def print_structures(self, static_structure, mobile_structure, pdb_file, single_pdb=False):
'''
Print all PDB decoys
'''
decoy_list = []
for decoy in self:
if singlePDB:
decoy_structure = decoy.get_structure(mobile_structure)
decoy_list.append((static_structure, decoy_structure))
else:
decoy.print_structure(static_structure, decoy_structure, pdb_file+'_'+str(decoy.get_num())+'.pdb')
if singlePDB:
PDB.write_pdb(decoy_list, pdb_file+'.pdb', multi_chain=True, multi_model=True)
def print_decoys(self, static, mobile, pdbFile, singlePDB=False):
'''
Print each decoy in a PDB format
@singlePDB = Prints each decoy as a model in a single PDB file
'''
staticDecoy = self.get_static_structure(static)
decoyList = []
for decoy in self.get_decoys():
mobileDecoy = self.get_mobile_structure(static, mobile, decoy)
if singlePDB:
DecoyList.append((staticDecoy, mobileDecoy))
else:
PDB.write_pdb((staticDecoy, mobileDecoy), pdbFile+'_'+str(decoy.get_id())+'.pdb' , multiChain=True, multiModel=False)
if singlePDB:
PDB.write_pdb(decoyList, pdbFile+'.pdb', multiChain=True, multiModel=True)
def get_structure(self, mobile_structure):
'''
Gets the structure of the given docking result
'''
ZDock_create = os.path.abspath(os.path.join(os.path.dirname(__file__), 'ZDock_create'))
if self.zdock.switch_num != '':
create_cmd = '%s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s' % (
ZDock_create, self.zdock.switch_num,
self.zdock.rec_rand1, self.zdock.rec_rand2, self.zdock.rec_rand3,
self.zdock.lig_rand1, self.zdock.lig_rand2, self.zdock.lig_rand3,
self.zdock.r1, self.zdock.r2, self.zdock.r3,
self.zdock.l1, self.zdock.l2, self.zdock.l3,
self.alpha, self.beta, self.gamma,
self.x, self.y, self.z,
self.zdock.n, self.zdock.spacing)
else:
create_cmd = '%s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s %s' % (
ZDock_create,
self.zdock.lig_rand1, self.zdock.lig_rand2, self.zdock.lig_rand3,
self.zdock.r1, self.zdock.r2, self.zdock.r3,
self.zdock.l1, self.zdock.l2, self.zdock.l3,
self.alpha, self.beta, self.gamma,
self.x, self.y, self.z,
self.zdock.n, self.zdock.spacing)
p = subprocess.Popen(create_cmd, stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True)
create_out, create_err = p.communicate(str(mobile_structure))
structure = PDB.read_pdb(create_out, from_string=True)
return structure
def print_structure(self, static_structure, mobile_structure, pdbFile):
decoy_structure = self.get_structure(mobile_structure)
PDB.write_pdb((static_structure, decoy_structure),
pdbFile + '.pdb',
multi_chain=True,
multi_model=False)