icolos.core.workflow_steps.calculation package

Submodules

icolos.core.workflow_steps.calculation.base module

class icolos.core.workflow_steps.calculation.base.StepCalculationBase(*, 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={}))

Bases: StepBase, BaseModel

data: StepData

execution: StepExecutionParameters

input: StepInputParameters

settings: StepSettingsParameters

step_id: str

type: str

work_dir: str

writeout: List[StepWriteoutParameters]

icolos.core.workflow_steps.calculation.boltzmann_weighting module

class icolos.core.workflow_steps.calculation.boltzmann_weighting.StepBoltzmannWeighting(*, 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={}))

Bases: StepCalculationBase, BaseModel

data: StepData

execute()

execution: StepExecutionParameters

input: StepInputParameters

settings: StepSettingsParameters

step_id: str

type: str

work_dir: str

writeout: List[StepWriteoutParameters]

icolos.core.workflow_steps.calculation.clustering module

class icolos.core.workflow_steps.calculation.clustering.StepClustering(*, 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={}))

Bases: StepCalculationBase, BaseModel

data: StepData

execute()

execution: StepExecutionParameters

input: StepInputParameters

settings: StepSettingsParameters

step_id: str

type: str

work_dir: str

writeout: List[StepWriteoutParameters]

icolos.core.workflow_steps.calculation.cosmo module

class icolos.core.workflow_steps.calculation.cosmo.StepCosmo(*, 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={}))

Bases: StepCalculationBase, BaseModel

Step that executes Cosmo.

Note, that the execution (especially in conjunction with a preceding turbomole step) is relatively complex. (1) Take the coord file from the additional data attached to the conformers, (2) run Cosmo, (3) extract the final XYZ snapshot with x2t, (4) translate it to a SDF file with obabel and (5) combined the new coordinates with the tags.

data: StepData

execute()

execution: StepExecutionParameters

input: StepInputParameters

settings: StepSettingsParameters

step_id: str

type: str

work_dir: str

writeout: List[StepWriteoutParameters]

icolos.core.workflow_steps.calculation.cresset_ec module

class icolos.core.workflow_steps.calculation.cresset_ec.StepCressetEC(*, 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={}))

Bases: StepBase, BaseModel

data: StepData

execute()

execution: StepExecutionParameters

input: StepInputParameters

settings: StepSettingsParameters

step_id: str

type: str

work_dir: str

writeout: List[StepWriteoutParameters]

icolos.core.workflow_steps.calculation.esp_sim module

class icolos.core.workflow_steps.calculation.esp_sim.StepEspSim(*, 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={}))

Bases: StepBase, BaseModel

data: StepData

execute()

esp-sim does molecular alignment with RDkit, then computes coulombic overlap integral + tanimoto similarity for shape measurement

Use case takes a reference compound (known binder) and compare to REINVENT compounds

Usage: * Define reference compound using settings.additional, as a smile string, to be embedded by RDkit * The remaining compounds are embedded using a preceeding RDkit embedding * attach the resulting scores to the enumeration

execution: StepExecutionParameters

input: StepInputParameters

settings: StepSettingsParameters

step_id: str

type: str

work_dir: str

writeout: List[StepWriteoutParameters]

icolos.core.workflow_steps.calculation.feature_counter module

class icolos.core.workflow_steps.calculation.feature_counter.StepFeatureCounter(*, 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={}))

Bases: StepCalculationBase, BaseModel

data: StepData

execute()

execution: StepExecutionParameters

input: StepInputParameters

settings: StepSettingsParameters

step_id: str

type: str

work_dir: str

writeout: List[StepWriteoutParameters]

icolos.core.workflow_steps.calculation.jazzy module

class icolos.core.workflow_steps.calculation.jazzy.JazzyAdditional(*, command: str = 'vec')

Bases: BaseModel

command: str

class icolos.core.workflow_steps.calculation.jazzy.StepJazzy(*, 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={}), jazzy_additional: ~icolos.core.workflow_steps.calculation.jazzy.JazzyAdditional = None)

Bases: StepCalculationBase, BaseModel

execute()

jazzy_additional: JazzyAdditional

icolos.core.workflow_steps.calculation.kallisto module

class icolos.core.workflow_steps.calculation.kallisto.KallistoAdditional(*, features: List[str] = ['alp', 'bonds'])

Bases: BaseModel

features: List[str]

class icolos.core.workflow_steps.calculation.kallisto.StepKallisto(*, 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={}), kallisto_additional: ~icolos.core.workflow_steps.calculation.kallisto.KallistoAdditional = None)

Bases: StepCalculationBase, BaseModel

execute()

kallisto_additional: KallistoAdditional

icolos.core.workflow_steps.calculation.lomap module

class icolos.core.workflow_steps.calculation.lomap.StepLomap(*, 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={}))

Bases: StepBase, BaseModel

execute()

icolos.core.workflow_steps.calculation.panther module

class icolos.core.workflow_steps.calculation.panther.StepPanther(*, 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={}), negative_images: ~typing.List = [])

Bases: StepCalculationBase, BaseModel

execute()

negative_images: List

icolos.core.workflow_steps.calculation.rms_filter module

class icolos.core.workflow_steps.calculation.rms_filter.StepRMSFilter(*, 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={}))

Bases: StepCalculationBase, BaseModel

data: StepData

execute()

execution: StepExecutionParameters

input: StepInputParameters

settings: StepSettingsParameters

step_id: str

type: str

work_dir: str

writeout: List[StepWriteoutParameters]

icolos.core.workflow_steps.calculation.rmsd module

class icolos.core.workflow_steps.calculation.rmsd.StepRMSD(*, 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={}))

Bases: StepCalculationBase, BaseModel

data: StepData

execute()

execution: StepExecutionParameters

input: StepInputParameters

settings: StepSettingsParameters

step_id: str

type: str

work_dir: str

writeout: List[StepWriteoutParameters]

icolos.core.workflow_steps.calculation.shaep module

class icolos.core.workflow_steps.calculation.shaep.StepShaep(*, 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={}))

Bases: StepCalculationBase, BaseModel

data: StepData

execute()

execution: StepExecutionParameters

input: StepInputParameters

settings: StepSettingsParameters

step_id: str

type: str

work_dir: str

writeout: List[StepWriteoutParameters]

icolos.core.workflow_steps.calculation.turbomole module

class icolos.core.workflow_steps.calculation.turbomole.StepTurbomole(*, 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={}))

Bases: StepCalculationBase, BaseModel

Step that executes Turbomole.

Note, that the execution (especially in conjunction with a subsequent cosmo step) is relatively complex. (1) Write the conformer as an SDF file to a temporary directory, (2) use obabel to translate it to an XYZ file, (3) use t2x to make a coord file out of it (input for turbomole; is updated during geometry optimization), (4) execute Turbomole, generating a (i) a final coord file and (ii) a trajectory (if specified), (5) use x2t to extract the final “snapshot” as an XYZ file and translate it to SDF and (6) update the coordinates and tags in the conformers

IMPORTANT: Keep the “mol.cosmo” file attached to the conformer as additional data for a possible cosmo step.

data: StepData

execute()

execution: StepExecutionParameters

get_original_conformer(conformer: Conformer) → Conformer

input: StepInputParameters

settings: StepSettingsParameters

step_id: str

type: str

work_dir: str

writeout: List[StepWriteoutParameters]

Module contents