from mpi4py import MPI from mpi4py.futures import MPICommExecutor from openbabel import pybel from Bio.PDB import * parser = PDBParser() import os molecular_weight_cutoff = 2500 def parse_ligand(fn): print(fn) try: struct = parser.get_structure('lig',fn) if len(list(struct.get_atoms())) > molecular_weight_cutoff: raise ValueError mol = next(pybel.readfile('pdb',fn)) if mol.molwt > molecular_weight_cutoff: raise ValueError smi = mol.write('can').split('\t')[0] return smi except: return None if __name__ == '__main__': import glob comm = MPI.COMM_WORLD with MPICommExecutor(comm, root=0) as executor: if executor is not None: import pandas as pd df = pd.read_table('biolip/data/BioLiP_2013-03-6_nr.txt',sep='\t',header=None,usecols=[0,4,5,6,13,14,15,16,19]) df = df.rename(columns={0:'pdb',4:'chain',5:'l_id',6:'l_chain', 13: 'affinity_lit',14: 'affinity_moad',15: 'affinity_pdbbind-cn',16:'affinity_bindingdb', 19: 'seq'}) base = 'biolip/data/ligand_nr/' df['ligand_fn'] = base + df['pdb']+'_'+df['chain']+'_'+df['l_id'].astype(str)+'_'+df['l_chain'].astype(str)+'.pdb' smiles = list(executor.map(parse_ligand, df['ligand_fn'])) df['smiles'] = smiles df.to_parquet('data/biolip_complex.parquet')