schrodinger.application.steps.enumerators module

schrodinger.application.steps.enumerators.get_transformer_reactions(file, logger=None, lead_in='')

Get the valid reaction SMARTS in file.

Parameters
  • file (str) – the json file to load the transformer reactions from

  • logger – the logger to write errors

  • logger – logging.Logger or NoneType

  • lead_in (str) – the lead in text for error logging

Returns

the valid reaction smarts in file

Return type

generator of ChemicalReaction

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

Bases: schrodinger.models.parameters.CompoundParam

smi: str

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str
transform_file: schrodinger.stepper.stepper.StepperFile

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str
DataClass

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error
__init__(default_value=<object object>, _param_type=<object object>, **kwargs)
classmethod addSubParam(name, param, update_owner=True)
blockSignals(self, b: bool) bool
block_signal_propagation()
childEvent(self, a0: QChildEvent)
children(self) List[QObject]
classmethod configureParam()

Override this class method to set up the abstract param class (e.g. setParamReference on child params.)

connectNotify(self, signal: QMetaMethod)
customEvent(self, a0: QEvent)
classmethod defaultValue()

Returns the default value for this abstract param:

default_atom = Atom.defaultValue()
assert Atom.coord.x == 0
deleteLater(self)
destroyed

destroyed(self, object: typing.Optional[QObject] = None) [signal]

disconnect(a0: QMetaObject.Connection) bool
disconnect(self) None
disconnectNotify(self, signal: QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) List[QByteArray]
event(self, a0: QEvent) bool
eventFilter(self, a0: QObject, a1: QEvent) bool
findChild(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) QObject
findChild(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) QObject
findChildren(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, type: type, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, types: Tuple, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
classmethod fromJson(json_obj)

A factory method which constructs a new object from a given dict loaded from a json string or file.

Parameters

json_obj (dict) – A json-loaded dictionary to create an object from.

Returns

An instance of this class.

Return type

cls

classmethod fromJsonImplementation(json_dict)

Sets the value of this compound param value object from a JSON dict.

Warning

This should never be called directly.

getAbstractParam()

Return the corresponding abstract param for this instance.

classmethod getJsonBlacklist()

Override to customize what params are serialized.

Implementations should return a list of abstract params that should be omitted from serialization.

..NOTE

Returned abstract params must be direct child params of cls, e.g. cls.name, not cls.coord.x.

classmethod getParamSignal(obj, signal_type='Changed')
classmethod getParamValue(obj)

Enables access to a param value on a compound param via an abstract param reference:

a = Atom()
assert Atom.coord.x.getParamValue(a) == 0 # ints default to 0
a.coord.x = 3
assert Atom.coord.x.getParamValue(a) == 3
Parameters

param (CompoundParam) – The owner param to get a param value from

classmethod getSubParam(name)

Get the value of a subparam using the string name:

c = Coord()
assert c.getSubParam('x') == 0

Note

Using the string name to access params is generally discouraged, but can be useful for serializing/deserializing param data.

Parameters

name (str) – The name of the subparam to get the value for.

classmethod getSubParams()

Return a dictionary mapping subparam names to their values.

getTypeHint()
get_version()

Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.

inherits(self, classname: str) bool
initAbstract()
initConcrete()

Override to customize initialization of concrete params.

initializeValue()

Override to dynamically set up the default value of the param. Useful for default values that are determined at runtime. This is called any time the param is reset.

installEventFilter(self, a0: QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

isDefault()

Whether the current value of this instance matches the default value.

isSignalConnected(self, signal: QMetaMethod) bool
isWidgetType(self) bool
isWindowType(self) bool
killTimer(self, id: int)
metaObject(self) QMetaObject
moveToThread(self, thread: QThread)
objectName(self) str
objectNameChanged

objectNameChanged(self, objectName: str) [signal]

classmethod owner()

Get the owner of the param:

# Can be called on an abstract param:
assert Coord.x.owner() == Coord

# ...or on an instance of a CompoundParam
a = Atom()
assert a.coord.owner() == a
classmethod ownerChain()

Returns a list of param owners starting from the toplevel param and ending with self. Examples:

foo.bar.atom.coord.ownerChain() will return [foo, bar, atom, coord] where every item is a concrete param.

Foo.bar.atom.coord.x.ownerChain() will return [Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x] where every item is an abstract params.

classmethod paramName()

Get the name of the param:

# Can be called on an abstract param:
print(Coord.x.paramName()) # 'x'

# ...or on an instance of a CompoundParam
a = Atom()
a.coord.paramName() # 'coord'
parent(self) QObject
property(self, name: str) Any
pyqtConfigure(...)

Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

receivers(self, signal: PYQT_SIGNAL) int
removeEventFilter(self, a0: QObject)
reset(*abstract_params)

Resets this compound param to its default value:

class Line(CompoundParam):
    start = Coord(x=1, y=2)
    end = Coord(x=4, y=5)
line = Line()
line.start.x = line.end.x = 10
assert line.start.x == line.end.x == 10
line.reset()
assert line.start.x == 1
assert line.end.x == 4

Any number of abstract params may be passed in to perform a partial reset of only the specified params:

line.start.x = line.end.x = 10
line.reset(Line.start.x)  # resets just start.x
assert line.start.x == 1
assert line.end.x == 10

line.reset(Line.end)      # resets the entire end point
assert line.end.x == 4

line.start.y = line.end.y = 10
line.reset(Line.start.y, Line.end.y)  # resets the y-coord of both
assert line.start.y == 2
assert line.end.y == 5
sender(self) QObject
senderSignalIndex(self) int
setObjectName(self, name: str)
classmethod setParamValue(obj, value)

Set the value of a param on an object by specifying the instance and the value:

# Setting the param value of a basic param
a = Atom()
Atom.coord.x.setParamValue(a, 5)
assert a.coord.x == 5

# setParamValue can also be used to set the value of CompoundParams
c = Coord()
c.x = 10
atom.coord.setParamValue(a, c)
assert atom.coord.x == 10
Parameters
  • param – The owner param to set a subparam value of.

  • value – The value to set the subparam value to.

setParent(self, a0: QObject)
setProperty(self, name: str, value: Any) bool
classmethod setReference(param1, param2)

Call this class method from configureParam to indicate that two params should be kept in sync. The initial values will start with the default value of param1. Example:

class Square(CompoundParam):
    width: float = 5
    height: float = 10

    @classmethod
    def configureParam(cls):
        super().configureParam()
        cls.setReference(cls.width, cls.height)

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6
Parameters
  • param1 – The first abstract param to keep synced

  • param2 – The second abstract param. After instantiation, this param will take on the value of param1.

setValue(value=None, **kwargs)

Set the value of this CompoundParam to match value.

Parameters
  • value – The value to set this CompoundParam to. It should be the same type as this CompoundParam.

  • kwargs – For internal use only.

signalsBlocked(self) bool
skip_eq_check()
smiChanged
smiReplaced
startTimer(self, interval: int, timerType: Qt.TimerType = Qt.CoarseTimer) int
staticMetaObject = <PyQt6.QtCore.QMetaObject object>
thread(self) QThread
timerEvent(self, a0: QTimerEvent)
toDict()

Return a dictionary version of this CompoundParam. The returned dictionary is fully nested and contains no CompoundParam instances

a = Atom()
a_dict = a.toDict()
assert a_dict['coord']['x'] == 0
assert a_dict['coord'] == {'x':0, 'y':0}
toJson(_mark_version=True)

Create and returns a data structure made up of jsonable items.

Return type

An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation()

Returns a JSON representation of this value object.

Warning

This should never be called directly.

tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) str
transform_fileChanged
transform_fileReplaced
valueChanged
class schrodinger.application.steps.enumerators.SmilesTransformPairer(settings=None, config=None, step_id=None, metrics_logger_depth=None, _run_info=None, **kwargs)

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

Yields all combinations of the input molecules’ SMILES with all json files in all the transform folders.

Raises

RuntimeWarning – when no json files can be found for any folder in transform_folders

Output

alias of schrodinger.application.steps.enumerators.SmilesTransformPair

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

Bases: schrodinger.models.parameters.CompoundParam

transform_folders: List[schrodinger.stepper.stepper.StepperFolder]

A Param to represent lists. Values of this param will have a mutated signal that will be emitted whenever any mutation method is called.

The constructor optionally takes a item_class keyword argument to specify what type of class the items in the list will be. This information will be used for jsonifying the list if specified.

DataClass

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error
__init__(default_value=<object object>, _param_type=<object object>, **kwargs)
classmethod addSubParam(name, param, update_owner=True)
blockSignals(self, b: bool) bool
block_signal_propagation()
childEvent(self, a0: QChildEvent)
children(self) List[QObject]
classmethod configureParam()

Override this class method to set up the abstract param class (e.g. setParamReference on child params.)

connectNotify(self, signal: QMetaMethod)
customEvent(self, a0: QEvent)
classmethod defaultValue()

Returns the default value for this abstract param:

default_atom = Atom.defaultValue()
assert Atom.coord.x == 0
deleteLater(self)
destroyed

destroyed(self, object: typing.Optional[QObject] = None) [signal]

disconnect(a0: QMetaObject.Connection) bool
disconnect(self) None
disconnectNotify(self, signal: QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) List[QByteArray]
event(self, a0: QEvent) bool
eventFilter(self, a0: QObject, a1: QEvent) bool
findChild(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) QObject
findChild(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) QObject
findChildren(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, type: type, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, types: Tuple, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
classmethod fromJson(json_obj)

A factory method which constructs a new object from a given dict loaded from a json string or file.

Parameters

json_obj (dict) – A json-loaded dictionary to create an object from.

Returns

An instance of this class.

Return type

cls

classmethod fromJsonImplementation(json_dict)

Sets the value of this compound param value object from a JSON dict.

Warning

This should never be called directly.

getAbstractParam()

Return the corresponding abstract param for this instance.

classmethod getJsonBlacklist()

Override to customize what params are serialized.

Implementations should return a list of abstract params that should be omitted from serialization.

..NOTE

Returned abstract params must be direct child params of cls, e.g. cls.name, not cls.coord.x.

classmethod getParamSignal(obj, signal_type='Changed')
classmethod getParamValue(obj)

Enables access to a param value on a compound param via an abstract param reference:

a = Atom()
assert Atom.coord.x.getParamValue(a) == 0 # ints default to 0
a.coord.x = 3
assert Atom.coord.x.getParamValue(a) == 3
Parameters

param (CompoundParam) – The owner param to get a param value from

classmethod getSubParam(name)

Get the value of a subparam using the string name:

c = Coord()
assert c.getSubParam('x') == 0

Note

Using the string name to access params is generally discouraged, but can be useful for serializing/deserializing param data.

Parameters

name (str) – The name of the subparam to get the value for.

classmethod getSubParams()

Return a dictionary mapping subparam names to their values.

getTypeHint()
get_version()

Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.

inherits(self, classname: str) bool
initAbstract()
initConcrete()

Override to customize initialization of concrete params.

initializeValue()

Override to dynamically set up the default value of the param. Useful for default values that are determined at runtime. This is called any time the param is reset.

installEventFilter(self, a0: QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

isDefault()

Whether the current value of this instance matches the default value.

isSignalConnected(self, signal: QMetaMethod) bool
isWidgetType(self) bool
isWindowType(self) bool
killTimer(self, id: int)
metaObject(self) QMetaObject
moveToThread(self, thread: QThread)
objectName(self) str
objectNameChanged

objectNameChanged(self, objectName: str) [signal]

classmethod owner()

Get the owner of the param:

# Can be called on an abstract param:
assert Coord.x.owner() == Coord

# ...or on an instance of a CompoundParam
a = Atom()
assert a.coord.owner() == a
classmethod ownerChain()

Returns a list of param owners starting from the toplevel param and ending with self. Examples:

foo.bar.atom.coord.ownerChain() will return [foo, bar, atom, coord] where every item is a concrete param.

Foo.bar.atom.coord.x.ownerChain() will return [Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x] where every item is an abstract params.

classmethod paramName()

Get the name of the param:

# Can be called on an abstract param:
print(Coord.x.paramName()) # 'x'

# ...or on an instance of a CompoundParam
a = Atom()
a.coord.paramName() # 'coord'
parent(self) QObject
property(self, name: str) Any
pyqtConfigure(...)

Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

receivers(self, signal: PYQT_SIGNAL) int
removeEventFilter(self, a0: QObject)
reset(*abstract_params)

Resets this compound param to its default value:

class Line(CompoundParam):
    start = Coord(x=1, y=2)
    end = Coord(x=4, y=5)
line = Line()
line.start.x = line.end.x = 10
assert line.start.x == line.end.x == 10
line.reset()
assert line.start.x == 1
assert line.end.x == 4

Any number of abstract params may be passed in to perform a partial reset of only the specified params:

line.start.x = line.end.x = 10
line.reset(Line.start.x)  # resets just start.x
assert line.start.x == 1
assert line.end.x == 10

line.reset(Line.end)      # resets the entire end point
assert line.end.x == 4

line.start.y = line.end.y = 10
line.reset(Line.start.y, Line.end.y)  # resets the y-coord of both
assert line.start.y == 2
assert line.end.y == 5
sender(self) QObject
senderSignalIndex(self) int
setObjectName(self, name: str)
classmethod setParamValue(obj, value)

Set the value of a param on an object by specifying the instance and the value:

# Setting the param value of a basic param
a = Atom()
Atom.coord.x.setParamValue(a, 5)
assert a.coord.x == 5

# setParamValue can also be used to set the value of CompoundParams
c = Coord()
c.x = 10
atom.coord.setParamValue(a, c)
assert atom.coord.x == 10
Parameters
  • param – The owner param to set a subparam value of.

  • value – The value to set the subparam value to.

setParent(self, a0: QObject)
setProperty(self, name: str, value: Any) bool
classmethod setReference(param1, param2)

Call this class method from configureParam to indicate that two params should be kept in sync. The initial values will start with the default value of param1. Example:

class Square(CompoundParam):
    width: float = 5
    height: float = 10

    @classmethod
    def configureParam(cls):
        super().configureParam()
        cls.setReference(cls.width, cls.height)

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6
Parameters
  • param1 – The first abstract param to keep synced

  • param2 – The second abstract param. After instantiation, this param will take on the value of param1.

setValue(value=None, **kwargs)

Set the value of this CompoundParam to match value.

Parameters
  • value – The value to set this CompoundParam to. It should be the same type as this CompoundParam.

  • kwargs – For internal use only.

signalsBlocked(self) bool
skip_eq_check()
startTimer(self, interval: int, timerType: Qt.TimerType = Qt.CoarseTimer) int
staticMetaObject = <PyQt6.QtCore.QMetaObject object>
thread(self) QThread
timerEvent(self, a0: QTimerEvent)
toDict()

Return a dictionary version of this CompoundParam. The returned dictionary is fully nested and contains no CompoundParam instances

a = Atom()
a_dict = a.toDict()
assert a_dict['coord']['x'] == 0
assert a_dict['coord'] == {'x':0, 'y':0}
toJson(_mark_version=True)

Create and returns a data structure made up of jsonable items.

Return type

An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation()

Returns a JSON representation of this value object.

Warning

This should never be called directly.

tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) str
transform_foldersChanged
transform_foldersReplaced
valueChanged
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)
Input

alias of rdkit.Chem.rdchem.Mol

InputSerializer

alias of schrodinger.application.steps.dataclasses.MolToSmilesSerializer

OutputSerializer

alias of schrodinger.stepper.stepper._DynamicSerializer

__init__(settings=None, config=None, step_id=None, metrics_logger_depth=None, _run_info=None, **kwargs)

See class docstring for info on the different constructor arguments.

blockSignals(self, b: bool) bool
childEvent(self, a0: QChildEvent)
children(self) List[QObject]
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.

connectNotify(self, signal: QMetaMethod)
customEvent(self, a0: QEvent)
deleteLater(self)
destroyed

destroyed(self, object: typing.Optional[QObject] = None) [signal]

disconnect(a0: QMetaObject.Connection) bool
disconnect(self) None
disconnectNotify(self, signal: QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) List[QByteArray]
event(self, a0: QEvent) bool
eventFilter(self, a0: QObject, a1: QEvent) bool
findChild(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) QObject
findChild(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) QObject
findChildren(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, type: type, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, types: Tuple, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
getLicenseRequirements()
getMetricsLoggerDepth() Optional[int]
getOutputSerializer()
getOutputs()

Gets all the outputs in a list by fully iterating the output generator.

getResources(param_type, resource_type)

Get the stepper resources in the settings that are instances of param_type and have a resource_type attribute that is resource_type.

Note does not work for list/set/tuple subparams in the settings.

Parameters
  • param_type (tasks._TaskResource) – the resource parameter type

  • resource_type (ResourceType) – the type of resource to get

Returns

the set of stepper resources of resource_type

Return type

set of tasks._TaskResource

getRunInfo()
getStepDepth() int

Get the depth of a step which is defined as how nested it is. A step run in isolation (i.e. not within a chain) has a depth level of 0.

getStepId()
inherits(self, classname: str) bool
inputs()
installEventFilter(self, a0: QObject)
isSignalConnected(self, signal: QMetaMethod) bool
isWidgetType(self) bool
isWindowType(self) bool
killTimer(self, id: int)
metaObject(self) QMetaObject
moveToThread(self, thread: QThread)
objectName(self) str
objectNameChanged

objectNameChanged(self, objectName: str) [signal]

outputs(*args, **kwargs)
parent(self) QObject
prettyPrintRunInfo()

Format and print info about the step’s run.

property(self, name: str) Any
pyqtConfigure(...)

Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

receivers(self, signal: PYQT_SIGNAL) int
removeEventFilter(self, a0: QObject)
report(prefix='')

Report the settings and batch settings for this step.

sender(self) QObject
senderSignalIndex(self) int
setInputFile(fname)
setInputs(*args, **kwargs)
setObjectName(self, name: str)
setParent(self, a0: QObject)
setProperty(self, name: str, value: Any) bool
setSettings(*args, **kwargs)
setUp()

Hook for adding any type of work that needs to happen before any outputs are created.

signalsBlocked(self) bool
startTimer(self, interval: int, timerType: Qt.TimerType = Qt.CoarseTimer) int
staticMetaObject = <PyQt6.QtCore.QMetaObject object>
thread(self) QThread
timerEvent(self, a0: QTimerEvent)
tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) str
writeOutputsToFile(fname)

Write outputs to fname. By default, the output file will consist of one line for each output with whatever is produced when passing the out- put to str. Override this method if more complex behavior is needed.

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

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

Yield all transformed molecules for the SmilesTranformPair input.

Input

alias of schrodinger.application.steps.enumerators.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):

InputSerializer

alias of schrodinger.stepper.stepper._DynamicSerializer

Output

alias of rdkit.Chem.rdchem.Mol

OutputSerializer

alias of schrodinger.application.steps.dataclasses.MolToSmilesSerializer

Settings

alias of schrodinger.models.parameters.CompoundParam

__init__(*args, **kwargs)
blockSignals(self, b: bool) bool
childEvent(self, a0: QChildEvent)
children(self) List[QObject]
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.

connectNotify(self, signal: QMetaMethod)
customEvent(self, a0: QEvent)
deleteLater(self)
destroyed

destroyed(self, object: typing.Optional[QObject] = None) [signal]

disconnect(a0: QMetaObject.Connection) bool
disconnect(self) None
disconnectNotify(self, signal: QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) List[QByteArray]
event(self, a0: QEvent) bool
eventFilter(self, a0: QObject, a1: QEvent) bool
findChild(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) QObject
findChild(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) QObject
findChildren(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, type: type, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, types: Tuple, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
getInputTopic() Optional[schrodinger.stepper.stepper.Topic]
getLicenseRequirements()
getMetricsLoggerDepth() Optional[int]
getOutputSerializer()
getOutputTopic() Optional[schrodinger.stepper.stepper.Topic]
getOutputs()

Gets all the outputs in a list by fully iterating the output generator.

getResources(param_type, resource_type)

Get the stepper resources in the settings that are instances of param_type and have a resource_type attribute that is resource_type.

Note does not work for list/set/tuple subparams in the settings.

Parameters
  • param_type (tasks._TaskResource) – the resource parameter type

  • resource_type (ResourceType) – the type of resource to get

Returns

the set of stepper resources of resource_type

Return type

set of tasks._TaskResource

getRunInfo()
getStepDepth() int

Get the depth of a step which is defined as how nested it is. A step run in isolation (i.e. not within a chain) has a depth level of 0.

getStepId()
inherits(self, classname: str) bool
initializeTopics()
inputs()
installEventFilter(self, a0: QObject)
isSignalConnected(self, signal: QMetaMethod) bool
isWidgetType(self) bool
isWindowType(self) bool
killTimer(self, id: int)
metaObject(self) QMetaObject
moveToThread(self, thread: QThread)
objectName(self) str
objectNameChanged

objectNameChanged(self, objectName: str) [signal]

outputs(*args, **kwargs)
parent(self) QObject
prettyPrintRunInfo()

Format and print info about the step’s run.

property(self, name: str) Any
pyqtConfigure(...)

Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

receivers(self, signal: PYQT_SIGNAL) int
reduceFunction(inputs)
removeEventFilter(self, a0: QObject)
report(prefix='')

Report the settings and batch settings for this step.

sender(self) QObject
senderSignalIndex(self) int
setBatchSettings(*args, **kwargs)
setInputFile(fname)
setInputTopic(inp_topic: Optional[schrodinger.stepper.stepper.Topic])
setInputs(*args, **kwargs)
setObjectName(self, name: str)
setOutputTopic(outp_topic: Optional[schrodinger.stepper.stepper.Topic])
setParent(self, a0: QObject)
setProperty(self, name: str, value: Any) bool
setSettings(*args, **kwargs)
setUp()

Hook for adding any type of work that needs to happen before any outputs are created.

signalsBlocked(self) bool
startTimer(self, interval: int, timerType: Qt.TimerType = Qt.CoarseTimer) int
staticMetaObject = <PyQt6.QtCore.QMetaObject object>
thread(self) QThread
timerEvent(self, a0: QTimerEvent)
property topic_prefix
property topic_suffix
tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) str
usingPubsub()
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]

writeOutputsToFile(fname)

Write outputs to fname. By default, the output file will consist of one line for each output with whatever is produced when passing the out- put to str. Override this method if more complex behavior is needed.

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

Bases: schrodinger.application.steps.dataclasses.MolMolMixin, schrodinger.stepper.stepper.Chain

Enumerates unique sanitized molecules from a combinatorial synthesis using routes based on the input molecules using the default reaction dictionary and reagent library.

If the maximum number of products is less than the total number of combinations the route synthesis will be done by random sampling, which may yield fewer products than requested. Otherwise a systematic set of unique products will be yielded.

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: schrodinger.models.parameters.CompoundParam

core_smarts: str

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str
depth: int

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str
reagent_lib: schrodinger.stepper.stepper.StepperFolder

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str
max_products: int

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str
seed: int

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str
yield_input: bool

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str
deduplicate_routes: bool

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str
DataClass

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error
__init__(default_value=<object object>, _param_type=<object object>, **kwargs)
classmethod addSubParam(name, param, update_owner=True)
blockSignals(self, b: bool) bool
block_signal_propagation()
childEvent(self, a0: QChildEvent)
children(self) List[QObject]
classmethod configureParam()

Override this class method to set up the abstract param class (e.g. setParamReference on child params.)

connectNotify(self, signal: QMetaMethod)
core_smartsChanged
core_smartsReplaced
customEvent(self, a0: QEvent)
deduplicate_routesChanged
deduplicate_routesReplaced
classmethod defaultValue()

Returns the default value for this abstract param:

default_atom = Atom.defaultValue()
assert Atom.coord.x == 0
deleteLater(self)
depthChanged
depthReplaced
destroyed

destroyed(self, object: typing.Optional[QObject] = None) [signal]

disconnect(a0: QMetaObject.Connection) bool
disconnect(self) None
disconnectNotify(self, signal: QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) List[QByteArray]
event(self, a0: QEvent) bool
eventFilter(self, a0: QObject, a1: QEvent) bool
findChild(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) QObject
findChild(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) QObject
findChildren(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, type: type, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, types: Tuple, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
classmethod fromJson(json_obj)

A factory method which constructs a new object from a given dict loaded from a json string or file.

Parameters

json_obj (dict) – A json-loaded dictionary to create an object from.

Returns

An instance of this class.

Return type

cls

classmethod fromJsonImplementation(json_dict)

Sets the value of this compound param value object from a JSON dict.

Warning

This should never be called directly.

getAbstractParam()

Return the corresponding abstract param for this instance.

classmethod getJsonBlacklist()

Override to customize what params are serialized.

Implementations should return a list of abstract params that should be omitted from serialization.

..NOTE

Returned abstract params must be direct child params of cls, e.g. cls.name, not cls.coord.x.

classmethod getParamSignal(obj, signal_type='Changed')
classmethod getParamValue(obj)

Enables access to a param value on a compound param via an abstract param reference:

a = Atom()
assert Atom.coord.x.getParamValue(a) == 0 # ints default to 0
a.coord.x = 3
assert Atom.coord.x.getParamValue(a) == 3
Parameters

param (CompoundParam) – The owner param to get a param value from

classmethod getSubParam(name)

Get the value of a subparam using the string name:

c = Coord()
assert c.getSubParam('x') == 0

Note

Using the string name to access params is generally discouraged, but can be useful for serializing/deserializing param data.

Parameters

name (str) – The name of the subparam to get the value for.

classmethod getSubParams()

Return a dictionary mapping subparam names to their values.

getTypeHint()
get_version()

Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.

inherits(self, classname: str) bool
initAbstract()
initConcrete()

Override to customize initialization of concrete params.

initializeValue()

Override to dynamically set up the default value of the param. Useful for default values that are determined at runtime. This is called any time the param is reset.

installEventFilter(self, a0: QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

isDefault()

Whether the current value of this instance matches the default value.

isSignalConnected(self, signal: QMetaMethod) bool
isWidgetType(self) bool
isWindowType(self) bool
killTimer(self, id: int)
max_productsChanged
max_productsReplaced
metaObject(self) QMetaObject
moveToThread(self, thread: QThread)
objectName(self) str
objectNameChanged

objectNameChanged(self, objectName: str) [signal]

classmethod owner()

Get the owner of the param:

# Can be called on an abstract param:
assert Coord.x.owner() == Coord

# ...or on an instance of a CompoundParam
a = Atom()
assert a.coord.owner() == a
classmethod ownerChain()

Returns a list of param owners starting from the toplevel param and ending with self. Examples:

foo.bar.atom.coord.ownerChain() will return [foo, bar, atom, coord] where every item is a concrete param.

Foo.bar.atom.coord.x.ownerChain() will return [Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x] where every item is an abstract params.

classmethod paramName()

Get the name of the param:

# Can be called on an abstract param:
print(Coord.x.paramName()) # 'x'

# ...or on an instance of a CompoundParam
a = Atom()
a.coord.paramName() # 'coord'
parent(self) QObject
property(self, name: str) Any
pyqtConfigure(...)

Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

reagent_libChanged
reagent_libReplaced
receivers(self, signal: PYQT_SIGNAL) int
removeEventFilter(self, a0: QObject)
reset(*abstract_params)

Resets this compound param to its default value:

class Line(CompoundParam):
    start = Coord(x=1, y=2)
    end = Coord(x=4, y=5)
line = Line()
line.start.x = line.end.x = 10
assert line.start.x == line.end.x == 10
line.reset()
assert line.start.x == 1
assert line.end.x == 4

Any number of abstract params may be passed in to perform a partial reset of only the specified params:

line.start.x = line.end.x = 10
line.reset(Line.start.x)  # resets just start.x
assert line.start.x == 1
assert line.end.x == 10

line.reset(Line.end)      # resets the entire end point
assert line.end.x == 4

line.start.y = line.end.y = 10
line.reset(Line.start.y, Line.end.y)  # resets the y-coord of both
assert line.start.y == 2
assert line.end.y == 5
seedChanged
seedReplaced
sender(self) QObject
senderSignalIndex(self) int
setObjectName(self, name: str)
classmethod setParamValue(obj, value)

Set the value of a param on an object by specifying the instance and the value:

# Setting the param value of a basic param
a = Atom()
Atom.coord.x.setParamValue(a, 5)
assert a.coord.x == 5

# setParamValue can also be used to set the value of CompoundParams
c = Coord()
c.x = 10
atom.coord.setParamValue(a, c)
assert atom.coord.x == 10
Parameters
  • param – The owner param to set a subparam value of.

  • value – The value to set the subparam value to.

setParent(self, a0: QObject)
setProperty(self, name: str, value: Any) bool
classmethod setReference(param1, param2)

Call this class method from configureParam to indicate that two params should be kept in sync. The initial values will start with the default value of param1. Example:

class Square(CompoundParam):
    width: float = 5
    height: float = 10

    @classmethod
    def configureParam(cls):
        super().configureParam()
        cls.setReference(cls.width, cls.height)

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6
Parameters
  • param1 – The first abstract param to keep synced

  • param2 – The second abstract param. After instantiation, this param will take on the value of param1.

setValue(value=None, **kwargs)

Set the value of this CompoundParam to match value.

Parameters
  • value – The value to set this CompoundParam to. It should be the same type as this CompoundParam.

  • kwargs – For internal use only.

signalsBlocked(self) bool
skip_eq_check()
startTimer(self, interval: int, timerType: Qt.TimerType = Qt.CoarseTimer) int
staticMetaObject = <PyQt6.QtCore.QMetaObject object>
thread(self) QThread
timerEvent(self, a0: QTimerEvent)
toDict()

Return a dictionary version of this CompoundParam. The returned dictionary is fully nested and contains no CompoundParam instances

a = Atom()
a_dict = a.toDict()
assert a_dict['coord']['x'] == 0
assert a_dict['coord'] == {'x':0, 'y':0}
toJson(_mark_version=True)

Create and returns a data structure made up of jsonable items.

Return type

An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation()

Returns a JSON representation of this value object.

Warning

This should never be called directly.

tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) str
valueChanged
yield_inputChanged
yield_inputReplaced
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.

Input

alias of rdkit.Chem.rdchem.Mol

InputSerializer

alias of schrodinger.application.steps.dataclasses.MolToSmilesSerializer

Output

alias of rdkit.Chem.rdchem.Mol

OutputSerializer

alias of schrodinger.application.steps.dataclasses.MolToSmilesSerializer

__init__(*args, **kwargs)
__len__()
addStep(step)
blockSignals(self, b: bool) bool
childEvent(self, a0: QChildEvent)
children(self) List[QObject]
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.

connectNotify(self, signal: QMetaMethod)
customEvent(self, a0: QEvent)
deleteLater(self)
destroyed

destroyed(self, object: typing.Optional[QObject] = None) [signal]

disconnect(a0: QMetaObject.Connection) bool
disconnect(self) None
disconnectNotify(self, signal: QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) List[QByteArray]
event(self, a0: QEvent) bool
eventFilter(self, a0: QObject, a1: QEvent) bool
findChild(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) QObject
findChild(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) QObject
findChildren(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, type: type, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, types: Tuple, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
getInputTopic() Optional[schrodinger.stepper.stepper.Topic]
getLicenseRequirements()
getMetricsLoggerDepth() Optional[int]
getOutputSerializer()
getOutputTopic() Optional[schrodinger.stepper.stepper.Topic]
getOutputs()

Gets all the outputs in a list by fully iterating the output generator.

getResources(param_type, resource_type)

Get the stepper resources in the settings for the chain as well as for every step in the chain that are instances of param_type and have a resource_type attribute that is resource_type.

Note does not work for list/set/tuple subparams in the settings.

Parameters
  • param_type (tasks._TaskResource) – the resource parameter type

  • resource_type (ResourceType) – the type of resource to get

Returns

the set of stepper resources of resource_type

Return type

set of tasks._TaskResource

getRunInfo()
getStepDepth() int

Get the depth of a step which is defined as how nested it is. A step run in isolation (i.e. not within a chain) has a depth level of 0.

getStepId()
inherits(self, classname: str) bool
initializeTopics()
inputs()
installEventFilter(self, a0: QObject)
isSignalConnected(self, signal: QMetaMethod) bool
isWidgetType(self) bool
isWindowType(self) bool
killTimer(self, id: int)
metaObject(self) QMetaObject
moveToThread(self, thread: QThread)
objectName(self) str
objectNameChanged

objectNameChanged(self, objectName: str) [signal]

outputs(*args, **kwargs)
parent(self) QObject
prettyPrintRunInfo()

Format and print info about the step’s run.

property(self, name: str) Any
pyqtConfigure(...)

Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

receivers(self, signal: PYQT_SIGNAL) int
reduceFunction(inputs)
removeEventFilter(self, a0: QObject)
report(prefix='')

Report the workflow steps and their settings (recursively).

Parameters

prefix (str) – the text to start each line with

sender(self) QObject
senderSignalIndex(self) int
setBatchSettings(*args, **kwargs)
setInputFile(input_file: str, starting_step_id: Optional[str] = None)

Set the input file for the chain. If starting_step_id is specified, then all steps before the specified starting step will be skipped. This is useful for resuming a chain’s computation.

setInputTopic(inp_topic: Optional[schrodinger.stepper.stepper.Topic])
setInputs(inputs: Iterable[Any], starting_step_id: Optional[str] = None)

Set the inputs for the chain. If starting_step_id is specified, then all steps before the specified starting step will be skipped. This is useful for resuming a chain’s computation.

setObjectName(self, name: str)
setOutputTopic(outp_topic: Optional[schrodinger.stepper.stepper.Topic])
setParent(self, a0: QObject)
setProperty(self, name: str, value: Any) bool
setSettings(*args, **kwargs)
setStartingStep(starting_step: str)
setUp()

Hook for adding any type of work that needs to happen before any outputs are created.

signalsBlocked(self) bool
startTimer(self, interval: int, timerType: Qt.TimerType = Qt.CoarseTimer) int
staticMetaObject = <PyQt6.QtCore.QMetaObject object>
thread(self) QThread
timerEvent(self, a0: QTimerEvent)
property topic_prefix
property topic_suffix
tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) str
usingPubsub()
validateChain()

Checks that the declaration of the chain is internally consistent - i.e. that each step is valid and each step’s Input class matches the preceding step’s Output class.

validateSettings()

Check whether the chain settings are valid and return a list of SettingsError and SettingsWarning to report any invalid settings. Default implementation simply returns problems from all child steps.

Return type

list[TaskError or TaskWarning]

writeOutputsToFile(fname)

Write outputs to fname. By default, the output file will consist of one line for each output with whatever is produced when passing the out- put to str. Override this method if more complex behavior is needed.

class schrodinger.application.steps.enumerators.RouteSerializer

Bases: schrodinger.stepper.stepper.Serializer

A serializer for RouteNodes

DataType

alias of schrodinger.application.pathfinder.route.RouteNode

toString(route: schrodinger.application.pathfinder.route.RouteNode) str
fromString(route_str: str) schrodinger.application.pathfinder.route.RouteNode
deserialize(fname)

Read in items from fname. :type fname: str :rtype: iterable[self.DataType]

serialize(items, fname)

Write items to a file named fname.

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

Bases: schrodinger.stepper.stepper.ReduceStep

Input

alias of schrodinger.application.pathfinder.route.RouteNode

Output

alias of schrodinger.application.pathfinder.route.RouteNode

InputSerializer

alias of schrodinger.application.steps.enumerators.RouteSerializer

OutputSerializer

alias of schrodinger.application.steps.enumerators.RouteSerializer

setUp()

Hook for adding any type of work that needs to happen before any outputs are created.

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
Settings

alias of schrodinger.models.parameters.CompoundParam

__init__(*args, **kwargs)

See class docstring for info on the different constructor arguments.

blockSignals(self, b: bool) bool
childEvent(self, a0: QChildEvent)
children(self) List[QObject]
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.

connectNotify(self, signal: QMetaMethod)
customEvent(self, a0: QEvent)
deleteLater(self)
destroyed

destroyed(self, object: typing.Optional[QObject] = None) [signal]

disconnect(a0: QMetaObject.Connection) bool
disconnect(self) None
disconnectNotify(self, signal: QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) List[QByteArray]
event(self, a0: QEvent) bool
eventFilter(self, a0: QObject, a1: QEvent) bool
findChild(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) QObject
findChild(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) QObject
findChildren(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, type: type, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, types: Tuple, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
getInputTopic() Optional[schrodinger.stepper.stepper.Topic]
getLicenseRequirements()
getMetricsLoggerDepth() Optional[int]
getOutputSerializer()
getOutputTopic() Optional[schrodinger.stepper.stepper.Topic]
getOutputs()

Gets all the outputs in a list by fully iterating the output generator.

getResources(param_type, resource_type)

Get the stepper resources in the settings that are instances of param_type and have a resource_type attribute that is resource_type.

Note does not work for list/set/tuple subparams in the settings.

Parameters
  • param_type (tasks._TaskResource) – the resource parameter type

  • resource_type (ResourceType) – the type of resource to get

Returns

the set of stepper resources of resource_type

Return type

set of tasks._TaskResource

getRunInfo()
getStepDepth() int

Get the depth of a step which is defined as how nested it is. A step run in isolation (i.e. not within a chain) has a depth level of 0.

getStepId()
inherits(self, classname: str) bool
initializeTopics()
inputs()
installEventFilter(self, a0: QObject)
isSignalConnected(self, signal: QMetaMethod) bool
isWidgetType(self) bool
isWindowType(self) bool
killTimer(self, id: int)
metaObject(self) QMetaObject
moveToThread(self, thread: QThread)
objectName(self) str
objectNameChanged

objectNameChanged(self, objectName: str) [signal]

outputs(*args, **kwargs)
parent(self) QObject
prettyPrintRunInfo()

Format and print info about the step’s run.

property(self, name: str) Any
pyqtConfigure(...)

Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

receivers(self, signal: PYQT_SIGNAL) int
removeEventFilter(self, a0: QObject)
report(prefix='')

Report the settings and batch settings for this step.

sender(self) QObject
senderSignalIndex(self) int
setBatchSettings(*args, **kwargs)
setInputFile(fname)
setInputTopic(inp_topic: Optional[schrodinger.stepper.stepper.Topic])
setInputs(*args, **kwargs)
setObjectName(self, name: str)
setOutputTopic(outp_topic: Optional[schrodinger.stepper.stepper.Topic])
setParent(self, a0: QObject)
setProperty(self, name: str, value: Any) bool
setSettings(*args, **kwargs)
signalsBlocked(self) bool
startTimer(self, interval: int, timerType: Qt.TimerType = Qt.CoarseTimer) int
staticMetaObject = <PyQt6.QtCore.QMetaObject object>
thread(self) QThread
timerEvent(self, a0: QTimerEvent)
property topic_prefix
property topic_suffix
tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) str
usingPubsub()
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]

writeOutputsToFile(fname)

Write outputs to fname. By default, the output file will consist of one line for each output with whatever is produced when passing the out- put to str. Override this method if more complex behavior is needed.

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

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

Mol -> (RouteEnumerator) -> RouteNode

Takes a Mol and enumerates the retrosynthetic routes that can produce it.

Output

alias of schrodinger.application.pathfinder.route.RouteNode

OutputSerializer

alias of schrodinger.application.steps.enumerators.RouteSerializer

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

Bases: schrodinger.models.parameters.CompoundParam

core_smarts: str

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str
depth: int

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str
DataClass

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error
__init__(default_value=<object object>, _param_type=<object object>, **kwargs)
classmethod addSubParam(name, param, update_owner=True)
blockSignals(self, b: bool) bool
block_signal_propagation()
childEvent(self, a0: QChildEvent)
children(self) List[QObject]
classmethod configureParam()

Override this class method to set up the abstract param class (e.g. setParamReference on child params.)

connectNotify(self, signal: QMetaMethod)
core_smartsChanged
core_smartsReplaced
customEvent(self, a0: QEvent)
classmethod defaultValue()

Returns the default value for this abstract param:

default_atom = Atom.defaultValue()
assert Atom.coord.x == 0
deleteLater(self)
depthChanged
depthReplaced
destroyed

destroyed(self, object: typing.Optional[QObject] = None) [signal]

disconnect(a0: QMetaObject.Connection) bool
disconnect(self) None
disconnectNotify(self, signal: QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) List[QByteArray]
event(self, a0: QEvent) bool
eventFilter(self, a0: QObject, a1: QEvent) bool
findChild(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) QObject
findChild(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) QObject
findChildren(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, type: type, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, types: Tuple, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
classmethod fromJson(json_obj)

A factory method which constructs a new object from a given dict loaded from a json string or file.

Parameters

json_obj (dict) – A json-loaded dictionary to create an object from.

Returns

An instance of this class.

Return type

cls

classmethod fromJsonImplementation(json_dict)

Sets the value of this compound param value object from a JSON dict.

Warning

This should never be called directly.

getAbstractParam()

Return the corresponding abstract param for this instance.

classmethod getJsonBlacklist()

Override to customize what params are serialized.

Implementations should return a list of abstract params that should be omitted from serialization.

..NOTE

Returned abstract params must be direct child params of cls, e.g. cls.name, not cls.coord.x.

classmethod getParamSignal(obj, signal_type='Changed')
classmethod getParamValue(obj)

Enables access to a param value on a compound param via an abstract param reference:

a = Atom()
assert Atom.coord.x.getParamValue(a) == 0 # ints default to 0
a.coord.x = 3
assert Atom.coord.x.getParamValue(a) == 3
Parameters

param (CompoundParam) – The owner param to get a param value from

classmethod getSubParam(name)

Get the value of a subparam using the string name:

c = Coord()
assert c.getSubParam('x') == 0

Note

Using the string name to access params is generally discouraged, but can be useful for serializing/deserializing param data.

Parameters

name (str) – The name of the subparam to get the value for.

classmethod getSubParams()

Return a dictionary mapping subparam names to their values.

getTypeHint()
get_version()

Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.

inherits(self, classname: str) bool
initAbstract()
initConcrete()

Override to customize initialization of concrete params.

initializeValue()

Override to dynamically set up the default value of the param. Useful for default values that are determined at runtime. This is called any time the param is reset.

installEventFilter(self, a0: QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

isDefault()

Whether the current value of this instance matches the default value.

isSignalConnected(self, signal: QMetaMethod) bool
isWidgetType(self) bool
isWindowType(self) bool
killTimer(self, id: int)
metaObject(self) QMetaObject
moveToThread(self, thread: QThread)
objectName(self) str
objectNameChanged

objectNameChanged(self, objectName: str) [signal]

classmethod owner()

Get the owner of the param:

# Can be called on an abstract param:
assert Coord.x.owner() == Coord

# ...or on an instance of a CompoundParam
a = Atom()
assert a.coord.owner() == a
classmethod ownerChain()

Returns a list of param owners starting from the toplevel param and ending with self. Examples:

foo.bar.atom.coord.ownerChain() will return [foo, bar, atom, coord] where every item is a concrete param.

Foo.bar.atom.coord.x.ownerChain() will return [Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x] where every item is an abstract params.

classmethod paramName()

Get the name of the param:

# Can be called on an abstract param:
print(Coord.x.paramName()) # 'x'

# ...or on an instance of a CompoundParam
a = Atom()
a.coord.paramName() # 'coord'
parent(self) QObject
property(self, name: str) Any
pyqtConfigure(...)

Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

receivers(self, signal: PYQT_SIGNAL) int
removeEventFilter(self, a0: QObject)
reset(*abstract_params)

Resets this compound param to its default value:

class Line(CompoundParam):
    start = Coord(x=1, y=2)
    end = Coord(x=4, y=5)
line = Line()
line.start.x = line.end.x = 10
assert line.start.x == line.end.x == 10
line.reset()
assert line.start.x == 1
assert line.end.x == 4

Any number of abstract params may be passed in to perform a partial reset of only the specified params:

line.start.x = line.end.x = 10
line.reset(Line.start.x)  # resets just start.x
assert line.start.x == 1
assert line.end.x == 10

line.reset(Line.end)      # resets the entire end point
assert line.end.x == 4

line.start.y = line.end.y = 10
line.reset(Line.start.y, Line.end.y)  # resets the y-coord of both
assert line.start.y == 2
assert line.end.y == 5
sender(self) QObject
senderSignalIndex(self) int
setObjectName(self, name: str)
classmethod setParamValue(obj, value)

Set the value of a param on an object by specifying the instance and the value:

# Setting the param value of a basic param
a = Atom()
Atom.coord.x.setParamValue(a, 5)
assert a.coord.x == 5

# setParamValue can also be used to set the value of CompoundParams
c = Coord()
c.x = 10
atom.coord.setParamValue(a, c)
assert atom.coord.x == 10
Parameters
  • param – The owner param to set a subparam value of.

  • value – The value to set the subparam value to.

setParent(self, a0: QObject)
setProperty(self, name: str, value: Any) bool
classmethod setReference(param1, param2)

Call this class method from configureParam to indicate that two params should be kept in sync. The initial values will start with the default value of param1. Example:

class Square(CompoundParam):
    width: float = 5
    height: float = 10

    @classmethod
    def configureParam(cls):
        super().configureParam()
        cls.setReference(cls.width, cls.height)

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6
Parameters
  • param1 – The first abstract param to keep synced

  • param2 – The second abstract param. After instantiation, this param will take on the value of param1.

setValue(value=None, **kwargs)

Set the value of this CompoundParam to match value.

Parameters
  • value – The value to set this CompoundParam to. It should be the same type as this CompoundParam.

  • kwargs – For internal use only.

signalsBlocked(self) bool
skip_eq_check()
startTimer(self, interval: int, timerType: Qt.TimerType = Qt.CoarseTimer) int
staticMetaObject = <PyQt6.QtCore.QMetaObject object>
thread(self) QThread
timerEvent(self, a0: QTimerEvent)
toDict()

Return a dictionary version of this CompoundParam. The returned dictionary is fully nested and contains no CompoundParam instances

a = Atom()
a_dict = a.toDict()
assert a_dict['coord']['x'] == 0
assert a_dict['coord'] == {'x':0, 'y':0}
toJson(_mark_version=True)

Create and returns a data structure made up of jsonable items.

Return type

An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation()

Returns a JSON representation of this value object.

Warning

This should never be called directly.

tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) str
valueChanged
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.

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):

Input

alias of rdkit.Chem.rdchem.Mol

InputSerializer

alias of schrodinger.application.steps.dataclasses.MolToSmilesSerializer

__init__(*args, **kwargs)
blockSignals(self, b: bool) bool
childEvent(self, a0: QChildEvent)
children(self) List[QObject]
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.

connectNotify(self, signal: QMetaMethod)
customEvent(self, a0: QEvent)
deleteLater(self)
destroyed

destroyed(self, object: typing.Optional[QObject] = None) [signal]

disconnect(a0: QMetaObject.Connection) bool
disconnect(self) None
disconnectNotify(self, signal: QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) List[QByteArray]
event(self, a0: QEvent) bool
eventFilter(self, a0: QObject, a1: QEvent) bool
findChild(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) QObject
findChild(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) QObject
findChildren(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, type: type, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, types: Tuple, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
getInputTopic() Optional[schrodinger.stepper.stepper.Topic]
getLicenseRequirements()
getMetricsLoggerDepth() Optional[int]
getOutputSerializer()
getOutputTopic() Optional[schrodinger.stepper.stepper.Topic]
getOutputs()

Gets all the outputs in a list by fully iterating the output generator.

getResources(param_type, resource_type)

Get the stepper resources in the settings that are instances of param_type and have a resource_type attribute that is resource_type.

Note does not work for list/set/tuple subparams in the settings.

Parameters
  • param_type (tasks._TaskResource) – the resource parameter type

  • resource_type (ResourceType) – the type of resource to get

Returns

the set of stepper resources of resource_type

Return type

set of tasks._TaskResource

getRunInfo()
getStepDepth() int

Get the depth of a step which is defined as how nested it is. A step run in isolation (i.e. not within a chain) has a depth level of 0.

getStepId()
inherits(self, classname: str) bool
initializeTopics()
inputs()
installEventFilter(self, a0: QObject)
isSignalConnected(self, signal: QMetaMethod) bool
isWidgetType(self) bool
isWindowType(self) bool
killTimer(self, id: int)
metaObject(self) QMetaObject
moveToThread(self, thread: QThread)
objectName(self) str
objectNameChanged

objectNameChanged(self, objectName: str) [signal]

outputs(*args, **kwargs)
parent(self) QObject
prettyPrintRunInfo()

Format and print info about the step’s run.

property(self, name: str) Any
pyqtConfigure(...)

Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

receivers(self, signal: PYQT_SIGNAL) int
reduceFunction(inputs)
removeEventFilter(self, a0: QObject)
report(prefix='')

Report the settings and batch settings for this step.

sender(self) QObject
senderSignalIndex(self) int
setBatchSettings(*args, **kwargs)
setInputFile(fname)
setInputTopic(inp_topic: Optional[schrodinger.stepper.stepper.Topic])
setInputs(*args, **kwargs)
setObjectName(self, name: str)
setOutputTopic(outp_topic: Optional[schrodinger.stepper.stepper.Topic])
setParent(self, a0: QObject)
setProperty(self, name: str, value: Any) bool
setSettings(*args, **kwargs)
signalsBlocked(self) bool
startTimer(self, interval: int, timerType: Qt.TimerType = Qt.CoarseTimer) int
staticMetaObject = <PyQt6.QtCore.QMetaObject object>
thread(self) QThread
timerEvent(self, a0: QTimerEvent)
property topic_prefix
property topic_suffix
tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) str
usingPubsub()
writeOutputsToFile(fname)

Write outputs to fname. By default, the output file will consist of one line for each output with whatever is produced when passing the out- put to str. Override this method if more complex behavior is needed.

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

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

RouteNode -> (RouteEvaluator) -> Mol

Takes a route and produces all products from it.

InputSerializer

alias of schrodinger.application.steps.enumerators.RouteSerializer

Input

alias of schrodinger.application.pathfinder.route.RouteNode

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

Bases: schrodinger.models.parameters.CompoundParam

max_products: int

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str
seed: int

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str
reagent_lib: schrodinger.stepper.stepper.StepperFolder

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str
DataClass

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error
__init__(default_value=<object object>, _param_type=<object object>, **kwargs)
classmethod addSubParam(name, param, update_owner=True)
blockSignals(self, b: bool) bool
block_signal_propagation()
childEvent(self, a0: QChildEvent)
children(self) List[QObject]
classmethod configureParam()

Override this class method to set up the abstract param class (e.g. setParamReference on child params.)

connectNotify(self, signal: QMetaMethod)
customEvent(self, a0: QEvent)
classmethod defaultValue()

Returns the default value for this abstract param:

default_atom = Atom.defaultValue()
assert Atom.coord.x == 0
deleteLater(self)
destroyed

destroyed(self, object: typing.Optional[QObject] = None) [signal]

disconnect(a0: QMetaObject.Connection) bool
disconnect(self) None
disconnectNotify(self, signal: QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) List[QByteArray]
event(self, a0: QEvent) bool
eventFilter(self, a0: QObject, a1: QEvent) bool
findChild(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) QObject
findChild(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) QObject
findChildren(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, type: type, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, types: Tuple, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
classmethod fromJson(json_obj)

A factory method which constructs a new object from a given dict loaded from a json string or file.

Parameters

json_obj (dict) – A json-loaded dictionary to create an object from.

Returns

An instance of this class.

Return type

cls

classmethod fromJsonImplementation(json_dict)

Sets the value of this compound param value object from a JSON dict.

Warning

This should never be called directly.

getAbstractParam()

Return the corresponding abstract param for this instance.

classmethod getJsonBlacklist()

Override to customize what params are serialized.

Implementations should return a list of abstract params that should be omitted from serialization.

..NOTE

Returned abstract params must be direct child params of cls, e.g. cls.name, not cls.coord.x.

classmethod getParamSignal(obj, signal_type='Changed')
classmethod getParamValue(obj)

Enables access to a param value on a compound param via an abstract param reference:

a = Atom()
assert Atom.coord.x.getParamValue(a) == 0 # ints default to 0
a.coord.x = 3
assert Atom.coord.x.getParamValue(a) == 3
Parameters

param (CompoundParam) – The owner param to get a param value from

classmethod getSubParam(name)

Get the value of a subparam using the string name:

c = Coord()
assert c.getSubParam('x') == 0

Note

Using the string name to access params is generally discouraged, but can be useful for serializing/deserializing param data.

Parameters

name (str) – The name of the subparam to get the value for.

classmethod getSubParams()

Return a dictionary mapping subparam names to their values.

getTypeHint()
get_version()

Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.

inherits(self, classname: str) bool
initAbstract()
initConcrete()

Override to customize initialization of concrete params.

initializeValue()

Override to dynamically set up the default value of the param. Useful for default values that are determined at runtime. This is called any time the param is reset.

installEventFilter(self, a0: QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

isDefault()

Whether the current value of this instance matches the default value.

isSignalConnected(self, signal: QMetaMethod) bool
isWidgetType(self) bool
isWindowType(self) bool
killTimer(self, id: int)
max_productsChanged
max_productsReplaced
metaObject(self) QMetaObject
moveToThread(self, thread: QThread)
objectName(self) str
objectNameChanged

objectNameChanged(self, objectName: str) [signal]

classmethod owner()

Get the owner of the param:

# Can be called on an abstract param:
assert Coord.x.owner() == Coord

# ...or on an instance of a CompoundParam
a = Atom()
assert a.coord.owner() == a
classmethod ownerChain()

Returns a list of param owners starting from the toplevel param and ending with self. Examples:

foo.bar.atom.coord.ownerChain() will return [foo, bar, atom, coord] where every item is a concrete param.

Foo.bar.atom.coord.x.ownerChain() will return [Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x] where every item is an abstract params.

classmethod paramName()

Get the name of the param:

# Can be called on an abstract param:
print(Coord.x.paramName()) # 'x'

# ...or on an instance of a CompoundParam
a = Atom()
a.coord.paramName() # 'coord'
parent(self) QObject
property(self, name: str) Any
pyqtConfigure(...)

Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

reagent_libChanged
reagent_libReplaced
receivers(self, signal: PYQT_SIGNAL) int
removeEventFilter(self, a0: QObject)
reset(*abstract_params)

Resets this compound param to its default value:

class Line(CompoundParam):
    start = Coord(x=1, y=2)
    end = Coord(x=4, y=5)
line = Line()
line.start.x = line.end.x = 10
assert line.start.x == line.end.x == 10
line.reset()
assert line.start.x == 1
assert line.end.x == 4

Any number of abstract params may be passed in to perform a partial reset of only the specified params:

line.start.x = line.end.x = 10
line.reset(Line.start.x)  # resets just start.x
assert line.start.x == 1
assert line.end.x == 10

line.reset(Line.end)      # resets the entire end point
assert line.end.x == 4

line.start.y = line.end.y = 10
line.reset(Line.start.y, Line.end.y)  # resets the y-coord of both
assert line.start.y == 2
assert line.end.y == 5
seedChanged
seedReplaced
sender(self) QObject
senderSignalIndex(self) int
setObjectName(self, name: str)
classmethod setParamValue(obj, value)

Set the value of a param on an object by specifying the instance and the value:

# Setting the param value of a basic param
a = Atom()
Atom.coord.x.setParamValue(a, 5)
assert a.coord.x == 5

# setParamValue can also be used to set the value of CompoundParams
c = Coord()
c.x = 10
atom.coord.setParamValue(a, c)
assert atom.coord.x == 10
Parameters
  • param – The owner param to set a subparam value of.

  • value – The value to set the subparam value to.

setParent(self, a0: QObject)
setProperty(self, name: str, value: Any) bool
classmethod setReference(param1, param2)

Call this class method from configureParam to indicate that two params should be kept in sync. The initial values will start with the default value of param1. Example:

class Square(CompoundParam):
    width: float = 5
    height: float = 10

    @classmethod
    def configureParam(cls):
        super().configureParam()
        cls.setReference(cls.width, cls.height)

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6
Parameters
  • param1 – The first abstract param to keep synced

  • param2 – The second abstract param. After instantiation, this param will take on the value of param1.

setValue(value=None, **kwargs)

Set the value of this CompoundParam to match value.

Parameters
  • value – The value to set this CompoundParam to. It should be the same type as this CompoundParam.

  • kwargs – For internal use only.

signalsBlocked(self) bool
skip_eq_check()
startTimer(self, interval: int, timerType: Qt.TimerType = Qt.CoarseTimer) int
staticMetaObject = <PyQt6.QtCore.QMetaObject object>
thread(self) QThread
timerEvent(self, a0: QTimerEvent)
toDict()

Return a dictionary version of this CompoundParam. The returned dictionary is fully nested and contains no CompoundParam instances

a = Atom()
a_dict = a.toDict()
assert a_dict['coord']['x'] == 0
assert a_dict['coord'] == {'x':0, 'y':0}
toJson(_mark_version=True)

Create and returns a data structure made up of jsonable items.

Return type

An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation()

Returns a JSON representation of this value object.

Warning

This should never be called directly.

tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) str
valueChanged
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.

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):

Output

alias of rdkit.Chem.rdchem.Mol

OutputSerializer

alias of schrodinger.application.steps.dataclasses.MolToSmilesSerializer

__init__(*args, **kwargs)
blockSignals(self, b: bool) bool
childEvent(self, a0: QChildEvent)
children(self) List[QObject]
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.

connectNotify(self, signal: QMetaMethod)
customEvent(self, a0: QEvent)
deleteLater(self)
destroyed

destroyed(self, object: typing.Optional[QObject] = None) [signal]

disconnect(a0: QMetaObject.Connection) bool
disconnect(self) None
disconnectNotify(self, signal: QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) List[QByteArray]
event(self, a0: QEvent) bool
eventFilter(self, a0: QObject, a1: QEvent) bool
findChild(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) QObject
findChild(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) QObject
findChildren(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, type: type, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, types: Tuple, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
getInputTopic() Optional[schrodinger.stepper.stepper.Topic]
getLicenseRequirements()
getMetricsLoggerDepth() Optional[int]
getOutputSerializer()
getOutputTopic() Optional[schrodinger.stepper.stepper.Topic]
getOutputs()

Gets all the outputs in a list by fully iterating the output generator.

getResources(param_type, resource_type)

Get the stepper resources in the settings that are instances of param_type and have a resource_type attribute that is resource_type.

Note does not work for list/set/tuple subparams in the settings.

Parameters
  • param_type (tasks._TaskResource) – the resource parameter type

  • resource_type (ResourceType) – the type of resource to get

Returns

the set of stepper resources of resource_type

Return type

set of tasks._TaskResource

getRunInfo()
getStepDepth() int

Get the depth of a step which is defined as how nested it is. A step run in isolation (i.e. not within a chain) has a depth level of 0.

getStepId()
inherits(self, classname: str) bool
initializeTopics()
inputs()
installEventFilter(self, a0: QObject)
isSignalConnected(self, signal: QMetaMethod) bool
isWidgetType(self) bool
isWindowType(self) bool
killTimer(self, id: int)
metaObject(self) QMetaObject
moveToThread(self, thread: QThread)
objectName(self) str
objectNameChanged

objectNameChanged(self, objectName: str) [signal]

outputs(*args, **kwargs)
parent(self) QObject
prettyPrintRunInfo()

Format and print info about the step’s run.

property(self, name: str) Any
pyqtConfigure(...)

Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

receivers(self, signal: PYQT_SIGNAL) int
reduceFunction(inputs)
removeEventFilter(self, a0: QObject)
report(prefix='')

Report the settings and batch settings for this step.

sender(self) QObject
senderSignalIndex(self) int
setBatchSettings(*args, **kwargs)
setInputFile(fname)
setInputTopic(inp_topic: Optional[schrodinger.stepper.stepper.Topic])
setInputs(*args, **kwargs)
setObjectName(self, name: str)
setOutputTopic(outp_topic: Optional[schrodinger.stepper.stepper.Topic])
setParent(self, a0: QObject)
setProperty(self, name: str, value: Any) bool
setSettings(*args, **kwargs)
signalsBlocked(self) bool
startTimer(self, interval: int, timerType: Qt.TimerType = Qt.CoarseTimer) int
staticMetaObject = <PyQt6.QtCore.QMetaObject object>
thread(self) QThread
timerEvent(self, a0: QTimerEvent)
property topic_prefix
property topic_suffix
tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) str
usingPubsub()
writeOutputsToFile(fname)

Write outputs to fname. By default, the output file will consist of one line for each output with whatever is produced when passing the out- put to str. Override this method if more complex behavior is needed.

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

Bases: schrodinger.application.steps.basesteps.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: schrodinger.application.steps.filters.ProfileSettings

rgroup_file: schrodinger.stepper.stepper.StepperFile

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str
core_smarts: str

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str
rgroup_atom_smarts: str

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str
validate(step)

Validate the settings on behalf of a step.

Parameters

step – stepper._BaseStep

Return type

list[TaskError or TaskWarning]

getReagentSmarts()
getReagentMol()
getReactionSmarts()
getRGroups()
DataClass

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error
__init__(default_value=<object object>, _param_type=<object object>, **kwargs)
classmethod addSubParam(name, param, update_owner=True)
blockSignals(self, b: bool) bool
block_signal_propagation()
childEvent(self, a0: QChildEvent)
children(self) List[QObject]
classmethod configureParam()

Override this class method to set up the abstract param class (e.g. setParamReference on child params.)

connectNotify(self, signal: QMetaMethod)
core_smartsChanged
core_smartsReplaced
customEvent(self, a0: QEvent)
classmethod defaultValue()

Returns the default value for this abstract param:

default_atom = Atom.defaultValue()
assert Atom.coord.x == 0
deleteLater(self)
destroyed

destroyed(self, object: typing.Optional[QObject] = None) [signal]

disconnect(a0: QMetaObject.Connection) bool
disconnect(self) None
disconnectNotify(self, signal: QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) List[QByteArray]
event(self, a0: QEvent) bool
eventFilter(self, a0: QObject, a1: QEvent) bool
findChild(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) QObject
findChild(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) QObject
findChildren(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, type: type, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, types: Tuple, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
classmethod fromJson(json_obj)

A factory method which constructs a new object from a given dict loaded from a json string or file.

Parameters

json_obj (dict) – A json-loaded dictionary to create an object from.

Returns

An instance of this class.

Return type

cls

classmethod fromJsonImplementation(json_dict)

Sets the value of this compound param value object from a JSON dict.

Warning

This should never be called directly.

getAbstractParam()

Return the corresponding abstract param for this instance.

classmethod getJsonBlacklist()

Override to customize what params are serialized.

Implementations should return a list of abstract params that should be omitted from serialization.

..NOTE

Returned abstract params must be direct child params of cls, e.g. cls.name, not cls.coord.x.

classmethod getParamSignal(obj, signal_type='Changed')
classmethod getParamValue(obj)

Enables access to a param value on a compound param via an abstract param reference:

a = Atom()
assert Atom.coord.x.getParamValue(a) == 0 # ints default to 0
a.coord.x = 3
assert Atom.coord.x.getParamValue(a) == 3
Parameters

param (CompoundParam) – The owner param to get a param value from

classmethod getSubParam(name)

Get the value of a subparam using the string name:

c = Coord()
assert c.getSubParam('x') == 0

Note

Using the string name to access params is generally discouraged, but can be useful for serializing/deserializing param data.

Parameters

name (str) – The name of the subparam to get the value for.

classmethod getSubParams()

Return a dictionary mapping subparam names to their values.

getTypeHint()
get_version()

Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.

inherits(self, classname: str) bool
initAbstract()
initConcrete()

Override to customize initialization of concrete params.

initializeValue()

Override to dynamically set up the default value of the param. Useful for default values that are determined at runtime. This is called any time the param is reset.

installEventFilter(self, a0: QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

isDefault()

Whether the current value of this instance matches the default value.

isSignalConnected(self, signal: QMetaMethod) bool
isWidgetType(self) bool
isWindowType(self) bool
killTimer(self, id: int)
metaObject(self) QMetaObject
moveToThread(self, thread: QThread)
objectName(self) str
objectNameChanged

objectNameChanged(self, objectName: str) [signal]

classmethod owner()

Get the owner of the param:

# Can be called on an abstract param:
assert Coord.x.owner() == Coord

# ...or on an instance of a CompoundParam
a = Atom()
assert a.coord.owner() == a
classmethod ownerChain()

Returns a list of param owners starting from the toplevel param and ending with self. Examples:

foo.bar.atom.coord.ownerChain() will return [foo, bar, atom, coord] where every item is a concrete param.

Foo.bar.atom.coord.x.ownerChain() will return [Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x] where every item is an abstract params.

classmethod paramName()

Get the name of the param:

# Can be called on an abstract param:
print(Coord.x.paramName()) # 'x'

# ...or on an instance of a CompoundParam
a = Atom()
a.coord.paramName() # 'coord'
parent(self) QObject
property(self, name: str) Any
property_ranges: Dict[str, List[float]]

A Param to represent dictionaries. Values of this param will have a mutated signal that will be emitted whenever any mutation method is called.

The constructor optionally takes a value_class keyword argument to specify what type of class the values will be. This information will be used for jsonifying the dictionary if specified. (Note that non-string keys are not currently supported for jsonification. This may change in the future. See PANEL-13029).

property_rangesChanged
property_rangesReplaced
pyqtConfigure(...)

Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

receivers(self, signal: PYQT_SIGNAL) int
removeEventFilter(self, a0: QObject)
reset(*abstract_params)

Resets this compound param to its default value:

class Line(CompoundParam):
    start = Coord(x=1, y=2)
    end = Coord(x=4, y=5)
line = Line()
line.start.x = line.end.x = 10
assert line.start.x == line.end.x == 10
line.reset()
assert line.start.x == 1
assert line.end.x == 4

Any number of abstract params may be passed in to perform a partial reset of only the specified params:

line.start.x = line.end.x = 10
line.reset(Line.start.x)  # resets just start.x
assert line.start.x == 1
assert line.end.x == 10

line.reset(Line.end)      # resets the entire end point
assert line.end.x == 4

line.start.y = line.end.y = 10
line.reset(Line.start.y, Line.end.y)  # resets the y-coord of both
assert line.start.y == 2
assert line.end.y == 5
rgroup_atom_smartsChanged
rgroup_atom_smartsReplaced
rgroup_fileChanged
rgroup_fileReplaced
sender(self) QObject
senderSignalIndex(self) int
setObjectName(self, name: str)
classmethod setParamValue(obj, value)

Set the value of a param on an object by specifying the instance and the value:

# Setting the param value of a basic param
a = Atom()
Atom.coord.x.setParamValue(a, 5)
assert a.coord.x == 5

# setParamValue can also be used to set the value of CompoundParams
c = Coord()
c.x = 10
atom.coord.setParamValue(a, c)
assert atom.coord.x == 10
Parameters
  • param – The owner param to set a subparam value of.

  • value – The value to set the subparam value to.

setParent(self, a0: QObject)
setProperty(self, name: str, value: Any) bool
classmethod setReference(param1, param2)

Call this class method from configureParam to indicate that two params should be kept in sync. The initial values will start with the default value of param1. Example:

class Square(CompoundParam):
    width: float = 5
    height: float = 10

    @classmethod
    def configureParam(cls):
        super().configureParam()
        cls.setReference(cls.width, cls.height)

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6
Parameters
  • param1 – The first abstract param to keep synced

  • param2 – The second abstract param. After instantiation, this param will take on the value of param1.

setValue(value=None, **kwargs)

Set the value of this CompoundParam to match value.

Parameters
  • value – The value to set this CompoundParam to. It should be the same type as this CompoundParam.

  • kwargs – For internal use only.

signalsBlocked(self) bool
skip_eq_check()
startTimer(self, interval: int, timerType: Qt.TimerType = Qt.CoarseTimer) int
staticMetaObject = <PyQt6.QtCore.QMetaObject object>
thread(self) QThread
timerEvent(self, a0: QTimerEvent)
toDict()

Return a dictionary version of this CompoundParam. The returned dictionary is fully nested and contains no CompoundParam instances

a = Atom()
a_dict = a.toDict()
assert a_dict['coord']['x'] == 0
assert a_dict['coord'] == {'x':0, 'y':0}
toJson(_mark_version=True)

Create and returns a data structure made up of jsonable items.

Return type

An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation()

Returns a JSON representation of this value object.

Warning

This should never be called directly.

tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) str
valueChanged
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.

Input

alias of rdkit.Chem.rdchem.Mol

InputSerializer

alias of schrodinger.application.steps.dataclasses.MolToSmilesSerializer

Output

alias of rdkit.Chem.rdchem.Mol

OutputSerializer

alias of schrodinger.application.steps.dataclasses.MolToSmilesSerializer

__init__(*args, **kwargs)
blockSignals(self, b: bool) bool
childEvent(self, a0: QChildEvent)
children(self) List[QObject]
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.

connectNotify(self, signal: QMetaMethod)
customEvent(self, a0: QEvent)
deleteLater(self)
destroyed

destroyed(self, object: typing.Optional[QObject] = None) [signal]

disconnect(a0: QMetaObject.Connection) bool
disconnect(self) None
disconnectNotify(self, signal: QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) List[QByteArray]
event(self, a0: QEvent) bool
eventFilter(self, a0: QObject, a1: QEvent) bool
findChild(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) QObject
findChild(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) QObject
findChildren(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, type: type, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, types: Tuple, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
getInputTopic() Optional[schrodinger.stepper.stepper.Topic]
getLicenseRequirements()
getMetricsLoggerDepth() Optional[int]
getOutputSerializer()
getOutputTopic() Optional[schrodinger.stepper.stepper.Topic]
getOutputs()

Gets all the outputs in a list by fully iterating the output generator.

getResources(param_type, resource_type)

Get the stepper resources in the settings that are instances of param_type and have a resource_type attribute that is resource_type.

Note does not work for list/set/tuple subparams in the settings.

Parameters
  • param_type (tasks._TaskResource) – the resource parameter type

  • resource_type (ResourceType) – the type of resource to get

Returns

the set of stepper resources of resource_type

Return type

set of tasks._TaskResource

getRunInfo()
getStepDepth() int

Get the depth of a step which is defined as how nested it is. A step run in isolation (i.e. not within a chain) has a depth level of 0.

getStepId()
inherits(self, classname: str) bool
initializeTopics()
inputs()
installEventFilter(self, a0: QObject)
isSignalConnected(self, signal: QMetaMethod) bool
isWidgetType(self) bool
isWindowType(self) bool
killTimer(self, id: int)
metaObject(self) QMetaObject
moveToThread(self, thread: QThread)
objectName(self) str
objectNameChanged

objectNameChanged(self, objectName: str) [signal]

outputs(*args, **kwargs)
parent(self) QObject
prettyPrintRunInfo()

Format and print info about the step’s run.

property(self, name: str) Any
pyqtConfigure(...)

Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

receivers(self, signal: PYQT_SIGNAL) int
reduceFunction(inputs)

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
removeEventFilter(self, a0: QObject)
report(prefix='')

Report the settings and batch settings for this step.

sender(self) QObject
senderSignalIndex(self) int
setBatchSettings(*args, **kwargs)
setInputFile(fname)
setInputTopic(inp_topic: Optional[schrodinger.stepper.stepper.Topic])
setInputs(*args, **kwargs)
setObjectName(self, name: str)
setOutputTopic(outp_topic: Optional[schrodinger.stepper.stepper.Topic])
setParent(self, a0: QObject)
setProperty(self, name: str, value: Any) bool
setSettings(*args, **kwargs)
signalsBlocked(self) bool
startTimer(self, interval: int, timerType: Qt.TimerType = Qt.CoarseTimer) int
staticMetaObject = <PyQt6.QtCore.QMetaObject object>
thread(self) QThread
timerEvent(self, a0: QTimerEvent)
property topic_prefix
property topic_suffix
tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) str
usingPubsub()
writeOutputsToFile(fname)

Write outputs to fname. By default, the output file will consist of one line for each output with whatever is produced when passing the out- put to str. Override this method if more complex behavior is needed.

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

Bases: schrodinger.application.steps.enumerators.BaseDecorator

mapFunction(mol)
Input

alias of rdkit.Chem.rdchem.Mol

InputSerializer

alias of schrodinger.application.steps.dataclasses.MolToSmilesSerializer

LEAVING_MOL_WT = 40.956
Output

alias of rdkit.Chem.rdchem.Mol

OutputSerializer

alias of schrodinger.application.steps.dataclasses.MolToSmilesSerializer

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

Bases: schrodinger.application.steps.filters.ProfileSettings

DataClass

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error
__init__(default_value=<object object>, _param_type=<object object>, **kwargs)
classmethod addSubParam(name, param, update_owner=True)
blockSignals(self, b: bool) bool
block_signal_propagation()
childEvent(self, a0: QChildEvent)
children(self) List[QObject]
classmethod configureParam()

Override this class method to set up the abstract param class (e.g. setParamReference on child params.)

connectNotify(self, signal: QMetaMethod)
core_smarts: str

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

class Coord(CompoundParam):
    x: int
    y: int

An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:

coord = Coord()
coord.x = 4

When a Param value is set, the valueChanged signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:

class Atom(CompoundParam):
    coord: Coord
    element: str
core_smartsChanged
core_smartsReplaced
customEvent(self, a0: QEvent)
classmethod defaultValue()

Returns the default value for this abstract param:

default_atom = Atom.defaultValue()
assert Atom.coord.x == 0
deleteLater(self)
destroyed

destroyed(self, object: typing.Optional[QObject] = None) [signal]

disconnect(a0: QMetaObject.Connection) bool
disconnect(self) None
disconnectNotify(self, signal: QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) List[QByteArray]
event(self, a0: QEvent) bool
eventFilter(self, a0: QObject, a1: QEvent) bool
findChild(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) QObject
findChild(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) QObject
findChildren(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, type: type, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
findChildren(self, types: Tuple, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) List[QObject]
classmethod fromJson(json_obj)

A factory method which constructs a new object from a given dict loaded from a json string or file.

Parameters

json_obj (dict) – A json-loaded dictionary to create an object from.

Returns

An instance of this class.

Return type

cls

classmethod fromJsonImplementation(json_dict)

Sets the value of this compound param value object from a JSON dict.

Warning

This should never be called directly.

getAbstractParam()

Return the corresponding abstract param for this instance.

classmethod getJsonBlacklist()

Override to customize what params are serialized.

Implementations should return a list of abstract params that should be omitted from serialization.

..NOTE

Returned abstract params must be direct child params of cls, e.g. cls.name, not cls.coord.x.

classmethod getParamSignal(obj, signal_type='Changed')
classmethod getParamValue(obj)

Enables access to a param value on a compound param via an abstract param reference:

a = Atom()
assert Atom.coord.x.getParamValue(a) == 0 # ints default to 0
a.coord.x = 3
assert Atom.coord.x.getParamValue(a) == 3
Parameters

param (CompoundParam) – The owner param to get a param value from

getRGroups()
getReactionSmarts()
getReagentMol()
getReagentSmarts()
classmethod getSubParam(name)

Get the value of a subparam using the string name:

c = Coord()
assert c.getSubParam('x') == 0

Note

Using the string name to access params is generally discouraged, but can be useful for serializing/deserializing param data.

Parameters

name (str) – The name of the subparam to get the value for.

classmethod getSubParams()

Return a dictionary mapping subparam names to their values.

getTypeHint()
get_version()

Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.

inherits(self, classname: str) bool
initAbstract()
initConcrete()

Override to customize initialization of concrete params.

initializeValue()

Override to dynamically set up the default value of the param. Useful for default values that are determined at runtime. This is called any time the param is reset.

installEventFilter(self, a0: QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

isDefault()

Whether the current value of this instance matches the default value.

isSignalConnected(self, signal: QMetaMethod) bool
isWidgetType(self) bool
isWindowType(self) bool
killTimer(self, id: int)
metaObject(self) QMetaObject
moveToThread(self, thread: QThread)
objectName(self) str
objectNameChanged

objectNameChanged(self, objectName: str) [signal]

classmethod owner()

Get the owner of the param:

# Can be called on an abstract param:
assert Coord.x.owner() == Coord