validate

REINVENT4 Input Validation

Validate SMILES files and TOML configs using Python/RDKit directly. No MCP server needed — requires RDKit and the toml package.

Workflow

1. Resolve paths

readlink -f <relative_path>

2. Detect file type

From $ARGUMENTS:

• .smi, .csv, .smiles → SMILES validation (Step 3a)
• .toml → TOML config validation (Step 3b)
• If ambiguous, ask the user

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3a. SMILES validation

Run this Python snippet (adapt the path and generator):

from rdkit import Chem
from collections import Counter

path = "/absolute/path/to/file.smi"  # or .csv
generator = "reinvent"  # reinvent | libinvent | linkinvent | mol2mol

smiles_list = []
with open(path) as f:
    for line in f:
        tok = line.strip().split()
        if tok:
            smiles_list.append(tok[0])

errors, dupes = [], Counter()
valid = []
for i, smi in enumerate(smiles_list, 1):
    mol = Chem.MolFromSmiles(smi)
    if mol is None:
        errors.append((i, smi, "invalid SMILES"))
        continue
    can = Chem.MolToSmiles(mol)
    # Generator-specific checks
    if generator == "libinvent" and "[*:0]" not in smi:
        errors.append((i, smi, "missing [*:0] attachment point"))
        continue
    if generator == "linkinvent" and "|" not in smi:
        errors.append((i, smi, "linkinvent requires two fragments separated by |"))
        continue
    valid.append(can)
    dupes[can] += 1

dup_count = sum(v - 1 for v in dupes.values() if v > 1)
print(f"Total: {len(smiles_list)}, Valid: {len(valid)}, Invalid: {len(errors)}, Duplicates: {dup_count}")
for idx, smi, reason in errors[:10]:
    print(f"  Line {idx}: {smi!r} — {reason}")

Report all findings. If invalid entries or duplicates exist, offer to write a cleaned file:

seen = set()
cleaned = []
for smi in smiles_list:
    mol = Chem.MolFromSmiles(smi)
    if mol is None:
        continue
    can = Chem.MolToSmiles(mol)
    if can not in seen:
        seen.add(can)
        cleaned.append(can)

out_path = path.replace(".smi", "_cleaned.smi")
with open(out_path, "w") as f:
    f.write("\n".join(cleaned) + "\n")
print(f"Wrote {len(cleaned)} molecules to {out_path}")