def fix_side_chain_pc(input_pdb_path, output_pdb_path, properties, **kwargs): try: fix_side_chain.FixSideChain(input_pdb_path=input_pdb_path, output_pdb_path=output_pdb_path, properties=properties, **kwargs).launch() except Exception: traceback.print_exc() fu.write_failed_output(output_pdb_path)
def reduce_remove_hydrogens_pc(input_path, output_path, properties, **kwargs): try: reduce_remove_hydrogens.ReduceRemoveHydrogens(input_path=input_path, output_path=output_path, properties=properties, **kwargs).launch() except Exception: traceback.print_exc() fu.write_failed_output(output_path)
def pdb_cluster_zip_pc(output_pdb_zip_path, properties, **kwargs): try: pdb_cluster_zip.MmbPdbClusterZip( output_pdb_zip_path=output_pdb_zip_path, properties=properties, **kwargs).launch() except Exception: traceback.print_exc() fu.write_failed_output(output_pdb_zip_path)
def babel_add_hydrogens_pc(input_path, output_path, properties, **kwargs): try: babel_add_hydrogens.BabelAddHydrogens(input_path=input_path, output_path=output_path, properties=properties, **kwargs).launch() except Exception: traceback.print_exc() fu.write_failed_output(output_path)
def babel_minimize_pc(input_path, output_path, properties, **kwargs): try: babel_minimize.BabelMinimize(input_path=input_path, output_path=output_path, properties=properties, **kwargs).launch() except Exception: traceback.print_exc() fu.write_failed_output(output_path)
def mutate_pc(input_pdb_path, output_pdb_path, properties, **kwargs): try: mutate.Mutate(input_pdb_path=input_pdb_path, output_pdb_path=output_pdb_path, properties=properties, **kwargs).launch() except Exception: traceback.print_exc() fu.write_failed_output(output_pdb_path)
def remove_pdb_water_pc(input_pdb_path, output_pdb_path, properties, **kwargs): try: remove_pdb_water.RemovePdbWater(input_pdb_path=input_pdb_path, output_pdb_path=output_pdb_path, properties=properties, **kwargs).launch() except Exception: traceback.print_exc() fu.write_failed_output(output_pdb_path)
def extract_chain_pc(input_structure_path, output_structure_path, properties, **kwargs): try: extract_chain.ExtractChain(input_structure_path=input_structure_path, output_structure_path=output_structure_path, properties=properties, **kwargs).launch() except Exception: traceback.print_exc() fu.write_failed_output(output_structure_path)
def cpptraj_dry_pc(input_top_path, input_traj_path, output_cpptraj_path, properties, **kwargs): try: cpptraj_dry.Dry(input_top_path=input_top_path, input_traj_path=input_traj_path, output_cpptraj_path=output_cpptraj_path, properties=properties, **kwargs).launch() except Exception: traceback.print_exc() fu.write_failed_output(output_cpptraj_path)
def extract_heteroatoms_pc(input_structure_path, output_heteroatom_path, properties, **kwargs): try: extract_heteroatoms.ExtractHeteroAtoms( input_structure_path=input_structure_path, output_heteroatom_path=output_heteroatom_path, properties=properties, **kwargs).launch() except Exception: traceback.print_exc() fu.write_failed_output(output_heteroatom_path)
def template_pc(input_file_path1, input_file_path2, output_file_path, properties, **kwargs): try: template.Template(input_file_path1=input_file_path1, input_file_path2=input_file_path2, output_file_path=output_file_path, properties=properties, **kwargs).launch() except Exception: traceback.print_exc() fu.write_failed_output(output_file_path)
def ndx2resttop_pc(input_ndx_path, input_top_zip_path, output_top_zip_path, properties, **kwargs): try: ndx2resttop.Ndx2resttop(input_ndx_path=input_ndx_path, input_top_zip_path=input_top_zip_path, output_top_zip_path=output_top_zip_path, properties=properties, **kwargs).launch() except Exception: traceback.print_exc() fu.write_failed_output(output_top_zip_path)
def gmx_rgyr_pc(input_structure_path, input_traj_path, output_xvg_path, input_index_path, properties, **kwargs): try: gmx_rgyr.GMXRgyr(input_structure_path=input_structure_path, input_traj_path=input_traj_path, output_xvg_path=output_xvg_path, input_index_path=input_index_path, properties=properties, **kwargs).launch() except Exception: traceback.print_exc() fu.write_failed_output(output_xvg_path)
def renumber_structures_pc(input_structure_path, output_structure_path, output_mapping_json_path, properties, **kwargs): try: renumber_structures.RenumberStructure( input_structure_path=input_structure_path, output_structure_path=output_structure_path, output_mapping_json_path=output_mapping_json_path, properties=properties, **kwargs).launch() except Exception: traceback.print_exc() fu.write_failed_output(output_structure_path) fu.write_failed_output(output_mapping_json_path)
def acpype_params_gmx_opls_pc(input_path, output_path_itp, output_path_top, properties, **kwargs): try: acpype_params_gmx_opls.AcpypeParamsGMXOPLS( input_path=input_path, output_path_itp=output_path_itp, output_path_top=output_path_top, properties=properties, **kwargs).launch() except Exception: traceback.print_exc() fu.write_failed_output(output_path_itp) fu.write_failed_output(output_path_top)
def gmx_energy_pc(input_energy_path, output_xvg_path, properties, **kwargs): try: gmx_energy.GMXEnergy(input_energy_path=input_energy_path, output_xvg_path=output_xvg_path, properties=properties, **kwargs).launch() if not os.path.exists(output_xvg_path): fu.write_failed_output(output_xvg_path) except Exception: traceback.print_exc() fu.write_failed_output(output_xvg_path) finally: sys.stdout.flush() sys.stderr.flush()
def gentop_pc(input_top_zip_path, output_top_zip_path, properties, **kwargs): try: os.environ.pop('PMI_FD', None) os.environ.pop('PMI_JOBID', None) os.environ.pop('PMI_RANK', None) os.environ.pop('PMI_SIZE', None) gentop.Gentop(input_top_zip_path=input_top_zip_path, output_top_zip_path=output_top_zip_path, properties=properties, **kwargs).launch() if not os.path.exists(output_top_zip_path): fu.write_failed_output(output_top_zip_path) except Exception: traceback.print_exc() fu.write_failed_output(output_top_zip_path) finally: sys.stdout.flush() sys.stderr.flush()
def mutate_bst_pc(input_structure_path, output_structure_path, input_b_structure_path, properties, **kwargs): try: mutate.Mutate(input_structure_path=input_structure_path, output_structure_path=output_structure_path, input_b_structure_path=input_b_structure_path, properties=properties, **kwargs).launch() if not os.path.exists(output_structure_path): fu.write_failed_output(output_structure_path) except Exception: traceback.print_exc() fu.write_failed_output(output_structure_path) finally: sys.stdout.flush() sys.stderr.flush()
def sort_gro_residues_pc(input_gro_path, output_gro_path, properties, **kwargs): try: os.environ.pop('PMI_FD', None) os.environ.pop('PMI_JOBID', None) os.environ.pop('PMI_RANK', None) os.environ.pop('PMI_SIZE', None) sort_gro_residues.SortGroResidues(input_gro_path=input_gro_path, output_gro_path=output_gro_path, properties=properties, **kwargs).launch() except Exception: traceback.print_exc() fu.write_failed_output(output_gro_path) finally: sys.stdout.flush() sys.stderr.flush()
def append_ligand_pc(input_top_zip_path, input_itp_path, output_top_zip_path, input_posres_itp_path, properties, **kwargs): try: os.environ.pop('PMI_FD', None) os.environ.pop('PMI_JOBID', None) os.environ.pop('PMI_RANK', None) os.environ.pop('PMI_SIZE', None) append_ligand.AppendLigand(input_top_zip_path=input_top_zip_path, input_itp_path=input_itp_path, output_top_zip_path=output_top_zip_path, input_posres_itp_path=input_posres_itp_path, properties=properties, **kwargs).launch() except Exception: traceback.print_exc() fu.write_failed_output(output_top_zip_path) finally: sys.stdout.flush() sys.stderr.flush()
def extract_atoms_pc(input_structure_path, output_structure_path, properties, **kwargs): try: os.environ.pop('PMI_FD', None) os.environ.pop('PMI_JOBID', None) os.environ.pop('PMI_RANK', None) os.environ.pop('PMI_SIZE', None) extract_atoms.ExtractAtoms(input_structure_path=input_structure_path, output_structure_path=output_structure_path, properties=properties, **kwargs).launch() if not os.path.exists(output_structure_path): fu.write_failed_output(output_structure_path) except Exception: traceback.print_exc() fu.write_failed_output(output_structure_path) finally: sys.stdout.flush() sys.stderr.flush()
def gmx_trjconv_str_ens_pc(input_traj_path, input_top_path, output_str_ens_path, properties, **kwargs): try: os.environ.pop('PMI_FD', None) os.environ.pop('PMI_JOBID', None) os.environ.pop('PMI_RANK', None) os.environ.pop('PMI_SIZE', None) gmx_trjconv_str_ens.GMXTrjConvStrEns( input_traj_path=input_traj_path, input_top_path=input_top_path, output_str_ens_path=output_str_ens_path, properties=properties, **kwargs).launch() if not os.path.exists(output_str_ens_path): fu.write_failed_output(output_str_ens_path) except Exception: traceback.print_exc() fu.write_failed_output(output_str_ens_path) finally: sys.stdout.flush() sys.stderr.flush()
def acpype_params_cns_pc(input_path, output_path_par, output_path_inp, output_path_top, properties, **kwargs): try: acpype_params_cns.AcpypeParamsCNS(input_path=input_path, output_path_par=output_path_par, output_path_inp=output_path_inp, output_path_top=output_path_top, properties=properties, **kwargs).launch() except Exception: traceback.print_exc() fu.write_failed_output(output_path_par) fu.write_failed_output(output_path_inp) fu.write_failed_output(output_path_top)
def acpype_params_ac_pc(input_path, output_path_frcmod, output_path_inpcrd, output_path_lib, output_path_prmtop, properties, **kwargs): try: acpype_params_ac.AcpypeParamsAC(input_path=input_path, output_path_frcmod=output_path_frcmod, output_path_inpcrd=output_path_inpcrd, output_path_lib=output_path_lib, output_path_prmtop=output_path_prmtop, properties=properties, **kwargs).launch() except Exception: traceback.print_exc() fu.write_failed_output(output_path_frcmod) fu.write_failed_output(output_path_inpcrd) fu.write_failed_output(output_path_lib) fu.write_failed_output(output_path_prmtop)
def analyse_pc(input_a_xvg_zip_path, input_b_xvg_zip_path, output_result_path, output_work_plot_path, properties, **kwargs): try: os.environ.pop('PMI_FD', None) os.environ.pop('PMI_JOBID', None) os.environ.pop('PMI_RANK', None) os.environ.pop('PMI_SIZE', None) analyse.Analyse(input_a_xvg_zip_path=input_a_xvg_zip_path, input_b_xvg_zip_path=input_b_xvg_zip_path, output_result_path=output_result_path, output_work_plot_path=output_work_plot_path, properties=properties, **kwargs).launch() if not os.path.exists(output_result_path): fu.write_failed_output(output_result_path) if not os.path.exists(output_work_plot_path): fu.write_failed_output(output_work_plot_path) except Exception: traceback.print_exc() fu.write_failed_output(output_result_path) fu.write_failed_output(output_work_plot_path) finally: sys.stdout.flush() sys.stderr.flush()
def cat_pdb_pc(input_structure1, input_structure2, output_structure_path, properties, **kwargs): try: cat_pdb.CatPDB(input_structure1=input_structure1, input_structure2=input_structure2, output_structure_path=output_structure_path, properties=properties, **kwargs).launch() except Exception: traceback.print_exc() fu.write_failed_output(output_structure_path)
def ligand_pc(output_pdb_path, properties, **kwargs): try: ligand.Ligand(output_pdb_path=output_pdb_path, properties=properties, **kwargs).launch() except Exception: traceback.print_exc() fu.write_failed_output(output_pdb_path)
def check_structure_and_run_ndx_pc( ensemble, output_structure_path, input_structure_path, output_ndx_path, properties_makendx, input_gro_path, input_top_zip_path, output_tpr_path, properties_grompp, output_trr_path, output_gro_path, output_edr_path, output_xtc_path, output_log_path, properties_mdrun, **kwargs): try: dummy = bool(os.path.getsize(output_structure_path)) if not dummy: #if ensemble == "stateA": from shutil import copyfile copyfile(input_gro_path, output_gro_path) fu.write_failed_output(output_ndx_path) fu.write_failed_output(output_tpr_path) fu.write_failed_output(output_trr_path) fu.write_failed_output(output_edr_path) fu.write_failed_output(output_xtc_path) fu.write_failed_output(output_log_path) else: # step4_gmx_makendx make_ndx_pc(input_structure_path=input_structure_path, output_ndx_path=output_ndx_path, properties=properties_makendx) # step5_gmx_grompp grompp_ndx_pc(input_gro_path=input_gro_path, input_top_zip_path=input_top_zip_path, output_tpr_path=output_tpr_path, input_ndx_path=output_ndx_path, properties=properties_grompp) # step6_gmx_mdrun mdrun_pc(input_tpr_path=output_tpr_path, output_trr_path=output_trr_path, output_gro_path=output_gro_path, output_edr_path=output_edr_path, output_xtc_path=output_xtc_path, output_log_path=output_log_path, properties=properties_mdrun) except Exception as e: raise Exception( "Error ocurred while checking the file containing dummy atoms")
def pdb_variants_pc(output_mutations_list_txt, properties, **kwargs): try: pdb_variants.MmbPdbVariants(output_mutations_list_txt=output_mutations_list_txt, properties=properties, **kwargs).launch() except Exception: traceback.print_exc() fu.write_failed_output(output_mutations_list_txt)
def gmx_trjconv_trj_pc(input_traj_path, output_traj_path, input_index_path, properties, **kwargs): try: gmx_trjconv_trj.GMXTrjConvTrj(input_traj_path=input_traj_path, output_traj_path=output_traj_path, input_index_path=input_index_path, properties=properties, **kwargs).launch() except Exception: traceback.print_exc() fu.write_failed_output(output_traj_path)