def test_shuffle(self):
# generate ensembles for 1b9vA
work_dir = "../data"
prt_pdb = "../data/1b9vA.pdb"
prt_code = "1b9vA"
lpc_result = "../data/RES1"
os.chdir(work_dir)
prt_ens.genProteinEnsemble(work_dir, prt_pdb, prt_code, lpc_result)
def test_shuffle(self):
# generate ensembles for 1b9vA
work_dir = "../data"
prt_pdb = "../data/1b9vA.pdb"
prt_code = "1b9vA"
lpc_result = "../data/RES1"
os.chdir(work_dir)
prt_ens.genProteinEnsemble(work_dir, prt_pdb, prt_code, lpc_result)
def help_run(self):
lpc = LPC(self.native_lig_sdf, self.native_prt_pdb)
lpc_result = lpc.runLPC()
pdb = os.path.join(self.dirname, os.path.split(self.native_prt_pdb)[-1])
shutil.copy(self.native_prt_pdb, pdb)
# TODO: IOError: openf______E> Cannot open file 3f9mA.seq: No such file or directory
genProteinEnsemble(self.dirname, pdb, self.ligand_code, lpc_result)
def help_run(self):
lpc = LPC(self.native_lig_sdf, self.native_prt_pdb)
lpc_result = lpc.runLPC()
pdb = os.path.join(self.dirname,
os.path.split(self.native_prt_pdb)[-1])
shutil.copy(self.native_prt_pdb, pdb)
# TODO: IOError: openf______E> Cannot open file 3f9mA.seq: No such file or directory
genProteinEnsemble(self.dirname, pdb, self.ligand_code, lpc_result)
# -d DIRECTORY, --directory DIRECTORY
# directory for data, must contain the native protein
# pdb file
# -p PROTEIN, --protein PROTEIN
# protein pdb file
# -c PROTEIN_CODE, --protein_code PROTEIN_CODE
# protein code
# -l LPC, --lpc LPC lpc result
##########################################################################
parser = argparse.ArgumentParser(
description="generate protein ensemble using Modeller")
parser.add_argument(
"-d",
"--directory",
type=str,
help="directory for data, must contain the native protein pdb file")
parser.add_argument("-p", "--protein", type=str, help="protein pdb file")
parser.add_argument("-c", "--protein_code", type=str, help="protein code")
parser.add_argument("-l", "--lpc", type=str, help="lpc result")
args = parser.parse_args()
work_dir = args.directory
prt_pdb = args.protein
prt_code = args.protein_code
lpc_result = args.lpc
os.chdir(work_dir)
prt_ens.genProteinEnsemble(work_dir, prt_pdb, prt_code, lpc_result)