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| #!/usr/bin/env python3 | |
| # update_modulus_csv.py | |
| # Usage: python update_modulus_csv.py PID | |
| # | |
| # Reads PID-prefixed modulus result files in the *current directory*: | |
| # {PID}_K_result.dat, {PID}_G1_result.dat, {PID}_G2_result.dat, | |
| # {PID}_G_result.dat, {PID}_nu_result.dat, {PID}_E_result.dat | |
| # | |
| # Writes/updates six separate CSVs in ../../RESULTS/: | |
| # K_MD.csv, G1_MD.csv, G2_MD.csv, G_MD.csv, NU_MD.csv, E_MD.csv | |
| # | |
| # Each CSV has columns: PID, SMILES, <property> | |
| # SMILES is looked up from ../../../SMILES.csv (expects headers: PID,SMILES) | |
| import sys, csv, re | |
| from pathlib import Path | |
| # --- Config --- | |
| OUT_DIR = Path("../../RESULTS") | |
| SMILES_CSV = Path("../../..") / "SMILES.csv" # run from POLYMER_DATA/MODULUS/<PID>/ | |
| PID_COL = "PID" | |
| SMILES_COL = "SMILES" | |
| # Input .dat files (PID-prefixed) | |
| PROP_FILES_BASE = { | |
| "K(GPa)" : "K_result.dat", | |
| "G1(GPa)": "G1_result.dat", | |
| "G2(GPa)": "G2_result.dat", | |
| "G(GPa)" : "G_result.dat", # combined shear modulus (Shear Modulus = ...) | |
| "nu" : "nu_result.dat", | |
| "E(GPa)" : "E_result.dat", | |
| } | |
| # Output CSV filenames per property | |
| PROP_OUTFILE = { | |
| "K(GPa)" : "K_MD.csv", | |
| "G1(GPa)": "G1_MD.csv", | |
| "G2(GPa)": "G2_MD.csv", | |
| "G(GPa)" : "G_MD.csv", # new CSV for combined shear modulus | |
| "nu" : "NU_MD.csv", | |
| "E(GPa)" : "E_MD.csv", | |
| } | |
| FLOAT_RE = re.compile(r"[-+]?(?:\d+\.?\d*|\.\d+)(?:[eE][-+]?\d+)?") | |
| def usage(): | |
| print("Usage: python update_modulus_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_k, smi_k = lower.get("pid"), lower.get("smiles") | |
| if not pid_k or not smi_k: | |
| return "" | |
| for row in rdr: | |
| if (row.get(pid_k) or "").strip() == pid: | |
| return (row.get(smi_k) or "").strip() | |
| return "" | |
| def read_existing_prop(csv_path: Path, prop_col: str): | |
| """Read an existing per-property CSV into a dict keyed by PID.""" | |
| rows = {} | |
| if csv_path.exists(): | |
| with csv_path.open(newline="", encoding="utf-8") as fh: | |
| rdr = csv.DictReader(fh) | |
| for row in rdr: | |
| k = (row.get(PID_COL) or "").strip() | |
| if not k: | |
| continue | |
| rows[k] = { | |
| PID_COL: k, | |
| SMILES_COL: (row.get(SMILES_COL) or "").strip(), | |
| prop_col: (row.get(prop_col) or "").strip(), | |
| } | |
| return rows | |
| def write_prop(csv_path: Path, rows: dict, prop_col: str): | |
| 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, prop_col]) | |
| w.writeheader() | |
| # Write in stable PID order | |
| for pid_key in sorted(rows.keys()): | |
| w.writerow(rows[pid_key]) | |
| def main(): | |
| if len(sys.argv) != 2: | |
| usage() | |
| pid = sys.argv[1].strip() | |
| if not pid: | |
| usage() | |
| # Gather values from PID-prefixed files in current directory | |
| updates = {} | |
| for prop_col, base in PROP_FILES_BASE.items(): | |
| fname = f"{pid}_{base}" | |
| p = Path(fname) | |
| if not p.exists(): | |
| print(f"[SKIP] {fname}: not found") | |
| continue | |
| try: | |
| txt = p.read_text(encoding="utf-8", errors="ignore") | |
| except Exception: | |
| print(f"[SKIP] {fname}: cannot read") | |
| continue | |
| val = first_number(txt) | |
| if val is None: | |
| print(f"[SKIP] {fname}: no numeric value found") | |
| continue | |
| updates[prop_col] = val | |
| print(f"[OK] {fname}: {prop_col}={val}") | |
| if not updates: | |
| print("[INFO] No modulus values found; nothing to write.") | |
| return | |
| smiles = load_smiles(pid) | |
| # Upsert each property into its own CSV | |
| for prop_col, val in updates.items(): | |
| out_csv = OUT_DIR / PROP_OUTFILE[prop_col] | |
| rows = read_existing_prop(out_csv, prop_col) | |
| row = rows.get(pid, {PID_COL: pid, SMILES_COL: "", prop_col: ""}) | |
| row[PID_COL] = pid | |
| # only overwrite SMILES if we have a non-empty lookup, else keep existing | |
| row[SMILES_COL] = smiles or row.get(SMILES_COL, "") | |
| row[prop_col] = val | |
| rows[pid] = row | |
| write_prop(out_csv, rows, prop_col) | |
| print(f"[DONE] Updated {out_csv.name} for PID={pid}") | |
| if __name__ == "__main__": | |
| main() | |