Upload src/01_build_list.py with huggingface_hub

src/01_build_list.py

@@ -0,0 +1,148 @@
+#!/usr/bin/env python3
+"""
+Scan pieces/2026_01_26 for cullpdb_* list and .fasta pairs. Writes:
+1) cullpdb_list_fasta_index.csv - paired only, with full paths
+2) cullpdb_full_compiled_list.csv - every list and every fasta found (full compiled list)
+"""
+import csv
+import re
+from pathlib import Path
+from typing import Optional
+
+SCRIPT_DIR = Path(__file__).resolve().parent
+BASE = SCRIPT_DIR.parent
+CULLPDB_DIR = BASE / "pieces" / "2026_01_26"
+CURATED_DIR = BASE / "curated_csv"
+OUT_CSV = CURATED_DIR / "cullpdb_list_fasta_index.csv"
+FULL_LIST_CSV = CURATED_DIR / "cullpdb_full_compiled_list.csv"
+
+# cullpdb_pc20.0_res0.0-1.0_noBrks_len40-10000_R0.2_Xray_d2026_01_26_chains300
+PAT = re.compile(
+    r"^cullpdb_pc([\d.]+)_res([\d.]+)-([\d.]+)_"
+    r"(?:(noBrks)_)?"
+    r"len40-10000_R([\d.]+)_"
+    r"(.+?)_d\d{4}_\d{2}_\d{2}_chains(\d+)$"
+)
+
+
+def parse_basename(name: str) -> Optional[dict]:
+    base = name.removesuffix(".fasta")
+    m = PAT.match(base)
+    if not m:
+        return None
+    pc, res_min, res_max, no_brks, r_cutoff, methods, n_chains = m.groups()
+    n = int(n_chains)
+    no_brk = no_brks is not None
+    return {
+        "list_basename": base,
+        "fasta_basename": base + ".fasta",
+        "n_chains": n,
+        "pc": float(pc),
+        "resolution": f"{res_min}-{res_max}",
+        "no_breaks": "yes" if no_brk else "no",
+        "R": float(r_cutoff),
+        "Nmethods": methods,
+    }
+
+
+def main():
+    dir_path = Path(CULLPDB_DIR)
+    if not dir_path.is_dir():
+        print(f"Missing cullpdb dir: {dir_path}")
+        return
+    dir_path = dir_path.resolve()
+    # Collect every basename that has a list and/or fasta
+    bases = set()
+    for p in dir_path.iterdir():
+        if not p.is_file():
+            continue
+        name = p.name
+        if not name.startswith("cullpdb_") or "len40-10000" not in name:
+            continue
+        base = name.removesuffix(".fasta")
+        bases.add(base)
+
+    # Full compiled list: one row per basename, list path + fasta path (full), and parsed params
+    full_rows = []
+    paired_rows = []
+    for base in sorted(bases):
+        list_path = dir_path / base
+        fasta_path = dir_path / (base + ".fasta")
+        list_exists = list_path.exists()
+        fasta_exists = fasta_path.exists()
+        parsed = parse_basename(base)
+        if not parsed:
+            full_rows.append({
+                "list_basename": base,
+                "fasta_basename": base + ".fasta",
+                "list_path": str(list_path) if list_exists else "",
+                "fasta_path": str(fasta_path) if fasta_exists else "",
+                "list_exists": list_exists,
+                "fasta_exists": fasta_exists,
+                "paired": list_exists and fasta_exists,
+                "n_chains": "",
+                "pc": "",
+                "resolution": "",
+                "no_breaks": "",
+                "R": "",
+                "Nmethods": "",
+            })
+            continue
+        row_full = {
+            "list_basename": base,
+            "fasta_basename": base + ".fasta",
+            "list_path": str(list_path) if list_exists else "",
+            "fasta_path": str(fasta_path) if fasta_exists else "",
+            "list_exists": list_exists,
+            "fasta_exists": fasta_exists,
+            "paired": list_exists and fasta_exists,
+            "n_chains": parsed["n_chains"],
+            "pc": parsed["pc"],
+            "resolution": parsed["resolution"],
+            "no_breaks": parsed["no_breaks"],
+            "R": parsed["R"],
+            "Nmethods": parsed["Nmethods"],
+        }
+        full_rows.append(row_full)
+        if list_exists and fasta_exists:
+            paired_rows.append({
+                "list_basename": base,
+                "fasta_basename": base + ".fasta",
+                "list_path": str(list_path),
+                "fasta_path": str(fasta_path),
+                "n_chains": parsed["n_chains"],
+                "pc": parsed["pc"],
+                "resolution": parsed["resolution"],
+                "no_breaks": parsed["no_breaks"],
+                "R": parsed["R"],
+                "Nmethods": parsed["Nmethods"],
+            })
+
+    CURATED_DIR.mkdir(parents=True, exist_ok=True)
+    # 1) Paired index with full paths
+    fieldnames = [
+        "list_basename", "fasta_basename", "list_path", "fasta_path",
+        "n_chains", "pc", "resolution", "no_breaks", "R", "Nmethods",
+    ]
+    with open(OUT_CSV, "w", newline="") as f:
+        w = csv.DictWriter(f, fieldnames=fieldnames)
+        w.writeheader()
+        w.writerows(paired_rows)
+    print(f"Wrote {OUT_CSV} with {len(paired_rows)} list↔fasta pairs (full paths).")
+
+    # 2) Full compiled list: every basename, list/fasta paths and exists flags
+    full_fieldnames = [
+        "list_basename", "fasta_basename", "list_path", "fasta_path",
+        "list_exists", "fasta_exists", "paired",
+        "n_chains", "pc", "resolution", "no_breaks", "R", "Nmethods",
+    ]
+    with open(FULL_LIST_CSV, "w", newline="") as f:
+        w = csv.DictWriter(f, fieldnames=full_fieldnames)
+        w.writeheader()
+        w.writerows(full_rows)
+    n_paired = sum(1 for r in full_rows if r["paired"])
+    print(f"Wrote {FULL_LIST_CSV} with {len(full_rows)} entries (full compiled list); {n_paired} paired.")
+
+
+if __name__ == "__main__":
+    main()