Exemple #1
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 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)
Exemple #2
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 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)
Exemple #3
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    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)
Exemple #4
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    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)
Exemple #5
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#   -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)