schrodinger.protein.predictors module¶
This module contains classes that wrap prime backends that predict sequence structures. Many of the parameters and class constants are from a time when documentation was sparse. In the future, it’s possible we’ll tweak these numbers as needed.
-
class
schrodinger.protein.predictors.
AbstractPredictor
(*args, **kwargs)¶ Bases:
schrodinger.tasks.tasks.SubprocessCmdTask
Base class for all predictors. Derived classes are expected to implement class constants for:
- EXE - A string that should match to the predictors executable.
- Most of the time this is the same as PREDICTOR_NAME
- PREDICTOR_NAME - A string with the name of the predictor. This is
- used to find the Prime data directory that holds the model parameters used by the predictor.
- CLASS_NUM - A parameter specific to the predictor. Usually found by
- looking through the Prime predictors source code.
NU - Another model parameter. NY - Another model parameter.
In addition, derived classes should implement the following methods:
- generateInputFile - Should generate the required input file at
- the file described by
input_fname
- prediction - Should read
self.stdout
and parse out the actual - prediction from the backend
- makeCmd - This only needs to be implemented if the backend
- takes a command different from the form:
executable model_fname input_fname
-
EXE
= NotImplemented¶
-
PREDICTOR_NAME
= NotImplemented¶
-
CLASS_NUM
= NotImplemented¶
-
NU
= NotImplemented¶
-
NY
= NotImplemented¶
-
class
Input
(default_value=<object object>, _param_type=<object object>, **kwargs)¶ Bases:
schrodinger.models.parameters.CompoundParam
-
seq
¶ Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:
class Coord(CompoundParam): x: int y: int
An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:
coord = Coord() coord.x = 4
When a Param value is set, the
valueChanged
signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:class Atom(CompoundParam): coord: Coord element: str
-
aln
¶ Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:
class Coord(CompoundParam): x: int y: int
An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:
coord = Coord() coord.x = 4
When a Param value is set, the
valueChanged
signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:class Atom(CompoundParam): coord: Coord element: str
-
DataClass
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
__init__
(default_value=<object object>, _param_type=<object object>, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
classmethod
addSubParam
(name, param, update_owner=True)¶
-
alnChanged
¶
-
alnReplaced
¶
-
blockSignals
(self, bool) → bool¶
-
block_signal_propagation
()¶
-
childEvent
(self, QChildEvent)¶
-
children
(self) → List[QObject]¶
-
classmethod
configureParam
()¶ Override this class method to set up the abstract param class (e.g. setParamReference on child params.)
-
connectNotify
(self, QMetaMethod)¶
-
customEvent
(self, QEvent)¶
-
classmethod
defaultValue
(*args, **kwargs)¶
-
deleteLater
(self)¶
-
destroyed
¶ destroyed(self, object: QObject = None) [signal]
-
disconnect
(self)¶
-
disconnectNotify
(self, QMetaMethod)¶
-
dumpObjectInfo
(self)¶
-
dumpObjectTree
(self)¶
-
dynamicPropertyNames
(self) → List[QByteArray]¶
-
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.
-
getAbstractParam
(*args, **kwargs)¶
-
classmethod
getJsonBlacklist
()¶ Override to customize what params are serialized.
Implementations should return a list of abstract params that should be omitted from serialization.
- ..NOTE
- Returned abstract params must be direct child params of
cls
, e.g.cls.name
, notcls.coord.x
.
-
classmethod
getParamSignal
(*args, **kwargs)¶
-
classmethod
getParamValue
(*args, **kwargs)¶
-
classmethod
getSubParam
(name)¶ Get the value of a subparam using the string name:
c = Coord() assert c.getSubParam('x') == 0
Note
Using the string name to accss params is generally discouraged, but can be useful for serializing/deserializing param data.
Parameters: name (str) – The name of the subparam to get the value for.
-
classmethod
getSubParams
()¶ Return a dictionary mapping subparam names to their values.
-
getTypeHint
()¶
-
get_version
()¶ Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.
-
inherits
(self, str) → bool¶
-
initAbstract
()¶
-
initConcrete
()¶ Override to customize initialization of concrete params.
-
initializeValue
()¶ Override to dynamically set up the default value of the param. Useful for default values that are determined at runtime. This is called any time the param is reset.
-
installEventFilter
(self, QObject)¶
-
classmethod
isAbstract
()¶ Whether the param is an “abstract” param.
-
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
()¶ Get the owner of the param:
# Can be called on an abstract param: assert Coord.x.owner() == Coord # ...or on an instance of a CompoundParam a = Atom() assert a.coord.owner() == a
-
classmethod
ownerChain
()¶ Returns a list of param owners starting from the toplevel param and ending with self. Examples:
foo.bar.atom.coord.ownerChain()
will return[foo, bar, atom, coord]
where every item is a concrete param.Foo.bar.atom.coord.x.ownerChain()
will return[Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x]
where every item is an abstract params.
-
classmethod
paramName
()¶ Get the name of the param:
# Can be called on an abstract param: print(Coord.x.paramName()) # 'x' # ...or on an instance of a CompoundParam a = Atom() a.coord.paramName() # 'coord'
-
parent
(self) → QObject¶
-
property
(self, 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¶
-
seqChanged
¶
-
seqReplaced
¶
-
setObjectName
(self, str)¶
-
classmethod
setParamValue
(*args, **kwargs)¶
-
setParent
(self, QObject)¶
-
setProperty
(self, str, Any) → bool¶
-
classmethod
setReference
(param1, param2)¶ Call this class method from configureParam to indicate that two params should be kept in sync. The initial values will start with the default value of
param1
. Example:class Square(CompoundParam): width: float = 5 height: float = 10 @classmethod def configureParam(cls): super().configureParam() cls.setReference(cls.width, cls.height) square = Square() assert square.width == square.height == 5 # Default value of width # takes priority square.height = 7 assert square.width == square.height == 7 square.width = 6 assert square.width == square.height == 6
Parameters: - param1 – The first abstract param to keep synced
- param2 – The second abstract param. After instantiation, this param will take on the value of param1.
-
setValue
(*args, **kwargs)¶
-
signalsBlocked
(self) → bool¶
-
skip_eq_check
()¶
-
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¶
-
valueChanged
¶
-
-
input
¶
-
input_fname
¶ Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:
class Coord(CompoundParam): x: int y: int
An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:
coord = Coord() coord.x = 4
When a Param value is set, the
valueChanged
signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:class Atom(CompoundParam): coord: Coord element: str
-
model_fname
¶ Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:
class Coord(CompoundParam): x: int y: int
An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:
coord = Coord() coord.x = 4
When a Param value is set, the
valueChanged
signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:class Atom(CompoundParam): coord: Coord element: str
-
generateInputFile
()¶ Generate the input file for the predictor. Typically includes a header (see
_getInputHeader
), the file name of the blast alignment, and the sequence to predict properties for.The input file should be written with the name
self.input_fname
.
-
prediction
()¶ Return the actual prediction. This can take various forms depending on the predictor.
-
generateAlignmentFile
()¶ Write the alignment file to be used as an input for the predictor. The file will be a temporary file and will be removed in
postprocess
.Gaps in the alignment file are represented as ‘.’.
-
generateModelFile
()¶ Generate the model definition file with the name
self.model_fname
. This is done by finding the Prime data directory for the predictor and getting the names of all the files in it.The model file includes a header describing the number of model files and the predictors class number (
self.CLASS_NUM
), and a list of the model files.
-
makeCmd
()¶ Return the command to run the predictor backend. The default implementation returns the predictor executable, the model file name, and the input file name.
Return type: list[str]
-
postprocess
()¶
-
AUTO_TASKDIR
= <object object>¶
-
CMDLINE
= 1¶
-
DEFAULT_TASKDIR_SETTING
= None¶
-
DONE
= 3¶
-
DataClass
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
FAILED
= 2¶
-
GUI
= 2¶
-
INTERRUPT_ENABLED
= False¶
-
RUNNING
= 1¶
-
TEMP_TASKDIR
= <object object>¶
-
WAITING
= 0¶
-
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
addFuncToGroup
(func, group=None, order=None)¶ Adds a function to the specified chain. Typically used for adding functions that are not methods of this object.
The function may optionally be decorated with a FuncGroupMarker. If so, the default group and order will be determined by the decorator. Any group or order explicitly passed in to addFuncToGroup will take precedence over the decorator settings.
Parameters: - func – the function to add
- group (FuncGroupMarker or None) – the group marker. If the function is decorated with a FuncGoupMarker, that group marker will be the default.
- order (float or None) – the sorting order. If the function is decorated with a FuncGoupMarker, the order specified in the decorator will be the default.
-
addPostprocessor
(func, order=0)¶ Adds a postproceessor function to this task instance. If the function has been decorated with
@postprocessor
, the order specified by the decorator will be used.Parameters: - func (typing.Callable) – the function to add
- order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.
-
addPreprocessor
(func, order=None)¶ Adds a preproceessor function to this task instance. If the function has been decorated with @preprocessor, the order specified by the decorator will be used as the default.
Parameters: - func – the function to add
- order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.
-
classmethod
addSubParam
(name, param, update_owner=True)¶
-
blockSignals
(self, bool) → bool¶
-
block_signal_propagation
()¶
-
calling_context
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
childEvent
(self, QChildEvent)¶
-
children
(self) → List[QObject]¶
-
cmd
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
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, object: QObject = None) [signal]
-
disconnect
(self)¶
-
disconnectNotify
(self, QMetaMethod)¶
-
dumpObjectInfo
(self)¶
-
dumpObjectTree
(self)¶
-
dynamicPropertyNames
(self) → List[QByteArray]¶
-
event
(self, QEvent) → bool¶
-
eventFilter
(self, QObject, QEvent) → bool¶
-
exit_code
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
failure_info
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
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)¶
-
getAddedFuncs
(group=None)¶
-
getFuncGroup
(group=None)¶ Retrieve the functions belonging to the specified group.
Parameters: group (FuncGroupMarker) – the group marker Returns: the functions in the specified group, in order Return type: list
-
classmethod
getJsonBlacklist
()¶ Override to customize what params are serialized.
Implementations should return a list of abstract params that should be omitted from serialization.
- ..NOTE
- Returned abstract params must be direct child params of
cls
, e.g.cls.name
, notcls.coord.x
.
-
getLogAsString
()¶
-
classmethod
getParamSignal
(*args, **kwargs)¶
-
classmethod
getParamValue
(*args, **kwargs)¶
-
classmethod
getSubParam
(name)¶ Get the value of a subparam using the string name:
c = Coord() assert c.getSubParam('x') == 0
Note
Using the string name to accss params is generally discouraged, but can be useful for serializing/deserializing param data.
Parameters: name (str) – The name of the subparam to get the value for.
-
classmethod
getSubParams
()¶ Return a dictionary mapping subparam names to their values.
-
getTaskDir
()¶ Returns the full path of the task directory. This is only available if the task directory exists (after creation of the taskdir or, if no task dir is specified, any time).
-
getTaskFilename
(fname)¶ Return the appropriate absolute path for an input or output file in the taskdir.
-
getTypeHint
()¶
-
get_version
()¶ Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.
-
guard
()¶ Context manager that saves any Exception raised inside
-
inherits
(self, str) → bool¶
-
initAbstract
()¶
-
initConcrete
()¶ Override to customize initialization of concrete params.
-
initializeValue
()¶ @overrides: parameters.CompoundParam
-
inputChanged
¶
-
inputReplaced
¶
-
input_fnameChanged
¶
-
input_fnameReplaced
¶
-
installEventFilter
(self, QObject)¶
-
classmethod
isAbstract
()¶ Whether the param is an “abstract” param.
-
isDefault
(*args, **kwargs)¶
-
isInterruptionRequested
()¶
-
isRunning
()¶
-
isSignalConnected
(self, QMetaMethod) → bool¶
-
isStartable
()¶
-
isWidgetType
(self) → bool¶
-
isWindowType
(self) → bool¶
-
kill
()¶ @overrides: AbstractTask
Kill the subprocess and set the status to FAILED.
-
killTimer
(self, int)¶
-
max_progress
¶
-
max_progressChanged
¶
-
max_progressReplaced
¶
-
metaObject
(self) → QMetaObject¶
-
model_fnameChanged
¶
-
model_fnameReplaced
¶
-
moveToThread
(self, QThread)¶
-
name
¶
-
nameChanged
¶
-
nameReplaced
¶
-
objectName
(self) → str¶
-
objectNameChanged
¶ objectNameChanged(self, str) [signal]
-
output
¶
-
outputChanged
¶
-
outputReplaced
¶
-
classmethod
owner
()¶ Get the owner of the param:
# Can be called on an abstract param: assert Coord.x.owner() == Coord # ...or on an instance of a CompoundParam a = Atom() assert a.coord.owner() == a
-
classmethod
ownerChain
()¶ Returns a list of param owners starting from the toplevel param and ending with self. Examples:
foo.bar.atom.coord.ownerChain()
will return[foo, bar, atom, coord]
where every item is a concrete param.Foo.bar.atom.coord.x.ownerChain()
will return[Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x]
where every item is an abstract params.
-
classmethod
paramName
()¶ Get the name of the param:
# Can be called on an abstract param: print(Coord.x.paramName()) # 'x' # ...or on an instance of a CompoundParam a = Atom() a.coord.paramName() # 'coord'
-
parent
(self) → QObject¶
-
postprocessors
()¶ Returns: A list of postprocessors, both decorated methods on the task and external functions that have been added via addPostprocessor()
Return type: list[typing.Callable]
-
preprocessors
()¶ Returns: A list of preprocessors (both decorated methods on the task and external functions that have been added via addPreprocessor)
-
printingOutputToTerminal
()¶ Returns: whether the StdOut
andStdErr
output from this task is being printed to the terminalReturn type: bool
-
processFuncChain
(chain=None, result_callback=None)¶ Execute each function in the specified chain sequentially in order.
The result_callback is called after each function with the return value of that function. This can be used to respond to the return value (e.g. present information to the user, get user feedback, log the result, etc.)
The return value of the result_callback determines whether processing will proceeed to the next function.
Parameters: - chain (FuncChainDecorator) – which chain to process
- result_callback – the callback that will get called with the result of each function in the chain
Returns: a list of the results from the functions
-
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.
-
qprocess
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
receivers
(self, PYQT_SIGNAL) → int¶
-
removeEventFilter
(self, QObject)¶
-
replicate
()¶ Create a new task with the same input and settings (but no output)
-
requestInterruption
()¶ Request the task to stop.
To enable this feature, subclasses should periodically check whether an interruption has been requested and terminate if it has been. If such logic has been included,
INTERRUPT_ENABLED
should be set toTrue
.
-
reset
(*args, **kwargs)¶
-
run
()¶
-
runCmd
(cmd)¶
-
classmethod
runFromCmdLine
()¶
-
runPostprocessing
(callback=None)¶
-
runPreprocessing
(callback=None, calling_context=None)¶ Run the preprocessors one-by-one. By default, any failing preprocessor will raise a TaskFailure exception and terminate processing. This behavior may be customized by supplying a callback function which will be called after each preprocessor with the result of that preprocessor.
This method is “final” so that all preprocessing logic will be enclosed in the try/finally block.
Parameters: - callback – a function that takes result and returns a bool that indicates whether to continue on to the next preprocessor
- calling_context – specify a value here to indicate the context in which this preprocessing is being called. This value will be stored in an instance variable, self.calling_context, which can be accessed from any preprocessor method on this task. Typically this value will be either self.GUI, self.CMDLINE, or None, but any value may be supplied here and checked for in the preprocessor methods. self.calling_context always reverts back to None at the end of runPreprocessing.
-
sender
(self) → QObject¶
-
senderSignalIndex
(self) → int¶
-
setObjectName
(self, str)¶
-
classmethod
setParamValue
(*args, **kwargs)¶
-
setParent
(self, QObject)¶
-
setPrintingOutputToTerminal
(print_to_terminal)¶ Set this task to print
StdOut
andStdErr
output to terminal, or not.Parameters: print_to_terminal (bool) – whether to send process output to terminal
-
setProperty
(self, str, Any) → bool¶
-
classmethod
setReference
(param1, param2)¶ Call this class method from configureParam to indicate that two params should be kept in sync. The initial values will start with the default value of
param1
. Example:class Square(CompoundParam): width: float = 5 height: float = 10 @classmethod def configureParam(cls): super().configureParam() cls.setReference(cls.width, cls.height) square = Square() assert square.width == square.height == 5 # Default value of width # takes priority square.height = 7 assert square.width == square.height == 7 square.width = 6 assert square.width == square.height == 6
Parameters: - param1 – The first abstract param to keep synced
- param2 – The second abstract param. After instantiation, this param will take on the value of param1.
-
setValue
(*args, **kwargs)¶
-
signalsBlocked
(self) → bool¶
-
skip_eq_check
()¶
-
specifyTaskDir
(taskdir_spec)¶ Specify the taskdir creation behavior. Use one of the following options:
A directory name (string). This may be a relative or absolute path
None - no taskdir is requested. The task will use the CWD as its taskdir
AUTO_TASKDIR - a new subdirectory will be created in the CWD using the task name as the directory name.
TEMP_TASKDIR - a temporary directory will be created in the schrodinger temp dir. This directory is cleaned up when the task is deleted.
Parameters: taskdir_spec – one of the four options listed above
-
start
(*args, **kwargs)¶
-
startTimer
(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int¶
-
staticMetaObject
= <PyQt5.QtCore.QMetaObject object>¶
-
status
¶
-
statusChanged
¶
-
statusReplaced
¶
-
stderr
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
stdout
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
taskDirSetting
()¶ Returns the taskdir spec. See specifyTaskDir() for details.
-
taskDone
¶
-
taskFailed
¶
-
taskStarted
¶
-
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¶
-
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.
-
class
schrodinger.protein.predictors.
SsproPredictor
(*args, **kwargs)¶ Bases:
schrodinger.protein.predictors.AbstractPredictor
Secondary structure predictor.
-
EXE
= 'sspro4'¶
-
PREDICTOR_NAME
= 'sspro'¶
-
CLASS_NUM
= 3¶
-
NU
= 20¶
-
NY
= 3¶
-
input_fname
¶ Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:
class Coord(CompoundParam): x: int y: int
An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:
coord = Coord() coord.x = 4
When a Param value is set, the
valueChanged
signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:class Atom(CompoundParam): coord: Coord element: str
-
model_fname
¶ Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:
class Coord(CompoundParam): x: int y: int
An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:
coord = Coord() coord.x = 4
When a Param value is set, the
valueChanged
signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:class Atom(CompoundParam): coord: Coord element: str
-
generateInputFile
()¶ Generate the input file for the predictor. Typically includes a header (see
_getInputHeader
), the file name of the blast alignment, and the sequence to predict properties for.The input file should be written with the name
self.input_fname
.
-
makeCmd
()¶ Usage: $PSP_PATH/sspro4 model_definition dataset_file alignment_directory dataset_format
-
rawPrediction
()¶ Returns: The raw prediction string containing one character per residue in the input sequence. :rtype : str
-
prediction
()¶ Returns: A list of ssa types from structure
, one for each element inself.input.sequence
:rtype : list
-
AUTO_TASKDIR
= <object object>¶
-
CMDLINE
= 1¶
-
DEFAULT_TASKDIR_SETTING
= None¶
-
DONE
= 3¶
-
DataClass
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
FAILED
= 2¶
-
GUI
= 2¶
-
INTERRUPT_ENABLED
= False¶
-
class
Input
(default_value=<object object>, _param_type=<object object>, **kwargs)¶ Bases:
schrodinger.models.parameters.CompoundParam
-
DataClass
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
__init__
(default_value=<object object>, _param_type=<object object>, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
classmethod
addSubParam
(name, param, update_owner=True)¶
-
aln
¶ Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:
class Coord(CompoundParam): x: int y: int
An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:
coord = Coord() coord.x = 4
When a Param value is set, the
valueChanged
signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:class Atom(CompoundParam): coord: Coord element: str
-
alnChanged
¶
-
alnReplaced
¶
-
blockSignals
(self, bool) → bool¶
-
block_signal_propagation
()¶
-
childEvent
(self, QChildEvent)¶
-
children
(self) → List[QObject]¶
-
classmethod
configureParam
()¶ Override this class method to set up the abstract param class (e.g. setParamReference on child params.)
-
connectNotify
(self, QMetaMethod)¶
-
customEvent
(self, QEvent)¶
-
classmethod
defaultValue
(*args, **kwargs)¶
-
deleteLater
(self)¶
-
destroyed
¶ destroyed(self, object: QObject = None) [signal]
-
disconnect
(self)¶
-
disconnectNotify
(self, QMetaMethod)¶
-
dumpObjectInfo
(self)¶
-
dumpObjectTree
(self)¶
-
dynamicPropertyNames
(self) → List[QByteArray]¶
-
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.
-
getAbstractParam
(*args, **kwargs)¶
-
classmethod
getJsonBlacklist
()¶ Override to customize what params are serialized.
Implementations should return a list of abstract params that should be omitted from serialization.
- ..NOTE
- Returned abstract params must be direct child params of
cls
, e.g.cls.name
, notcls.coord.x
.
-
classmethod
getParamSignal
(*args, **kwargs)¶
-
classmethod
getParamValue
(*args, **kwargs)¶
-
classmethod
getSubParam
(name)¶ Get the value of a subparam using the string name:
c = Coord() assert c.getSubParam('x') == 0
Note
Using the string name to accss params is generally discouraged, but can be useful for serializing/deserializing param data.
Parameters: name (str) – The name of the subparam to get the value for.
-
classmethod
getSubParams
()¶ Return a dictionary mapping subparam names to their values.
-
getTypeHint
()¶
-
get_version
()¶ Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.
-
inherits
(self, str) → bool¶
-
initAbstract
()¶
-
initConcrete
()¶ Override to customize initialization of concrete params.
-
initializeValue
()¶ Override to dynamically set up the default value of the param. Useful for default values that are determined at runtime. This is called any time the param is reset.
-
installEventFilter
(self, QObject)¶
-
classmethod
isAbstract
()¶ Whether the param is an “abstract” param.
-
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
()¶ Get the owner of the param:
# Can be called on an abstract param: assert Coord.x.owner() == Coord # ...or on an instance of a CompoundParam a = Atom() assert a.coord.owner() == a
-
classmethod
ownerChain
()¶ Returns a list of param owners starting from the toplevel param and ending with self. Examples:
foo.bar.atom.coord.ownerChain()
will return[foo, bar, atom, coord]
where every item is a concrete param.Foo.bar.atom.coord.x.ownerChain()
will return[Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x]
where every item is an abstract params.
-
classmethod
paramName
()¶ Get the name of the param:
# Can be called on an abstract param: print(Coord.x.paramName()) # 'x' # ...or on an instance of a CompoundParam a = Atom() a.coord.paramName() # 'coord'
-
parent
(self) → QObject¶
-
property
(self, 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¶
-
seq
¶ Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:
class Coord(CompoundParam): x: int y: int
An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:
coord = Coord() coord.x = 4
When a Param value is set, the
valueChanged
signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:class Atom(CompoundParam): coord: Coord element: str
-
seqChanged
¶
-
seqReplaced
¶
-
setObjectName
(self, str)¶
-
classmethod
setParamValue
(*args, **kwargs)¶
-
setParent
(self, QObject)¶
-
setProperty
(self, str, Any) → bool¶
-
classmethod
setReference
(param1, param2)¶ Call this class method from configureParam to indicate that two params should be kept in sync. The initial values will start with the default value of
param1
. Example:class Square(CompoundParam): width: float = 5 height: float = 10 @classmethod def configureParam(cls): super().configureParam() cls.setReference(cls.width, cls.height) square = Square() assert square.width == square.height == 5 # Default value of width # takes priority square.height = 7 assert square.width == square.height == 7 square.width = 6 assert square.width == square.height == 6
Parameters: - param1 – The first abstract param to keep synced
- param2 – The second abstract param. After instantiation, this param will take on the value of param1.
-
setValue
(*args, **kwargs)¶
-
signalsBlocked
(self) → bool¶
-
skip_eq_check
()¶
-
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¶
-
valueChanged
¶
-
-
RUNNING
= 1¶
-
TEMP_TASKDIR
= <object object>¶
-
WAITING
= 0¶
-
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
addFuncToGroup
(func, group=None, order=None)¶ Adds a function to the specified chain. Typically used for adding functions that are not methods of this object.
The function may optionally be decorated with a FuncGroupMarker. If so, the default group and order will be determined by the decorator. Any group or order explicitly passed in to addFuncToGroup will take precedence over the decorator settings.
Parameters: - func – the function to add
- group (FuncGroupMarker or None) – the group marker. If the function is decorated with a FuncGoupMarker, that group marker will be the default.
- order (float or None) – the sorting order. If the function is decorated with a FuncGoupMarker, the order specified in the decorator will be the default.
-
addPostprocessor
(func, order=0)¶ Adds a postproceessor function to this task instance. If the function has been decorated with
@postprocessor
, the order specified by the decorator will be used.Parameters: - func (typing.Callable) – the function to add
- order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.
-
addPreprocessor
(func, order=None)¶ Adds a preproceessor function to this task instance. If the function has been decorated with @preprocessor, the order specified by the decorator will be used as the default.
Parameters: - func – the function to add
- order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.
-
classmethod
addSubParam
(name, param, update_owner=True)¶
-
blockSignals
(self, bool) → bool¶
-
block_signal_propagation
()¶
-
calling_context
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
childEvent
(self, QChildEvent)¶
-
children
(self) → List[QObject]¶
-
cmd
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
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, object: QObject = None) [signal]
-
disconnect
(self)¶
-
disconnectNotify
(self, QMetaMethod)¶
-
dumpObjectInfo
(self)¶
-
dumpObjectTree
(self)¶
-
dynamicPropertyNames
(self) → List[QByteArray]¶
-
event
(self, QEvent) → bool¶
-
eventFilter
(self, QObject, QEvent) → bool¶
-
exit_code
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
failure_info
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
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.
-
generateAlignmentFile
()¶ Write the alignment file to be used as an input for the predictor. The file will be a temporary file and will be removed in
postprocess
.Gaps in the alignment file are represented as ‘.’.
-
generateModelFile
()¶ Generate the model definition file with the name
self.model_fname
. This is done by finding the Prime data directory for the predictor and getting the names of all the files in it.The model file includes a header describing the number of model files and the predictors class number (
self.CLASS_NUM
), and a list of the model files.
-
getAbstractParam
(*args, **kwargs)¶
-
getAddedFuncs
(group=None)¶
-
getFuncGroup
(group=None)¶ Retrieve the functions belonging to the specified group.
Parameters: group (FuncGroupMarker) – the group marker Returns: the functions in the specified group, in order Return type: list
-
classmethod
getJsonBlacklist
()¶ Override to customize what params are serialized.
Implementations should return a list of abstract params that should be omitted from serialization.
- ..NOTE
- Returned abstract params must be direct child params of
cls
, e.g.cls.name
, notcls.coord.x
.
-
getLogAsString
()¶
-
classmethod
getParamSignal
(*args, **kwargs)¶
-
classmethod
getParamValue
(*args, **kwargs)¶
-
classmethod
getSubParam
(name)¶ Get the value of a subparam using the string name:
c = Coord() assert c.getSubParam('x') == 0
Note
Using the string name to accss params is generally discouraged, but can be useful for serializing/deserializing param data.
Parameters: name (str) – The name of the subparam to get the value for.
-
classmethod
getSubParams
()¶ Return a dictionary mapping subparam names to their values.
-
getTaskDir
()¶ Returns the full path of the task directory. This is only available if the task directory exists (after creation of the taskdir or, if no task dir is specified, any time).
-
getTaskFilename
(fname)¶ Return the appropriate absolute path for an input or output file in the taskdir.
-
getTypeHint
()¶
-
get_version
()¶ Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.
-
guard
()¶ Context manager that saves any Exception raised inside
-
inherits
(self, str) → bool¶
-
initAbstract
()¶
-
initConcrete
()¶ Override to customize initialization of concrete params.
-
initializeValue
()¶ @overrides: parameters.CompoundParam
-
input
¶
-
inputChanged
¶
-
inputReplaced
¶
-
input_fnameChanged
¶
-
input_fnameReplaced
¶
-
installEventFilter
(self, QObject)¶
-
classmethod
isAbstract
()¶ Whether the param is an “abstract” param.
-
isDefault
(*args, **kwargs)¶
-
isInterruptionRequested
()¶
-
isRunning
()¶
-
isSignalConnected
(self, QMetaMethod) → bool¶
-
isStartable
()¶
-
isWidgetType
(self) → bool¶
-
isWindowType
(self) → bool¶
-
kill
()¶ @overrides: AbstractTask
Kill the subprocess and set the status to FAILED.
-
killTimer
(self, int)¶
-
max_progress
¶
-
max_progressChanged
¶
-
max_progressReplaced
¶
-
metaObject
(self) → QMetaObject¶
-
model_fnameChanged
¶
-
model_fnameReplaced
¶
-
moveToThread
(self, QThread)¶
-
name
¶
-
nameChanged
¶
-
nameReplaced
¶
-
objectName
(self) → str¶
-
objectNameChanged
¶ objectNameChanged(self, str) [signal]
-
output
¶
-
outputChanged
¶
-
outputReplaced
¶
-
classmethod
owner
()¶ Get the owner of the param:
# Can be called on an abstract param: assert Coord.x.owner() == Coord # ...or on an instance of a CompoundParam a = Atom() assert a.coord.owner() == a
-
classmethod
ownerChain
()¶ Returns a list of param owners starting from the toplevel param and ending with self. Examples:
foo.bar.atom.coord.ownerChain()
will return[foo, bar, atom, coord]
where every item is a concrete param.Foo.bar.atom.coord.x.ownerChain()
will return[Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x]
where every item is an abstract params.
-
classmethod
paramName
()¶ Get the name of the param:
# Can be called on an abstract param: print(Coord.x.paramName()) # 'x' # ...or on an instance of a CompoundParam a = Atom() a.coord.paramName() # 'coord'
-
parent
(self) → QObject¶
-
postprocess
()¶
-
postprocessors
()¶ Returns: A list of postprocessors, both decorated methods on the task and external functions that have been added via addPostprocessor()
Return type: list[typing.Callable]
-
preprocessors
()¶ Returns: A list of preprocessors (both decorated methods on the task and external functions that have been added via addPreprocessor)
-
printingOutputToTerminal
()¶ Returns: whether the StdOut
andStdErr
output from this task is being printed to the terminalReturn type: bool
-
processFuncChain
(chain=None, result_callback=None)¶ Execute each function in the specified chain sequentially in order.
The result_callback is called after each function with the return value of that function. This can be used to respond to the return value (e.g. present information to the user, get user feedback, log the result, etc.)
The return value of the result_callback determines whether processing will proceeed to the next function.
Parameters: - chain (FuncChainDecorator) – which chain to process
- result_callback – the callback that will get called with the result of each function in the chain
Returns: a list of the results from the functions
-
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.
-
qprocess
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
receivers
(self, PYQT_SIGNAL) → int¶
-
removeEventFilter
(self, QObject)¶
-
replicate
()¶ Create a new task with the same input and settings (but no output)
-
requestInterruption
()¶ Request the task to stop.
To enable this feature, subclasses should periodically check whether an interruption has been requested and terminate if it has been. If such logic has been included,
INTERRUPT_ENABLED
should be set toTrue
.
-
reset
(*args, **kwargs)¶
-
run
()¶
-
runCmd
(cmd)¶
-
classmethod
runFromCmdLine
()¶
-
runPostprocessing
(callback=None)¶
-
runPreprocessing
(callback=None, calling_context=None)¶ Run the preprocessors one-by-one. By default, any failing preprocessor will raise a TaskFailure exception and terminate processing. This behavior may be customized by supplying a callback function which will be called after each preprocessor with the result of that preprocessor.
This method is “final” so that all preprocessing logic will be enclosed in the try/finally block.
Parameters: - callback – a function that takes result and returns a bool that indicates whether to continue on to the next preprocessor
- calling_context – specify a value here to indicate the context in which this preprocessing is being called. This value will be stored in an instance variable, self.calling_context, which can be accessed from any preprocessor method on this task. Typically this value will be either self.GUI, self.CMDLINE, or None, but any value may be supplied here and checked for in the preprocessor methods. self.calling_context always reverts back to None at the end of runPreprocessing.
-
sender
(self) → QObject¶
-
senderSignalIndex
(self) → int¶
-
setObjectName
(self, str)¶
-
classmethod
setParamValue
(*args, **kwargs)¶
-
setParent
(self, QObject)¶
-
setPrintingOutputToTerminal
(print_to_terminal)¶ Set this task to print
StdOut
andStdErr
output to terminal, or not.Parameters: print_to_terminal (bool) – whether to send process output to terminal
-
setProperty
(self, str, Any) → bool¶
-
classmethod
setReference
(param1, param2)¶ Call this class method from configureParam to indicate that two params should be kept in sync. The initial values will start with the default value of
param1
. Example:class Square(CompoundParam): width: float = 5 height: float = 10 @classmethod def configureParam(cls): super().configureParam() cls.setReference(cls.width, cls.height) square = Square() assert square.width == square.height == 5 # Default value of width # takes priority square.height = 7 assert square.width == square.height == 7 square.width = 6 assert square.width == square.height == 6
Parameters: - param1 – The first abstract param to keep synced
- param2 – The second abstract param. After instantiation, this param will take on the value of param1.
-
setValue
(*args, **kwargs)¶
-
signalsBlocked
(self) → bool¶
-
skip_eq_check
()¶
-
specifyTaskDir
(taskdir_spec)¶ Specify the taskdir creation behavior. Use one of the following options:
A directory name (string). This may be a relative or absolute path
None - no taskdir is requested. The task will use the CWD as its taskdir
AUTO_TASKDIR - a new subdirectory will be created in the CWD using the task name as the directory name.
TEMP_TASKDIR - a temporary directory will be created in the schrodinger temp dir. This directory is cleaned up when the task is deleted.
Parameters: taskdir_spec – one of the four options listed above
-
start
(*args, **kwargs)¶
-
startTimer
(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int¶
-
staticMetaObject
= <PyQt5.QtCore.QMetaObject object>¶
-
status
¶
-
statusChanged
¶
-
statusReplaced
¶
-
stderr
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
stdout
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
taskDirSetting
()¶ Returns the taskdir spec. See specifyTaskDir() for details.
-
taskDone
¶
-
taskFailed
¶
-
taskStarted
¶
-
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¶
-
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.
-
-
class
schrodinger.protein.predictors.
SolventAccessibility
(*args, **kwargs)¶ Bases:
schrodinger.models.jsonable.JsonableEnum
An enumeration.
-
BURIED
= 1¶
-
EXPOSED
= 2¶
-
-
class
schrodinger.protein.predictors.
AccproPredictor
(*args, **kwargs)¶ Bases:
schrodinger.protein.predictors.AbstractPredictor
Solvent accessibility predictor.
-
EXE
= 'accpro'¶
-
PREDICTOR_NAME
= 'accpro'¶
-
CLASS_NUM
= 20¶
-
NU
= 20¶
-
NY
= 3¶
-
input_fname
¶ Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:
class Coord(CompoundParam): x: int y: int
An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:
coord = Coord() coord.x = 4
When a Param value is set, the
valueChanged
signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:class Atom(CompoundParam): coord: Coord element: str
-
model_fname
¶ Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:
class Coord(CompoundParam): x: int y: int
An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:
coord = Coord() coord.x = 4
When a Param value is set, the
valueChanged
signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:class Atom(CompoundParam): coord: Coord element: str
-
CHAR_TO_ACC_MAP
= {'b': <SolventAccessibility.BURIED: 1>, 'e': <SolventAccessibility.EXPOSED: 2>}¶
-
generateInputFile
()¶ Generate the input file for the predictor. Typically includes a header (see
_getInputHeader
), the file name of the blast alignment, and the sequence to predict properties for.The input file should be written with the name
self.input_fname
.
-
makeCmd
()¶ Usage: $PSP_PATH/accpro model_definition dataset_file alignment_directory dataset_format threshold_index
-
rawPrediction
()¶ - Example:
- eeebbbebebebebbebbebebeebbbbbbbeeeee
e = exposed b = buried
-
prediction
()¶ Return the actual prediction. This can take various forms depending on the predictor.
-
AUTO_TASKDIR
= <object object>¶
-
CMDLINE
= 1¶
-
DEFAULT_TASKDIR_SETTING
= None¶
-
DONE
= 3¶
-
DataClass
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
FAILED
= 2¶
-
GUI
= 2¶
-
INTERRUPT_ENABLED
= False¶
-
class
Input
(default_value=<object object>, _param_type=<object object>, **kwargs)¶ Bases:
schrodinger.models.parameters.CompoundParam
-
DataClass
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
__init__
(default_value=<object object>, _param_type=<object object>, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
classmethod
addSubParam
(name, param, update_owner=True)¶
-
aln
¶ Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:
class Coord(CompoundParam): x: int y: int
An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:
coord = Coord() coord.x = 4
When a Param value is set, the
valueChanged
signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:class Atom(CompoundParam): coord: Coord element: str
-
alnChanged
¶
-
alnReplaced
¶
-
blockSignals
(self, bool) → bool¶
-
block_signal_propagation
()¶
-
childEvent
(self, QChildEvent)¶
-
children
(self) → List[QObject]¶
-
classmethod
configureParam
()¶ Override this class method to set up the abstract param class (e.g. setParamReference on child params.)
-
connectNotify
(self, QMetaMethod)¶
-
customEvent
(self, QEvent)¶
-
classmethod
defaultValue
(*args, **kwargs)¶
-
deleteLater
(self)¶
-
destroyed
¶ destroyed(self, object: QObject = None) [signal]
-
disconnect
(self)¶
-
disconnectNotify
(self, QMetaMethod)¶
-
dumpObjectInfo
(self)¶
-
dumpObjectTree
(self)¶
-
dynamicPropertyNames
(self) → List[QByteArray]¶
-
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.
-
getAbstractParam
(*args, **kwargs)¶
-
classmethod
getJsonBlacklist
()¶ Override to customize what params are serialized.
Implementations should return a list of abstract params that should be omitted from serialization.
- ..NOTE
- Returned abstract params must be direct child params of
cls
, e.g.cls.name
, notcls.coord.x
.
-
classmethod
getParamSignal
(*args, **kwargs)¶
-
classmethod
getParamValue
(*args, **kwargs)¶
-
classmethod
getSubParam
(name)¶ Get the value of a subparam using the string name:
c = Coord() assert c.getSubParam('x') == 0
Note
Using the string name to accss params is generally discouraged, but can be useful for serializing/deserializing param data.
Parameters: name (str) – The name of the subparam to get the value for.
-
classmethod
getSubParams
()¶ Return a dictionary mapping subparam names to their values.
-
getTypeHint
()¶
-
get_version
()¶ Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.
-
inherits
(self, str) → bool¶
-
initAbstract
()¶
-
initConcrete
()¶ Override to customize initialization of concrete params.
-
initializeValue
()¶ Override to dynamically set up the default value of the param. Useful for default values that are determined at runtime. This is called any time the param is reset.
-
installEventFilter
(self, QObject)¶
-
classmethod
isAbstract
()¶ Whether the param is an “abstract” param.
-
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
()¶ Get the owner of the param:
# Can be called on an abstract param: assert Coord.x.owner() == Coord # ...or on an instance of a CompoundParam a = Atom() assert a.coord.owner() == a
-
classmethod
ownerChain
()¶ Returns a list of param owners starting from the toplevel param and ending with self. Examples:
foo.bar.atom.coord.ownerChain()
will return[foo, bar, atom, coord]
where every item is a concrete param.Foo.bar.atom.coord.x.ownerChain()
will return[Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x]
where every item is an abstract params.
-
classmethod
paramName
()¶ Get the name of the param:
# Can be called on an abstract param: print(Coord.x.paramName()) # 'x' # ...or on an instance of a CompoundParam a = Atom() a.coord.paramName() # 'coord'
-
parent
(self) → QObject¶
-
property
(self, 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¶
-
seq
¶ Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:
class Coord(CompoundParam): x: int y: int
An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:
coord = Coord() coord.x = 4
When a Param value is set, the
valueChanged
signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:class Atom(CompoundParam): coord: Coord element: str
-
seqChanged
¶
-
seqReplaced
¶
-
setObjectName
(self, str)¶
-
classmethod
setParamValue
(*args, **kwargs)¶
-
setParent
(self, QObject)¶
-
setProperty
(self, str, Any) → bool¶
-
classmethod
setReference
(param1, param2)¶ Call this class method from configureParam to indicate that two params should be kept in sync. The initial values will start with the default value of
param1
. Example:class Square(CompoundParam): width: float = 5 height: float = 10 @classmethod def configureParam(cls): super().configureParam() cls.setReference(cls.width, cls.height) square = Square() assert square.width == square.height == 5 # Default value of width # takes priority square.height = 7 assert square.width == square.height == 7 square.width = 6 assert square.width == square.height == 6
Parameters: - param1 – The first abstract param to keep synced
- param2 – The second abstract param. After instantiation, this param will take on the value of param1.
-
setValue
(*args, **kwargs)¶
-
signalsBlocked
(self) → bool¶
-
skip_eq_check
()¶
-
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¶
-
valueChanged
¶
-
-
RUNNING
= 1¶
-
TEMP_TASKDIR
= <object object>¶
-
WAITING
= 0¶
-
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
addFuncToGroup
(func, group=None, order=None)¶ Adds a function to the specified chain. Typically used for adding functions that are not methods of this object.
The function may optionally be decorated with a FuncGroupMarker. If so, the default group and order will be determined by the decorator. Any group or order explicitly passed in to addFuncToGroup will take precedence over the decorator settings.
Parameters: - func – the function to add
- group (FuncGroupMarker or None) – the group marker. If the function is decorated with a FuncGoupMarker, that group marker will be the default.
- order (float or None) – the sorting order. If the function is decorated with a FuncGoupMarker, the order specified in the decorator will be the default.
-
addPostprocessor
(func, order=0)¶ Adds a postproceessor function to this task instance. If the function has been decorated with
@postprocessor
, the order specified by the decorator will be used.Parameters: - func (typing.Callable) – the function to add
- order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.
-
addPreprocessor
(func, order=None)¶ Adds a preproceessor function to this task instance. If the function has been decorated with @preprocessor, the order specified by the decorator will be used as the default.
Parameters: - func – the function to add
- order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.
-
classmethod
addSubParam
(name, param, update_owner=True)¶
-
blockSignals
(self, bool) → bool¶
-
block_signal_propagation
()¶
-
calling_context
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
childEvent
(self, QChildEvent)¶
-
children
(self) → List[QObject]¶
-
cmd
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
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, object: QObject = None) [signal]
-
disconnect
(self)¶
-
disconnectNotify
(self, QMetaMethod)¶
-
dumpObjectInfo
(self)¶
-
dumpObjectTree
(self)¶
-
dynamicPropertyNames
(self) → List[QByteArray]¶
-
event
(self, QEvent) → bool¶
-
eventFilter
(self, QObject, QEvent) → bool¶
-
exit_code
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
failure_info
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
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.
-
generateAlignmentFile
()¶ Write the alignment file to be used as an input for the predictor. The file will be a temporary file and will be removed in
postprocess
.Gaps in the alignment file are represented as ‘.’.
-
generateModelFile
()¶ Generate the model definition file with the name
self.model_fname
. This is done by finding the Prime data directory for the predictor and getting the names of all the files in it.The model file includes a header describing the number of model files and the predictors class number (
self.CLASS_NUM
), and a list of the model files.
-
getAbstractParam
(*args, **kwargs)¶
-
getAddedFuncs
(group=None)¶
-
getFuncGroup
(group=None)¶ Retrieve the functions belonging to the specified group.
Parameters: group (FuncGroupMarker) – the group marker Returns: the functions in the specified group, in order Return type: list
-
classmethod
getJsonBlacklist
()¶ Override to customize what params are serialized.
Implementations should return a list of abstract params that should be omitted from serialization.
- ..NOTE
- Returned abstract params must be direct child params of
cls
, e.g.cls.name
, notcls.coord.x
.
-
getLogAsString
()¶
-
classmethod
getParamSignal
(*args, **kwargs)¶
-
classmethod
getParamValue
(*args, **kwargs)¶
-
classmethod
getSubParam
(name)¶ Get the value of a subparam using the string name:
c = Coord() assert c.getSubParam('x') == 0
Note
Using the string name to accss params is generally discouraged, but can be useful for serializing/deserializing param data.
Parameters: name (str) – The name of the subparam to get the value for.
-
classmethod
getSubParams
()¶ Return a dictionary mapping subparam names to their values.
-
getTaskDir
()¶ Returns the full path of the task directory. This is only available if the task directory exists (after creation of the taskdir or, if no task dir is specified, any time).
-
getTaskFilename
(fname)¶ Return the appropriate absolute path for an input or output file in the taskdir.
-
getTypeHint
()¶
-
get_version
()¶ Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.
-
guard
()¶ Context manager that saves any Exception raised inside
-
inherits
(self, str) → bool¶
-
initAbstract
()¶
-
initConcrete
()¶ Override to customize initialization of concrete params.
-
initializeValue
()¶ @overrides: parameters.CompoundParam
-
input
¶
-
inputChanged
¶
-
inputReplaced
¶
-
input_fnameChanged
¶
-
input_fnameReplaced
¶
-
installEventFilter
(self, QObject)¶
-
classmethod
isAbstract
()¶ Whether the param is an “abstract” param.
-
isDefault
(*args, **kwargs)¶
-
isInterruptionRequested
()¶
-
isRunning
()¶
-
isSignalConnected
(self, QMetaMethod) → bool¶
-
isStartable
()¶
-
isWidgetType
(self) → bool¶
-
isWindowType
(self) → bool¶
-
kill
()¶ @overrides: AbstractTask
Kill the subprocess and set the status to FAILED.
-
killTimer
(self, int)¶
-
max_progress
¶
-
max_progressChanged
¶
-
max_progressReplaced
¶
-
metaObject
(self) → QMetaObject¶
-
model_fnameChanged
¶
-
model_fnameReplaced
¶
-
moveToThread
(self, QThread)¶
-
name
¶
-
nameChanged
¶
-
nameReplaced
¶
-
objectName
(self) → str¶
-
objectNameChanged
¶ objectNameChanged(self, str) [signal]
-
output
¶
-
outputChanged
¶
-
outputReplaced
¶
-
classmethod
owner
()¶ Get the owner of the param:
# Can be called on an abstract param: assert Coord.x.owner() == Coord # ...or on an instance of a CompoundParam a = Atom() assert a.coord.owner() == a
-
classmethod
ownerChain
()¶ Returns a list of param owners starting from the toplevel param and ending with self. Examples:
foo.bar.atom.coord.ownerChain()
will return[foo, bar, atom, coord]
where every item is a concrete param.Foo.bar.atom.coord.x.ownerChain()
will return[Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x]
where every item is an abstract params.
-
classmethod
paramName
()¶ Get the name of the param:
# Can be called on an abstract param: print(Coord.x.paramName()) # 'x' # ...or on an instance of a CompoundParam a = Atom() a.coord.paramName() # 'coord'
-
parent
(self) → QObject¶
-
postprocess
()¶
-
postprocessors
()¶ Returns: A list of postprocessors, both decorated methods on the task and external functions that have been added via addPostprocessor()
Return type: list[typing.Callable]
-
preprocessors
()¶ Returns: A list of preprocessors (both decorated methods on the task and external functions that have been added via addPreprocessor)
-
printingOutputToTerminal
()¶ Returns: whether the StdOut
andStdErr
output from this task is being printed to the terminalReturn type: bool
-
processFuncChain
(chain=None, result_callback=None)¶ Execute each function in the specified chain sequentially in order.
The result_callback is called after each function with the return value of that function. This can be used to respond to the return value (e.g. present information to the user, get user feedback, log the result, etc.)
The return value of the result_callback determines whether processing will proceeed to the next function.
Parameters: - chain (FuncChainDecorator) – which chain to process
- result_callback – the callback that will get called with the result of each function in the chain
Returns: a list of the results from the functions
-
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.
-
qprocess
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
receivers
(self, PYQT_SIGNAL) → int¶
-
removeEventFilter
(self, QObject)¶
-
replicate
()¶ Create a new task with the same input and settings (but no output)
-
requestInterruption
()¶ Request the task to stop.
To enable this feature, subclasses should periodically check whether an interruption has been requested and terminate if it has been. If such logic has been included,
INTERRUPT_ENABLED
should be set toTrue
.
-
reset
(*args, **kwargs)¶
-
run
()¶
-
runCmd
(cmd)¶
-
classmethod
runFromCmdLine
()¶
-
runPostprocessing
(callback=None)¶
-
runPreprocessing
(callback=None, calling_context=None)¶ Run the preprocessors one-by-one. By default, any failing preprocessor will raise a TaskFailure exception and terminate processing. This behavior may be customized by supplying a callback function which will be called after each preprocessor with the result of that preprocessor.
This method is “final” so that all preprocessing logic will be enclosed in the try/finally block.
Parameters: - callback – a function that takes result and returns a bool that indicates whether to continue on to the next preprocessor
- calling_context – specify a value here to indicate the context in which this preprocessing is being called. This value will be stored in an instance variable, self.calling_context, which can be accessed from any preprocessor method on this task. Typically this value will be either self.GUI, self.CMDLINE, or None, but any value may be supplied here and checked for in the preprocessor methods. self.calling_context always reverts back to None at the end of runPreprocessing.
-
sender
(self) → QObject¶
-
senderSignalIndex
(self) → int¶
-
setObjectName
(self, str)¶
-
classmethod
setParamValue
(*args, **kwargs)¶
-
setParent
(self, QObject)¶
-
setPrintingOutputToTerminal
(print_to_terminal)¶ Set this task to print
StdOut
andStdErr
output to terminal, or not.Parameters: print_to_terminal (bool) – whether to send process output to terminal
-
setProperty
(self, str, Any) → bool¶
-
classmethod
setReference
(param1, param2)¶ Call this class method from configureParam to indicate that two params should be kept in sync. The initial values will start with the default value of
param1
. Example:class Square(CompoundParam): width: float = 5 height: float = 10 @classmethod def configureParam(cls): super().configureParam() cls.setReference(cls.width, cls.height) square = Square() assert square.width == square.height == 5 # Default value of width # takes priority square.height = 7 assert square.width == square.height == 7 square.width = 6 assert square.width == square.height == 6
Parameters: - param1 – The first abstract param to keep synced
- param2 – The second abstract param. After instantiation, this param will take on the value of param1.
-
setValue
(*args, **kwargs)¶
-
signalsBlocked
(self) → bool¶
-
skip_eq_check
()¶
-
specifyTaskDir
(taskdir_spec)¶ Specify the taskdir creation behavior. Use one of the following options:
A directory name (string). This may be a relative or absolute path
None - no taskdir is requested. The task will use the CWD as its taskdir
AUTO_TASKDIR - a new subdirectory will be created in the CWD using the task name as the directory name.
TEMP_TASKDIR - a temporary directory will be created in the schrodinger temp dir. This directory is cleaned up when the task is deleted.
Parameters: taskdir_spec – one of the four options listed above
-
start
(*args, **kwargs)¶
-
startTimer
(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int¶
-
staticMetaObject
= <PyQt5.QtCore.QMetaObject object>¶
-
status
¶
-
statusChanged
¶
-
statusReplaced
¶
-
stderr
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
stdout
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
taskDirSetting
()¶ Returns the taskdir spec. See specifyTaskDir() for details.
-
taskDone
¶
-
taskFailed
¶
-
taskStarted
¶
-
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¶
-
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.predictors.
encode_acc
(acc)¶
-
class
schrodinger.protein.predictors.
Disordered
(*args, **kwargs)¶ Bases:
schrodinger.models.jsonable.JsonableEnum
An enumeration.
-
HIGHSCORE
= 1¶
-
LOWSCORE
= 3¶
-
MEDIUMSCORE
= 2¶
-
-
class
schrodinger.protein.predictors.
SsAccDependentPredictors
(*args, **kwargs)¶ Bases:
schrodinger.protein.predictors.AbstractPredictor
Base class for predictors that use secondary structure and solvent accessibility predictions as inputs.
-
class
Input
(default_value=<object object>, _param_type=<object object>, **kwargs)¶ Bases:
schrodinger.models.parameters.CompoundParam
-
seq
¶ Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:
class Coord(CompoundParam): x: int y: int
An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:
coord = Coord() coord.x = 4
When a Param value is set, the
valueChanged
signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:class Atom(CompoundParam): coord: Coord element: str
-
aln
¶ Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:
class Coord(CompoundParam): x: int y: int
An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:
coord = Coord() coord.x = 4
When a Param value is set, the
valueChanged
signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:class Atom(CompoundParam): coord: Coord element: str
-
ss_prediction
¶ Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:
class Coord(CompoundParam): x: int y: int
An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:
coord = Coord() coord.x = 4
When a Param value is set, the
valueChanged
signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:class Atom(CompoundParam): coord: Coord element: str
-
acc_prediction
¶ Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:
class Coord(CompoundParam): x: int y: int
An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:
coord = Coord() coord.x = 4
When a Param value is set, the
valueChanged
signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:class Atom(CompoundParam): coord: Coord element: str
-
DataClass
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
__init__
(default_value=<object object>, _param_type=<object object>, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
acc_predictionChanged
¶
-
acc_predictionReplaced
¶
-
classmethod
addSubParam
(name, param, update_owner=True)¶
-
alnChanged
¶
-
alnReplaced
¶
-
blockSignals
(self, bool) → bool¶
-
block_signal_propagation
()¶
-
childEvent
(self, QChildEvent)¶
-
children
(self) → List[QObject]¶
-
classmethod
configureParam
()¶ Override this class method to set up the abstract param class (e.g. setParamReference on child params.)
-
connectNotify
(self, QMetaMethod)¶
-
customEvent
(self, QEvent)¶
-
classmethod
defaultValue
(*args, **kwargs)¶
-
deleteLater
(self)¶
-
destroyed
¶ destroyed(self, object: QObject = None) [signal]
-
disconnect
(self)¶
-
disconnectNotify
(self, QMetaMethod)¶
-
dumpObjectInfo
(self)¶
-
dumpObjectTree
(self)¶
-
dynamicPropertyNames
(self) → List[QByteArray]¶
-
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.
-
getAbstractParam
(*args, **kwargs)¶
-
classmethod
getJsonBlacklist
()¶ Override to customize what params are serialized.
Implementations should return a list of abstract params that should be omitted from serialization.
- ..NOTE
- Returned abstract params must be direct child params of
cls
, e.g.cls.name
, notcls.coord.x
.
-
classmethod
getParamSignal
(*args, **kwargs)¶
-
classmethod
getParamValue
(*args, **kwargs)¶
-
classmethod
getSubParam
(name)¶ Get the value of a subparam using the string name:
c = Coord() assert c.getSubParam('x') == 0
Note
Using the string name to accss params is generally discouraged, but can be useful for serializing/deserializing param data.
Parameters: name (str) – The name of the subparam to get the value for.
-
classmethod
getSubParams
()¶ Return a dictionary mapping subparam names to their values.
-
getTypeHint
()¶
-
get_version
()¶ Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.
-
inherits
(self, str) → bool¶
-
initAbstract
()¶
-
initConcrete
()¶ Override to customize initialization of concrete params.
-
initializeValue
()¶ Override to dynamically set up the default value of the param. Useful for default values that are determined at runtime. This is called any time the param is reset.
-
installEventFilter
(self, QObject)¶
-
classmethod
isAbstract
()¶ Whether the param is an “abstract” param.
-
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
()¶ Get the owner of the param:
# Can be called on an abstract param: assert Coord.x.owner() == Coord # ...or on an instance of a CompoundParam a = Atom() assert a.coord.owner() == a
-
classmethod
ownerChain
()¶ Returns a list of param owners starting from the toplevel param and ending with self. Examples:
foo.bar.atom.coord.ownerChain()
will return[foo, bar, atom, coord]
where every item is a concrete param.Foo.bar.atom.coord.x.ownerChain()
will return[Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x]
where every item is an abstract params.
-
classmethod
paramName
()¶ Get the name of the param:
# Can be called on an abstract param: print(Coord.x.paramName()) # 'x' # ...or on an instance of a CompoundParam a = Atom() a.coord.paramName() # 'coord'
-
parent
(self) → QObject¶
-
property
(self, 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¶
-
seqChanged
¶
-
seqReplaced
¶
-
setObjectName
(self, str)¶
-
classmethod
setParamValue
(*args, **kwargs)¶
-
setParent
(self, QObject)¶
-
setProperty
(self, str, Any) → bool¶
-
classmethod
setReference
(param1, param2)¶ Call this class method from configureParam to indicate that two params should be kept in sync. The initial values will start with the default value of
param1
. Example:class Square(CompoundParam): width: float = 5 height: float = 10 @classmethod def configureParam(cls): super().configureParam() cls.setReference(cls.width, cls.height) square = Square() assert square.width == square.height == 5 # Default value of width # takes priority square.height = 7 assert square.width == square.height == 7 square.width = 6 assert square.width == square.height == 6
Parameters: - param1 – The first abstract param to keep synced
- param2 – The second abstract param. After instantiation, this param will take on the value of param1.
-
setValue
(*args, **kwargs)¶
-
signalsBlocked
(self) → bool¶
-
skip_eq_check
()¶
-
ss_predictionChanged
¶
-
ss_predictionReplaced
¶
-
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¶
-
valueChanged
¶
-
-
input
¶
-
AUTO_TASKDIR
= <object object>¶
-
CLASS_NUM
= NotImplemented¶
-
CMDLINE
= 1¶
-
DEFAULT_TASKDIR_SETTING
= None¶
-
DONE
= 3¶
-
DataClass
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
EXE
= NotImplemented¶
-
FAILED
= 2¶
-
GUI
= 2¶
-
INTERRUPT_ENABLED
= False¶
-
NU
= NotImplemented¶
-
NY
= NotImplemented¶
-
PREDICTOR_NAME
= NotImplemented¶
-
RUNNING
= 1¶
-
TEMP_TASKDIR
= <object object>¶
-
WAITING
= 0¶
-
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
addFuncToGroup
(func, group=None, order=None)¶ Adds a function to the specified chain. Typically used for adding functions that are not methods of this object.
The function may optionally be decorated with a FuncGroupMarker. If so, the default group and order will be determined by the decorator. Any group or order explicitly passed in to addFuncToGroup will take precedence over the decorator settings.
Parameters: - func – the function to add
- group (FuncGroupMarker or None) – the group marker. If the function is decorated with a FuncGoupMarker, that group marker will be the default.
- order (float or None) – the sorting order. If the function is decorated with a FuncGoupMarker, the order specified in the decorator will be the default.
-
addPostprocessor
(func, order=0)¶ Adds a postproceessor function to this task instance. If the function has been decorated with
@postprocessor
, the order specified by the decorator will be used.Parameters: - func (typing.Callable) – the function to add
- order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.
-
addPreprocessor
(func, order=None)¶ Adds a preproceessor function to this task instance. If the function has been decorated with @preprocessor, the order specified by the decorator will be used as the default.
Parameters: - func – the function to add
- order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.
-
classmethod
addSubParam
(name, param, update_owner=True)¶
-
blockSignals
(self, bool) → bool¶
-
block_signal_propagation
()¶
-
calling_context
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
childEvent
(self, QChildEvent)¶
-
children
(self) → List[QObject]¶
-
cmd
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
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, object: QObject = None) [signal]
-
disconnect
(self)¶
-
disconnectNotify
(self, QMetaMethod)¶
-
dumpObjectInfo
(self)¶
-
dumpObjectTree
(self)¶
-
dynamicPropertyNames
(self) → List[QByteArray]¶
-
event
(self, QEvent) → bool¶
-
eventFilter
(self, QObject, QEvent) → bool¶
-
exit_code
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
failure_info
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
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.
-
generateAlignmentFile
()¶ Write the alignment file to be used as an input for the predictor. The file will be a temporary file and will be removed in
postprocess
.Gaps in the alignment file are represented as ‘.’.
-
generateInputFile
()¶ Generate the input file for the predictor. Typically includes a header (see
_getInputHeader
), the file name of the blast alignment, and the sequence to predict properties for.The input file should be written with the name
self.input_fname
.
-
generateModelFile
()¶ Generate the model definition file with the name
self.model_fname
. This is done by finding the Prime data directory for the predictor and getting the names of all the files in it.The model file includes a header describing the number of model files and the predictors class number (
self.CLASS_NUM
), and a list of the model files.
-
getAbstractParam
(*args, **kwargs)¶
-
getAddedFuncs
(group=None)¶
-
getFuncGroup
(group=None)¶ Retrieve the functions belonging to the specified group.
Parameters: group (FuncGroupMarker) – the group marker Returns: the functions in the specified group, in order Return type: list
-
classmethod
getJsonBlacklist
()¶ Override to customize what params are serialized.
Implementations should return a list of abstract params that should be omitted from serialization.
- ..NOTE
- Returned abstract params must be direct child params of
cls
, e.g.cls.name
, notcls.coord.x
.
-
getLogAsString
()¶
-
classmethod
getParamSignal
(*args, **kwargs)¶
-
classmethod
getParamValue
(*args, **kwargs)¶
-
classmethod
getSubParam
(name)¶ Get the value of a subparam using the string name:
c = Coord() assert c.getSubParam('x') == 0
Note
Using the string name to accss params is generally discouraged, but can be useful for serializing/deserializing param data.
Parameters: name (str) – The name of the subparam to get the value for.
-
classmethod
getSubParams
()¶ Return a dictionary mapping subparam names to their values.
-
getTaskDir
()¶ Returns the full path of the task directory. This is only available if the task directory exists (after creation of the taskdir or, if no task dir is specified, any time).
-
getTaskFilename
(fname)¶ Return the appropriate absolute path for an input or output file in the taskdir.
-
getTypeHint
()¶
-
get_version
()¶ Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.
-
guard
()¶ Context manager that saves any Exception raised inside
-
inherits
(self, str) → bool¶
-
initAbstract
()¶
-
initConcrete
()¶ Override to customize initialization of concrete params.
-
initializeValue
()¶ @overrides: parameters.CompoundParam
-
inputChanged
¶
-
inputReplaced
¶
-
input_fname
¶ Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:
class Coord(CompoundParam): x: int y: int
An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:
coord = Coord() coord.x = 4
When a Param value is set, the
valueChanged
signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:class Atom(CompoundParam): coord: Coord element: str
-
input_fnameChanged
¶
-
input_fnameReplaced
¶
-
installEventFilter
(self, QObject)¶
-
classmethod
isAbstract
()¶ Whether the param is an “abstract” param.
-
isDefault
(*args, **kwargs)¶
-
isInterruptionRequested
()¶
-
isRunning
()¶
-
isSignalConnected
(self, QMetaMethod) → bool¶
-
isStartable
()¶
-
isWidgetType
(self) → bool¶
-
isWindowType
(self) → bool¶
-
kill
()¶ @overrides: AbstractTask
Kill the subprocess and set the status to FAILED.
-
killTimer
(self, int)¶
-
makeCmd
()¶ Return the command to run the predictor backend. The default implementation returns the predictor executable, the model file name, and the input file name.
Return type: list[str]
-
max_progress
¶
-
max_progressChanged
¶
-
max_progressReplaced
¶
-
metaObject
(self) → QMetaObject¶
-
model_fname
¶ Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:
class Coord(CompoundParam): x: int y: int
An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:
coord = Coord() coord.x = 4
When a Param value is set, the
valueChanged
signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:class Atom(CompoundParam): coord: Coord element: str
-
model_fnameChanged
¶
-
model_fnameReplaced
¶
-
moveToThread
(self, QThread)¶
-
name
¶
-
nameChanged
¶
-
nameReplaced
¶
-
objectName
(self) → str¶
-
objectNameChanged
¶ objectNameChanged(self, str) [signal]
-
output
¶
-
outputChanged
¶
-
outputReplaced
¶
-
classmethod
owner
()¶ Get the owner of the param:
# Can be called on an abstract param: assert Coord.x.owner() == Coord # ...or on an instance of a CompoundParam a = Atom() assert a.coord.owner() == a
-
classmethod
ownerChain
()¶ Returns a list of param owners starting from the toplevel param and ending with self. Examples:
foo.bar.atom.coord.ownerChain()
will return[foo, bar, atom, coord]
where every item is a concrete param.Foo.bar.atom.coord.x.ownerChain()
will return[Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x]
where every item is an abstract params.
-
classmethod
paramName
()¶ Get the name of the param:
# Can be called on an abstract param: print(Coord.x.paramName()) # 'x' # ...or on an instance of a CompoundParam a = Atom() a.coord.paramName() # 'coord'
-
parent
(self) → QObject¶
-
postprocess
()¶
-
postprocessors
()¶ Returns: A list of postprocessors, both decorated methods on the task and external functions that have been added via addPostprocessor()
Return type: list[typing.Callable]
-
prediction
()¶ Return the actual prediction. This can take various forms depending on the predictor.
-
preprocessors
()¶ Returns: A list of preprocessors (both decorated methods on the task and external functions that have been added via addPreprocessor)
-
printingOutputToTerminal
()¶ Returns: whether the StdOut
andStdErr
output from this task is being printed to the terminalReturn type: bool
-
processFuncChain
(chain=None, result_callback=None)¶ Execute each function in the specified chain sequentially in order.
The result_callback is called after each function with the return value of that function. This can be used to respond to the return value (e.g. present information to the user, get user feedback, log the result, etc.)
The return value of the result_callback determines whether processing will proceeed to the next function.
Parameters: - chain (FuncChainDecorator) – which chain to process
- result_callback – the callback that will get called with the result of each function in the chain
Returns: a list of the results from the functions
-
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.
-
qprocess
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
receivers
(self, PYQT_SIGNAL) → int¶
-
removeEventFilter
(self, QObject)¶
-
replicate
()¶ Create a new task with the same input and settings (but no output)
-
requestInterruption
()¶ Request the task to stop.
To enable this feature, subclasses should periodically check whether an interruption has been requested and terminate if it has been. If such logic has been included,
INTERRUPT_ENABLED
should be set toTrue
.
-
reset
(*args, **kwargs)¶
-
run
()¶
-
runCmd
(cmd)¶
-
classmethod
runFromCmdLine
()¶
-
runPostprocessing
(callback=None)¶
-
runPreprocessing
(callback=None, calling_context=None)¶ Run the preprocessors one-by-one. By default, any failing preprocessor will raise a TaskFailure exception and terminate processing. This behavior may be customized by supplying a callback function which will be called after each preprocessor with the result of that preprocessor.
This method is “final” so that all preprocessing logic will be enclosed in the try/finally block.
Parameters: - callback – a function that takes result and returns a bool that indicates whether to continue on to the next preprocessor
- calling_context – specify a value here to indicate the context in which this preprocessing is being called. This value will be stored in an instance variable, self.calling_context, which can be accessed from any preprocessor method on this task. Typically this value will be either self.GUI, self.CMDLINE, or None, but any value may be supplied here and checked for in the preprocessor methods. self.calling_context always reverts back to None at the end of runPreprocessing.
-
sender
(self) → QObject¶
-
senderSignalIndex
(self) → int¶
-
setObjectName
(self, str)¶
-
classmethod
setParamValue
(*args, **kwargs)¶
-
setParent
(self, QObject)¶
-
setPrintingOutputToTerminal
(print_to_terminal)¶ Set this task to print
StdOut
andStdErr
output to terminal, or not.Parameters: print_to_terminal (bool) – whether to send process output to terminal
-
setProperty
(self, str, Any) → bool¶
-
classmethod
setReference
(param1, param2)¶ Call this class method from configureParam to indicate that two params should be kept in sync. The initial values will start with the default value of
param1
. Example:class Square(CompoundParam): width: float = 5 height: float = 10 @classmethod def configureParam(cls): super().configureParam() cls.setReference(cls.width, cls.height) square = Square() assert square.width == square.height == 5 # Default value of width # takes priority square.height = 7 assert square.width == square.height == 7 square.width = 6 assert square.width == square.height == 6
Parameters: - param1 – The first abstract param to keep synced
- param2 – The second abstract param. After instantiation, this param will take on the value of param1.
-
setValue
(*args, **kwargs)¶
-
signalsBlocked
(self) → bool¶
-
skip_eq_check
()¶
-
specifyTaskDir
(taskdir_spec)¶ Specify the taskdir creation behavior. Use one of the following options:
A directory name (string). This may be a relative or absolute path
None - no taskdir is requested. The task will use the CWD as its taskdir
AUTO_TASKDIR - a new subdirectory will be created in the CWD using the task name as the directory name.
TEMP_TASKDIR - a temporary directory will be created in the schrodinger temp dir. This directory is cleaned up when the task is deleted.
Parameters: taskdir_spec – one of the four options listed above
-
start
(*args, **kwargs)¶
-
startTimer
(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int¶
-
staticMetaObject
= <PyQt5.QtCore.QMetaObject object>¶
-
status
¶
-
statusChanged
¶
-
statusReplaced
¶
-
stderr
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
stdout
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
taskDirSetting
()¶ Returns the taskdir spec. See specifyTaskDir() for details.
-
taskDone
¶
-
taskFailed
¶
-
taskStarted
¶
-
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¶
-
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.
-
class
-
class
schrodinger.protein.predictors.
DisproPredictor
(*args, **kwargs)¶ Bases:
schrodinger.protein.predictors.SsAccDependentPredictors
Disordered regions predictor.
-
EXE
= 'dispro'¶
-
PREDICTOR_NAME
= 'dispro'¶
-
CLASS_NUM
= 2¶
-
NU
= 25¶
-
NY
= 2¶
-
input_fname
¶ Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:
class Coord(CompoundParam): x: int y: int
An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:
coord = Coord() coord.x = 4
When a Param value is set, the
valueChanged
signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:class Atom(CompoundParam): coord: Coord element: str
-
model_fname
¶ Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:
class Coord(CompoundParam): x: int y: int
An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:
coord = Coord() coord.x = 4
When a Param value is set, the
valueChanged
signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:class Atom(CompoundParam): coord: Coord element: str
-
makeCmd
()¶ Return the command to run the predictor backend. The default implementation returns the predictor executable, the model file name, and the input file name.
Return type: list[str]
-
generateInputFile
()¶ Generate the input file for the predictor. Typically includes a header (see
_getInputHeader
), the file name of the blast alignment, and the sequence to predict properties for.The input file should be written with the name
self.input_fname
.
-
rawPrediction
()¶
-
prediction
()¶ Return the actual prediction. This can take various forms depending on the predictor.
-
AUTO_TASKDIR
= <object object>¶
-
CMDLINE
= 1¶
-
DEFAULT_TASKDIR_SETTING
= None¶
-
DONE
= 3¶
-
DataClass
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
FAILED
= 2¶
-
GUI
= 2¶
-
INTERRUPT_ENABLED
= False¶
-
class
Input
(default_value=<object object>, _param_type=<object object>, **kwargs)¶ Bases:
schrodinger.models.parameters.CompoundParam
-
DataClass
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
__init__
(default_value=<object object>, _param_type=<object object>, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
acc_prediction
¶ Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:
class Coord(CompoundParam): x: int y: int
An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:
coord = Coord() coord.x = 4
When a Param value is set, the
valueChanged
signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:class Atom(CompoundParam): coord: Coord element: str
-
acc_predictionChanged
¶
-
acc_predictionReplaced
¶
-
classmethod
addSubParam
(name, param, update_owner=True)¶
-
aln
¶ Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:
class Coord(CompoundParam): x: int y: int
An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:
coord = Coord() coord.x = 4
When a Param value is set, the
valueChanged
signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:class Atom(CompoundParam): coord: Coord element: str
-
alnChanged
¶
-
alnReplaced
¶
-
blockSignals
(self, bool) → bool¶
-
block_signal_propagation
()¶
-
childEvent
(self, QChildEvent)¶
-
children
(self) → List[QObject]¶
-
classmethod
configureParam
()¶ Override this class method to set up the abstract param class (e.g. setParamReference on child params.)
-
connectNotify
(self, QMetaMethod)¶
-
customEvent
(self, QEvent)¶
-
classmethod
defaultValue
(*args, **kwargs)¶
-
deleteLater
(self)¶
-
destroyed
¶ destroyed(self, object: QObject = None) [signal]
-
disconnect
(self)¶
-
disconnectNotify
(self, QMetaMethod)¶
-
dumpObjectInfo
(self)¶
-
dumpObjectTree
(self)¶
-
dynamicPropertyNames
(self) → List[QByteArray]¶
-
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.
-
getAbstractParam
(*args, **kwargs)¶
-
classmethod
getJsonBlacklist
()¶ Override to customize what params are serialized.
Implementations should return a list of abstract params that should be omitted from serialization.
- ..NOTE
- Returned abstract params must be direct child params of
cls
, e.g.cls.name
, notcls.coord.x
.
-
classmethod
getParamSignal
(*args, **kwargs)¶
-
classmethod
getParamValue
(*args, **kwargs)¶
-
classmethod
getSubParam
(name)¶ Get the value of a subparam using the string name:
c = Coord() assert c.getSubParam('x') == 0
Note
Using the string name to accss params is generally discouraged, but can be useful for serializing/deserializing param data.
Parameters: name (str) – The name of the subparam to get the value for.
-
classmethod
getSubParams
()¶ Return a dictionary mapping subparam names to their values.
-
getTypeHint
()¶
-
get_version
()¶ Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.
-
inherits
(self, str) → bool¶
-
initAbstract
()¶
-
initConcrete
()¶ Override to customize initialization of concrete params.
-
initializeValue
()¶ Override to dynamically set up the default value of the param. Useful for default values that are determined at runtime. This is called any time the param is reset.
-
installEventFilter
(self, QObject)¶
-
classmethod
isAbstract
()¶ Whether the param is an “abstract” param.
-
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
()¶ Get the owner of the param:
# Can be called on an abstract param: assert Coord.x.owner() == Coord # ...or on an instance of a CompoundParam a = Atom() assert a.coord.owner() == a
-
classmethod
ownerChain
()¶ Returns a list of param owners starting from the toplevel param and ending with self. Examples:
foo.bar.atom.coord.ownerChain()
will return[foo, bar, atom, coord]
where every item is a concrete param.Foo.bar.atom.coord.x.ownerChain()
will return[Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x]
where every item is an abstract params.
-
classmethod
paramName
()¶ Get the name of the param:
# Can be called on an abstract param: print(Coord.x.paramName()) # 'x' # ...or on an instance of a CompoundParam a = Atom() a.coord.paramName() # 'coord'
-
parent
(self) → QObject¶
-
property
(self, 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¶
-
seq
¶ Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:
class Coord(CompoundParam): x: int y: int
An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:
coord = Coord() coord.x = 4
When a Param value is set, the
valueChanged
signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:class Atom(CompoundParam): coord: Coord element: str
-
seqChanged
¶
-
seqReplaced
¶
-
setObjectName
(self, str)¶
-
classmethod
setParamValue
(*args, **kwargs)¶
-
setParent
(self, QObject)¶
-
setProperty
(self, str, Any) → bool¶
-
classmethod
setReference
(param1, param2)¶ Call this class method from configureParam to indicate that two params should be kept in sync. The initial values will start with the default value of
param1
. Example:class Square(CompoundParam): width: float = 5 height: float = 10 @classmethod def configureParam(cls): super().configureParam() cls.setReference(cls.width, cls.height) square = Square() assert square.width == square.height == 5 # Default value of width # takes priority square.height = 7 assert square.width == square.height == 7 square.width = 6 assert square.width == square.height == 6
Parameters: - param1 – The first abstract param to keep synced
- param2 – The second abstract param. After instantiation, this param will take on the value of param1.
-
setValue
(*args, **kwargs)¶
-
signalsBlocked
(self) → bool¶
-
skip_eq_check
()¶
-
ss_prediction
¶ Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:
class Coord(CompoundParam): x: int y: int
An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:
coord = Coord() coord.x = 4
When a Param value is set, the
valueChanged
signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:class Atom(CompoundParam): coord: Coord element: str
-
ss_predictionChanged
¶
-
ss_predictionReplaced
¶
-
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¶
-
valueChanged
¶
-
-
RUNNING
= 1¶
-
TEMP_TASKDIR
= <object object>¶
-
WAITING
= 0¶
-
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
addFuncToGroup
(func, group=None, order=None)¶ Adds a function to the specified chain. Typically used for adding functions that are not methods of this object.
The function may optionally be decorated with a FuncGroupMarker. If so, the default group and order will be determined by the decorator. Any group or order explicitly passed in to addFuncToGroup will take precedence over the decorator settings.
Parameters: - func – the function to add
- group (FuncGroupMarker or None) – the group marker. If the function is decorated with a FuncGoupMarker, that group marker will be the default.
- order (float or None) – the sorting order. If the function is decorated with a FuncGoupMarker, the order specified in the decorator will be the default.
-
addPostprocessor
(func, order=0)¶ Adds a postproceessor function to this task instance. If the function has been decorated with
@postprocessor
, the order specified by the decorator will be used.Parameters: - func (typing.Callable) – the function to add
- order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.
-
addPreprocessor
(func, order=None)¶ Adds a preproceessor function to this task instance. If the function has been decorated with @preprocessor, the order specified by the decorator will be used as the default.
Parameters: - func – the function to add
- order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.
-
classmethod
addSubParam
(name, param, update_owner=True)¶
-
blockSignals
(self, bool) → bool¶
-
block_signal_propagation
()¶
-
calling_context
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
childEvent
(self, QChildEvent)¶
-
children
(self) → List[QObject]¶
-
cmd
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
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, object: QObject = None) [signal]
-
disconnect
(self)¶
-
disconnectNotify
(self, QMetaMethod)¶
-
dumpObjectInfo
(self)¶
-
dumpObjectTree
(self)¶
-
dynamicPropertyNames
(self) → List[QByteArray]¶
-
event
(self, QEvent) → bool¶
-
eventFilter
(self, QObject, QEvent) → bool¶
-
exit_code
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
failure_info
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
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.
-
generateAlignmentFile
()¶ Write the alignment file to be used as an input for the predictor. The file will be a temporary file and will be removed in
postprocess
.Gaps in the alignment file are represented as ‘.’.
-
generateModelFile
()¶ Generate the model definition file with the name
self.model_fname
. This is done by finding the Prime data directory for the predictor and getting the names of all the files in it.The model file includes a header describing the number of model files and the predictors class number (
self.CLASS_NUM
), and a list of the model files.
-
getAbstractParam
(*args, **kwargs)¶
-
getAddedFuncs
(group=None)¶
-
getFuncGroup
(group=None)¶ Retrieve the functions belonging to the specified group.
Parameters: group (FuncGroupMarker) – the group marker Returns: the functions in the specified group, in order Return type: list
-
classmethod
getJsonBlacklist
()¶ Override to customize what params are serialized.
Implementations should return a list of abstract params that should be omitted from serialization.
- ..NOTE
- Returned abstract params must be direct child params of
cls
, e.g.cls.name
, notcls.coord.x
.
-
getLogAsString
()¶
-
classmethod
getParamSignal
(*args, **kwargs)¶
-
classmethod
getParamValue
(*args, **kwargs)¶
-
classmethod
getSubParam
(name)¶ Get the value of a subparam using the string name:
c = Coord() assert c.getSubParam('x') == 0
Note
Using the string name to accss params is generally discouraged, but can be useful for serializing/deserializing param data.
Parameters: name (str) – The name of the subparam to get the value for.
-
classmethod
getSubParams
()¶ Return a dictionary mapping subparam names to their values.
-
getTaskDir
()¶ Returns the full path of the task directory. This is only available if the task directory exists (after creation of the taskdir or, if no task dir is specified, any time).
-
getTaskFilename
(fname)¶ Return the appropriate absolute path for an input or output file in the taskdir.
-
getTypeHint
()¶
-
get_version
()¶ Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.
-
guard
()¶ Context manager that saves any Exception raised inside
-
inherits
(self, str) → bool¶
-
initAbstract
()¶
-
initConcrete
()¶ Override to customize initialization of concrete params.
-
initializeValue
()¶ @overrides: parameters.CompoundParam
-
input
¶
-
inputChanged
¶
-
inputReplaced
¶
-
input_fnameChanged
¶
-
input_fnameReplaced
¶
-
installEventFilter
(self, QObject)¶
-
classmethod
isAbstract
()¶ Whether the param is an “abstract” param.
-
isDefault
(*args, **kwargs)¶
-
isInterruptionRequested
()¶
-
isRunning
()¶
-
isSignalConnected
(self, QMetaMethod) → bool¶
-
isStartable
()¶
-
isWidgetType
(self) → bool¶
-
isWindowType
(self) → bool¶
-
kill
()¶ @overrides: AbstractTask
Kill the subprocess and set the status to FAILED.
-
killTimer
(self, int)¶
-
max_progress
¶
-
max_progressChanged
¶
-
max_progressReplaced
¶
-
metaObject
(self) → QMetaObject¶
-
model_fnameChanged
¶
-
model_fnameReplaced
¶
-
moveToThread
(self, QThread)¶
-
name
¶
-
nameChanged
¶
-
nameReplaced
¶
-
objectName
(self) → str¶
-
objectNameChanged
¶ objectNameChanged(self, str) [signal]
-
output
¶
-
outputChanged
¶
-
outputReplaced
¶
-
classmethod
owner
()¶ Get the owner of the param:
# Can be called on an abstract param: assert Coord.x.owner() == Coord # ...or on an instance of a CompoundParam a = Atom() assert a.coord.owner() == a
-
classmethod
ownerChain
()¶ Returns a list of param owners starting from the toplevel param and ending with self. Examples:
foo.bar.atom.coord.ownerChain()
will return[foo, bar, atom, coord]
where every item is a concrete param.Foo.bar.atom.coord.x.ownerChain()
will return[Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x]
where every item is an abstract params.
-
classmethod
paramName
()¶ Get the name of the param:
# Can be called on an abstract param: print(Coord.x.paramName()) # 'x' # ...or on an instance of a CompoundParam a = Atom() a.coord.paramName() # 'coord'
-
parent
(self) → QObject¶
-
postprocess
()¶
-
postprocessors
()¶ Returns: A list of postprocessors, both decorated methods on the task and external functions that have been added via addPostprocessor()
Return type: list[typing.Callable]
-
preprocessors
()¶ Returns: A list of preprocessors (both decorated methods on the task and external functions that have been added via addPreprocessor)
-
printingOutputToTerminal
()¶ Returns: whether the StdOut
andStdErr
output from this task is being printed to the terminalReturn type: bool
-
processFuncChain
(chain=None, result_callback=None)¶ Execute each function in the specified chain sequentially in order.
The result_callback is called after each function with the return value of that function. This can be used to respond to the return value (e.g. present information to the user, get user feedback, log the result, etc.)
The return value of the result_callback determines whether processing will proceeed to the next function.
Parameters: - chain (FuncChainDecorator) – which chain to process
- result_callback – the callback that will get called with the result of each function in the chain
Returns: a list of the results from the functions
-
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.
-
qprocess
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
receivers
(self, PYQT_SIGNAL) → int¶
-
removeEventFilter
(self, QObject)¶
-
replicate
()¶ Create a new task with the same input and settings (but no output)
-
requestInterruption
()¶ Request the task to stop.
To enable this feature, subclasses should periodically check whether an interruption has been requested and terminate if it has been. If such logic has been included,
INTERRUPT_ENABLED
should be set toTrue
.
-
reset
(*args, **kwargs)¶
-
run
()¶
-
runCmd
(cmd)¶
-
classmethod
runFromCmdLine
()¶
-
runPostprocessing
(callback=None)¶
-
runPreprocessing
(callback=None, calling_context=None)¶ Run the preprocessors one-by-one. By default, any failing preprocessor will raise a TaskFailure exception and terminate processing. This behavior may be customized by supplying a callback function which will be called after each preprocessor with the result of that preprocessor.
This method is “final” so that all preprocessing logic will be enclosed in the try/finally block.
Parameters: - callback – a function that takes result and returns a bool that indicates whether to continue on to the next preprocessor
- calling_context – specify a value here to indicate the context in which this preprocessing is being called. This value will be stored in an instance variable, self.calling_context, which can be accessed from any preprocessor method on this task. Typically this value will be either self.GUI, self.CMDLINE, or None, but any value may be supplied here and checked for in the preprocessor methods. self.calling_context always reverts back to None at the end of runPreprocessing.
-
sender
(self) → QObject¶
-
senderSignalIndex
(self) → int¶
-
setObjectName
(self, str)¶
-
classmethod
setParamValue
(*args, **kwargs)¶
-
setParent
(self, QObject)¶
-
setPrintingOutputToTerminal
(print_to_terminal)¶ Set this task to print
StdOut
andStdErr
output to terminal, or not.Parameters: print_to_terminal (bool) – whether to send process output to terminal
-
setProperty
(self, str, Any) → bool¶
-
classmethod
setReference
(param1, param2)¶ Call this class method from configureParam to indicate that two params should be kept in sync. The initial values will start with the default value of
param1
. Example:class Square(CompoundParam): width: float = 5 height: float = 10 @classmethod def configureParam(cls): super().configureParam() cls.setReference(cls.width, cls.height) square = Square() assert square.width == square.height == 5 # Default value of width # takes priority square.height = 7 assert square.width == square.height == 7 square.width = 6 assert square.width == square.height == 6
Parameters: - param1 – The first abstract param to keep synced
- param2 – The second abstract param. After instantiation, this param will take on the value of param1.
-
setValue
(*args, **kwargs)¶
-
signalsBlocked
(self) → bool¶
-
skip_eq_check
()¶
-
specifyTaskDir
(taskdir_spec)¶ Specify the taskdir creation behavior. Use one of the following options:
A directory name (string). This may be a relative or absolute path
None - no taskdir is requested. The task will use the CWD as its taskdir
AUTO_TASKDIR - a new subdirectory will be created in the CWD using the task name as the directory name.
TEMP_TASKDIR - a temporary directory will be created in the schrodinger temp dir. This directory is cleaned up when the task is deleted.
Parameters: taskdir_spec – one of the four options listed above
-
start
(*args, **kwargs)¶
-
startTimer
(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int¶
-
staticMetaObject
= <PyQt5.QtCore.QMetaObject object>¶
-
status
¶
-
statusChanged
¶
-
statusReplaced
¶
-
stderr
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
stdout
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
taskDirSetting
()¶ Returns the taskdir spec. See specifyTaskDir() for details.
-
taskDone
¶
-
taskFailed
¶
-
taskStarted
¶
-
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¶
-
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.
-
-
class
schrodinger.protein.predictors.
DomainArrangement
(*args, **kwargs)¶ Bases:
schrodinger.models.jsonable.JsonableEnum
An enumeration.
-
DomainForming
= 2¶
-
Interdomain
= 1¶
-
-
class
schrodinger.protein.predictors.
DomproPredictor
(*args, **kwargs)¶ Bases:
schrodinger.protein.predictors.SsAccDependentPredictors
Domain arrangement predictor.
-
EXE
= 'dompro'¶
-
PREDICTOR_NAME
= 'dompro'¶
-
CLASS_NUM
= 2¶
-
NU
= 25¶
-
NY
= 3¶
-
input_fname
¶ Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:
class Coord(CompoundParam): x: int y: int
An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:
coord = Coord() coord.x = 4
When a Param value is set, the
valueChanged
signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:class Atom(CompoundParam): coord: Coord element: str
-
model_fname
¶ Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:
class Coord(CompoundParam): x: int y: int
An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:
coord = Coord() coord.x = 4
When a Param value is set, the
valueChanged
signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:class Atom(CompoundParam): coord: Coord element: str
-
makeCmd
()¶ Return the command to run the predictor backend. The default implementation returns the predictor executable, the model file name, and the input file name.
Return type: list[str]
-
generateInputFile
()¶ Generate the input file for the predictor. Typically includes a header (see
_getInputHeader
), the file name of the blast alignment, and the sequence to predict properties for.The input file should be written with the name
self.input_fname
.
-
rawPrediction
()¶
-
prediction
()¶ Return the actual prediction. This can take various forms depending on the predictor.
-
AUTO_TASKDIR
= <object object>¶
-
CMDLINE
= 1¶
-
DEFAULT_TASKDIR_SETTING
= None¶
-
DONE
= 3¶
-
DataClass
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
FAILED
= 2¶
-
GUI
= 2¶
-
INTERRUPT_ENABLED
= False¶
-
class
Input
(default_value=<object object>, _param_type=<object object>, **kwargs)¶ Bases:
schrodinger.models.parameters.CompoundParam
-
DataClass
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
__init__
(default_value=<object object>, _param_type=<object object>, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
acc_prediction
¶ Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:
class Coord(CompoundParam): x: int y: int
An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:
coord = Coord() coord.x = 4
When a Param value is set, the
valueChanged
signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:class Atom(CompoundParam): coord: Coord element: str
-
acc_predictionChanged
¶
-
acc_predictionReplaced
¶
-
classmethod
addSubParam
(name, param, update_owner=True)¶
-
aln
¶ Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:
class Coord(CompoundParam): x: int y: int
An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:
coord = Coord() coord.x = 4
When a Param value is set, the
valueChanged
signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:class Atom(CompoundParam): coord: Coord element: str
-
alnChanged
¶
-
alnReplaced
¶
-
blockSignals
(self, bool) → bool¶
-
block_signal_propagation
()¶
-
childEvent
(self, QChildEvent)¶
-
children
(self) → List[QObject]¶
-
classmethod
configureParam
()¶ Override this class method to set up the abstract param class (e.g. setParamReference on child params.)
-
connectNotify
(self, QMetaMethod)¶
-
customEvent
(self, QEvent)¶
-
classmethod
defaultValue
(*args, **kwargs)¶
-
deleteLater
(self)¶
-
destroyed
¶ destroyed(self, object: QObject = None) [signal]
-
disconnect
(self)¶
-
disconnectNotify
(self, QMetaMethod)¶
-
dumpObjectInfo
(self)¶
-
dumpObjectTree
(self)¶
-
dynamicPropertyNames
(self) → List[QByteArray]¶
-
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.
-
getAbstractParam
(*args, **kwargs)¶
-
classmethod
getJsonBlacklist
()¶ Override to customize what params are serialized.
Implementations should return a list of abstract params that should be omitted from serialization.
- ..NOTE
- Returned abstract params must be direct child params of
cls
, e.g.cls.name
, notcls.coord.x
.
-
classmethod
getParamSignal
(*args, **kwargs)¶
-
classmethod
getParamValue
(*args, **kwargs)¶
-
classmethod
getSubParam
(name)¶ Get the value of a subparam using the string name:
c = Coord() assert c.getSubParam('x') == 0
Note
Using the string name to accss params is generally discouraged, but can be useful for serializing/deserializing param data.
Parameters: name (str) – The name of the subparam to get the value for.
-
classmethod
getSubParams
()¶ Return a dictionary mapping subparam names to their values.
-
getTypeHint
()¶
-
get_version
()¶ Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.
-
inherits
(self, str) → bool¶
-
initAbstract
()¶
-
initConcrete
()¶ Override to customize initialization of concrete params.
-
initializeValue
()¶ Override to dynamically set up the default value of the param. Useful for default values that are determined at runtime. This is called any time the param is reset.
-
installEventFilter
(self, QObject)¶
-
classmethod
isAbstract
()¶ Whether the param is an “abstract” param.
-
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
()¶ Get the owner of the param:
# Can be called on an abstract param: assert Coord.x.owner() == Coord # ...or on an instance of a CompoundParam a = Atom() assert a.coord.owner() == a
-
classmethod
ownerChain
()¶ Returns a list of param owners starting from the toplevel param and ending with self. Examples:
foo.bar.atom.coord.ownerChain()
will return[foo, bar, atom, coord]
where every item is a concrete param.Foo.bar.atom.coord.x.ownerChain()
will return[Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x]
where every item is an abstract params.
-
classmethod
paramName
()¶ Get the name of the param:
# Can be called on an abstract param: print(Coord.x.paramName()) # 'x' # ...or on an instance of a CompoundParam a = Atom() a.coord.paramName() # 'coord'
-
parent
(self) → QObject¶
-
property
(self, 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¶
-
seq
¶ Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:
class Coord(CompoundParam): x: int y: int
An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:
coord = Coord() coord.x = 4
When a Param value is set, the
valueChanged
signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:class Atom(CompoundParam): coord: Coord element: str
-
seqChanged
¶
-
seqReplaced
¶
-
setObjectName
(self, str)¶
-
classmethod
setParamValue
(*args, **kwargs)¶
-
setParent
(self, QObject)¶
-
setProperty
(self, str, Any) → bool¶
-
classmethod
setReference
(param1, param2)¶ Call this class method from configureParam to indicate that two params should be kept in sync. The initial values will start with the default value of
param1
. Example:class Square(CompoundParam): width: float = 5 height: float = 10 @classmethod def configureParam(cls): super().configureParam() cls.setReference(cls.width, cls.height) square = Square() assert square.width == square.height == 5 # Default value of width # takes priority square.height = 7 assert square.width == square.height == 7 square.width = 6 assert square.width == square.height == 6
Parameters: - param1 – The first abstract param to keep synced
- param2 – The second abstract param. After instantiation, this param will take on the value of param1.
-
setValue
(*args, **kwargs)¶
-
signalsBlocked
(self) → bool¶
-
skip_eq_check
()¶
-
ss_prediction
¶ Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:
class Coord(CompoundParam): x: int y: int
An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:
coord = Coord() coord.x = 4
When a Param value is set, the
valueChanged
signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:class Atom(CompoundParam): coord: Coord element: str
-
ss_predictionChanged
¶
-
ss_predictionReplaced
¶
-
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¶
-
valueChanged
¶
-
-
RUNNING
= 1¶
-
TEMP_TASKDIR
= <object object>¶
-
WAITING
= 0¶
-
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
addFuncToGroup
(func, group=None, order=None)¶ Adds a function to the specified chain. Typically used for adding functions that are not methods of this object.
The function may optionally be decorated with a FuncGroupMarker. If so, the default group and order will be determined by the decorator. Any group or order explicitly passed in to addFuncToGroup will take precedence over the decorator settings.
Parameters: - func – the function to add
- group (FuncGroupMarker or None) – the group marker. If the function is decorated with a FuncGoupMarker, that group marker will be the default.
- order (float or None) – the sorting order. If the function is decorated with a FuncGoupMarker, the order specified in the decorator will be the default.
-
addPostprocessor
(func, order=0)¶ Adds a postproceessor function to this task instance. If the function has been decorated with
@postprocessor
, the order specified by the decorator will be used.Parameters: - func (typing.Callable) – the function to add
- order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.
-
addPreprocessor
(func, order=None)¶ Adds a preproceessor function to this task instance. If the function has been decorated with @preprocessor, the order specified by the decorator will be used as the default.
Parameters: - func – the function to add
- order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.
-
classmethod
addSubParam
(name, param, update_owner=True)¶
-
blockSignals
(self, bool) → bool¶
-
block_signal_propagation
()¶
-
calling_context
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
childEvent
(self, QChildEvent)¶
-
children
(self) → List[QObject]¶
-
cmd
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
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, object: QObject = None) [signal]
-
disconnect
(self)¶
-
disconnectNotify
(self, QMetaMethod)¶
-
dumpObjectInfo
(self)¶
-
dumpObjectTree
(self)¶
-
dynamicPropertyNames
(self) → List[QByteArray]¶
-
event
(self, QEvent) → bool¶
-
eventFilter
(self, QObject, QEvent) → bool¶
-
exit_code
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
failure_info
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
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.
-
generateAlignmentFile
()¶ Write the alignment file to be used as an input for the predictor. The file will be a temporary file and will be removed in
postprocess
.Gaps in the alignment file are represented as ‘.’.
-
generateModelFile
()¶ Generate the model definition file with the name
self.model_fname
. This is done by finding the Prime data directory for the predictor and getting the names of all the files in it.The model file includes a header describing the number of model files and the predictors class number (
self.CLASS_NUM
), and a list of the model files.
-
getAbstractParam
(*args, **kwargs)¶
-
getAddedFuncs
(group=None)¶
-
getFuncGroup
(group=None)¶ Retrieve the functions belonging to the specified group.
Parameters: group (FuncGroupMarker) – the group marker Returns: the functions in the specified group, in order Return type: list
-
classmethod
getJsonBlacklist
()¶ Override to customize what params are serialized.
Implementations should return a list of abstract params that should be omitted from serialization.
- ..NOTE
- Returned abstract params must be direct child params of
cls
, e.g.cls.name
, notcls.coord.x
.
-
getLogAsString
()¶
-
classmethod
getParamSignal
(*args, **kwargs)¶
-
classmethod
getParamValue
(*args, **kwargs)¶
-
classmethod
getSubParam
(name)¶ Get the value of a subparam using the string name:
c = Coord() assert c.getSubParam('x') == 0
Note
Using the string name to accss params is generally discouraged, but can be useful for serializing/deserializing param data.
Parameters: name (str) – The name of the subparam to get the value for.
-
classmethod
getSubParams
()¶ Return a dictionary mapping subparam names to their values.
-
getTaskDir
()¶ Returns the full path of the task directory. This is only available if the task directory exists (after creation of the taskdir or, if no task dir is specified, any time).
-
getTaskFilename
(fname)¶ Return the appropriate absolute path for an input or output file in the taskdir.
-
getTypeHint
()¶
-
get_version
()¶ Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.
-
guard
()¶ Context manager that saves any Exception raised inside
-
inherits
(self, str) → bool¶
-
initAbstract
()¶
-
initConcrete
()¶ Override to customize initialization of concrete params.
-
initializeValue
()¶ @overrides: parameters.CompoundParam
-
input
¶
-
inputChanged
¶
-
inputReplaced
¶
-
input_fnameChanged
¶
-
input_fnameReplaced
¶
-
installEventFilter
(self, QObject)¶
-
classmethod
isAbstract
()¶ Whether the param is an “abstract” param.
-
isDefault
(*args, **kwargs)¶
-
isInterruptionRequested
()¶
-
isRunning
()¶
-
isSignalConnected
(self, QMetaMethod) → bool¶
-
isStartable
()¶
-
isWidgetType
(self) → bool¶
-
isWindowType
(self) → bool¶
-
kill
()¶ @overrides: AbstractTask
Kill the subprocess and set the status to FAILED.
-
killTimer
(self, int)¶
-
max_progress
¶
-
max_progressChanged
¶
-
max_progressReplaced
¶
-
metaObject
(self) → QMetaObject¶
-
model_fnameChanged
¶
-
model_fnameReplaced
¶
-
moveToThread
(self, QThread)¶
-
name
¶
-
nameChanged
¶
-
nameReplaced
¶
-
objectName
(self) → str¶
-
objectNameChanged
¶ objectNameChanged(self, str) [signal]
-
output
¶
-
outputChanged
¶
-
outputReplaced
¶
-
classmethod
owner
()¶ Get the owner of the param:
# Can be called on an abstract param: assert Coord.x.owner() == Coord # ...or on an instance of a CompoundParam a = Atom() assert a.coord.owner() == a
-
classmethod
ownerChain
()¶ Returns a list of param owners starting from the toplevel param and ending with self. Examples:
foo.bar.atom.coord.ownerChain()
will return[foo, bar, atom, coord]
where every item is a concrete param.Foo.bar.atom.coord.x.ownerChain()
will return[Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x]
where every item is an abstract params.
-
classmethod
paramName
()¶ Get the name of the param:
# Can be called on an abstract param: print(Coord.x.paramName()) # 'x' # ...or on an instance of a CompoundParam a = Atom() a.coord.paramName() # 'coord'
-
parent
(self) → QObject¶
-
postprocess
()¶
-
postprocessors
()¶ Returns: A list of postprocessors, both decorated methods on the task and external functions that have been added via addPostprocessor()
Return type: list[typing.Callable]
-
preprocessors
()¶ Returns: A list of preprocessors (both decorated methods on the task and external functions that have been added via addPreprocessor)
-
printingOutputToTerminal
()¶ Returns: whether the StdOut
andStdErr
output from this task is being printed to the terminalReturn type: bool
-
processFuncChain
(chain=None, result_callback=None)¶ Execute each function in the specified chain sequentially in order.
The result_callback is called after each function with the return value of that function. This can be used to respond to the return value (e.g. present information to the user, get user feedback, log the result, etc.)
The return value of the result_callback determines whether processing will proceeed to the next function.
Parameters: - chain (FuncChainDecorator) – which chain to process
- result_callback – the callback that will get called with the result of each function in the chain
Returns: a list of the results from the functions
-
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.
-
qprocess
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
receivers
(self, PYQT_SIGNAL) → int¶
-
removeEventFilter
(self, QObject)¶
-
replicate
()¶ Create a new task with the same input and settings (but no output)
-
requestInterruption
()¶ Request the task to stop.
To enable this feature, subclasses should periodically check whether an interruption has been requested and terminate if it has been. If such logic has been included,
INTERRUPT_ENABLED
should be set toTrue
.
-
reset
(*args, **kwargs)¶
-
run
()¶
-
runCmd
(cmd)¶
-
classmethod
runFromCmdLine
()¶
-
runPostprocessing
(callback=None)¶
-
runPreprocessing
(callback=None, calling_context=None)¶ Run the preprocessors one-by-one. By default, any failing preprocessor will raise a TaskFailure exception and terminate processing. This behavior may be customized by supplying a callback function which will be called after each preprocessor with the result of that preprocessor.
This method is “final” so that all preprocessing logic will be enclosed in the try/finally block.
Parameters: - callback – a function that takes result and returns a bool that indicates whether to continue on to the next preprocessor
- calling_context – specify a value here to indicate the context in which this preprocessing is being called. This value will be stored in an instance variable, self.calling_context, which can be accessed from any preprocessor method on this task. Typically this value will be either self.GUI, self.CMDLINE, or None, but any value may be supplied here and checked for in the preprocessor methods. self.calling_context always reverts back to None at the end of runPreprocessing.
-
sender
(self) → QObject¶
-
senderSignalIndex
(self) → int¶
-
setObjectName
(self, str)¶
-
classmethod
setParamValue
(*args, **kwargs)¶
-
setParent
(self, QObject)¶
-
setPrintingOutputToTerminal
(print_to_terminal)¶ Set this task to print
StdOut
andStdErr
output to terminal, or not.Parameters: print_to_terminal (bool) – whether to send process output to terminal
-
setProperty
(self, str, Any) → bool¶
-
classmethod
setReference
(param1, param2)¶ Call this class method from configureParam to indicate that two params should be kept in sync. The initial values will start with the default value of
param1
. Example:class Square(CompoundParam): width: float = 5 height: float = 10 @classmethod def configureParam(cls): super().configureParam() cls.setReference(cls.width, cls.height) square = Square() assert square.width == square.height == 5 # Default value of width # takes priority square.height = 7 assert square.width == square.height == 7 square.width = 6 assert square.width == square.height == 6
Parameters: - param1 – The first abstract param to keep synced
- param2 – The second abstract param. After instantiation, this param will take on the value of param1.
-
setValue
(*args, **kwargs)¶
-
signalsBlocked
(self) → bool¶
-
skip_eq_check
()¶
-
specifyTaskDir
(taskdir_spec)¶ Specify the taskdir creation behavior. Use one of the following options:
A directory name (string). This may be a relative or absolute path
None - no taskdir is requested. The task will use the CWD as its taskdir
AUTO_TASKDIR - a new subdirectory will be created in the CWD using the task name as the directory name.
TEMP_TASKDIR - a temporary directory will be created in the schrodinger temp dir. This directory is cleaned up when the task is deleted.
Parameters: taskdir_spec – one of the four options listed above
-
start
(*args, **kwargs)¶
-
startTimer
(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int¶
-
staticMetaObject
= <PyQt5.QtCore.QMetaObject object>¶
-
status
¶
-
statusChanged
¶
-
statusReplaced
¶
-
stderr
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
stdout
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
taskDirSetting
()¶ Returns the taskdir spec. See specifyTaskDir() for details.
-
taskDone
¶
-
taskFailed
¶
-
taskStarted
¶
-
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¶
-
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.
-
-
class
schrodinger.protein.predictors.
DiproPredictor
(*args, **kwargs)¶ Bases:
schrodinger.protein.predictors.SsAccDependentPredictors
Disulfide bonds predictor.
-
EXE
= 'dipro'¶
-
PREDICTOR_NAME
= 'dipro'¶
-
CLASS_NUM
= 0.5¶
-
input_fname
¶ Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:
class Coord(CompoundParam): x: int y: int
An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:
coord = Coord() coord.x = 4
When a Param value is set, the
valueChanged
signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:class Atom(CompoundParam): coord: Coord element: str
-
model_fname
¶ Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:
class Coord(CompoundParam): x: int y: int
An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:
coord = Coord() coord.x = 4
When a Param value is set, the
valueChanged
signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:class Atom(CompoundParam): coord: Coord element: str
-
class
DiproFormat
¶ Bases:
enum.IntEnum
For use with command line invocation.
-
Alessandro
= 1¶
-
NewDipro
= 2¶
-
-
makeCmd
()¶ Usage: $PSP_PATH/dipro model_file sequence_file alignment_file format
-
generateInputFile
()¶ Generate the input file for the predictor. Typically includes a header (see
_getInputHeader
), the file name of the blast alignment, and the sequence to predict properties for.The input file should be written with the name
self.input_fname
.
-
prediction
()¶ Returns: A list of disulfide bonds represented by 2-tuples with two residue indexes :rtype : list[tuple[int]]
-
AUTO_TASKDIR
= <object object>¶
-
CMDLINE
= 1¶
-
DEFAULT_TASKDIR_SETTING
= None¶
-
DONE
= 3¶
-
DataClass
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
FAILED
= 2¶
-
GUI
= 2¶
-
INTERRUPT_ENABLED
= False¶
-
class
Input
(default_value=<object object>, _param_type=<object object>, **kwargs)¶ Bases:
schrodinger.models.parameters.CompoundParam
-
DataClass
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
__init__
(default_value=<object object>, _param_type=<object object>, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
acc_prediction
¶ Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:
class Coord(CompoundParam): x: int y: int
An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:
coord = Coord() coord.x = 4
When a Param value is set, the
valueChanged
signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:class Atom(CompoundParam): coord: Coord element: str
-
acc_predictionChanged
¶
-
acc_predictionReplaced
¶
-
classmethod
addSubParam
(name, param, update_owner=True)¶
-
aln
¶ Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:
class Coord(CompoundParam): x: int y: int
An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:
coord = Coord() coord.x = 4
When a Param value is set, the
valueChanged
signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:class Atom(CompoundParam): coord: Coord element: str
-
alnChanged
¶
-
alnReplaced
¶
-
blockSignals
(self, bool) → bool¶
-
block_signal_propagation
()¶
-
childEvent
(self, QChildEvent)¶
-
children
(self) → List[QObject]¶
-
classmethod
configureParam
()¶ Override this class method to set up the abstract param class (e.g. setParamReference on child params.)
-
connectNotify
(self, QMetaMethod)¶
-
customEvent
(self, QEvent)¶
-
classmethod
defaultValue
(*args, **kwargs)¶
-
deleteLater
(self)¶
-
destroyed
¶ destroyed(self, object: QObject = None) [signal]
-
disconnect
(self)¶
-
disconnectNotify
(self, QMetaMethod)¶
-
dumpObjectInfo
(self)¶
-
dumpObjectTree
(self)¶
-
dynamicPropertyNames
(self) → List[QByteArray]¶
-
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.
-
getAbstractParam
(*args, **kwargs)¶
-
classmethod
getJsonBlacklist
()¶ Override to customize what params are serialized.
Implementations should return a list of abstract params that should be omitted from serialization.
- ..NOTE
- Returned abstract params must be direct child params of
cls
, e.g.cls.name
, notcls.coord.x
.
-
classmethod
getParamSignal
(*args, **kwargs)¶
-
classmethod
getParamValue
(*args, **kwargs)¶
-
classmethod
getSubParam
(name)¶ Get the value of a subparam using the string name:
c = Coord() assert c.getSubParam('x') == 0
Note
Using the string name to accss params is generally discouraged, but can be useful for serializing/deserializing param data.
Parameters: name (str) – The name of the subparam to get the value for.
-
classmethod
getSubParams
()¶ Return a dictionary mapping subparam names to their values.
-
getTypeHint
()¶
-
get_version
()¶ Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.
-
inherits
(self, str) → bool¶
-
initAbstract
()¶
-
initConcrete
()¶ Override to customize initialization of concrete params.
-
initializeValue
()¶ Override to dynamically set up the default value of the param. Useful for default values that are determined at runtime. This is called any time the param is reset.
-
installEventFilter
(self, QObject)¶
-
classmethod
isAbstract
()¶ Whether the param is an “abstract” param.
-
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
()¶ Get the owner of the param:
# Can be called on an abstract param: assert Coord.x.owner() == Coord # ...or on an instance of a CompoundParam a = Atom() assert a.coord.owner() == a
-
classmethod
ownerChain
()¶ Returns a list of param owners starting from the toplevel param and ending with self. Examples:
foo.bar.atom.coord.ownerChain()
will return[foo, bar, atom, coord]
where every item is a concrete param.Foo.bar.atom.coord.x.ownerChain()
will return[Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x]
where every item is an abstract params.
-
classmethod
paramName
()¶ Get the name of the param:
# Can be called on an abstract param: print(Coord.x.paramName()) # 'x' # ...or on an instance of a CompoundParam a = Atom() a.coord.paramName() # 'coord'
-
parent
(self) → QObject¶
-
property
(self, 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¶
-
seq
¶ Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:
class Coord(CompoundParam): x: int y: int
An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:
coord = Coord() coord.x = 4
When a Param value is set, the
valueChanged
signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:class Atom(CompoundParam): coord: Coord element: str
-
seqChanged
¶
-
seqReplaced
¶
-
setObjectName
(self, str)¶
-
classmethod
setParamValue
(*args, **kwargs)¶
-
setParent
(self, QObject)¶
-
setProperty
(self, str, Any) → bool¶
-
classmethod
setReference
(param1, param2)¶ Call this class method from configureParam to indicate that two params should be kept in sync. The initial values will start with the default value of
param1
. Example:class Square(CompoundParam): width: float = 5 height: float = 10 @classmethod def configureParam(cls): super().configureParam() cls.setReference(cls.width, cls.height) square = Square() assert square.width == square.height == 5 # Default value of width # takes priority square.height = 7 assert square.width == square.height == 7 square.width = 6 assert square.width == square.height == 6
Parameters: - param1 – The first abstract param to keep synced
- param2 – The second abstract param. After instantiation, this param will take on the value of param1.
-
setValue
(*args, **kwargs)¶
-
signalsBlocked
(self) → bool¶
-
skip_eq_check
()¶
-
ss_prediction
¶ Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:
class Coord(CompoundParam): x: int y: int
An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:
coord = Coord() coord.x = 4
When a Param value is set, the
valueChanged
signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:class Atom(CompoundParam): coord: Coord element: str
-
ss_predictionChanged
¶
-
ss_predictionReplaced
¶
-
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¶
-
valueChanged
¶
-
-
NU
= NotImplemented¶
-
NY
= NotImplemented¶
-
RUNNING
= 1¶
-
TEMP_TASKDIR
= <object object>¶
-
WAITING
= 0¶
-
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
addFuncToGroup
(func, group=None, order=None)¶ Adds a function to the specified chain. Typically used for adding functions that are not methods of this object.
The function may optionally be decorated with a FuncGroupMarker. If so, the default group and order will be determined by the decorator. Any group or order explicitly passed in to addFuncToGroup will take precedence over the decorator settings.
Parameters: - func – the function to add
- group (FuncGroupMarker or None) – the group marker. If the function is decorated with a FuncGoupMarker, that group marker will be the default.
- order (float or None) – the sorting order. If the function is decorated with a FuncGoupMarker, the order specified in the decorator will be the default.
-
addPostprocessor
(func, order=0)¶ Adds a postproceessor function to this task instance. If the function has been decorated with
@postprocessor
, the order specified by the decorator will be used.Parameters: - func (typing.Callable) – the function to add
- order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.
-
addPreprocessor
(func, order=None)¶ Adds a preproceessor function to this task instance. If the function has been decorated with @preprocessor, the order specified by the decorator will be used as the default.
Parameters: - func – the function to add
- order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.
-
classmethod
addSubParam
(name, param, update_owner=True)¶
-
blockSignals
(self, bool) → bool¶
-
block_signal_propagation
()¶
-
calling_context
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
childEvent
(self, QChildEvent)¶
-
children
(self) → List[QObject]¶
-
cmd
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
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, object: QObject = None) [signal]
-
disconnect
(self)¶
-
disconnectNotify
(self, QMetaMethod)¶
-
dumpObjectInfo
(self)¶
-
dumpObjectTree
(self)¶
-
dynamicPropertyNames
(self) → List[QByteArray]¶
-
event
(self, QEvent) → bool¶
-
eventFilter
(self, QObject, QEvent) → bool¶
-
exit_code
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
failure_info
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
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.
-
generateAlignmentFile
()¶ Write the alignment file to be used as an input for the predictor. The file will be a temporary file and will be removed in
postprocess
.Gaps in the alignment file are represented as ‘.’.
-
generateModelFile
()¶ Generate the model definition file with the name
self.model_fname
. This is done by finding the Prime data directory for the predictor and getting the names of all the files in it.The model file includes a header describing the number of model files and the predictors class number (
self.CLASS_NUM
), and a list of the model files.
-
getAbstractParam
(*args, **kwargs)¶
-
getAddedFuncs
(group=None)¶
-
getFuncGroup
(group=None)¶ Retrieve the functions belonging to the specified group.
Parameters: group (FuncGroupMarker) – the group marker Returns: the functions in the specified group, in order Return type: list
-
classmethod
getJsonBlacklist
()¶ Override to customize what params are serialized.
Implementations should return a list of abstract params that should be omitted from serialization.
- ..NOTE
- Returned abstract params must be direct child params of
cls
, e.g.cls.name
, notcls.coord.x
.
-
getLogAsString
()¶
-
classmethod
getParamSignal
(*args, **kwargs)¶
-
classmethod
getParamValue
(*args, **kwargs)¶
-
classmethod
getSubParam
(name)¶ Get the value of a subparam using the string name:
c = Coord() assert c.getSubParam('x') == 0
Note
Using the string name to accss params is generally discouraged, but can be useful for serializing/deserializing param data.
Parameters: name (str) – The name of the subparam to get the value for.
-
classmethod
getSubParams
()¶ Return a dictionary mapping subparam names to their values.
-
getTaskDir
()¶ Returns the full path of the task directory. This is only available if the task directory exists (after creation of the taskdir or, if no task dir is specified, any time).
-
getTaskFilename
(fname)¶ Return the appropriate absolute path for an input or output file in the taskdir.
-
getTypeHint
()¶
-
get_version
()¶ Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.
-
guard
()¶ Context manager that saves any Exception raised inside
-
inherits
(self, str) → bool¶
-
initAbstract
()¶
-
initConcrete
()¶ Override to customize initialization of concrete params.
-
initializeValue
()¶ @overrides: parameters.CompoundParam
-
input
¶
-
inputChanged
¶
-
inputReplaced
¶
-
input_fnameChanged
¶
-
input_fnameReplaced
¶
-
installEventFilter
(self, QObject)¶
-
classmethod
isAbstract
()¶ Whether the param is an “abstract” param.
-
isDefault
(*args, **kwargs)¶
-
isInterruptionRequested
()¶
-
isRunning
()¶
-
isSignalConnected
(self, QMetaMethod) → bool¶
-
isStartable
()¶
-
isWidgetType
(self) → bool¶
-
isWindowType
(self) → bool¶
-
kill
()¶ @overrides: AbstractTask
Kill the subprocess and set the status to FAILED.
-
killTimer
(self, int)¶
-
max_progress
¶
-
max_progressChanged
¶
-
max_progressReplaced
¶
-
metaObject
(self) → QMetaObject¶
-
model_fnameChanged
¶
-
model_fnameReplaced
¶
-
moveToThread
(self, QThread)¶
-
name
¶
-
nameChanged
¶
-
nameReplaced
¶
-
objectName
(self) → str¶
-
objectNameChanged
¶ objectNameChanged(self, str) [signal]
-
output
¶
-
outputChanged
¶
-
outputReplaced
¶
-
classmethod
owner
()¶ Get the owner of the param:
# Can be called on an abstract param: assert Coord.x.owner() == Coord # ...or on an instance of a CompoundParam a = Atom() assert a.coord.owner() == a
-
classmethod
ownerChain
()¶ Returns a list of param owners starting from the toplevel param and ending with self. Examples:
foo.bar.atom.coord.ownerChain()
will return[foo, bar, atom, coord]
where every item is a concrete param.Foo.bar.atom.coord.x.ownerChain()
will return[Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x]
where every item is an abstract params.
-
classmethod
paramName
()¶ Get the name of the param:
# Can be called on an abstract param: print(Coord.x.paramName()) # 'x' # ...or on an instance of a CompoundParam a = Atom() a.coord.paramName() # 'coord'
-
parent
(self) → QObject¶
-
postprocess
()¶
-
postprocessors
()¶ Returns: A list of postprocessors, both decorated methods on the task and external functions that have been added via addPostprocessor()
Return type: list[typing.Callable]
-
preprocessors
()¶ Returns: A list of preprocessors (both decorated methods on the task and external functions that have been added via addPreprocessor)
-
printingOutputToTerminal
()¶ Returns: whether the StdOut
andStdErr
output from this task is being printed to the terminalReturn type: bool
-
processFuncChain
(chain=None, result_callback=None)¶ Execute each function in the specified chain sequentially in order.
The result_callback is called after each function with the return value of that function. This can be used to respond to the return value (e.g. present information to the user, get user feedback, log the result, etc.)
The return value of the result_callback determines whether processing will proceeed to the next function.
Parameters: - chain (FuncChainDecorator) – which chain to process
- result_callback – the callback that will get called with the result of each function in the chain
Returns: a list of the results from the functions
-
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.
-
qprocess
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
receivers
(self, PYQT_SIGNAL) → int¶
-
removeEventFilter
(self, QObject)¶
-
replicate
()¶ Create a new task with the same input and settings (but no output)
-
requestInterruption
()¶ Request the task to stop.
To enable this feature, subclasses should periodically check whether an interruption has been requested and terminate if it has been. If such logic has been included,
INTERRUPT_ENABLED
should be set toTrue
.
-
reset
(*args, **kwargs)¶
-
run
()¶
-
runCmd
(cmd)¶
-
classmethod
runFromCmdLine
()¶
-
runPostprocessing
(callback=None)¶
-
runPreprocessing
(callback=None, calling_context=None)¶ Run the preprocessors one-by-one. By default, any failing preprocessor will raise a TaskFailure exception and terminate processing. This behavior may be customized by supplying a callback function which will be called after each preprocessor with the result of that preprocessor.
This method is “final” so that all preprocessing logic will be enclosed in the try/finally block.
Parameters: - callback – a function that takes result and returns a bool that indicates whether to continue on to the next preprocessor
- calling_context – specify a value here to indicate the context in which this preprocessing is being called. This value will be stored in an instance variable, self.calling_context, which can be accessed from any preprocessor method on this task. Typically this value will be either self.GUI, self.CMDLINE, or None, but any value may be supplied here and checked for in the preprocessor methods. self.calling_context always reverts back to None at the end of runPreprocessing.
-
sender
(self) → QObject¶
-
senderSignalIndex
(self) → int¶
-
setObjectName
(self, str)¶
-
classmethod
setParamValue
(*args, **kwargs)¶
-
setParent
(self, QObject)¶
-
setPrintingOutputToTerminal
(print_to_terminal)¶ Set this task to print
StdOut
andStdErr
output to terminal, or not.Parameters: print_to_terminal (bool) – whether to send process output to terminal
-
setProperty
(self, str, Any) → bool¶
-
classmethod
setReference
(param1, param2)¶ Call this class method from configureParam to indicate that two params should be kept in sync. The initial values will start with the default value of
param1
. Example:class Square(CompoundParam): width: float = 5 height: float = 10 @classmethod def configureParam(cls): super().configureParam() cls.setReference(cls.width, cls.height) square = Square() assert square.width == square.height == 5 # Default value of width # takes priority square.height = 7 assert square.width == square.height == 7 square.width = 6 assert square.width == square.height == 6
Parameters: - param1 – The first abstract param to keep synced
- param2 – The second abstract param. After instantiation, this param will take on the value of param1.
-
setValue
(*args, **kwargs)¶
-
signalsBlocked
(self) → bool¶
-
skip_eq_check
()¶
-
specifyTaskDir
(taskdir_spec)¶ Specify the taskdir creation behavior. Use one of the following options:
A directory name (string). This may be a relative or absolute path
None - no taskdir is requested. The task will use the CWD as its taskdir
AUTO_TASKDIR - a new subdirectory will be created in the CWD using the task name as the directory name.
TEMP_TASKDIR - a temporary directory will be created in the schrodinger temp dir. This directory is cleaned up when the task is deleted.
Parameters: taskdir_spec – one of the four options listed above
-
start
(*args, **kwargs)¶
-
startTimer
(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int¶
-
staticMetaObject
= <PyQt5.QtCore.QMetaObject object>¶
-
status
¶
-
statusChanged
¶
-
statusReplaced
¶
-
stderr
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
stdout
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
taskDirSetting
()¶ Returns the taskdir spec. See specifyTaskDir() for details.
-
taskDone
¶
-
taskFailed
¶
-
taskStarted
¶
-
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¶
-
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.
-
-
class
schrodinger.protein.predictors.
BetaproPredictor
(*args, **kwargs)¶ Bases:
schrodinger.protein.predictors.AbstractPredictor
Beta strand contacts predictor
-
EXE
= 'betapro'¶
-
PREDICTOR_NAME
= 'betapro'¶
-
CLASS_NUM
= ''¶
-
NU
= 20¶
-
NY
= 3¶
-
input_fname
¶ Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:
class Coord(CompoundParam): x: int y: int
An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:
coord = Coord() coord.x = 4
When a Param value is set, the
valueChanged
signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:class Atom(CompoundParam): coord: Coord element: str
-
model_fname
¶ Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:
class Coord(CompoundParam): x: int y: int
An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:
coord = Coord() coord.x = 4
When a Param value is set, the
valueChanged
signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:class Atom(CompoundParam): coord: Coord element: str
-
class
Input
(default_value=<object object>, _param_type=<object object>, **kwargs)¶ Bases:
schrodinger.models.parameters.CompoundParam
-
seq
¶ Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:
class Coord(CompoundParam): x: int y: int
An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:
coord = Coord() coord.x = 4
When a Param value is set, the
valueChanged
signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:class Atom(CompoundParam): coord: Coord element: str
-
aln
¶ Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:
class Coord(CompoundParam): x: int y: int
An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:
coord = Coord() coord.x = 4
When a Param value is set, the
valueChanged
signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:class Atom(CompoundParam): coord: Coord element: str
-
ss_prediction
¶ Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:
class Coord(CompoundParam): x: int y: int
An instance of the Coord class can be created normally, and Params can be accessed as normal attributes:
coord = Coord() coord.x = 4
When a Param value is set, the
valueChanged
signal is emitted. Params can be serialized and deserialized to and from JSON. Params can also be nested:class Atom(CompoundParam): coord: Coord element: str
-
DataClass
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
__init__
(default_value=<object object>, _param_type=<object object>, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
classmethod
addSubParam
(name, param, update_owner=True)¶
-
alnChanged
¶
-
alnReplaced
¶
-
blockSignals
(self, bool) → bool¶
-
block_signal_propagation
()¶
-
childEvent
(self, QChildEvent)¶
-
children
(self) → List[QObject]¶
-
classmethod
configureParam
()¶ Override this class method to set up the abstract param class (e.g. setParamReference on child params.)
-
connectNotify
(self, QMetaMethod)¶
-
customEvent
(self, QEvent)¶
-
classmethod
defaultValue
(*args, **kwargs)¶
-
deleteLater
(self)¶
-
destroyed
¶ destroyed(self, object: QObject = None) [signal]
-
disconnect
(self)¶
-
disconnectNotify
(self, QMetaMethod)¶
-
dumpObjectInfo
(self)¶
-
dumpObjectTree
(self)¶
-
dynamicPropertyNames
(self) → List[QByteArray]¶
-
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.
-
getAbstractParam
(*args, **kwargs)¶
-
classmethod
getJsonBlacklist
()¶ Override to customize what params are serialized.
Implementations should return a list of abstract params that should be omitted from serialization.
- ..NOTE
- Returned abstract params must be direct child params of
cls
, e.g.cls.name
, notcls.coord.x
.
-
classmethod
getParamSignal
(*args, **kwargs)¶
-
classmethod
getParamValue
(*args, **kwargs)¶
-
classmethod
getSubParam
(name)¶ Get the value of a subparam using the string name:
c = Coord() assert c.getSubParam('x') == 0
Note
Using the string name to accss params is generally discouraged, but can be useful for serializing/deserializing param data.
Parameters: name (str) – The name of the subparam to get the value for.
-
classmethod
getSubParams
()¶ Return a dictionary mapping subparam names to their values.
-
getTypeHint
()¶
-
get_version
()¶ Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.
-
inherits
(self, str) → bool¶
-
initAbstract
()¶
-
initConcrete
()¶ Override to customize initialization of concrete params.
-
initializeValue
()¶ Override to dynamically set up the default value of the param. Useful for default values that are determined at runtime. This is called any time the param is reset.
-
installEventFilter
(self, QObject)¶
-
classmethod
isAbstract
()¶ Whether the param is an “abstract” param.
-
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
()¶ Get the owner of the param:
# Can be called on an abstract param: assert Coord.x.owner() == Coord # ...or on an instance of a CompoundParam a = Atom() assert a.coord.owner() == a
-
classmethod
ownerChain
()¶ Returns a list of param owners starting from the toplevel param and ending with self. Examples:
foo.bar.atom.coord.ownerChain()
will return[foo, bar, atom, coord]
where every item is a concrete param.Foo.bar.atom.coord.x.ownerChain()
will return[Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x]
where every item is an abstract params.
-
classmethod
paramName
()¶ Get the name of the param:
# Can be called on an abstract param: print(Coord.x.paramName()) # 'x' # ...or on an instance of a CompoundParam a = Atom() a.coord.paramName() # 'coord'
-
parent
(self) → QObject¶
-
property
(self, 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¶
-
seqChanged
¶
-
seqReplaced
¶
-
setObjectName
(self, str)¶
-
classmethod
setParamValue
(*args, **kwargs)¶
-
setParent
(self, QObject)¶
-
setProperty
(self, str, Any) → bool¶
-
classmethod
setReference
(param1, param2)¶ Call this class method from configureParam to indicate that two params should be kept in sync. The initial values will start with the default value of
param1
. Example:class Square(CompoundParam): width: float = 5 height: float = 10 @classmethod def configureParam(cls): super().configureParam() cls.setReference(cls.width, cls.height) square = Square() assert square.width == square.height == 5 # Default value of width # takes priority square.height = 7 assert square.width == square.height == 7 square.width = 6 assert square.width == square.height == 6
Parameters: - param1 – The first abstract param to keep synced
- param2 – The second abstract param. After instantiation, this param will take on the value of param1.
-
setValue
(*args, **kwargs)¶
-
signalsBlocked
(self) → bool¶
-
skip_eq_check
()¶
-
ss_predictionChanged
¶
-
ss_predictionReplaced
¶
-
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¶
-
valueChanged
¶
-
-
input
¶
-
generateInputFile
()¶ Generate the input file for the predictor. Typically includes a header (see
_getInputHeader
), the file name of the blast alignment, and the sequence to predict properties for.The input file should be written with the name
self.input_fname
.
-
makeCmd
()¶ Usage: $PSP_PATH/betapro model_file, protein_file, alignment_file
-
prediction
()¶ Return the actual prediction. This can take various forms depending on the predictor.
-
AUTO_TASKDIR
= <object object>¶
-
CMDLINE
= 1¶
-
DEFAULT_TASKDIR_SETTING
= None¶
-
DONE
= 3¶
-
DataClass
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
FAILED
= 2¶
-
GUI
= 2¶
-
INTERRUPT_ENABLED
= False¶
-
RUNNING
= 1¶
-
TEMP_TASKDIR
= <object object>¶
-
WAITING
= 0¶
-
__init__
(*args, **kwargs)¶ Initialize self. See help(type(self)) for accurate signature.
-
addFuncToGroup
(func, group=None, order=None)¶ Adds a function to the specified chain. Typically used for adding functions that are not methods of this object.
The function may optionally be decorated with a FuncGroupMarker. If so, the default group and order will be determined by the decorator. Any group or order explicitly passed in to addFuncToGroup will take precedence over the decorator settings.
Parameters: - func – the function to add
- group (FuncGroupMarker or None) – the group marker. If the function is decorated with a FuncGoupMarker, that group marker will be the default.
- order (float or None) – the sorting order. If the function is decorated with a FuncGoupMarker, the order specified in the decorator will be the default.
-
addPostprocessor
(func, order=0)¶ Adds a postproceessor function to this task instance. If the function has been decorated with
@postprocessor
, the order specified by the decorator will be used.Parameters: - func (typing.Callable) – the function to add
- order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.
-
addPreprocessor
(func, order=None)¶ Adds a preproceessor function to this task instance. If the function has been decorated with @preprocessor, the order specified by the decorator will be used as the default.
Parameters: - func – the function to add
- order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.
-
classmethod
addSubParam
(name, param, update_owner=True)¶
-
blockSignals
(self, bool) → bool¶
-
block_signal_propagation
()¶
-
calling_context
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
childEvent
(self, QChildEvent)¶
-
children
(self) → List[QObject]¶
-
cmd
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
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, object: QObject = None) [signal]
-
disconnect
(self)¶
-
disconnectNotify
(self, QMetaMethod)¶
-
dumpObjectInfo
(self)¶
-
dumpObjectTree
(self)¶
-
dynamicPropertyNames
(self) → List[QByteArray]¶
-
event
(self, QEvent) → bool¶
-
eventFilter
(self, QObject, QEvent) → bool¶
-
exit_code
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
failure_info
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
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.
-
generateAlignmentFile
()¶ Write the alignment file to be used as an input for the predictor. The file will be a temporary file and will be removed in
postprocess
.Gaps in the alignment file are represented as ‘.’.
-
generateModelFile
()¶ Generate the model definition file with the name
self.model_fname
. This is done by finding the Prime data directory for the predictor and getting the names of all the files in it.The model file includes a header describing the number of model files and the predictors class number (
self.CLASS_NUM
), and a list of the model files.
-
getAbstractParam
(*args, **kwargs)¶
-
getAddedFuncs
(group=None)¶
-
getFuncGroup
(group=None)¶ Retrieve the functions belonging to the specified group.
Parameters: group (FuncGroupMarker) – the group marker Returns: the functions in the specified group, in order Return type: list
-
classmethod
getJsonBlacklist
()¶ Override to customize what params are serialized.
Implementations should return a list of abstract params that should be omitted from serialization.
- ..NOTE
- Returned abstract params must be direct child params of
cls
, e.g.cls.name
, notcls.coord.x
.
-
getLogAsString
()¶
-
classmethod
getParamSignal
(*args, **kwargs)¶
-
classmethod
getParamValue
(*args, **kwargs)¶
-
classmethod
getSubParam
(name)¶ Get the value of a subparam using the string name:
c = Coord() assert c.getSubParam('x') == 0
Note
Using the string name to accss params is generally discouraged, but can be useful for serializing/deserializing param data.
Parameters: name (str) – The name of the subparam to get the value for.
-
classmethod
getSubParams
()¶ Return a dictionary mapping subparam names to their values.
-
getTaskDir
()¶ Returns the full path of the task directory. This is only available if the task directory exists (after creation of the taskdir or, if no task dir is specified, any time).
-
getTaskFilename
(fname)¶ Return the appropriate absolute path for an input or output file in the taskdir.
-
getTypeHint
()¶
-
get_version
()¶ Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.
-
guard
()¶ Context manager that saves any Exception raised inside
-
inherits
(self, str) → bool¶
-
initAbstract
()¶
-
initConcrete
()¶ Override to customize initialization of concrete params.
-
initializeValue
()¶ @overrides: parameters.CompoundParam
-
inputChanged
¶
-
inputReplaced
¶
-
input_fnameChanged
¶
-
input_fnameReplaced
¶
-
installEventFilter
(self, QObject)¶
-
classmethod
isAbstract
()¶ Whether the param is an “abstract” param.
-
isDefault
(*args, **kwargs)¶
-
isInterruptionRequested
()¶
-
isRunning
()¶
-
isSignalConnected
(self, QMetaMethod) → bool¶
-
isStartable
()¶
-
isWidgetType
(self) → bool¶
-
isWindowType
(self) → bool¶
-
kill
()¶ @overrides: AbstractTask
Kill the subprocess and set the status to FAILED.
-
killTimer
(self, int)¶
-
max_progress
¶
-
max_progressChanged
¶
-
max_progressReplaced
¶
-
metaObject
(self) → QMetaObject¶
-
model_fnameChanged
¶
-
model_fnameReplaced
¶
-
moveToThread
(self, QThread)¶
-
name
¶
-
nameChanged
¶
-
nameReplaced
¶
-
objectName
(self) → str¶
-
objectNameChanged
¶ objectNameChanged(self, str) [signal]
-
output
¶
-
outputChanged
¶
-
outputReplaced
¶
-
classmethod
owner
()¶ Get the owner of the param:
# Can be called on an abstract param: assert Coord.x.owner() == Coord # ...or on an instance of a CompoundParam a = Atom() assert a.coord.owner() == a
-
classmethod
ownerChain
()¶ Returns a list of param owners starting from the toplevel param and ending with self. Examples:
foo.bar.atom.coord.ownerChain()
will return[foo, bar, atom, coord]
where every item is a concrete param.Foo.bar.atom.coord.x.ownerChain()
will return[Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x]
where every item is an abstract params.
-
classmethod
paramName
()¶ Get the name of the param:
# Can be called on an abstract param: print(Coord.x.paramName()) # 'x' # ...or on an instance of a CompoundParam a = Atom() a.coord.paramName() # 'coord'
-
parent
(self) → QObject¶
-
postprocess
()¶
-
postprocessors
()¶ Returns: A list of postprocessors, both decorated methods on the task and external functions that have been added via addPostprocessor()
Return type: list[typing.Callable]
-
preprocessors
()¶ Returns: A list of preprocessors (both decorated methods on the task and external functions that have been added via addPreprocessor)
-
printingOutputToTerminal
()¶ Returns: whether the StdOut
andStdErr
output from this task is being printed to the terminalReturn type: bool
-
processFuncChain
(chain=None, result_callback=None)¶ Execute each function in the specified chain sequentially in order.
The result_callback is called after each function with the return value of that function. This can be used to respond to the return value (e.g. present information to the user, get user feedback, log the result, etc.)
The return value of the result_callback determines whether processing will proceeed to the next function.
Parameters: - chain (FuncChainDecorator) – which chain to process
- result_callback – the callback that will get called with the result of each function in the chain
Returns: a list of the results from the functions
-
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.
-
qprocess
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
receivers
(self, PYQT_SIGNAL) → int¶
-
removeEventFilter
(self, QObject)¶
-
replicate
()¶ Create a new task with the same input and settings (but no output)
-
requestInterruption
()¶ Request the task to stop.
To enable this feature, subclasses should periodically check whether an interruption has been requested and terminate if it has been. If such logic has been included,
INTERRUPT_ENABLED
should be set toTrue
.
-
reset
(*args, **kwargs)¶
-
run
()¶
-
runCmd
(cmd)¶
-
classmethod
runFromCmdLine
()¶
-
runPostprocessing
(callback=None)¶
-
runPreprocessing
(callback=None, calling_context=None)¶ Run the preprocessors one-by-one. By default, any failing preprocessor will raise a TaskFailure exception and terminate processing. This behavior may be customized by supplying a callback function which will be called after each preprocessor with the result of that preprocessor.
This method is “final” so that all preprocessing logic will be enclosed in the try/finally block.
Parameters: - callback – a function that takes result and returns a bool that indicates whether to continue on to the next preprocessor
- calling_context – specify a value here to indicate the context in which this preprocessing is being called. This value will be stored in an instance variable, self.calling_context, which can be accessed from any preprocessor method on this task. Typically this value will be either self.GUI, self.CMDLINE, or None, but any value may be supplied here and checked for in the preprocessor methods. self.calling_context always reverts back to None at the end of runPreprocessing.
-
sender
(self) → QObject¶
-
senderSignalIndex
(self) → int¶
-
setObjectName
(self, str)¶
-
classmethod
setParamValue
(*args, **kwargs)¶
-
setParent
(self, QObject)¶
-
setPrintingOutputToTerminal
(print_to_terminal)¶ Set this task to print
StdOut
andStdErr
output to terminal, or not.Parameters: print_to_terminal (bool) – whether to send process output to terminal
-
setProperty
(self, str, Any) → bool¶
-
classmethod
setReference
(param1, param2)¶ Call this class method from configureParam to indicate that two params should be kept in sync. The initial values will start with the default value of
param1
. Example:class Square(CompoundParam): width: float = 5 height: float = 10 @classmethod def configureParam(cls): super().configureParam() cls.setReference(cls.width, cls.height) square = Square() assert square.width == square.height == 5 # Default value of width # takes priority square.height = 7 assert square.width == square.height == 7 square.width = 6 assert square.width == square.height == 6
Parameters: - param1 – The first abstract param to keep synced
- param2 – The second abstract param. After instantiation, this param will take on the value of param1.
-
setValue
(*args, **kwargs)¶
-
signalsBlocked
(self) → bool¶
-
skip_eq_check
()¶
-
specifyTaskDir
(taskdir_spec)¶ Specify the taskdir creation behavior. Use one of the following options:
A directory name (string). This may be a relative or absolute path
None - no taskdir is requested. The task will use the CWD as its taskdir
AUTO_TASKDIR - a new subdirectory will be created in the CWD using the task name as the directory name.
TEMP_TASKDIR - a temporary directory will be created in the schrodinger temp dir. This directory is cleaned up when the task is deleted.
Parameters: taskdir_spec – one of the four options listed above
-
start
(*args, **kwargs)¶
-
startTimer
(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int¶
-
staticMetaObject
= <PyQt5.QtCore.QMetaObject object>¶
-
status
¶
-
statusChanged
¶
-
statusReplaced
¶
-
stderr
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
stdout
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
taskDirSetting
()¶ Returns the taskdir spec. See specifyTaskDir() for details.
-
taskDone
¶
-
taskFailed
¶
-
taskStarted
¶
-
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¶
-
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.
-
-
class
schrodinger.protein.predictors.
PredictorWrapperTask
(anno, seq, blast_ann)¶ Bases:
schrodinger.tasks.tasks.BlockingFunctionTask
Task to run a specific predictor.
-
__init__
(anno, seq, blast_ann)¶ Initialize self. See help(type(self)) for accurate signature.
-
mainFunction
()¶
-
AUTO_TASKDIR
= <object object>¶
-
CMDLINE
= 1¶
-
DEFAULT_TASKDIR_SETTING
= None¶
-
DONE
= 3¶
-
DataClass
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
FAILED
= 2¶
-
GUI
= 2¶
-
INTERRUPT_ENABLED
= False¶
-
RUNNING
= 1¶
-
TEMP_TASKDIR
= <object object>¶
-
WAITING
= 0¶
-
addFuncToGroup
(func, group=None, order=None)¶ Adds a function to the specified chain. Typically used for adding functions that are not methods of this object.
The function may optionally be decorated with a FuncGroupMarker. If so, the default group and order will be determined by the decorator. Any group or order explicitly passed in to addFuncToGroup will take precedence over the decorator settings.
Parameters: - func – the function to add
- group (FuncGroupMarker or None) – the group marker. If the function is decorated with a FuncGoupMarker, that group marker will be the default.
- order (float or None) – the sorting order. If the function is decorated with a FuncGoupMarker, the order specified in the decorator will be the default.
-
addPostprocessor
(func, order=0)¶ Adds a postproceessor function to this task instance. If the function has been decorated with
@postprocessor
, the order specified by the decorator will be used.Parameters: - func (typing.Callable) – the function to add
- order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.
-
addPreprocessor
(func, order=None)¶ Adds a preproceessor function to this task instance. If the function has been decorated with @preprocessor, the order specified by the decorator will be used as the default.
Parameters: - func – the function to add
- order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.
-
classmethod
addSubParam
(name, param, update_owner=True)¶
-
blockSignals
(self, bool) → bool¶
-
block_signal_propagation
()¶
-
calling_context
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
childEvent
(self, QChildEvent)¶
-
children
(self) → List[QObject]¶
-
classmethod
configureParam
()¶ Override this class method to set up the abstract param class (e.g. setParamReference on child params.)
-
connectNotify
(self, QMetaMethod)¶
-
customEvent
(self, QEvent)¶
-
classmethod
defaultValue
(*args, **kwargs)¶
-
deleteLater
(self)¶
-
destroyed
¶ destroyed(self, object: QObject = None) [signal]
-
disconnect
(self)¶
-
disconnectNotify
(self, QMetaMethod)¶
-
dumpObjectInfo
(self)¶
-
dumpObjectTree
(self)¶
-
dynamicPropertyNames
(self) → List[QByteArray]¶
-
event
(self, QEvent) → bool¶
-
eventFilter
(self, QObject, QEvent) → bool¶
-
failure_info
¶ This class can be used to declare a public attribute on a
CompoundParam
. Declared public attributes can be used without error.Example usage:
class Coord(CompoundParam): x: int y: int note = NonParamAttribute() coord = Coord() coord.note = "hello" # No error
-
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)¶
-
getAddedFuncs
(group=None)¶
-
getFuncGroup
(group=None)¶ Retrieve the functions belonging to the specified group.
Parameters: group (FuncGroupMarker) – the group marker Returns: the functions in the specified group, in order Return type: list
-
classmethod
getJsonBlacklist
()¶ Override to customize what params are serialized.
Implementations should return a list of abstract params that should be omitted from serialization.
- ..NOTE
- Returned abstract params must be direct child params of
cls
, e.g.cls.name
, notcls.coord.x
.
-
classmethod
getParamSignal
(*args, **kwargs)¶
-
classmethod
getParamValue
(*args, **kwargs)¶
-
classmethod
getSubParam
(name)¶ Get the value of a subparam using the string name:
c = Coord() assert c.getSubParam('x') == 0
Note
Using the string name to accss params is generally discouraged, but can be useful for serializing/deserializing param data.
Parameters: name (str) – The name of the subparam to get the value for.
-
classmethod
getSubParams
()¶ Return a dictionary mapping subparam names to their values.
-
getTaskDir
()¶ Returns the full path of the task directory. This is only available if the task directory exists (after creation of the taskdir or, if no task dir is specified, any time).
-
getTaskFilename
(fname)¶ Return the appropriate absolute path for an input or output file in the taskdir.
-
getTypeHint
()¶
-
get_version
()¶ Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.
-
guard
()¶ Context manager that saves any Exception raised inside
-
inherits
(self, str) → bool¶
-
initAbstract
()¶
-
initConcrete
()¶ Override to customize initialization of concrete params.
-
initializeValue
()¶ @overrides: parameters.CompoundParam
-
input
¶
-
inputChanged
¶
-
inputReplaced
¶
-
installEventFilter
(self, QObject)¶
-
classmethod
isAbstract
()¶ Whether the param is an “abstract” param.
-
isDefault
(*args, **kwargs)¶
-
isInterruptionRequested
()¶
-
isRunning
()¶
-
isSignalConnected
(self, QMetaMethod) → bool¶
-
isStartable
()¶
-
isWidgetType
(self) → bool¶
-
isWindowType
(self) → bool¶
-
kill
()¶ Implementations are responsible for immediately stopping the task. No threads or processes should be running after this method is complete.
This method should be called sparingly since in many contexts the task will be forced to terminate without a chance to clean up or free resources.
-
killTimer
(self, int)¶
-
max_progress
¶
-
max_progressChanged
¶
-
max_progressReplaced
¶
-
metaObject
(self) → QMetaObject¶
-
moveToThread
(self, QThread)¶
-
name
¶
-
nameChanged
¶
-
nameReplaced
¶
-
objectName
(self) → str¶
-
objectNameChanged
¶ objectNameChanged(self, str) [signal]
-
output
¶
-
outputChanged
¶
-
outputReplaced
¶
-
classmethod
owner
()¶ Get the owner of the param:
# Can be called on an abstract param: assert Coord.x.owner() == Coord # ...or on an instance of a CompoundParam a = Atom() assert a.coord.owner() == a
-
classmethod
ownerChain
()¶ Returns a list of param owners starting from the toplevel param and ending with self. Examples:
foo.bar.atom.coord.ownerChain()
will return[foo, bar, atom, coord]
where every item is a concrete param.Foo.bar.atom.coord.x.ownerChain()
will return[Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x]
where every item is an abstract params.
-
classmethod
paramName
()¶ Get the name of the param:
# Can be called on an abstract param: print(Coord.x.paramName()) # 'x' # ...or on an instance of a CompoundParam a = Atom() a.coord.paramName() # 'coord'
-
parent
(self) → QObject¶
-
postprocessors
()¶ Returns: A list of postprocessors, both decorated methods on the task and external functions that have been added via addPostprocessor()
Return type: list[typing.Callable]
-
preprocessors
()¶ Returns: A list of preprocessors (both decorated methods on the task and external functions that have been added via addPreprocessor)
-
processFuncChain
(chain=None, result_callback=None)¶ Execute each function in the specified chain sequentially in order.
The result_callback is called after each function with the return value of that function. This can be used to respond to the return value (e.g. present information to the user, get user feedback, log the result, etc.)
The return value of the result_callback determines whether processing will proceeed to the next function.
Parameters: - chain (FuncChainDecorator) – which chain to process
- result_callback – the callback that will get called with the result of each function in the chain
Returns: a list of the results from the functions
-
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)
-
requestInterruption
()¶ Request the task to stop.
To enable this feature, subclasses should periodically check whether an interruption has been requested and terminate if it has been. If such logic has been included,
INTERRUPT_ENABLED
should be set toTrue
.
-
reset
(*args, **kwargs)¶
-
run
()¶
-
classmethod
runFromCmdLine
()¶
-
runPostprocessing
(callback=None)¶
-
runPreprocessing
(callback=None, calling_context=None)¶ Run the preprocessors one-by-one. By default, any failing preprocessor will raise a TaskFailure exception and terminate processing. This behavior may be customized by supplying a callback function which will be called after each preprocessor with the result of that preprocessor.
This method is “final” so that all preprocessing logic will be enclosed in the try/finally block.
Parameters: - callback – a function that takes result and returns a bool that indicates whether to continue on to the next preprocessor
- calling_context – specify a value here to indicate the context in which this preprocessing is being called. This value will be stored in an instance variable, self.calling_context, which can be accessed from any preprocessor method on this task. Typically this value will be either self.GUI, self.CMDLINE, or None, but any value may be supplied here and checked for in the preprocessor methods. self.calling_context always reverts back to None at the end of runPreprocessing.
-
sender
(self) → QObject¶
-
senderSignalIndex
(self) → int¶
-
setObjectName
(self, str)¶
-
classmethod
setParamValue
(*args, **kwargs)¶
-
setParent
(self, QObject)¶
-
setProperty
(self, str, Any) → bool¶
-
classmethod
setReference
(param1, param2)¶ Call this class method from configureParam to indicate that two params should be kept in sync. The initial values will start with the default value of
param1
. Example:class Square(CompoundParam): width: float = 5 height: float = 10 @classmethod def configureParam(cls): super().configureParam() cls.setReference(cls.width, cls.height) square = Square() assert square.width == square.height == 5 # Default value of width # takes priority square.height = 7 assert square.width == square.height == 7 square.width = 6 assert square.width == square.height == 6
Parameters: - param1 – The first abstract param to keep synced
- param2 – The second abstract param. After instantiation, this param will take on the value of param1.
-
setValue
(*args, **kwargs)¶
-
signalsBlocked
(self) → bool¶
-
skip_eq_check
()¶
-
specifyTaskDir
(taskdir_spec)¶ Specify the taskdir creation behavior. Use one of the following options:
A directory name (string). This may be a relative or absolute path
None - no taskdir is requested. The task will use the CWD as its taskdir
AUTO_TASKDIR - a new subdirectory will be created in the CWD using the task name as the directory name.
TEMP_TASKDIR - a temporary directory will be created in the schrodinger temp dir. This directory is cleaned up when the task is deleted.
Parameters: taskdir_spec – one of the four options listed above
-
start
(skip_preprocessing=False)¶ This is the main method for starting a task. Start will check if a task is not already running, run preprocessing, and then run the task.
Failures in preprocessing will interrupt the task start, and the task will never enter the RUNNING state.
Parameters: skip_preprocessing (bool) – whether to skip preprocessing. This can be useful if preprocessing was already performed prior to calling start.
-
startTimer
(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int¶
-
staticMetaObject
= <PyQt5.QtCore.QMetaObject object>¶
-
status
¶
-
statusChanged
¶
-
statusReplaced
¶
-
taskDirSetting
()¶ Returns the taskdir spec. See specifyTaskDir() for details.
-
taskDone
¶
-
taskFailed
¶
-
taskStarted
¶
-
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¶
-
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.predictors.
predict_secondary_structure
(seq, aln, mutate_in_place=True)¶
-
schrodinger.protein.predictors.
predict_solvent_accessibility
(seq, aln, mutate_in_place=True)¶
-
schrodinger.protein.predictors.
predict_disordered_regions
(seq, aln, mutate_in_place=True)¶
-
schrodinger.protein.predictors.
predict_domain_arrangement
(seq, aln, mutate_in_place=True)¶
-
schrodinger.protein.predictors.
predict_disulfide_bond
(seq, aln, mutate_in_place=True)¶
-
schrodinger.protein.predictors.
encode_ssa
(ssa)¶