File size: 3,173 Bytes
930ea3d | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 | #!/usr/bin/env python3
# update_tc_csv.py
# Usage: python update_tc_csv.py PID
#
# Reads thermal conductivity result in the *current directory*:
# {PID}_TC_result.dat -> ../../RESULTS/TC_MD.csv (columns: PID,SMILES,TC)
#
# Looks up SMILES for PID from ../../../SMILES.csv (expects headers: PID,SMILES)
import sys, csv, re
from pathlib import Path
PID_COL, SMILES_COL, VALUE_COL = "PID", "SMILES", "TC"
SMILES_CSV = Path("../../..") / "SMILES.csv" # from POLYMER_DATA/THERMAL_CONDUCTIVITY/<PID>/
OUT_DIR = Path("../../RESULTS")
OUT_CSV = OUT_DIR / "TC_MD.csv"
FLOAT_RE = re.compile(r"[-+]?(?:\d+\.?\d*|\.\d+)(?:[eE][-+]?\d+)?")
def usage():
print("Usage: python update_tc_csv.py PID")
sys.exit(1)
def first_number(text: str):
m = FLOAT_RE.search(text)
return m.group(0) if m else None
def load_smiles(pid: str) -> str:
if not SMILES_CSV.exists():
return ""
with SMILES_CSV.open(newline="", encoding="utf-8") as fh:
rdr = csv.DictReader(fh)
if not rdr.fieldnames:
return ""
lower = {k.lower(): k for k in rdr.fieldnames}
pid_key = lower.get("pid"); smi_key = lower.get("smiles")
if not pid_key or not smi_key:
return ""
for row in rdr:
if (row.get(pid_key) or "").strip() == pid:
return (row.get(smi_key) or "").strip()
return ""
def upsert(csv_path: Path, pid: str, smiles: str, value: str):
# Simple upsert keyed by PID; expects columns PID,SMILES,TC
data = {}
if csv_path.exists():
with csv_path.open(newline="", encoding="utf-8") as fh:
rdr = csv.DictReader(fh)
if rdr.fieldnames and {PID_COL, SMILES_COL, VALUE_COL}.issubset(rdr.fieldnames):
for row in rdr:
k = (row.get(PID_COL) or "").strip()
if k:
data[k] = {
PID_COL: k,
SMILES_COL: row.get(SMILES_COL, ""),
VALUE_COL: row.get(VALUE_COL, ""),
}
data[pid] = {PID_COL: pid, SMILES_COL: smiles, VALUE_COL: value}
csv_path.parent.mkdir(parents=True, exist_ok=True)
with csv_path.open("w", newline="", encoding="utf-8") as fh:
w = csv.DictWriter(fh, fieldnames=[PID_COL, SMILES_COL, VALUE_COL])
w.writeheader()
for row in data.values():
w.writerow(row)
def main():
if len(sys.argv) != 2:
usage()
pid = sys.argv[1].strip()
if not pid:
usage()
src = Path(f"{pid}_TC_result.dat")
if not src.exists():
print(f"[SKIP] {src.name}: not found")
sys.exit(0)
try:
text = src.read_text(encoding="utf-8", errors="ignore")
except Exception:
print(f"[SKIP] {src.name}: cannot read")
sys.exit(0)
val = first_number(text)
if val is None:
print(f"[SKIP] {src.name}: no numeric value found")
sys.exit(0)
smiles = load_smiles(pid)
upsert(OUT_CSV, pid, smiles, val)
print(f"[OK] {src.name} → {OUT_CSV.name}: PID={pid} {VALUE_COL}={val}")
if __name__ == "__main__":
main()
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