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import pandas as pd
import argparse
import os
def safe_float(value):
try:
# Handle malformed scientific notation like 2.1997*^-6
clean_value = value.replace("*^-", "e-").replace("*^", "e")
return float(clean_value)
except Exception as e:
raise ValueError(f"Failed to parse float from '{value}': {e}")
def process_xyz(filepath):
data = {}
with open(filepath, 'r') as f:
lines = f.readlines()
data["n_atoms"] = int(lines[0].strip())
values = lines[1].split()
data["ID"] = values[1]
#data["SMILES_GDB17"], data["SMILES_B3LYP"] = lines[-2].strip().split()
data["SMILES_GDB17"] = lines[-2].strip().split()[0]
data["Rotational_Constant_A"] = safe_float(values[2])
data["Rotational_Constant_B"] = safe_float(values[3])
data["Rotational_Constant_C"] = safe_float(values[4])
data["Dipole_Moment"] = safe_float(values[5])
data["Isotropic_polarizability"] = safe_float(values[6])
data["Energy_of_HOMO"] = safe_float(values[7])
data["Energy_of_LUMO"] = safe_float(values[8])
data["LUMO_HOMO_GAP"] = safe_float(values[9])
data["Electronic_spatial_extent"] = safe_float(values[10])
data["Zero_point_vibrational_energy"] = safe_float(values[11])
data["Internal_energy_at_0_K"] = safe_float(values[12])
data["Internal_energy_at_298.15_K"] = safe_float(values[13])
data["Enthalpy_at_298.15_K"] = safe_float(values[14])
data["Free_energy_at_298.15_K"] = safe_float(values[15])
data["Heat_capacity_at_298.15_K"] = safe_float(values[16])
for i in range(data["n_atoms"]):
atom = lines[2 + i].split()
data[f"element_{i}"] = atom[0]
data[f"x_{i}"] = safe_float(atom[1])
data[f"y_{i}"] = safe_float(atom[2])
data[f"z_{i}"] = safe_float(atom[3])
data[f"charge_{i}"] = safe_float(atom[4])
return data
def main():
parser = argparse.ArgumentParser()
parser.add_argument("--file_list", required=True, help="Path to .txt file listing input .xyz files")
parser.add_argument("--output_file", required=True, help="Path to output .parquet file (checkpointed)")
parser.add_argument("--checkpoint_every", type=int, default=100, help="Save after every N molecules")
args = parser.parse_args()
print("Processing",args.file_list)
with open(args.file_list, 'r') as f:
files = [line.strip() for line in f if line.strip()]
records = {}
for i, path in enumerate(files):
try:
data = process_xyz(path)
n_atoms=data["n_atoms"]
records[n_atoms]=data
except Exception as e:
print(f" Failed on {path}: {e}")
if (i + 1) % args.checkpoint_every == 0:
df = pd.DataFrame(records)
df.to_parquet(args.output_file, index=False)
print(f"Checkpointed {len(df)} molecules at {i+1}/{len(files)}")
# Final save
if records:
df = pd.DataFrame(records)
df.to_parquet(args.output_file, index=False)
print(f" Final write: {len(df)} molecules → {args.output_file}")
else:
print(" No valid data to save.")
if __name__ == "__main__":
main() |