icolos.core.workflow_steps.autodockvina package

Submodules

icolos.core.workflow_steps.autodockvina.docking module

class icolos.core.workflow_steps.autodockvina.docking.ADVAdditional(*, configuration: ADVConfiguration = ADVConfiguration(seed=42, number_poses=1, search_space=ADVSearchSpace(center_x=None, center_y=None, center_z=None, size_x=15.0, size_y=15.0, size_z=15.0), receptor_path=None), grid_ids: List[str] = ['grid0'])

Bases: BaseModel

configuration: ADVConfiguration

grid_ids: List[str]

class icolos.core.workflow_steps.autodockvina.docking.ADVConfiguration(*, seed: int = 42, number_poses: int = 1, search_space: ADVSearchSpace = ADVSearchSpace(center_x=None, center_y=None, center_z=None, size_x=15.0, size_y=15.0, size_z=15.0), receptor_path: str = None)

Bases: BaseModel

number_poses: int

receptor_path: str

search_space: ADVSearchSpace

seed: int

class icolos.core.workflow_steps.autodockvina.docking.ADVSearchSpace(**extra_data: Any)

Bases: BaseModel

center_x: float

center_y: float

center_z: float

size_x: float

size_y: float

size_z: float

class icolos.core.workflow_steps.autodockvina.docking.StepAutoDockVina(*, 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={}), adv_additional: ~icolos.core.workflow_steps.autodockvina.docking.ADVAdditional = None)

Bases: StepBase, BaseModel

adv_additional: ADVAdditional

execute()

icolos.core.workflow_steps.autodockvina.target_preparation module

class icolos.core.workflow_steps.autodockvina.target_preparation.ADVAdditionalTP(*, pH: float = 7.4, input_receptor_pdb: str = None, output_receptor_pdbqt: str = None, extract_box: ADVExtractBoxTP = ADVExtractBoxTP(reference_ligand_path=None, reference_ligand_format='PDB'))

Bases: BaseModel

extract_box: ADVExtractBoxTP

input_receptor_pdb: str

output_receptor_pdbqt: str

pH: float

class icolos.core.workflow_steps.autodockvina.target_preparation.ADVExtractBoxTP(*, reference_ligand_path: str = None, reference_ligand_format: str = 'PDB')

Bases: BaseModel

reference_ligand_format: str

reference_ligand_path: str

class icolos.core.workflow_steps.autodockvina.target_preparation.StepAutoDockVinaTargetPreparation(*, 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={}), adv_additional: ~icolos.core.workflow_steps.autodockvina.target_preparation.ADVAdditionalTP = None)

Bases: StepBase, BaseModel

adv_additional: ADVAdditionalTP

execute()

Module contents