plin1112 / process_pubchem_smiles

process_PubChem_SMILES

python scripts used to process the SMILES files obtained from PubChem

General Information

• sort_CID_SMILES_byElements.py split the CID-SMILES by element groups, and by complex types, ion or neutral, etc.
• sort_CID_SMILES_byHeavyAtoms.py split the CID-SMILES by number of heavy atoms
• sort_stat_CID_SMILES_ECFP_r3.py process each splitted CID-SMILES, calculate fingerprints and count and save the statistics (recommand to run through splitted element groups and by number of heavy atoms
• csv2pqz_CID_SMILES_ECFP_r3.py split the statistics of fingerprints based on radius used and save in dataframe
• sort_pick_split_smiles_RDKit.py further splitting SMILES presenting the unique fingerprint by charge and multiplicity
• gen_xtbxyz_RDKit_from_csv.py Generate xyz files ready for xTB calculation from csv formatted file