def restart(
start: str,
results: str,
skip_stages: Optional[List[str]] = None,
end: Optional[str] = None,
config: Optional[str] = None,
cores: Optional[int] = None,
memory: Optional[int] = None,
) -> None:
"""Restart a QUBEKit parametrisation job from the given stage.
Must be started from within an old workflow folder.
"""
# try and load the results file
results = WorkFlowResult.parse_file(results)
if config is None:
# if we have no new config load from results
workflow = prep_config(results=results, cores=cores, memory=memory)
else:
# load the new config file
workflow = prep_config(config_file=config, cores=cores, memory=memory)
# now run the workflow
workflow.restart_workflow(start=start,
result=results,
skip_stages=skip_stages,
end=end)
def run(
input_file: Optional[str] = None,
smiles: Optional[str] = None,
name: Optional[str] = None,
multiplicity: int = 1,
end: Optional[str] = None,
skip_stages: Optional[List[str]] = None,
config: Optional[str] = None,
protocol: Optional[str] = None,
cores: Optional[int] = None,
memory: Optional[int] = None,
):
"""Run the QUBEKit parametrisation workflow on an input molecule."""
# make sure we have an input or smiles not both
if input_file is not None and smiles is not None:
raise RuntimeError(
"Please supply either the name of the input file or a smiles string not both."
)
# load the molecule
if input_file is not None:
molecule = Ligand.from_file(file_name=input_file,
multiplicity=multiplicity)
else:
if name is None:
raise RuntimeError(
"Please also pass a name for the molecule when starting from smiles."
)
molecule = Ligand.from_smiles(smiles_string=smiles,
name=name,
multiplicity=multiplicity)
# load workflow
workflow = prep_config(config_file=config,
memory=memory,
cores=cores,
protocol=protocol)
# move into the working folder and run
with folder_setup(
f"QUBEKit_{molecule.name}_{datetime.now().strftime('%Y_%m_%d')}"):
# write the starting molecule
molecule.to_file(file_name=f"{molecule.name}.pdb")
workflow.new_workflow(molecule=molecule,
skip_stages=skip_stages,
end=end)
def run(
bulk_file: str,
skip_stages: Optional[List[str]] = None,
end: Optional[str] = None,
restart: Optional[str] = None,
config: Optional[str] = None,
protocol: Optional[str] = None,
cores: Optional[int] = None,
memory: Optional[int] = None,
) -> None:
"""Run the QUBEKit parametrisation workflow on a collection of molecules in serial.
Loop over the molecules in order of the CSV file.
"""
import glob
import os
from qubekit.utils.helpers import mol_data_from_csv
home = os.getcwd()
# load all inputs
bulk_data = mol_data_from_csv(bulk_file)
# start main molecule loop
for name, mol_data in bulk_data.items():
print(f"Analysing: {name}")
try:
if restart is not None or mol_data["restart"] is not None:
# we are trying to restart a run, find the folder
# should only be one
fname = name.split(".")[0]
folder = glob.glob(f"QUBEKit_{fname}_*")[0]
with folder_setup(folder):
results = WorkFlowResult.parse_file("workflow_result.json")
if config is None:
# if we have no new config load from results
workflow = prep_config(
results=results, cores=cores, memory=memory, protocol=None
)
else:
# load the new config file
workflow = prep_config(
config_file=config, cores=cores, memory=memory
)
workflow.restart_workflow(
start=restart or mol_data["restart"],
skip_stages=skip_stages,
end=end or mol_data["end"],
result=results,
)
else:
if mol_data["smiles"] is not None:
molecule = Ligand.from_smiles(
smiles_string=mol_data["smiles"], name=name
)
else:
molecule = Ligand.from_file(file_name=name)
# load the CLI config or the csv config, else default
workflow = prep_config(
config_file=config or mol_data["config_file"],
memory=memory,
cores=cores,
protocol=protocol,
)
# move into the working folder and run
with folder_setup(
f"QUBEKit_{molecule.name}_{datetime.now().strftime('%Y_%m_%d')}"
):
# write the starting molecule
molecule.to_file(file_name=f"{molecule.name}.pdb")
workflow.new_workflow(
molecule=molecule,
skip_stages=skip_stages,
end=end or mol_data["end"],
)
except WorkFlowExecutionError:
os.chdir(home)
print(
f"An error was encountered while running {name} see folder for more info."
)
continue