schrodinger.application.steps.converters module

class schrodinger.application.steps.converters.SmilesToMolConverter(*args, **kwargs)

Bases: schrodinger.application.steps.dataclasses.MolOutMixin, schrodinger.stepper.stepper.MapStep

Creates a molecule from the first word in the input string, interpreted as SMILES.

Input

alias of str

mapFunction(string)

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.converters.MolToSmilesConverter(*args, **kwargs)

Bases: schrodinger.application.steps.dataclasses.MolInMixin, schrodinger.stepper.stepper.MapStep

Creates the canonical smiles string for the molecule.

Output

alias of str

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.converters.MolToStructureConverter(*args, **kwargs)

Bases: schrodinger.application.steps.dataclasses.MolInMixin, schrodinger.application.steps.dataclasses.MaeOutMixin, schrodinger.stepper.stepper.MapStep

Step for converting Chem.Mol to structure.Structure objects.

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

Bases: schrodinger.models.parameters.CompoundParam

generate_coordinates: bool

A parameter of the class.

generate_coordinatesChanged

A pyqtSignal emitted by instances of the class.

generate_coordinatesReplaced

A pyqtSignal emitted by instances of the class.

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.converters.StructureToMolConverter(*args, **kwargs)

Bases: schrodinger.application.steps.dataclasses.MaeInMixin, schrodinger.application.steps.dataclasses.MolOutMixin, schrodinger.stepper.stepper.MapStep

Step for converting structure.Structure to Chem.Mol objects.

mapFunction(st)

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.converters.MaeFileWriter(*args, **kwargs)

Bases: schrodinger.application.steps.dataclasses.MaeInMixin, schrodinger.stepper.stepper.ReduceStep

A class to write the input Structure objects to a Maestro file.

Output

alias of schrodinger.stepper.stepper.StepperFile

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

Bases: schrodinger.models.parameters.CompoundParam

filename: str

A parameter of the class.

filenameChanged

A pyqtSignal emitted by instances of the class.

filenameReplaced

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(strucs)

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