schrodinger.application.steps.enumerators module¶

class schrodinger.application.steps.enumerators.SmilesTransformPair(*args, _param_type=<object object>, **kwargs)¶

Bases: CompoundParam

smi: str¶: A parameter of the class.

transform_file: StepperFile¶: A parameter of the class.

smiChanged¶: A pyqtSignal emitted by instances of the class.

smiReplaced¶: A pyqtSignal emitted by instances of the class.

transform_fileChanged¶: A pyqtSignal emitted by instances of the class.

transform_fileReplaced¶: A pyqtSignal emitted by instances of the class.

class schrodinger.application.steps.enumerators.SmilesTransformPairer(settings=None, config=None, step_id=None, metrics_logger_depth=None, _run_info=None, **kwargs)¶

Bases: MolInMixin, UnbatchedReduceStep

For backwards compatibility, this step only implements the validation.

Output¶: alias of SmilesTransformPair

class Settings(*args, _param_type=<object object>, **kwargs)¶

Bases: CompoundParam

transform_folders: List[StepperFolder]¶: A parameter of the class.

transform_foldersChanged¶: A pyqtSignal emitted by instances of the class.

transform_foldersReplaced¶: A pyqtSignal emitted by instances of the class.

validateSettings()¶

Check whether the step settings are valid and return a list of SettingsError and SettingsWarning to report any invalid settings. Default implementation checks that all stepper files are set to valid file paths.

Return type:: list[TaskError or TaskWarning]

reduceFunction(mols)¶

class schrodinger.application.steps.enumerators.TransformApplyer(*args, **kwargs)¶

Bases: MolOutMixin, MapStep

For backwards compatibility, this step only implements the validation.

Input¶: alias of SmilesTransformPair

mapFunction(smiles_transform_pair)¶

The main computation for this step. This function should take in a single input item and return an iterable of outputs. This allows a single output to produce multiple ouputs (e.g. enumeration).

The output may be yielded as a generator, in order to reduce memory usage.

If only a single output is produced for each input, return it as a single-element list.

Parameters:

input –

this will be a single input item from the input source. Implementer is encouraged to use a more descriptive, context- specific variable name. Example:

def mapFunction(self, starting_smiles):
…

class schrodinger.application.steps.enumerators.Synthesizer(*args, **kwargs)¶

Bases: MolMolMixin, Chain

For backwards compatibility, this step only implements the validation.

The settings contain:

core_smarts: the SMARTS that the products should have and needs to be part of the input molecule.

depth: the maximum depth of the retrosynthetic routes to use.

reagent_lib: an optional directory to prepend to the standard reagent library search path

max_products: the maximum number of products try to synthesize for each input molecule per route. Use 0 to force an exhaustive synthesis.

seed: seed for random number generator. If None, the random number generator will not be seeded.

yield_input: whether the input molecule should be returned first

class Settings(*args, _param_type=<object object>, **kwargs)¶

Bases: CompoundParam

core_smarts: str¶: A parameter of the class.

depth: int¶: A parameter of the class.

reagent_lib: StepperFolder¶: A parameter of the class.

max_products: int¶: A parameter of the class.

seed: int¶: A parameter of the class.

yield_input: bool¶: A parameter of the class.

deduplicate_routes: bool¶: A parameter of the class.

core_smartsChanged¶: A pyqtSignal emitted by instances of the class.

core_smartsReplaced¶: A pyqtSignal emitted by instances of the class.

deduplicate_routesChanged¶: A pyqtSignal emitted by instances of the class.

deduplicate_routesReplaced¶: A pyqtSignal emitted by instances of the class.

depthChanged¶: A pyqtSignal emitted by instances of the class.

depthReplaced¶: A pyqtSignal emitted by instances of the class.

max_productsChanged¶: A pyqtSignal emitted by instances of the class.

max_productsReplaced¶: A pyqtSignal emitted by instances of the class.

reagent_libChanged¶: A pyqtSignal emitted by instances of the class.

reagent_libReplaced¶: A pyqtSignal emitted by instances of the class.

seedChanged¶: A pyqtSignal emitted by instances of the class.

seedReplaced¶: A pyqtSignal emitted by instances of the class.

yield_inputChanged¶: A pyqtSignal emitted by instances of the class.

yield_inputReplaced¶: A pyqtSignal emitted by instances of the class.

buildChain()¶: This method must be implemented by subclasses to build the chain. The chain is built by modifying self.steps. The chain’s composition may be dependent on self.settings.

class schrodinger.application.steps.enumerators.RouteSerializer¶

Bases: Serializer

A serializer for RouteNodes

DataType¶: alias of RouteNode

toString(route: RouteNode) → str¶

fromString(route_str: str) → RouteNode¶

class schrodinger.application.steps.enumerators.RouteDeduplicator(*args, **kwargs)¶

Bases: ReduceStep

For backwards compatibility, this step only implements the validation.

Input¶: alias of RouteNode

Output¶: alias of RouteNode

InputSerializer¶: alias of RouteSerializer

OutputSerializer¶: alias of RouteSerializer

reduceFunction(routes)¶

The main computation for this step. This function should take in a iterable of inputs and return an iterable of outputs.

Example:

def reduceFunction(self, words):
    # Find all unique words
    seen_words = set()
    for word in words:
        if word not in seen_words:
            seen_words.add(word)
            yield word

class schrodinger.application.steps.enumerators.RouteEnumerator(*args, **kwargs)¶

Bases: LoggerMixin, MolInMixin, MapStep

For backwards compatibility, this step only implements the validation.

Output¶: alias of RouteNode

OutputSerializer¶: alias of RouteSerializer

class Settings(*args, _param_type=<object object>, **kwargs)¶

Bases: CompoundParam

core_smarts: str¶: A parameter of the class.

depth: int¶: A parameter of the class.

core_smartsChanged¶: A pyqtSignal emitted by instances of the class.

core_smartsReplaced¶: A pyqtSignal emitted by instances of the class.

depthChanged¶: A pyqtSignal emitted by instances of the class.

depthReplaced¶: A pyqtSignal emitted by instances of the class.

validateSettings()¶

Check whether the step settings are valid and return a list of SettingsError and SettingsWarning to report any invalid settings. Default implementation checks that all stepper files are set to valid file paths.

Return type:: list[TaskError or TaskWarning]

mapFunction(mol)¶

The main computation for this step. This function should take in a single input item and return an iterable of outputs. This allows a single output to produce multiple ouputs (e.g. enumeration).

The output may be yielded as a generator, in order to reduce memory usage.

If only a single output is produced for each input, return it as a single-element list.

Parameters:

input –

this will be a single input item from the input source. Implementer is encouraged to use a more descriptive, context- specific variable name. Example:

def mapFunction(self, starting_smiles):
…

class schrodinger.application.steps.enumerators.RouteEvaluator(*args, **kwargs)¶

Bases: MolOutMixin, MapStep

For backwards compatibility, this step only implements the validation.

InputSerializer¶: alias of RouteSerializer

Input¶: alias of RouteNode

class Settings(*args, _param_type=<object object>, **kwargs)¶

Bases: CompoundParam

max_products: int¶: A parameter of the class.

seed: int¶: A parameter of the class.

reagent_lib: StepperFolder¶: A parameter of the class.

max_productsChanged¶: A pyqtSignal emitted by instances of the class.

max_productsReplaced¶: A pyqtSignal emitted by instances of the class.

reagent_libChanged¶: A pyqtSignal emitted by instances of the class.

reagent_libReplaced¶: A pyqtSignal emitted by instances of the class.

seedChanged¶: A pyqtSignal emitted by instances of the class.

seedReplaced¶: A pyqtSignal emitted by instances of the class.

validateSettings()¶

Check whether the step settings are valid and return a list of SettingsError and SettingsWarning to report any invalid settings. Default implementation checks that all stepper files are set to valid file paths.

Return type:: list[TaskError or TaskWarning]

mapFunction(route)¶

The main computation for this step. This function should take in a single input item and return an iterable of outputs. This allows a single output to produce multiple ouputs (e.g. enumeration).

The output may be yielded as a generator, in order to reduce memory usage.

If only a single output is produced for each input, return it as a single-element list.

Parameters:

input –

this will be a single input item from the input source. Implementer is encouraged to use a more descriptive, context- specific variable name. Example:

def mapFunction(self, starting_smiles):
…

class schrodinger.application.steps.enumerators.BaseDecorator(*args, **kwargs)¶

Bases: MolMapStep

The base class for decorators. To use this class you must implement the mapFunction.

Enumerates unique sanitized molecules formed by replacing a hydrogen on a C, N, or O atom in the ligand with an R-group that was attached to an Ar.

The rgroup_atom_smarts setting allows for filtering of which reagents in the rgroup_file are used for the decoration reaction. The default value of ‘#6,#7,#8,#9,#16,#17,#35,#53’ is used if the rgroup_atom_smarts is an empty string or None.

The settings is a filters.ProfileSettings instance whose property_ranges are used to determine with R-groups are allowed to react. The property_ranges are optional.

seealso:: filters.ProfileSettings

Example R-group reagents:

C[Ar]
N[Ar]

Example of a Decorator definition in a yaml file:

Decorator:
    rgroup_atom_smarts: '*'  # allow all unique rgroup reagents
    rgroup_file: rgroups_small.smi
    core_smarts: c1ccccc1
    property_ranges:
        MolWt: [250, 500]
        RingCount: [0, 5]
        NumAromaticRings: [0, 3]
        NumAliphaticRings: [0, 5]
        NumSpiroAtoms: [0, 0]

LEAVING_MOL_WT = 40.956¶

class Settings(*args, _param_type=<object object>, **kwargs)¶

Bases: ProfileSettings

rgroup_file: StepperFile¶: A parameter of the class.

core_smarts: str¶: A parameter of the class.

rgroup_atom_smarts: str¶: A parameter of the class.

validate(step)¶

Validate the settings on behalf of a step.

Parameters:: step – stepper._BaseStep
Return type:: list[TaskError or TaskWarning]

getReagentSmarts()¶

getReagentMol()¶

getReactionSmarts()¶

getRGroups()¶

core_smartsChanged¶: A pyqtSignal emitted by instances of the class.

core_smartsReplaced¶: A pyqtSignal emitted by instances of the class.

property_rangesChanged¶: A pyqtSignal emitted by instances of the class.

property_rangesReplaced¶: A pyqtSignal emitted by instances of the class.

rgroup_atom_smartsChanged¶: A pyqtSignal emitted by instances of the class.

rgroup_atom_smartsReplaced¶: A pyqtSignal emitted by instances of the class.

rgroup_fileChanged¶: A pyqtSignal emitted by instances of the class.

rgroup_fileReplaced¶: A pyqtSignal emitted by instances of the class.

validateSettings()¶

Check whether the step settings are valid and return a list of SettingsError and SettingsWarning to report any invalid settings. Default implementation checks that all stepper files are set to valid file paths.

Return type:: list[TaskError or TaskWarning]

setUp()¶: Hook for adding any type of work that needs to happen before any outputs are created.

class schrodinger.application.steps.enumerators.Decorator(*args, **kwargs)¶

Bases: BaseDecorator

mapFunction(mol)¶

class schrodinger.application.steps.enumerators.FastFragmenter(*args, **kwargs)¶

Bases: MolMapStep

For backwards compatibility, this step only implements the validation.

class Settings(*args, _param_type=<object object>, **kwargs)¶

Bases: CompoundParam

core_smarts: str¶: A parameter of the class.

max_out: int¶: A parameter of the class.

max_mol_wt: float¶: A parameter of the class.

core_smartsChanged¶: A pyqtSignal emitted by instances of the class.

core_smartsReplaced¶: A pyqtSignal emitted by instances of the class.

max_mol_wtChanged¶: A pyqtSignal emitted by instances of the class.

max_mol_wtReplaced¶: A pyqtSignal emitted by instances of the class.

max_outChanged¶: A pyqtSignal emitted by instances of the class.

max_outReplaced¶: A pyqtSignal emitted by instances of the class.

validateSettings()¶

Check whether the step settings are valid and return a list of SettingsError and SettingsWarning to report any invalid settings. Default implementation checks that all stepper files are set to valid file paths.

Return type:: list[TaskError or TaskWarning]

mapFunction(mol)¶