training_classifiers/binding_affinity_iptm.py

#!/usr/bin/env python3
"""
extract_iptm_affinity_csv_all.py

Writes:
  - out_dir/wt_iptm_affinity_all.csv
  - out_dir/smiles_iptm_affinity_all.csv

Also prints:
  - N
  - Spearman rho (affinity vs iptm)
  - Pearson r (affinity vs iptm)
"""

from pathlib import Path
import numpy as np
import pandas as pd


def corr_stats(df: pd.DataFrame, x: str, y: str):
    # pandas handles NaNs if we already dropped them; still be safe
    xx = pd.to_numeric(df[x], errors="coerce")
    yy = pd.to_numeric(df[y], errors="coerce")
    m = xx.notna() & yy.notna()
    xx = xx[m]
    yy = yy[m]
    n = int(m.sum())

    # Pearson r
    pearson_r = float(xx.corr(yy, method="pearson")) if n > 1 else float("nan")
    # Spearman rho
    spearman_rho = float(xx.corr(yy, method="spearman")) if n > 1 else float("nan")

    return {"n": n, "pearson_r": pearson_r, "spearman_rho": spearman_rho}


def clean_one(
    in_csv: Path,
    out_csv: Path,
    iptm_col: str,
    affinity_col: str = "affinity",
    keep_cols=(),
):
    df = pd.read_csv(in_csv)

    # affinity + iptm must exist
    need = [affinity_col, iptm_col]
    missing = [c for c in need if c not in df.columns]
    if missing:
        raise ValueError(f"{in_csv} missing columns: {missing}. Found: {list(df.columns)}")

    # coerce numeric
    df[affinity_col] = pd.to_numeric(df[affinity_col], errors="coerce")
    df[iptm_col] = pd.to_numeric(df[iptm_col], errors="coerce")

    # drop NaNs in either
    df = df.dropna(subset=[affinity_col, iptm_col]).reset_index(drop=True)

    # output cols (standardize names)
    out = pd.DataFrame({
        "affinity": df[affinity_col].astype(float),
        "iptm": df[iptm_col].astype(float),
    })

    # keep split if present (handy for coloring later, but not used for corr)
    if "split" in df.columns:
        out.insert(0, "split", df["split"].astype(str))

    # optional extras for labeling/debug
    for c in keep_cols:
        if c in df.columns:
            out[c] = df[c]

    out_csv.parent.mkdir(parents=True, exist_ok=True)
    out.to_csv(out_csv, index=False)

    stats = corr_stats(out, "iptm", "affinity")
    print(f"[write] {out_csv}")
    print(f"  N={stats['n']} | Pearson r={stats['pearson_r']:.4f} | Spearman rho={stats['spearman_rho']:.4f}")

    # also save stats json next to csv
    stats_path = out_csv.with_suffix(".stats.json")
    with open(stats_path, "w") as f:
        import json
        json.dump(
            {
                "input_csv": str(in_csv),
                "output_csv": str(out_csv),
                "iptm_col": iptm_col,
                "affinity_col": affinity_col,
                **stats,
            },
            f,
            indent=2,
        )


def main():
    import argparse
    ap = argparse.ArgumentParser()
    ap.add_argument("--wt_meta_csv", type=str, required=True)
    ap.add_argument("--smiles_meta_csv", type=str, required=True)
    ap.add_argument("--out_dir", type=str, required=True)

    ap.add_argument("--wt_iptm_col", type=str, default="wt_iptm_score")
    ap.add_argument("--smiles_iptm_col", type=str, default="smiles_iptm_score")
    ap.add_argument("--affinity_col", type=str, default="affinity")
    args = ap.parse_args()

    out_dir = Path(args.out_dir)

    clean_one(
        Path(args.wt_meta_csv),
        out_dir / "wt_iptm_affinity_all.csv",
        iptm_col=args.wt_iptm_col,
        affinity_col=args.affinity_col,
        keep_cols=("seq1", "seq2", "Fasta2SMILES", "REACT_SMILES"),
    )

    clean_one(
        Path(args.smiles_meta_csv),
        out_dir / "smiles_iptm_affinity_all.csv",
        iptm_col=args.smiles_iptm_col,
        affinity_col=args.affinity_col,
        keep_cols=("seq1", "seq2", "Fasta2SMILES", "REACT_SMILES", "smiles_sequence"),
    )

    print(f"\n[DONE] CSVs + stats JSONs in: {out_dir}")


if __name__ == "__main__":
    main()