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
andquestion
methods have been defined in the subclass, as in e.g.widget_mixins.MessageBoxMixin
.Parameters: results ( validation.ValidationResults
) – Set of validation results generated byvalidate
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- 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
-
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
andquestion
methods have been defined in the subclass, as in e.g.widget_mixins.MessageBoxMixin
.Parameters: results ( validation.ValidationResults
) – Set of validation results generated byvalidate
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- 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
-
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)¶
-