']}: {r['method']:<25} {r['resolution']} Å  — {r['title'][:50]}")

import requests, time

SEARCH = "https://search.rcsb.org/rcsbsearch/v2/query"
DATA   = "https://data.rcsb.org/graphql"

payload = {
    "query": {
        "type": "group", "logical_operator": "and",
        "nodes": [
            {"type": "terminal", "service": "full_text",
             "parameters": {"value": "EGFR epidermal growth factor receptor"}},
            {"type": "terminal", "service": "text",
             "parameters": {"attribute": "rcsb_entity_source_organism.scientific_name",
                            "operator": "exact_match", "value": "Homo sapiens"}},
            {"type": "terminal", "service": "text",
             "parameters": {"attribute": "rcsb_entry_info.resolution_combined",
                            "operator": "less", "value": 2.5}},
        ],
    },
    "return_type": "entry",
    "request_options": {"paginate": {"rows": 50}},
}
r = requests.post(SEARCH, json=payload, timeout=30)
r.raise_for_status()
pdb_ids = [h["identifier"] for h in r.json()["result_set"]]
print(f"EGFR ≤2.5 Å human structures: {len(pdb_ids)}")

# Filter to entries with bound ligands via batch GraphQL
ids_str = ", ".join(f'"{p}"' for p in pdb_ids[:20])
gql = f"""{{ entries(entry_ids: [{ids_str}]) {{
    rcsb_id
    struct {{ title }}
    rcsb_entry_info {{ resolution_combined nonpolymer_entity_count }}
}} }}"""
r2 = requests.post(DATA, json={"query": gql}, timeout=60)
for e in r2.json()["data"]["entries"]:
    n_lig = e["rcsb_entry_info"]["nonpolymer_entity_count"] or 0
    if n_lig > 0:
        res = e["rcsb_entry_info"]["resolution_combined"]
        res_v = res[0] if isinstance(res, list) else res
        print(f"  {e['rcsb_id']}: {res_v} Å, ligands={n_lig}  — {e['struct']['title'][:60]}")
    time.sleep(0.05)

import requests, time

SEARCH = "https://search.rcsb.org/rcsbsearch/v2/query"
DATA   = "https://data.rcsb.org/graphql"

kras_seq = ("MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQ"
            "EEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPS"
            "RTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEKMSK")

payload = {
    "query": {
        "type": "terminal", "service": "sequence",
        "parameters": {"target": "pdb_protein_sequence", "value": kras_seq,
                       "evalue_cutoff": 1e-5, "identity_cutoff": 0.5},
    },
    "return_type": "polymer_entity",
    "request_options": {"paginate": {"rows": 20}},
}
r = requests.post(SEARCH, json=payload, timeout=30)
hits = r.json()["result_set"]
print(f"KRAS family hits: {len(hits)}")

# Unique PDB IDs from polymer_entity identifiers (e.g., "4OBE_1" -> "4OBE")
entry_ids = sorted({h["identifier"].split("_")[0] for h in hits})

# Batch metadata
ids_str = ", ".join(f'"{p}"' for p in entry_ids)
gql = f"""{{ entries(entry_ids: [{ids_str}]) {{
    rcsb_id
    struct {{ title }}
    exptl {{ method }}
    rcsb_entry_info {{ resolution_combined }}
}} }}"""
r2 = requests.post(DATA, json={"query": gql}, timeout=60)
for e in sorted(r2.json()["data"]["entries"],
                key=lambda x: (x["rcsb_entry_info"]["resolution_combined"] or [99])[0] if isinstance(x["rcsb_entry_info"]["resolution_combined"], list) else (x["rcsb_entry_info"]["resolution_combined"] or 99)):
    res = e["rcsb_entry_info"]["resolution_combined"]
    res_v = res[0] if isinstance(res, list) else res
    print(f"  {e['rcsb_id']}: {res_v} Å  {e['exptl'][0]['method']:<25} {e['struct']['title'][:50]}")

import requests
from Bio.PDB import MMCIFParser

pdb_id = "4HHB"
r = requests.get(f"https://files.rcsb.org/download/{pdb_id}.cif", timeout=60)
r.raise_for_status()
with open(f"{pdb_id}.cif", "w") as f:
    f.write(r.text)

parser = MMCIFParser(QUIET=True)
structure = parser.get_structure(pdb_id, f"{pdb_id}.cif")
for model in structure:
    for chain in model:
        std_res = [r for r in chain if r.id[0] == " "]
        atoms = sum(len(list(r.get_atoms())) for r in std_res)
        print(f"Chain {chain.id}: {len(std_res)} residues, {atoms} atoms")