schrodinger.protein.tasks.blast module

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

Bases: schrodinger.models.json.JsonableEnum

An enumeration.

BLAST = 1
PSIBLAST = 2
class schrodinger.protein.tasks.blast.BlastDatabase(*args, **kwargs)

Bases: schrodinger.models.json.JsonableEnum

An enumeration.

AlignJobDB = 4
GPCR = 3
NR = 2
PDB = 1
class schrodinger.protein.tasks.blast.SimilarityMatrix(*args, **kwargs)

Bases: schrodinger.models.json.JsonableEnum

An enumeration.

BLOSUM45 = 1
BLOSUM62 = 2
BLOSUM80 = 3
PAM30 = 4
PAM70 = 5
class schrodinger.protein.tasks.blast.BlastSettings(default_value=<object object>, param_type=<object object>, **kwargs)

Bases: schrodinger.models.parameters.ParamModel

progname
use_local

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.
database_name
word_size

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.
filter_query

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.
gap_open_cost

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.
gap_extend_cost

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.
similarity_matrix
num_iterations

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.
evalue_threshold

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.
inclusion_threshold

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.
getBlastSettings()

Returns BLAST settings as a dictionary.

Returns:Dictionary of BLAST settings.
Return type:dict
DataClass

alias of builtins.object

__init__(default_value=<object object>, param_type=<object object>, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

classmethod addSubParam(name, param, update_owner=True)
blockSignals(self, bool) → bool
block_signal_propagation()
childEvent(self, QChildEvent)
children(self) → object
classmethod configureParam()

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

connectNotify(self, QMetaMethod)
customEvent(self, QEvent)
database_nameChanged
database_nameReplaced
classmethod defaultValue(*args, **kwargs)
deleteLater(self)
destroyed

destroyed(self, QObject = None) [signal]

disconnect(self)
disconnectNotify(self, QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → object
evalue_thresholdChanged
evalue_thresholdReplaced
event(self, QEvent) → bool
eventFilter(self, QObject, QEvent) → bool
filter_queryChanged
filter_queryReplaced
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 fromJsonImplementation(json_dict)

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

gap_extend_costChanged
gap_extend_costReplaced
gap_open_costChanged
gap_open_costReplaced
getAbstractParam(*args, **kwargs)
classmethod getParamSignal(*args, **kwargs)
classmethod getParamValue(*args, **kwargs)
classmethod getSubParam(name)
classmethod getSubParams()
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.

inclusion_thresholdChanged
inclusion_thresholdReplaced
inherits(self, str) → bool
initAbstract()
initConcrete()
initializeValue()
installEventFilter(self, QObject)
classmethod isAbstract()
isDefault(*args, **kwargs)
isSignalConnected(self, QMetaMethod) → bool
isWidgetType(self) → bool
isWindowType(self) → bool
killTimer(self, int)
metaObject(self) → QMetaObject
moveToThread(self, QThread)
num_iterationsChanged
num_iterationsReplaced
objectName(self) → str
objectNameChanged

objectNameChanged(self, str) [signal]

classmethod owner()
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()
parent(self) → QObject
prognameChanged
prognameReplaced
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.

receivers(self, PYQT_SIGNAL) → int
removeEventFilter(self, QObject)
reset(*args, **kwargs)
sender(self) → QObject
senderSignalIndex(self) → int
setObjectName(self, str)
classmethod setParamValue(*args, **kwargs)
setParent(self, QObject)
setProperty(self, str, Any) → bool
setValue(*args, **kwargs)
signalsBlocked(self) → bool
similarity_matrixChanged
similarity_matrixReplaced
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
thread(self) → QThread
timerEvent(self, QTimerEvent)
toDict(*args, **kwargs)
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(*args, **kwargs)
tr(self, str, disambiguation: str = None, n: int = -1) → str
use_localChanged
use_localReplaced
valueChanged
word_sizeChanged
word_sizeReplaced
class schrodinger.protein.tasks.blast.BlastTaskTester(*args, cmd_list=None, **kwargs)

Bases: schrodinger.protein.tasks.blast.BlastTask

DONE = 3
DataClass

alias of builtins.object

FAILED = 2
class Input(default_value=<object object>, param_type=<object object>, **kwargs)

Bases: schrodinger.tasks.jobtasks.JobInput

DASH_STRING = '--'
DataClass

alias of builtins.object

__init__(default_value=<object object>, param_type=<object object>, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

classmethod addSubParam(name, param, update_owner=True)
blockSignals(self, bool) → bool
block_signal_propagation()
childEvent(self, QChildEvent)
children(self) → object
classmethod configureParam()

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

connectNotify(self, QMetaMethod)
customEvent(self, QEvent)
classmethod defaultValue(*args, **kwargs)
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 fromJsonImplementation(json_dict)

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

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.

genomesChanged
genomesReplaced
getAbstractParam(*args, **kwargs)
classmethod getParamSignal(*args, **kwargs)
classmethod getParamValue(*args, **kwargs)
classmethod getSubParam(name)
classmethod getSubParams()
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, str) → bool
initAbstract()
initConcrete()
initializeValue()
installEventFilter(self, QObject)
classmethod isAbstract()
isDefault(*args, **kwargs)
isSignalConnected(self, QMetaMethod) → bool
isWidgetType(self) → bool
isWindowType(self) → bool
killTimer(self, int)
metaObject(self) → QMetaObject
moveToThread(self, QThread)
objectName(self) → str
objectNameChanged

objectNameChanged(self, str) [signal]

classmethod owner()
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()
parent(self) → QObject
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_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.
query_sequenceChanged
query_sequenceReplaced
receivers(self, PYQT_SIGNAL) → int
removeEventFilter(self, QObject)
reset(*args, **kwargs)
sender(self) → QObject
senderSignalIndex(self) → int
setObjectName(self, str)
classmethod setParamValue(*args, **kwargs)
setParent(self, QObject)
setProperty(self, str, Any) → bool
setValue(*args, **kwargs)
settings
settingsChanged
settingsReplaced
signalsBlocked(self) → bool
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
thread(self) → QThread
timerEvent(self, QTimerEvent)
toCmdArgs()
toDict(*args, **kwargs)
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(*args, **kwargs)
tr(self, str, disambiguation: str = None, n: int = -1) → str
valueChanged
RUNNING = 1
WAITING = 0
__init__(*args, cmd_list=None, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

classmethod addSubParam(name, param, update_owner=True)
backendMain()
backend_name = 'combojobtask_entry_point.py'
blast_plus
blockSignals(self, bool) → bool
block_signal_propagation()
childEvent(self, QChildEvent)
children(self) → object
config
configChanged
configReplaced
classmethod configureParam()

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

connectNotify(self, QMetaMethod)
customEvent(self, QEvent)
classmethod defaultValue(*args, **kwargs)
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.

getAbstractParam(*args, **kwargs)
getBlastAlignment()
getInputArgs()
classmethod getParamSignal(*args, **kwargs)
classmethod getParamValue(*args, **kwargs)
classmethod getSubParam(name)
classmethod getSubParams()
getTaskDirectory()

Return the absolute path of the task directory

getTaskFilename(fname)

Return the appropriate absolute path for an input or output file

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.

guard()

Context manager that saves any Exception raised inside

inherits(self, str) → bool
initAbstract()
initConcrete(*args, **kwargs)
initializeValue()
input
inputChanged
inputReplaced
input_files

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.

input_filesChanged
input_filesReplaced
installEventFilter(self, QObject)
classmethod isAbstract()
isDefault(*args, **kwargs)
isSignalConnected(self, QMetaMethod) → bool
isStartable()
isWidgetType(self) → bool
isWindowType(self) → bool
json_filename
json_out_filename
killTimer(self, int)
makeJobSpecFromCmd(cmd)
makeLaunchParams()
max_progress
max_progressChanged
max_progressReplaced
metaObject(self) → QMetaObject
moveToThread(self, QThread)
name
nameChanged
nameReplaced
objectName(self) → str
objectNameChanged

objectNameChanged(self, str) [signal]

output

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.

outputChanged
outputReplaced
output_files

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.

output_filesChanged
output_filesReplaced
classmethod owner()
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()
parent(self) → QObject
prepareStart()
preprocessors()
Returns:A list of bound preprocessing methods
progress
progressChanged
progressReplaced
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.

receivers(self, PYQT_SIGNAL) → int
removeEventFilter(self, QObject)
replicate()

Create a new task with the same input and settings (but no output)

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, **kwargs)
run()
runBackend()
classmethod runFromCmdLine()
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
sender(self) → QObject
senderSignalIndex(self) → int
setAutoTaskDir(auto_task_dir)
setObjectName(self, str)
classmethod setParamValue(*args, **kwargs)
setParent(self, QObject)
setProperty(self, str, Any) → bool
setValue(*args, **kwargs)
signalsBlocked(self) → bool
start(*args, **kwargs)
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
status
statusChanged
statusReplaced
taskDone
taskFailed
taskStarted
taskdir
thread(self) → QThread
timerEvent(self, QTimerEvent)
toCmd()
toDict(*args, **kwargs)
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(*args, **kwargs)
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.
wrapCmdInLaunchApi(cmd)
writeJsonFile(filename)
class schrodinger.protein.tasks.blast.BlastTask(*args, cmd_list=None, **kwargs)

Bases: schrodinger.tasks.jobtasks.ComboJobTask

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

To enable DEBUG_MODE, set DEBUG_MODE to True at the bottom of this class. In DEBUG_MODE, no blast call will actually be made and the first top 10 hits of a BLAST search with 1cmy:a will be returned as the output.

output

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.

class Input(default_value=<object object>, param_type=<object object>, **kwargs)

Bases: schrodinger.tasks.jobtasks.JobInput

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.
settings
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.

DASH_STRING = '--'
DataClass

alias of builtins.object

__init__(default_value=<object object>, param_type=<object object>, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

classmethod addSubParam(name, param, update_owner=True)
blockSignals(self, bool) → bool
block_signal_propagation()
childEvent(self, QChildEvent)
children(self) → object
classmethod configureParam()

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

connectNotify(self, QMetaMethod)
customEvent(self, QEvent)
classmethod defaultValue(*args, **kwargs)
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 fromJsonImplementation(json_dict)

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

genomesChanged
genomesReplaced
getAbstractParam(*args, **kwargs)
classmethod getParamSignal(*args, **kwargs)
classmethod getParamValue(*args, **kwargs)
classmethod getSubParam(name)
classmethod getSubParams()
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, str) → bool
initAbstract()
initConcrete()
initializeValue()
installEventFilter(self, QObject)
classmethod isAbstract()
isDefault(*args, **kwargs)
isSignalConnected(self, QMetaMethod) → bool
isWidgetType(self) → bool
isWindowType(self) → bool
killTimer(self, int)
metaObject(self) → QMetaObject
moveToThread(self, QThread)
objectName(self) → str
objectNameChanged

objectNameChanged(self, str) [signal]

classmethod owner()
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()
parent(self) → QObject
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)
reset(*args, **kwargs)
sender(self) → QObject
senderSignalIndex(self) → int
setObjectName(self, str)
classmethod setParamValue(*args, **kwargs)
setParent(self, QObject)
setProperty(self, str, Any) → bool
setValue(*args, **kwargs)
settingsChanged
settingsReplaced
signalsBlocked(self) → bool
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
thread(self) → QThread
timerEvent(self, QTimerEvent)
toCmdArgs()
toDict(*args, **kwargs)
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(*args, **kwargs)
tr(self, str, disambiguation: str = None, n: int = -1) → str
valueChanged
backendMain()
getBlastAlignment()
DONE = 3
DataClass

alias of builtins.object

FAILED = 2
RUNNING = 1
WAITING = 0
__init__(*args, cmd_list=None, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

classmethod addSubParam(name, param, update_owner=True)
backend_name = 'combojobtask_entry_point.py'
blockSignals(self, bool) → bool
block_signal_propagation()
childEvent(self, QChildEvent)
children(self) → object
config
configChanged
configReplaced
classmethod configureParam()

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

connectNotify(self, QMetaMethod)
customEvent(self, QEvent)
classmethod defaultValue(*args, **kwargs)
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.

getAbstractParam(*args, **kwargs)
getInputArgs()
classmethod getParamSignal(*args, **kwargs)
classmethod getParamValue(*args, **kwargs)
classmethod getSubParam(name)
classmethod getSubParams()
getTaskDirectory()

Return the absolute path of the task directory

getTaskFilename(fname)

Return the appropriate absolute path for an input or output file

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.

guard()

Context manager that saves any Exception raised inside

inherits(self, str) → bool
initAbstract()
initConcrete(*args, **kwargs)
initializeValue()
input
inputChanged
inputReplaced
input_files

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.

input_filesChanged
input_filesReplaced
installEventFilter(self, QObject)
classmethod isAbstract()
isDefault(*args, **kwargs)
isSignalConnected(self, QMetaMethod) → bool
isStartable()
isWidgetType(self) → bool
isWindowType(self) → bool
json_filename
json_out_filename
killTimer(self, int)
makeJobSpecFromCmd(cmd)
makeLaunchParams()
max_progress
max_progressChanged
max_progressReplaced
metaObject(self) → QMetaObject
moveToThread(self, QThread)
name
nameChanged
nameReplaced
objectName(self) → str
objectNameChanged

objectNameChanged(self, str) [signal]

outputChanged
outputReplaced
output_files

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.

output_filesChanged
output_filesReplaced
classmethod owner()
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()
parent(self) → QObject
prepareStart()
preprocessors()
Returns:A list of bound preprocessing methods
progress
progressChanged
progressReplaced
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.

receivers(self, PYQT_SIGNAL) → int
removeEventFilter(self, QObject)
replicate()

Create a new task with the same input and settings (but no output)

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, **kwargs)
run()
runBackend()
classmethod runFromCmdLine()
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
sender(self) → QObject
senderSignalIndex(self) → int
setAutoTaskDir(auto_task_dir)
setObjectName(self, str)
classmethod setParamValue(*args, **kwargs)
setParent(self, QObject)
setProperty(self, str, Any) → bool
setValue(*args, **kwargs)
signalsBlocked(self) → bool
start(*args, **kwargs)
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
status
statusChanged
statusReplaced
taskDone
taskFailed
taskStarted
taskdir
thread(self) → QThread
timerEvent(self, QTimerEvent)
toCmd()
toDict(*args, **kwargs)
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(*args, **kwargs)
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.
wrapCmdInLaunchApi(cmd)
writeJsonFile(filename)