icolos.core.workflow_steps.fpocket package#

Submodules#

icolos.core.workflow_steps.fpocket.base module#

class icolos.core.workflow_steps.fpocket.base.StepFpocketBase(*, step_id: str, work_dir: str = None, type: str = None, data: ~icolos.core.step_utils.input_preparator.StepData = StepData(compounds=[], generic=<icolos.core.containers.generic.GenericContainer object>, gmx_state=Gromacs Topology object: System: [] | Molecules: [] | FF: amber03 | itp files: [] | posre files []), input: ~icolos.core.step_utils.input_preparator.StepInputParameters = StepInputParameters(compounds=[], generic=[], gmx_state={}, perturbation_map=None, merge=StepMerge(compounds=True, enumerations=False, merge_compounds_by=<StepBaseEnum.INPUT_MERGE_BY_NAME: 'name'>, merge_enumerations_by=<StepBaseEnum.INPUT_MERGE_BY_ID: 'id'>), work_dir=None), writeout: ~typing.List[~icolos.core.step_utils.step_writeout.StepWriteoutParameters] = [], execution: ~icolos.core.workflow_steps.step.StepExecutionParameters = StepExecutionParameters(prefix_execution=None, binary_location=None, pipe_input=None, parallelization=StepExecutionParallelizationParameters(jobs=1, max_length_sublists=None), failure_policy=StepFailurePolicyParameters(n_tries=1, retry_wait_seconds=10), check_backend_availability=False, resources=StepExecutionResourceParameters(partition=<ExecutionPlatformEnum.CORE: 'core'>, time='12:00:00', gres=None, tasks=None, mem=None, cores=None, modules=[], other_args={}, additional_lines=[]), platform=<ExecutionPlatformEnum.LOCAL: 'local'>), settings: ~icolos.core.workflow_steps.step.StepSettingsParameters = StepSettingsParameters(arguments=StepSettingsArgsParameters(flags=[], parameters={}), additional={}), eps: float = None, iso_value: int = None, threshold: float = None, min_samples: int = None, format_: str = None)[source]#

Bases: StepBase, BaseModel

eps: float#

format_: str#

iso_value: int#

min_samples: int#

threshold: float#

icolos.core.workflow_steps.fpocket.mdpocket module#

class icolos.core.workflow_steps.fpocket.mdpocket.StepMDpocket(*, step_id: str, work_dir: str = None, type: str = None, data: ~icolos.core.step_utils.input_preparator.StepData = StepData(compounds=[], generic=<icolos.core.containers.generic.GenericContainer object>, gmx_state=Gromacs Topology object: System: [] | Molecules: [] | FF: amber03 | itp files: [] | posre files []), input: ~icolos.core.step_utils.input_preparator.StepInputParameters = StepInputParameters(compounds=[], generic=[], gmx_state={}, perturbation_map=None, merge=StepMerge(compounds=True, enumerations=False, merge_compounds_by=<StepBaseEnum.INPUT_MERGE_BY_NAME: 'name'>, merge_enumerations_by=<StepBaseEnum.INPUT_MERGE_BY_ID: 'id'>), work_dir=None), writeout: ~typing.List[~icolos.core.step_utils.step_writeout.StepWriteoutParameters] = [], execution: ~icolos.core.workflow_steps.step.StepExecutionParameters = StepExecutionParameters(prefix_execution=None, binary_location=None, pipe_input=None, parallelization=StepExecutionParallelizationParameters(jobs=1, max_length_sublists=None), failure_policy=StepFailurePolicyParameters(n_tries=1, retry_wait_seconds=10), check_backend_availability=False, resources=StepExecutionResourceParameters(partition=<ExecutionPlatformEnum.CORE: 'core'>, time='12:00:00', gres=None, tasks=None, mem=None, cores=None, modules=[], other_args={}, additional_lines=[]), platform=<ExecutionPlatformEnum.LOCAL: 'local'>), settings: ~icolos.core.workflow_steps.step.StepSettingsParameters = StepSettingsParameters(arguments=StepSettingsArgsParameters(flags=[], parameters={}), additional={}), eps: float = None, iso_value: int = None, threshold: float = None, min_samples: int = None, format_: str = None)[source]#