schrodinger.application.steps.ligprep module

class schrodinger.application.steps.ligprep.LigPrepStep(*args, **kwargs)

Bases: schrodinger.stepper.stepper.MapStep

A step that implements the basic lig prep functionality of Structure objects.

The settings is the list of command line arguments that are usually passed to the ligprep script, excluding the input and output arguments.

Within one process more than one LigPrepStep is allowed to be created only if the settings are the same, to avoid problems if both use ‘-epik’.

There are issues with generating tautomers even if the first generator is closed (LIGPREP-1941).

getLicenseRequirements()

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

Bases: schrodinger.models.parameters.CompoundParam

arg_string: str

A parameter of the class.

ligprep_filter_file: schrodinger.stepper.stepper.StepperFile

A parameter of the class.

arg_stringChanged

A pyqtSignal emitted by instances of the class.

arg_stringReplaced

A pyqtSignal emitted by instances of the class.

ligprep_filter_fileChanged

A pyqtSignal emitted by instances of the class.

ligprep_filter_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]

mapFunction(struc)

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):

…

cleanUp()

Hook for adding any type of work that needs to happen after all outputs are exhausted or if some outputs are created and the step is destroyed.

class schrodinger.application.steps.ligprep.LigandPrepper(*args, **kwargs)

Bases: schrodinger.application.steps.dataclasses.MolMolMixin, schrodinger.application.steps.ligprep.LigPrepStep

See also LigPrepMixin

mapFunction(inp_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.ligprep.MaeLigandPrepper(*args, **kwargs)

Bases: schrodinger.application.steps.dataclasses.MaeMaeMixin, schrodinger.application.steps.ligprep.LigPrepStep

See also LigPrepStep