Provide new mol file to sdf writer.

[TJGorrie]

fragalysis-api/fragalysis_api/xcimporter/conversion_pdb_mol.py

Lines 583 to 598 in ae3e3f6

	new.create_mol_file(
	directory=new.mol_dict["directory"][i],
	file_base=new.mol_dict["file_base"][i],
	mol_obj=new.mol_dict["mol"][i],
	smiles_file=smiles_file,
	) # creates mol file for each ligand
	writer = Chem.rdmolfiles.SDWriter(
	os.path.join(
	new.mol_dict["directory"][i],
	str(new.mol_dict["file_base"][i] + ".sdf"),
	)
	)
	new.create_sd_file(
	new.mol_lst[i], writer
	) # creates sd file containing all mol files
	writer.close() # this is important to make sure the file overwrites each time