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)
