schrodinger.protein.tasks.blast module¶

class schrodinger.protein.tasks.blast.BlastTask(*args, **kwargs)¶

Bases: schrodinger.tasks.tasks_.ThreadFunctionTask

This is a thin wrapper over BlastPlus object that implements job running and incorporation.

query_sequence¶

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 Owner(object):
    data_x = IntParam()
    data_y = IntParam()

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

owner_instance = Owner()
owner_instance.data_x = 4

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

Warning

As descriptors, instances of this class will not behave correctly if used as class variables.

Variables:

DataClass (type) – The type of data the param describes.
is_abstract (bool) – Whether this param is an abstract (ie class attribute) param.
valueChanged (QtCore.pyqtSignal) – A signal emitted whenever the param is changed.
default_value (DataClass) – The default value of the param. If unset, the default value is whatever value is created when calling DataClass()
param_name (str) – The name of the attribute this param is set as. For example, Owner.data_x.param_name would be ‘data_x’.
instance_attr_name (str) – The name of the attribute used to store param values on instances.
abstract_attr_name (str) – The name of the attribute used to store abstract params on class objects.

settings¶

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).

genomes¶

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.

hits¶

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.

start(*args, **kwargs)¶

mainFunction()¶: Creates an instance of BlastPlus and runs BLAST job.

getBlastAlignment()¶

DONE = 4¶

DataClass¶: alias of builtins.object

FAILED = 3¶

MAX_THREAD_TASKS = 500¶

NOTRUNNING = 0¶

RUNNING = 2¶

STARTING = 1¶

__init__(*args, **kwargs)¶: Initialize self. See help(type(self)) for accurate signature.

aboutToReplace¶

blockSignals(self, bool) → bool¶

childEvent(self, QChildEvent)¶

children(self) → object¶

connectNotify(self, QMetaMethod)¶

customEvent(self, QEvent)¶

deleteLater(self)¶

destroyed¶: destroyed(self, QObject = None) [signal]

disconnect(self)¶

disconnectNotify(self, QMetaMethod)¶

dumpObjectInfo(self)¶

dumpObjectTree(self)¶

dynamicPropertyNames(self) → object¶

event(self, QEvent) → bool¶

eventFilter(self, QObject, QEvent) → bool¶

findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject¶: findChild(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> QObject

findChildren(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]¶: findChildren(self, Tuple, name: str = ‘’, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegExp, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, type, QRegularExpression, options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) -> List[QObject] findChildren(self, Tuple, QRegularExpression, options: Union[Qt.FindChildOptions, 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.

:rtype : cls

classmethod fromJsonFilename(filename)¶

classmethod fromJsonImplementation(json_dict)¶: Sets the value of this compound param value object from a JSON dict.

genomesChanged¶

genomesReplaced¶

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.

hitsChanged¶

hitsReplaced¶

inherits(self, str) → bool¶

initAbstract()¶: Override this method to define logic specfically for initializing abstract instances of this param.

initConcrete()¶: Override this method to define logic specfically for initializing concrete instances of this param. This will generally only run for compound params, as atomic params are not typically instantiated outside of class declaration.

input¶

Inherit all functionality of CompoundParam with name that designates this class as a model. Models should themselves be parameters so that their corresponding view can be easily incorporated into a parent view. In this case, the model of the parent view will contain the model of the child view as a parameter.

WARNING: as descriptors, instances of this class will not behave normally if used as class variables.

inputChanged¶

inputReplaced¶

installEventFilter(self, QObject)¶

isDefault()¶

isSignalConnected(self, QMetaMethod) → bool¶

isStartable()¶

isWidgetType(self) → bool¶

isWindowType(self) → bool¶

is_abstract = True¶

killTimer(self, int)¶

metaObject(self) → QMetaObject¶

moveToThread(self, QThread)¶

name¶

nameChanged¶

nameReplaced¶

objectName(self) → str¶

objectNameChanged¶: objectNameChanged(self, str) [signal]

output¶

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 Owner(object):
    data_x = IntParam()
    data_y = IntParam()

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

owner_instance = Owner()
owner_instance.data_x = 4

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

Warning

As descriptors, instances of this class will not behave correctly if used as class variables.

Variables:

DataClass (type) – The type of data the param describes.
is_abstract (bool) – Whether this param is an abstract (ie class attribute) param.
valueChanged (QtCore.pyqtSignal) – A signal emitted whenever the param is changed.
default_value (DataClass) – The default value of the param. If unset, the default value is whatever value is created when calling DataClass()
param_name (str) – The name of the attribute this param is set as. For example, Owner.data_x.param_name would be ‘data_x’.
instance_attr_name (str) – The name of the attribute used to store param values on instances.
abstract_attr_name (str) – The name of the attribute used to store abstract params on class objects.

outputChanged¶

outputReplaced¶

owner()¶: Returns the owner of this param. Works for both concrete and abstract params. Returns None if the param has no owner. Follows the same rules as ownerChain.

ownerChain()¶

Returns the owner chain for this param. This works for concrete params and abstract params. Examples:

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

Foo.bar.atom.coord.x.ownerChain() will return [Foo, bar, atom.coord, x] where Foo is a class and all other items are abstract params.

parent(self) → QObject¶

postprocess()¶

preprocess()¶

property(self, 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.

query_sequenceChanged¶

query_sequenceReplaced¶

receivers(self, PYQT_SIGNAL) → int¶

removeEventFilter(self, QObject)¶

reportValidation(results)¶

Present validation messages to the user. This is an implmentation of the ValidationMixin interface and does not need to be called directly.

This method assumes that error and question methods have been defined in the subclass, as in e.g. widget_mixins.MessageBoxMixin.

Parameters:	results (`validation.ValidationResults`) – Set of validation results generated by `validate`
Returns:	if True, there were no validation errors and the user decided to continue despite any warnings. If False, there was at least one validation error or the user decided to abort when faced with a warning.

reset(*args)¶

Resets this compound param to its default value. If no arguments are passed in, the entire param is reset. Any number of abstract params may be optionally passed in to perform a partial reset to default value of specified sub-params. For example, given a compound param with two xyz coordinates as endpoints:

class Line(CompoundParam):

start = Coord(x=1, y=2, z=3) end = Coord(x=4, y=5, z=6)

line = Line()

We can reset the entire line:

line.reset()

Or just certain parts:

line.reset(Line.start.x) # resets just start.x line.start.reset(Coord.x) # another way to reset start.x line.reset(Line.end) # resets the entire end point line.reset(Line.start.z, Line.end.z) # resets the z-coord of both

Parameters:	args – abstract sub-params of self

runValidation(silent=False, validate_children=True, stop_on_fail=True)¶

Runs validation and reports the results (unless run silently).

Parameters:	silent (bool) – run without any reporting (i.e. error messages to the user). This is useful if we want to programmatically test validity. Changes return value of this method from `ValidationResults` to a boolean. validate_children (bool) – run validation on all child objects. See `_validateChildren` for documentation on what this entails. stop_on_fail (bool) – stop validation when first failure is encountered
Returns:	if silent is False, returns the validation results. If silent is True, returns a boolean generated by `reportValidation`.
Return type:	`ValidationResults` or bool

running_tasks = []¶

sender(self) → QObject¶

senderSignalIndex(self) → int¶

setObjectName(self, str)¶

setParent(self, QObject)¶

setProperty(self, str, Any) → bool¶

setValue(value=None, **kwargs)¶

Set the value of this compound param instance. This mutates the compound param to be equal to value; it does not make the compound param /identical/ to value.

Parameters:	value (self.DataClass or dict) – either another param instance of the same type or a dictionary mapping the sub-param names to values.

settingsChanged¶

settingsReplaced¶

signalsBlocked(self) → bool¶

startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int¶

staticMetaObject = <PyQt5.QtCore.QMetaObject object>¶

status¶

statusChanged¶

statusReplaced¶

suspend_signals()¶

thread(self) → QThread¶

timerEvent(self, QTimerEvent)¶

toDict()¶

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.

tr(self, str, disambiguation: str = None, n: int = -1) → str¶

valueChanged¶

wait(timeout=None)¶

Block until the task is finished executing or timeout seconds have passed.

Parameters:	timeout (NoneType or int) – Amount of time in seconds to wait before timing out. If None or a negative number, this method will wait until the task is finished.

schrodinger.protein.tasks.blast module¶

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