def clean_pdb(pdb_file, pdb_chain, out_dir):
out_dir_chain = out_dir + '/' + 'chain'
if not os.path.isfile(pdb_file):
raise argparse.ArgumentTypeError("PDB file could not be found.")
# Create output directories if they do not already exist
if not os.path.exists(out_dir):
os.makedirs(out_dir)
if not os.path.exists(out_dir_chain):
os.makedirs(out_dir_chain)
# Grab PDB name and make sure it's converted to uppercase
pdb_name = os.path.basename(pdb_file).split('.')[0].upper()
# Extract chain of interest
structure = parsePDBStructure(pdb_file)
# Make sure chain exists, otherwise throw an error
try:
chain = structure[0][pdb_chain]
except KeyError:
print("\nERROR:\n\n\t"+pdb_name+": chain "+pdb_chain+" could not be found.\n")
return
io = PDBIO()
chain_select = ChainSelect(pdb_chain)
io.set_structure(structure)
pdb_chain_file = out_dir_chain+'/'+pdb_name+'_'+pdb_chain+'_temp.pdb'
io.save(pdb_chain_file, chain_select)
# Remove HetAtoms
temp_file = out_dir + "/" + pdb_name + "_temp.pdb"
removeHetAtoms(pdb_file, temp_file)
temp_file_chain = out_dir_chain + "/" + pdb_name + '_' + pdb_chain + "_temp2.pdb"
removeHetAtoms(pdb_chain_file, temp_file_chain)
# Renumber PDB
structure = parsePDBStructure(temp_file)
(new_pdb, renumbered_pdb) = renumberResidues(structure, pdb_name)
structure_chain = parsePDBStructure(temp_file_chain)
(new_pdb_chain, renumbered_pdb) = renumberResidues(structure_chain, pdb_name + '_' + pdb_chain)
# Remove waters
removeWaters(new_pdb, out_dir + "/" + pdb_name + ".pdb")
removeWaters(new_pdb_chain, out_dir_chain+'/'+pdb_name+'_'+pdb_chain+'.pdb')
# Clean up temporary files
os.remove(pdb_chain_file)
os.remove(temp_file)
os.remove(temp_file_chain)
os.remove(new_pdb_chain)
os.remove(new_pdb)
def main():
args = sys.argv
pdb = args[1]
pdb_name = os.path.basename(pdb).split('.')[0].upper()
usage = "\nUsage:\n\n\textract_state.py <pdb>\n\n" \
"\tThis script prints whether a given PDB is monomeric or multimeric. Must be used with RAW biological assembly for accurate results."
assert os.path.exists(pdb), usage
structure = parsePDBStructure(pdb)
print pdb_name,",",checkMultimer(structure)
return 0