schrodinger.application.steps.ligprep module

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

Bases: schrodinger.stepper.stepper.MapStep

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

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

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

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

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

Bases: schrodinger.models.parameters.CompoundParam

arg_string: str

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
ligprep_filter_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)
arg_stringChanged
arg_stringReplaced
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)
ligprep_filter_fileChanged
ligprep_filter_fileReplaced
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]

mapFunction(struc)

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

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

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

Parameters

input –

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

def mapFunction(self, starting_smiles):

…

cleanUp()

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

Input = None
InputSerializer

alias of schrodinger.stepper.stepper._DynamicSerializer

Output = None
OutputSerializer

alias of schrodinger.stepper.stepper._DynamicSerializer

__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]
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]
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()
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.ligprep.LigandPrepper(*args, **kwargs)

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

See also LigPrepMixin

mapFunction(inp_mol)

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

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

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

Parameters

input –

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

def mapFunction(self, starting_smiles):

…

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

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

Bases: schrodinger.models.parameters.CompoundParam

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)
arg_string: 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
arg_stringChanged
arg_stringReplaced
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)
ligprep_filter_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
ligprep_filter_fileChanged
ligprep_filter_fileReplaced
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
__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.ligprep.MaeLigandPrepper(*args, **kwargs)

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

See also LigPrepStep

Input

alias of schrodinger.structure._structure.Structure

InputSerializer

alias of schrodinger.stepper.stepper._DynamicSerializer

Output

alias of schrodinger.structure._structure.Structure

OutputSerializer

alias of schrodinger.stepper.stepper._DynamicSerializer

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

Bases: schrodinger.models.parameters.CompoundParam

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)
arg_string: 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
arg_stringChanged
arg_stringReplaced
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)
ligprep_filter_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
ligprep_filter_fileChanged
ligprep_filter_fileReplaced
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
__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)
mapFunction(struc)

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

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

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

Parameters

input –

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

def mapFunction(self, starting_smiles):

…

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.