def output_multiple_chains(chains, filename, file_type="pdb"):
'''
Dump multiple chains to an output file. Remove the hydrogen atoms.
:param chains: An iterable of Bio.PDB.Chain to dump.
:param filename: The place to dump it.
'''
class HSelect(bpdb.Select):
def accept_atom(self, atom):
if atom.name.find('H') >= 0:
return False
else:
return True
m = bpdb.Model.Model(0)
s = bpdb.Structure.Structure('stru')
for chain in chains:
log.debug("Adding chain %s with %s residues", chain.id, len(chain))
m.add(chain)
if file_type=="pdb" and len(chain.id)!=1:
raise ValueError("Cannot save chain with name %s (not a single character) "
"in PDB format. Use cif format instead!")
s.add(m)
if file_type == "pdb":
io = bpdb.PDBIO()
else:
io = bpdb.MMCIFIO()
io.set_structure(s)
try:
io.save(filename, HSelect())
except Exception as e:
with log_to_exception(log, e):
log.error("Could not output PDB with chains and residues:")
for chain in s[0]:
log.error("%s: %s", chain.id, [r.id for r in chain])
raise
def split_chains(pdbid):
if not os.path.isfile(pdbid):
print("Error: Function split_chains: file does not exist:" + pdbid +
"\n")
return
if '.gz' in pdbid:
handle = gzip.open(pdbid, "rt")
parser = PDB.MMCIFParser(QUIET=True)
structure = parser.get_structure(pdbid[:-7], handle)
else:
handle = open(pdbid, "rt")
parser = PDB.MMCIFParser(QUIET=True)
structure = parser.get_structure(pdbid[:-4], handle)
for model in structure:
for chain in model:
#io=PDB.PDBIO() Section to output .pdb format
#io.set_structure(chain)
#chain_filename=(structure.id+chain.id+".pdb") #Output in PDB format
#io.save(chain_filename)
#cmd=('gzip -f '+chain_filename)
#subprocess.call(cmd, shell=True)
io = PDB.MMCIFIO()
io.set_structure(chain)
chain_filename = (structure.id + chain.id + ".cif"
) #Output in MMCIF format
io.save(chain_filename)
cmd = ('gzip -f ' + chain_filename)
subprocess.call(cmd, shell=True)
def saving_file(id, struct):
"""
saving the file in cif format
:param id: the file's id
:param struct: the structure we want to save
"""
io = pdb.MMCIFIO()
io.set_structure(struct)
io.save("{0}.cif".format(id))
def export_structure(structure, name, format):
"""
Writes the strucuture into a file. The file can be either a pdb or a mmcif.
"""
if format == "pdb":
io = PDBIO()
elif format == "cif":
io = pdb.MMCIFIO()
io.set_structure(structure)
io.save(name)
def write_structure_into_file(structure, name, format):
"""
Writes the strcuture into a file. The file can be either a pdb or a mmcif.
Format needs to be either "pdb" or "mmcif" depending on the desired output
file.
"""
if format == "pdb":
io = pdb.PDBIO()
elif format == "mmcif":
io = pdb.MMCIFIO()
io.set_structure(structure)
io.save(name)