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.ParamModel

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

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

owner_instance = Owner()
owner_instance.data_x = 4

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

Warning

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

Variables:DataClass (type) – The type of data the param describes.

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

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

owner_instance = Owner()
owner_instance.data_x = 4

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

Warning

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

Variables:DataClass (type) – The type of data the param describes.

DataClass

alias of builtins.object

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

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

classmethod addSubParam(name, param, update_owner=True)

alnChanged

alnReplaced

blockSignals(self, bool) → bool

block_signal_propagation()

childEvent(self, QChildEvent)

children(self) → object

classmethod configureParam()

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

connectNotify(self, QMetaMethod)

customEvent(self, QEvent)

classmethod defaultValue(*args, **kwargs)

deleteLater(self)

destroyed

destroyed(self, QObject = None) [signal]

disconnect(self)

disconnectNotify(self, QMetaMethod)

dumpObjectInfo(self)

dumpObjectTree(self)

dynamicPropertyNames(self) → object

event(self, QEvent) → bool

eventFilter(self, QObject, QEvent) → bool

findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject

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

findChildren(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]

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

classmethod fromJson(json_obj)

A factory method which constructs a new object from a given dict loaded from a json string or file.

Parameters:json_obj (dict) – A json-loaded dictionary to create an object from. Returns:An instance of this class.

:rtype : cls

classmethod fromJsonImplementation(json_dict)

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

getAbstractParam(*args, **kwargs)

classmethod getParamSignal(*args, **kwargs)

classmethod getParamValue(*args, **kwargs)

classmethod getSubParam(name)

classmethod getSubParams()

get_version()

Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.

inherits(self, str) → bool

initAbstract()

initConcrete()

initializeValue()

installEventFilter(self, QObject)

classmethod isAbstract()

isDefault(*args, **kwargs)

isSignalConnected(self, QMetaMethod) → bool

isWidgetType(self) → bool

isWindowType(self) → bool

killTimer(self, int)

metaObject(self) → QMetaObject

moveToThread(self, QThread)

objectName(self) → str

objectNameChanged

objectNameChanged(self, str) [signal]

classmethod owner()

classmethod ownerChain()

Returns a list of param owners starting from the toplevel param and ending with self. Examples:

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

Foo.bar.atom.coord.x.ownerChain() will return [Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x] where every item is an abstract params.

classmethod paramName()

parent(self) → QObject

property(self, str) → Any

pyqtConfigure(...)

Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

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

setValue(*args, **kwargs)

signalsBlocked(self) → bool

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

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

owner_instance = Owner()
owner_instance.data_x = 4

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

Warning

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

Variables:DataClass (type) – The type of data the param describes.

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

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

owner_instance = Owner()
owner_instance.data_x = 4

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

Warning

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

Variables:DataClass (type) – The type of data the param describes.

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()

DONE = 3

DataClass

alias of builtins.object

FAILED = 2

RUNNING = 1

WAITING = 0

__init__(*args, **kwargs)

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

classmethod addSubParam(name, param, update_owner=True)

blockSignals(self, bool) → bool

block_signal_propagation()

childEvent(self, QChildEvent)

children(self) → object

classmethod configureParam()

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

connectNotify(self, QMetaMethod)

customEvent(self, QEvent)

classmethod defaultValue(*args, **kwargs)

deleteLater(self)

destroyed

destroyed(self, QObject = None) [signal]

disconnect(self)

disconnectNotify(self, QMetaMethod)

dumpObjectInfo(self)

dumpObjectTree(self)

dynamicPropertyNames(self) → object

event(self, QEvent) → bool

eventFilter(self, QObject, QEvent) → bool

findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject

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

findChildren(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]

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

classmethod fromJson(json_obj)

A factory method which constructs a new object from a given dict loaded from a json string or file.

Parameters:json_obj (dict) – A json-loaded dictionary to create an object from. Returns:An instance of this class.

:rtype : cls

classmethod fromJsonFilename(filename)

classmethod fromJsonImplementation(json_dict)

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

getAbstractParam(*args, **kwargs)

classmethod getParamSignal(*args, **kwargs)

classmethod getParamValue(*args, **kwargs)

classmethod getSubParam(name)

classmethod getSubParams()

getTaskDirectory()

Return the absolute path of the task directory

getTaskFilename(fname)

Return the appropriate absolute path for an input or output file

get_version()

Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.

guard()

Context manager that saves any Exception raised inside

inherits(self, str) → bool

initAbstract()

initConcrete(auto_task_dir=False)

initializeValue()

inputChanged

inputReplaced

input_fnameChanged

input_fnameReplaced

installEventFilter(self, QObject)

classmethod isAbstract()

isDefault(*args, **kwargs)

isSignalConnected(self, QMetaMethod) → bool

isStartable()

isWidgetType(self) → bool

isWindowType(self) → bool

kill()

Kill the subprocess and reset the status to FAILED. If the task is not currently running, this is a no-op.

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

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

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

outputChanged

outputReplaced

classmethod owner()

classmethod ownerChain()

Returns a list of param owners starting from the toplevel param and ending with self. Examples:

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

Foo.bar.atom.coord.x.ownerChain() will return [Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x] where every item is an abstract params.

classmethod paramName()

parent(self) → QObject

preprocessors()

Returns:A list of bound preprocessing methods

progress

progressChanged

progressReplaced

property(self, str) → Any

pyqtConfigure(...)

Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

receivers(self, PYQT_SIGNAL) → int

removeEventFilter(self, QObject)

replicate()

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

reportValidation(results)

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

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

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

reset(*args, **kwargs)

run()

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

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

Parameters:

• silent (bool) – run without any reporting (i.e. error messages to the user). This is useful if we want to programmatically test validity. Changes return value of this method from ValidationResults to a boolean.
• validate_children (bool) – run validation on all child objects. See _validateChildren for documentation on what this entails.
• stop_on_fail (bool) – stop validation when first failure is encountered

Returns:

if silent is False, returns the validation results. If silent is True, returns a boolean generated by reportValidation.

Return type:

ValidationResults or bool

sender(self) → QObject

senderSignalIndex(self) → int

setAutoTaskDir(auto_task_dir)

setObjectName(self, str)

classmethod setParamValue(*args, **kwargs)

setParent(self, QObject)

setProperty(self, str, Any) → bool

setValue(*args, **kwargs)

signalsBlocked(self) → bool

start(skip_preprocessing=False)

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

staticMetaObject = <PyQt5.QtCore.QMetaObject object>

status

statusChanged

statusReplaced

taskDone

taskFailed

taskStarted

taskdir

thread(self) → QThread

timerEvent(self, QTimerEvent)

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.

SSA_MAP = {'': None, 'B': 2, 'C': -1, 'E': 2, 'G': 1, 'H': 1, 'I': 1, 'S': -1, 'T': 3}

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

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

owner_instance = Owner()
owner_instance.data_x = 4

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

Warning

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

Variables:DataClass (type) – The type of data the param describes.

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

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

owner_instance = Owner()
owner_instance.data_x = 4

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

Warning

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

Variables:DataClass (type) – The type of data the param describes.

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 in self.input.sequence

:rtype : list

DONE = 3

DataClass

alias of builtins.object

FAILED = 2

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

Bases: schrodinger.models.parameters.ParamModel

DataClass

alias of builtins.object

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

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

classmethod addSubParam(name, param, update_owner=True)

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

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

owner_instance = Owner()
owner_instance.data_x = 4

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

Warning

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

Variables:DataClass (type) – The type of data the param describes.

alnChanged

alnReplaced

blockSignals(self, bool) → bool

block_signal_propagation()

childEvent(self, QChildEvent)

children(self) → object

classmethod configureParam()

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

connectNotify(self, QMetaMethod)

customEvent(self, QEvent)

classmethod defaultValue(*args, **kwargs)

deleteLater(self)

destroyed

destroyed(self, QObject = None) [signal]

disconnect(self)

disconnectNotify(self, QMetaMethod)

dumpObjectInfo(self)

dumpObjectTree(self)

dynamicPropertyNames(self) → object

event(self, QEvent) → bool

eventFilter(self, QObject, QEvent) → bool

findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject

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

findChildren(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]

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

classmethod fromJson(json_obj)

A factory method which constructs a new object from a given dict loaded from a json string or file.

Parameters:json_obj (dict) – A json-loaded dictionary to create an object from. Returns:An instance of this class.

:rtype : cls

classmethod fromJsonImplementation(json_dict)

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

getAbstractParam(*args, **kwargs)

classmethod getParamSignal(*args, **kwargs)

classmethod getParamValue(*args, **kwargs)

classmethod getSubParam(name)

classmethod getSubParams()

get_version()

Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.

inherits(self, str) → bool

initAbstract()

initConcrete()

initializeValue()

installEventFilter(self, QObject)

classmethod isAbstract()

isDefault(*args, **kwargs)

isSignalConnected(self, QMetaMethod) → bool

isWidgetType(self) → bool

isWindowType(self) → bool

killTimer(self, int)

metaObject(self) → QMetaObject

moveToThread(self, QThread)

objectName(self) → str

objectNameChanged

objectNameChanged(self, str) [signal]

classmethod owner()

classmethod ownerChain()

Returns a list of param owners starting from the toplevel param and ending with self. Examples:

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

Foo.bar.atom.coord.x.ownerChain() will return [Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x] where every item is an abstract params.

classmethod paramName()

parent(self) → QObject

property(self, str) → Any

pyqtConfigure(...)

Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

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

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

owner_instance = Owner()
owner_instance.data_x = 4

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

Warning

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

Variables:DataClass (type) – The type of data the param describes.

seqChanged

seqReplaced

setObjectName(self, str)

classmethod setParamValue(*args, **kwargs)

setParent(self, QObject)

setProperty(self, str, Any) → bool

setValue(*args, **kwargs)

signalsBlocked(self) → bool

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

WAITING = 0

__init__(*args, **kwargs)

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

classmethod addSubParam(name, param, update_owner=True)

blockSignals(self, bool) → bool

block_signal_propagation()

childEvent(self, QChildEvent)

children(self) → object

classmethod configureParam()

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

connectNotify(self, QMetaMethod)

customEvent(self, QEvent)

classmethod defaultValue(*args, **kwargs)

deleteLater(self)

destroyed

destroyed(self, QObject = None) [signal]

disconnect(self)

disconnectNotify(self, QMetaMethod)

dumpObjectInfo(self)

dumpObjectTree(self)

dynamicPropertyNames(self) → object

event(self, QEvent) → bool

eventFilter(self, QObject, QEvent) → bool

findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject

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

findChildren(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]

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

classmethod fromJson(json_obj)

A factory method which constructs a new object from a given dict loaded from a json string or file.

Parameters:json_obj (dict) – A json-loaded dictionary to create an object from. Returns:An instance of this class.

:rtype : cls

classmethod 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)

classmethod getParamSignal(*args, **kwargs)

classmethod getParamValue(*args, **kwargs)

classmethod getSubParam(name)

classmethod getSubParams()

getTaskDirectory()

Return the absolute path of the task directory

getTaskFilename(fname)

Return the appropriate absolute path for an input or output file

get_version()

Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.

guard()

Context manager that saves any Exception raised inside

inherits(self, str) → bool

initAbstract()

initConcrete(auto_task_dir=False)

initializeValue()

input

inputChanged

inputReplaced

input_fnameChanged

input_fnameReplaced

installEventFilter(self, QObject)

classmethod isAbstract()

isDefault(*args, **kwargs)

isSignalConnected(self, QMetaMethod) → bool

isStartable()

isWidgetType(self) → bool

isWindowType(self) → bool

kill()

Kill the subprocess and reset the status to FAILED. If the task is not currently running, this is a no-op.

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

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

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

outputChanged

outputReplaced

classmethod owner()

classmethod ownerChain()

Returns a list of param owners starting from the toplevel param and ending with self. Examples:

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

Foo.bar.atom.coord.x.ownerChain() will return [Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x] where every item is an abstract params.

classmethod paramName()

parent(self) → QObject

postprocess()

preprocessors()

Returns:A list of bound preprocessing methods

progress

progressChanged

progressReplaced

property(self, str) → Any

pyqtConfigure(...)

Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

receivers(self, PYQT_SIGNAL) → int

removeEventFilter(self, QObject)

replicate()

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

reportValidation(results)

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

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

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

reset(*args, **kwargs)

run()

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

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

Parameters:

• silent (bool) – run without any reporting (i.e. error messages to the user). This is useful if we want to programmatically test validity. Changes return value of this method from ValidationResults to a boolean.
• validate_children (bool) – run validation on all child objects. See _validateChildren for documentation on what this entails.
• stop_on_fail (bool) – stop validation when first failure is encountered

Returns:

if silent is False, returns the validation results. If silent is True, returns a boolean generated by reportValidation.

Return type:

ValidationResults or bool

sender(self) → QObject

senderSignalIndex(self) → int

setAutoTaskDir(auto_task_dir)

setObjectName(self, str)

classmethod setParamValue(*args, **kwargs)

setParent(self, QObject)

setProperty(self, str, Any) → bool

setValue(*args, **kwargs)

signalsBlocked(self) → bool

start(skip_preprocessing=False)

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

staticMetaObject = <PyQt5.QtCore.QMetaObject object>

status

statusChanged

statusReplaced

taskDone

taskFailed

taskStarted

taskdir

thread(self) → QThread

timerEvent(self, QTimerEvent)

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

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

owner_instance = Owner()
owner_instance.data_x = 4

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

Warning

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

Variables:DataClass (type) – The type of data the param describes.

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

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

owner_instance = Owner()
owner_instance.data_x = 4

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

Warning

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

Variables:DataClass (type) – The type of data the param describes.

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.

DONE = 3

DataClass

alias of builtins.object

FAILED = 2

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

Bases: schrodinger.models.parameters.ParamModel

DataClass

alias of builtins.object

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

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

classmethod addSubParam(name, param, update_owner=True)

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

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

owner_instance = Owner()
owner_instance.data_x = 4

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

Warning

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

Variables:DataClass (type) – The type of data the param describes.

alnChanged

alnReplaced

blockSignals(self, bool) → bool

block_signal_propagation()

childEvent(self, QChildEvent)

children(self) → object

classmethod configureParam()

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

connectNotify(self, QMetaMethod)

customEvent(self, QEvent)

classmethod defaultValue(*args, **kwargs)

deleteLater(self)

destroyed

destroyed(self, QObject = None) [signal]

disconnect(self)

disconnectNotify(self, QMetaMethod)

dumpObjectInfo(self)

dumpObjectTree(self)

dynamicPropertyNames(self) → object

event(self, QEvent) → bool

eventFilter(self, QObject, QEvent) → bool

findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject

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

findChildren(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]

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

classmethod fromJson(json_obj)

A factory method which constructs a new object from a given dict loaded from a json string or file.

Parameters:json_obj (dict) – A json-loaded dictionary to create an object from. Returns:An instance of this class.

:rtype : cls

classmethod fromJsonImplementation(json_dict)

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

getAbstractParam(*args, **kwargs)

classmethod getParamSignal(*args, **kwargs)

classmethod getParamValue(*args, **kwargs)

classmethod getSubParam(name)

classmethod getSubParams()

get_version()

Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.

inherits(self, str) → bool

initAbstract()

initConcrete()

initializeValue()

installEventFilter(self, QObject)

classmethod isAbstract()

isDefault(*args, **kwargs)

isSignalConnected(self, QMetaMethod) → bool

isWidgetType(self) → bool

isWindowType(self) → bool

killTimer(self, int)

metaObject(self) → QMetaObject

moveToThread(self, QThread)

objectName(self) → str

objectNameChanged

objectNameChanged(self, str) [signal]

classmethod owner()

classmethod ownerChain()

Returns a list of param owners starting from the toplevel param and ending with self. Examples:

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

Foo.bar.atom.coord.x.ownerChain() will return [Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x] where every item is an abstract params.

classmethod paramName()

parent(self) → QObject

property(self, str) → Any

pyqtConfigure(...)

Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

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

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

owner_instance = Owner()
owner_instance.data_x = 4

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

Warning

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

Variables:DataClass (type) – The type of data the param describes.

seqChanged

seqReplaced

setObjectName(self, str)

classmethod setParamValue(*args, **kwargs)

setParent(self, QObject)

setProperty(self, str, Any) → bool

setValue(*args, **kwargs)

signalsBlocked(self) → bool

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

WAITING = 0

__init__(*args, **kwargs)

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

classmethod addSubParam(name, param, update_owner=True)

blockSignals(self, bool) → bool

block_signal_propagation()

childEvent(self, QChildEvent)

children(self) → object

classmethod configureParam()

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

connectNotify(self, QMetaMethod)

customEvent(self, QEvent)

classmethod defaultValue(*args, **kwargs)

deleteLater(self)

destroyed

destroyed(self, QObject = None) [signal]

disconnect(self)

disconnectNotify(self, QMetaMethod)

dumpObjectInfo(self)

dumpObjectTree(self)

dynamicPropertyNames(self) → object

event(self, QEvent) → bool

eventFilter(self, QObject, QEvent) → bool

findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject

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

findChildren(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]

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

classmethod fromJson(json_obj)

A factory method which constructs a new object from a given dict loaded from a json string or file.

Parameters:json_obj (dict) – A json-loaded dictionary to create an object from. Returns:An instance of this class.

:rtype : cls

classmethod 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)

classmethod getParamSignal(*args, **kwargs)

classmethod getParamValue(*args, **kwargs)

classmethod getSubParam(name)

classmethod getSubParams()

getTaskDirectory()

Return the absolute path of the task directory

getTaskFilename(fname)

Return the appropriate absolute path for an input or output file

get_version()

Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.

guard()

Context manager that saves any Exception raised inside

inherits(self, str) → bool

initAbstract()

initConcrete(auto_task_dir=False)

initializeValue()

input

inputChanged

inputReplaced

input_fnameChanged

input_fnameReplaced

installEventFilter(self, QObject)

classmethod isAbstract()

isDefault(*args, **kwargs)

isSignalConnected(self, QMetaMethod) → bool

isStartable()

isWidgetType(self) → bool

isWindowType(self) → bool

kill()

Kill the subprocess and reset the status to FAILED. If the task is not currently running, this is a no-op.

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

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

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

outputChanged

outputReplaced

classmethod owner()

classmethod ownerChain()

Returns a list of param owners starting from the toplevel param and ending with self. Examples:

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

Foo.bar.atom.coord.x.ownerChain() will return [Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x] where every item is an abstract params.

classmethod paramName()

parent(self) → QObject

postprocess()

preprocessors()

Returns:A list of bound preprocessing methods

progress

progressChanged

progressReplaced

property(self, str) → Any

pyqtConfigure(...)

Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

receivers(self, PYQT_SIGNAL) → int

removeEventFilter(self, QObject)

replicate()

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

reportValidation(results)

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

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

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

reset(*args, **kwargs)

run()

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

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

Parameters:

• silent (bool) – run without any reporting (i.e. error messages to the user). This is useful if we want to programmatically test validity. Changes return value of this method from ValidationResults to a boolean.
• validate_children (bool) – run validation on all child objects. See _validateChildren for documentation on what this entails.
• stop_on_fail (bool) – stop validation when first failure is encountered

Returns:

if silent is False, returns the validation results. If silent is True, returns a boolean generated by reportValidation.

Return type:

ValidationResults or bool

sender(self) → QObject

senderSignalIndex(self) → int

setAutoTaskDir(auto_task_dir)

setObjectName(self, str)

classmethod setParamValue(*args, **kwargs)

setParent(self, QObject)

setProperty(self, str, Any) → bool

setValue(*args, **kwargs)

signalsBlocked(self) → bool

start(skip_preprocessing=False)

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

staticMetaObject = <PyQt5.QtCore.QMetaObject object>

status

statusChanged

statusReplaced

taskDone

taskFailed

taskStarted

taskdir

thread(self) → QThread

timerEvent(self, QTimerEvent)

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.json.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.ParamModel

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

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

owner_instance = Owner()
owner_instance.data_x = 4

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

Warning

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

Variables:DataClass (type) – The type of data the param describes.

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

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

owner_instance = Owner()
owner_instance.data_x = 4

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

Warning

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

Variables:DataClass (type) – The type of data the param describes.

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

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

owner_instance = Owner()
owner_instance.data_x = 4

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

Warning

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

Variables:DataClass (type) – The type of data the param describes.

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

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

owner_instance = Owner()
owner_instance.data_x = 4

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

Warning

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

Variables:DataClass (type) – The type of data the param describes.

DataClass

alias of builtins.object

__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) → object

classmethod configureParam()

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

connectNotify(self, QMetaMethod)

customEvent(self, QEvent)

classmethod defaultValue(*args, **kwargs)

deleteLater(self)

destroyed

destroyed(self, QObject = None) [signal]

disconnect(self)

disconnectNotify(self, QMetaMethod)

dumpObjectInfo(self)

dumpObjectTree(self)

dynamicPropertyNames(self) → object

event(self, QEvent) → bool

eventFilter(self, QObject, QEvent) → bool

findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject

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

findChildren(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]

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

classmethod fromJson(json_obj)

A factory method which constructs a new object from a given dict loaded from a json string or file.

Parameters:json_obj (dict) – A json-loaded dictionary to create an object from. Returns:An instance of this class.

:rtype : cls

classmethod fromJsonImplementation(json_dict)

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

getAbstractParam(*args, **kwargs)

classmethod getParamSignal(*args, **kwargs)

classmethod getParamValue(*args, **kwargs)

classmethod getSubParam(name)

classmethod getSubParams()

get_version()

Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.

inherits(self, str) → bool

initAbstract()

initConcrete()

initializeValue()

installEventFilter(self, QObject)

classmethod isAbstract()

isDefault(*args, **kwargs)

isSignalConnected(self, QMetaMethod) → bool

isWidgetType(self) → bool

isWindowType(self) → bool

killTimer(self, int)

metaObject(self) → QMetaObject

moveToThread(self, QThread)

objectName(self) → str

objectNameChanged

objectNameChanged(self, str) [signal]

classmethod owner()

classmethod ownerChain()

Returns a list of param owners starting from the toplevel param and ending with self. Examples:

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

Foo.bar.atom.coord.x.ownerChain() will return [Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x] where every item is an abstract params.

classmethod paramName()

parent(self) → QObject

property(self, str) → Any

pyqtConfigure(...)

Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

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

setValue(*args, **kwargs)

signalsBlocked(self) → bool

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

CLASS_NUM = NotImplemented

DONE = 3

DataClass

alias of builtins.object

EXE = NotImplemented

FAILED = 2

NU = NotImplemented

NY = NotImplemented

PREDICTOR_NAME = NotImplemented

RUNNING = 1

WAITING = 0

__init__(*args, **kwargs)

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

classmethod addSubParam(name, param, update_owner=True)

blockSignals(self, bool) → bool

block_signal_propagation()

childEvent(self, QChildEvent)

children(self) → object

classmethod configureParam()

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

connectNotify(self, QMetaMethod)

customEvent(self, QEvent)

classmethod defaultValue(*args, **kwargs)

deleteLater(self)

destroyed

destroyed(self, QObject = None) [signal]

disconnect(self)

disconnectNotify(self, QMetaMethod)

dumpObjectInfo(self)

dumpObjectTree(self)

dynamicPropertyNames(self) → object

event(self, QEvent) → bool

eventFilter(self, QObject, QEvent) → bool

findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject

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

findChildren(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]

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

classmethod fromJson(json_obj)

A factory method which constructs a new object from a given dict loaded from a json string or file.

Parameters:json_obj (dict) – A json-loaded dictionary to create an object from. Returns:An instance of this class.

:rtype : cls

classmethod 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)

classmethod getParamSignal(*args, **kwargs)

classmethod getParamValue(*args, **kwargs)

classmethod getSubParam(name)

classmethod getSubParams()

getTaskDirectory()

Return the absolute path of the task directory

getTaskFilename(fname)

Return the appropriate absolute path for an input or output file

get_version()

Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.

guard()

Context manager that saves any Exception raised inside

inherits(self, str) → bool

initAbstract()

initConcrete(auto_task_dir=False)

initializeValue()

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

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

owner_instance = Owner()
owner_instance.data_x = 4

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

Warning

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

Variables:DataClass (type) – The type of data the param describes.

input_fnameChanged

input_fnameReplaced

installEventFilter(self, QObject)

classmethod isAbstract()

isDefault(*args, **kwargs)

isSignalConnected(self, QMetaMethod) → bool

isStartable()

isWidgetType(self) → bool

isWindowType(self) → bool

kill()

Kill the subprocess and reset the status to FAILED. If the task is not currently running, this is a no-op.

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

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

owner_instance = Owner()
owner_instance.data_x = 4

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

Warning

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

Variables:DataClass (type) – The type of data the param describes.

model_fnameChanged

model_fnameReplaced

moveToThread(self, QThread)

name

nameChanged

nameReplaced

objectName(self) → str

objectNameChanged

objectNameChanged(self, str) [signal]

output

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

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

outputChanged

outputReplaced

classmethod owner()

classmethod ownerChain()

Returns a list of param owners starting from the toplevel param and ending with self. Examples:

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

Foo.bar.atom.coord.x.ownerChain() will return [Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x] where every item is an abstract params.

classmethod paramName()

parent(self) → QObject

postprocess()

prediction()

Return the actual prediction. This can take various forms depending on the predictor.

preprocessors()

Returns:A list of bound preprocessing methods

progress

progressChanged

progressReplaced

property(self, str) → Any

pyqtConfigure(...)

Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

receivers(self, PYQT_SIGNAL) → int

removeEventFilter(self, QObject)

replicate()

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

reportValidation(results)

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

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

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

reset(*args, **kwargs)

run()

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

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

Parameters:

• silent (bool) – run without any reporting (i.e. error messages to the user). This is useful if we want to programmatically test validity. Changes return value of this method from ValidationResults to a boolean.
• validate_children (bool) – run validation on all child objects. See _validateChildren for documentation on what this entails.
• stop_on_fail (bool) – stop validation when first failure is encountered

Returns:

if silent is False, returns the validation results. If silent is True, returns a boolean generated by reportValidation.

Return type:

ValidationResults or bool

sender(self) → QObject

senderSignalIndex(self) → int

setAutoTaskDir(auto_task_dir)

setObjectName(self, str)

classmethod setParamValue(*args, **kwargs)

setParent(self, QObject)

setProperty(self, str, Any) → bool

setValue(*args, **kwargs)

signalsBlocked(self) → bool

start(skip_preprocessing=False)

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

staticMetaObject = <PyQt5.QtCore.QMetaObject object>

status

statusChanged

statusReplaced

taskDone

taskFailed

taskStarted

taskdir

thread(self) → QThread

timerEvent(self, QTimerEvent)

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

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

owner_instance = Owner()
owner_instance.data_x = 4

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

Warning

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

Variables:DataClass (type) – The type of data the param describes.

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

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

owner_instance = Owner()
owner_instance.data_x = 4

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

Warning

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

Variables:DataClass (type) – The type of data the param describes.

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.

DONE = 3

DataClass

alias of builtins.object

FAILED = 2

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

Bases: schrodinger.models.parameters.ParamModel

DataClass

alias of builtins.object

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

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

owner_instance = Owner()
owner_instance.data_x = 4

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

Warning

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

Variables:DataClass (type) – The type of data the param describes.

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

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

owner_instance = Owner()
owner_instance.data_x = 4

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

Warning

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

Variables:DataClass (type) – The type of data the param describes.

alnChanged

alnReplaced

blockSignals(self, bool) → bool

block_signal_propagation()

childEvent(self, QChildEvent)

children(self) → object

classmethod configureParam()

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

connectNotify(self, QMetaMethod)

customEvent(self, QEvent)

classmethod defaultValue(*args, **kwargs)

deleteLater(self)

destroyed

destroyed(self, QObject = None) [signal]

disconnect(self)

disconnectNotify(self, QMetaMethod)

dumpObjectInfo(self)

dumpObjectTree(self)

dynamicPropertyNames(self) → object

event(self, QEvent) → bool

eventFilter(self, QObject, QEvent) → bool

findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject

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

findChildren(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]

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

classmethod fromJson(json_obj)

A factory method which constructs a new object from a given dict loaded from a json string or file.

Parameters:json_obj (dict) – A json-loaded dictionary to create an object from. Returns:An instance of this class.

:rtype : cls

classmethod fromJsonImplementation(json_dict)

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

getAbstractParam(*args, **kwargs)

classmethod getParamSignal(*args, **kwargs)

classmethod getParamValue(*args, **kwargs)

classmethod getSubParam(name)

classmethod getSubParams()

get_version()

Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.

inherits(self, str) → bool

initAbstract()

initConcrete()

initializeValue()

installEventFilter(self, QObject)

classmethod isAbstract()

isDefault(*args, **kwargs)

isSignalConnected(self, QMetaMethod) → bool

isWidgetType(self) → bool

isWindowType(self) → bool

killTimer(self, int)

metaObject(self) → QMetaObject

moveToThread(self, QThread)

objectName(self) → str

objectNameChanged

objectNameChanged(self, str) [signal]

classmethod owner()

classmethod ownerChain()

Returns a list of param owners starting from the toplevel param and ending with self. Examples:

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

Foo.bar.atom.coord.x.ownerChain() will return [Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x] where every item is an abstract params.

classmethod paramName()

parent(self) → QObject

property(self, str) → Any

pyqtConfigure(...)

Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

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

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

owner_instance = Owner()
owner_instance.data_x = 4

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

Warning

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

Variables:DataClass (type) – The type of data the param describes.

seqChanged

seqReplaced

setObjectName(self, str)

classmethod setParamValue(*args, **kwargs)

setParent(self, QObject)

setProperty(self, str, Any) → bool

setValue(*args, **kwargs)

signalsBlocked(self) → bool

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

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

owner_instance = Owner()
owner_instance.data_x = 4

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

Warning

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

Variables:DataClass (type) – The type of data the param describes.

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

WAITING = 0

__init__(*args, **kwargs)

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

classmethod addSubParam(name, param, update_owner=True)

blockSignals(self, bool) → bool

block_signal_propagation()

childEvent(self, QChildEvent)

children(self) → object

classmethod configureParam()

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

connectNotify(self, QMetaMethod)

customEvent(self, QEvent)

classmethod defaultValue(*args, **kwargs)

deleteLater(self)

destroyed

destroyed(self, QObject = None) [signal]

disconnect(self)

disconnectNotify(self, QMetaMethod)

dumpObjectInfo(self)

dumpObjectTree(self)

dynamicPropertyNames(self) → object

event(self, QEvent) → bool

eventFilter(self, QObject, QEvent) → bool

findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject

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

findChildren(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]

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

classmethod fromJson(json_obj)

A factory method which constructs a new object from a given dict loaded from a json string or file.

Parameters:json_obj (dict) – A json-loaded dictionary to create an object from. Returns:An instance of this class.

:rtype : cls

classmethod 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)

classmethod getParamSignal(*args, **kwargs)

classmethod getParamValue(*args, **kwargs)

classmethod getSubParam(name)

classmethod getSubParams()

getTaskDirectory()

Return the absolute path of the task directory

getTaskFilename(fname)

Return the appropriate absolute path for an input or output file

get_version()

Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.

guard()

Context manager that saves any Exception raised inside

inherits(self, str) → bool

initAbstract()

initConcrete(auto_task_dir=False)

initializeValue()

input

inputChanged

inputReplaced

input_fnameChanged

input_fnameReplaced

installEventFilter(self, QObject)

classmethod isAbstract()

isDefault(*args, **kwargs)

isSignalConnected(self, QMetaMethod) → bool

isStartable()

isWidgetType(self) → bool

isWindowType(self) → bool

kill()

Kill the subprocess and reset the status to FAILED. If the task is not currently running, this is a no-op.

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

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

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

outputChanged

outputReplaced

classmethod owner()

classmethod ownerChain()

Returns a list of param owners starting from the toplevel param and ending with self. Examples:

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

Foo.bar.atom.coord.x.ownerChain() will return [Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x] where every item is an abstract params.

classmethod paramName()

parent(self) → QObject

postprocess()

preprocessors()

Returns:A list of bound preprocessing methods

progress

progressChanged

progressReplaced

property(self, str) → Any

pyqtConfigure(...)

Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

receivers(self, PYQT_SIGNAL) → int

removeEventFilter(self, QObject)

replicate()

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

reportValidation(results)

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

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

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

reset(*args, **kwargs)

run()

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

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

Parameters:

• silent (bool) – run without any reporting (i.e. error messages to the user). This is useful if we want to programmatically test validity. Changes return value of this method from ValidationResults to a boolean.
• validate_children (bool) – run validation on all child objects. See _validateChildren for documentation on what this entails.
• stop_on_fail (bool) – stop validation when first failure is encountered

Returns:

if silent is False, returns the validation results. If silent is True, returns a boolean generated by reportValidation.

Return type:

ValidationResults or bool

sender(self) → QObject

senderSignalIndex(self) → int

setAutoTaskDir(auto_task_dir)

setObjectName(self, str)

classmethod setParamValue(*args, **kwargs)

setParent(self, QObject)

setProperty(self, str, Any) → bool

setValue(*args, **kwargs)

signalsBlocked(self) → bool

start(skip_preprocessing=False)

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

staticMetaObject = <PyQt5.QtCore.QMetaObject object>

status

statusChanged

statusReplaced

taskDone

taskFailed

taskStarted

taskdir

thread(self) → QThread

timerEvent(self, QTimerEvent)

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

Bases: enum.Enum

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

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

owner_instance = Owner()
owner_instance.data_x = 4

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

Warning

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

Variables:DataClass (type) – The type of data the param describes.

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

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

owner_instance = Owner()
owner_instance.data_x = 4

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

Warning

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

Variables:DataClass (type) – The type of data the param describes.

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.

DONE = 3

DataClass

alias of builtins.object

FAILED = 2

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

Bases: schrodinger.models.parameters.ParamModel

DataClass

alias of builtins.object

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

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

owner_instance = Owner()
owner_instance.data_x = 4

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

Warning

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

Variables:DataClass (type) – The type of data the param describes.

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

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

owner_instance = Owner()
owner_instance.data_x = 4

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

Warning

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

Variables:DataClass (type) – The type of data the param describes.

alnChanged

alnReplaced

blockSignals(self, bool) → bool

block_signal_propagation()

childEvent(self, QChildEvent)

children(self) → object

classmethod configureParam()

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

connectNotify(self, QMetaMethod)

customEvent(self, QEvent)

classmethod defaultValue(*args, **kwargs)

deleteLater(self)

destroyed

destroyed(self, QObject = None) [signal]

disconnect(self)

disconnectNotify(self, QMetaMethod)

dumpObjectInfo(self)

dumpObjectTree(self)

dynamicPropertyNames(self) → object

event(self, QEvent) → bool

eventFilter(self, QObject, QEvent) → bool

findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject

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

findChildren(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]

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

classmethod fromJson(json_obj)

A factory method which constructs a new object from a given dict loaded from a json string or file.

Parameters:json_obj (dict) – A json-loaded dictionary to create an object from. Returns:An instance of this class.

:rtype : cls

classmethod fromJsonImplementation(json_dict)

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

getAbstractParam(*args, **kwargs)

classmethod getParamSignal(*args, **kwargs)

classmethod getParamValue(*args, **kwargs)

classmethod getSubParam(name)

classmethod getSubParams()

get_version()

Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.

inherits(self, str) → bool

initAbstract()

initConcrete()

initializeValue()

installEventFilter(self, QObject)

classmethod isAbstract()

isDefault(*args, **kwargs)

isSignalConnected(self, QMetaMethod) → bool

isWidgetType(self) → bool

isWindowType(self) → bool

killTimer(self, int)

metaObject(self) → QMetaObject

moveToThread(self, QThread)

objectName(self) → str

objectNameChanged

objectNameChanged(self, str) [signal]

classmethod owner()

classmethod ownerChain()

Returns a list of param owners starting from the toplevel param and ending with self. Examples:

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

Foo.bar.atom.coord.x.ownerChain() will return [Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x] where every item is an abstract params.

classmethod paramName()

parent(self) → QObject

property(self, str) → Any

pyqtConfigure(...)

Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

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

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

owner_instance = Owner()
owner_instance.data_x = 4

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

Warning

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

Variables:DataClass (type) – The type of data the param describes.

seqChanged

seqReplaced

setObjectName(self, str)

classmethod setParamValue(*args, **kwargs)

setParent(self, QObject)

setProperty(self, str, Any) → bool

setValue(*args, **kwargs)

signalsBlocked(self) → bool

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

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

owner_instance = Owner()
owner_instance.data_x = 4

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

Warning

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

Variables:DataClass (type) – The type of data the param describes.

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

WAITING = 0

__init__(*args, **kwargs)

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

classmethod addSubParam(name, param, update_owner=True)

blockSignals(self, bool) → bool

block_signal_propagation()

childEvent(self, QChildEvent)

children(self) → object

classmethod configureParam()

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

connectNotify(self, QMetaMethod)

customEvent(self, QEvent)

classmethod defaultValue(*args, **kwargs)

deleteLater(self)

destroyed

destroyed(self, QObject = None) [signal]

disconnect(self)

disconnectNotify(self, QMetaMethod)

dumpObjectInfo(self)

dumpObjectTree(self)

dynamicPropertyNames(self) → object

event(self, QEvent) → bool

eventFilter(self, QObject, QEvent) → bool

findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject

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

findChildren(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]

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

classmethod fromJson(json_obj)

A factory method which constructs a new object from a given dict loaded from a json string or file.

Parameters:json_obj (dict) – A json-loaded dictionary to create an object from. Returns:An instance of this class.

:rtype : cls

classmethod 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)

classmethod getParamSignal(*args, **kwargs)

classmethod getParamValue(*args, **kwargs)

classmethod getSubParam(name)

classmethod getSubParams()

getTaskDirectory()

Return the absolute path of the task directory

getTaskFilename(fname)

Return the appropriate absolute path for an input or output file

get_version()

Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.

guard()

Context manager that saves any Exception raised inside

inherits(self, str) → bool

initAbstract()

initConcrete(auto_task_dir=False)

initializeValue()

input

inputChanged

inputReplaced

input_fnameChanged

input_fnameReplaced

installEventFilter(self, QObject)

classmethod isAbstract()

isDefault(*args, **kwargs)

isSignalConnected(self, QMetaMethod) → bool

isStartable()

isWidgetType(self) → bool

isWindowType(self) → bool

kill()

Kill the subprocess and reset the status to FAILED. If the task is not currently running, this is a no-op.

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

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

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

outputChanged

outputReplaced

classmethod owner()

classmethod ownerChain()

Returns a list of param owners starting from the toplevel param and ending with self. Examples:

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

Foo.bar.atom.coord.x.ownerChain() will return [Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x] where every item is an abstract params.

classmethod paramName()

parent(self) → QObject

postprocess()

preprocessors()

Returns:A list of bound preprocessing methods

progress

progressChanged

progressReplaced

property(self, str) → Any

pyqtConfigure(...)

Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

receivers(self, PYQT_SIGNAL) → int

removeEventFilter(self, QObject)

replicate()

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

reportValidation(results)

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

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

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

reset(*args, **kwargs)

run()

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

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

Parameters:

• silent (bool) – run without any reporting (i.e. error messages to the user). This is useful if we want to programmatically test validity. Changes return value of this method from ValidationResults to a boolean.
• validate_children (bool) – run validation on all child objects. See _validateChildren for documentation on what this entails.
• stop_on_fail (bool) – stop validation when first failure is encountered

Returns:

if silent is False, returns the validation results. If silent is True, returns a boolean generated by reportValidation.

Return type:

ValidationResults or bool

sender(self) → QObject

senderSignalIndex(self) → int

setAutoTaskDir(auto_task_dir)

setObjectName(self, str)

classmethod setParamValue(*args, **kwargs)

setParent(self, QObject)

setProperty(self, str, Any) → bool

setValue(*args, **kwargs)

signalsBlocked(self) → bool

start(skip_preprocessing=False)

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

staticMetaObject = <PyQt5.QtCore.QMetaObject object>

status

statusChanged

statusReplaced

taskDone

taskFailed

taskStarted

taskdir

thread(self) → QThread

timerEvent(self, QTimerEvent)

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

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

owner_instance = Owner()
owner_instance.data_x = 4

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

Warning

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

Variables:DataClass (type) – The type of data the param describes.

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

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

owner_instance = Owner()
owner_instance.data_x = 4

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

Warning

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

Variables:DataClass (type) – The type of data the param describes.

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]]

DONE = 3

DataClass

alias of builtins.object

FAILED = 2

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

Bases: schrodinger.models.parameters.ParamModel

DataClass

alias of builtins.object

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

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

owner_instance = Owner()
owner_instance.data_x = 4

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

Warning

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

Variables:DataClass (type) – The type of data the param describes.

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

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

owner_instance = Owner()
owner_instance.data_x = 4

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

Warning

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

Variables:DataClass (type) – The type of data the param describes.

alnChanged

alnReplaced

blockSignals(self, bool) → bool

block_signal_propagation()

childEvent(self, QChildEvent)

children(self) → object

classmethod configureParam()

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

connectNotify(self, QMetaMethod)

customEvent(self, QEvent)

classmethod defaultValue(*args, **kwargs)

deleteLater(self)

destroyed

destroyed(self, QObject = None) [signal]

disconnect(self)

disconnectNotify(self, QMetaMethod)

dumpObjectInfo(self)

dumpObjectTree(self)

dynamicPropertyNames(self) → object

event(self, QEvent) → bool

eventFilter(self, QObject, QEvent) → bool

findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject

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

findChildren(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]

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

classmethod fromJson(json_obj)

A factory method which constructs a new object from a given dict loaded from a json string or file.

Parameters:json_obj (dict) – A json-loaded dictionary to create an object from. Returns:An instance of this class.

:rtype : cls

classmethod fromJsonImplementation(json_dict)

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

getAbstractParam(*args, **kwargs)

classmethod getParamSignal(*args, **kwargs)

classmethod getParamValue(*args, **kwargs)

classmethod getSubParam(name)

classmethod getSubParams()

get_version()

Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.

inherits(self, str) → bool

initAbstract()

initConcrete()

initializeValue()

installEventFilter(self, QObject)

classmethod isAbstract()

isDefault(*args, **kwargs)

isSignalConnected(self, QMetaMethod) → bool

isWidgetType(self) → bool

isWindowType(self) → bool

killTimer(self, int)

metaObject(self) → QMetaObject

moveToThread(self, QThread)

objectName(self) → str

objectNameChanged

objectNameChanged(self, str) [signal]

classmethod owner()

classmethod ownerChain()

Returns a list of param owners starting from the toplevel param and ending with self. Examples:

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

Foo.bar.atom.coord.x.ownerChain() will return [Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x] where every item is an abstract params.

classmethod paramName()

parent(self) → QObject

property(self, str) → Any

pyqtConfigure(...)

Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

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

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

owner_instance = Owner()
owner_instance.data_x = 4

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

Warning

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

Variables:DataClass (type) – The type of data the param describes.

seqChanged

seqReplaced

setObjectName(self, str)

classmethod setParamValue(*args, **kwargs)

setParent(self, QObject)

setProperty(self, str, Any) → bool

setValue(*args, **kwargs)

signalsBlocked(self) → bool

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

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

owner_instance = Owner()
owner_instance.data_x = 4

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

Warning

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

Variables:DataClass (type) – The type of data the param describes.

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

WAITING = 0

__init__(*args, **kwargs)

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

classmethod addSubParam(name, param, update_owner=True)

blockSignals(self, bool) → bool

block_signal_propagation()

childEvent(self, QChildEvent)

children(self) → object

classmethod configureParam()

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

connectNotify(self, QMetaMethod)

customEvent(self, QEvent)

classmethod defaultValue(*args, **kwargs)

deleteLater(self)

destroyed

destroyed(self, QObject = None) [signal]

disconnect(self)

disconnectNotify(self, QMetaMethod)

dumpObjectInfo(self)

dumpObjectTree(self)

dynamicPropertyNames(self) → object

event(self, QEvent) → bool

eventFilter(self, QObject, QEvent) → bool

findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject

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

findChildren(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]

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

classmethod fromJson(json_obj)

A factory method which constructs a new object from a given dict loaded from a json string or file.

Parameters:json_obj (dict) – A json-loaded dictionary to create an object from. Returns:An instance of this class.

:rtype : cls

classmethod 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)

classmethod getParamSignal(*args, **kwargs)

classmethod getParamValue(*args, **kwargs)

classmethod getSubParam(name)

classmethod getSubParams()

getTaskDirectory()

Return the absolute path of the task directory

getTaskFilename(fname)

Return the appropriate absolute path for an input or output file

get_version()

Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.

guard()

Context manager that saves any Exception raised inside

inherits(self, str) → bool

initAbstract()

initConcrete(auto_task_dir=False)

initializeValue()

input

inputChanged

inputReplaced

input_fnameChanged

input_fnameReplaced

installEventFilter(self, QObject)

classmethod isAbstract()

isDefault(*args, **kwargs)

isSignalConnected(self, QMetaMethod) → bool

isStartable()

isWidgetType(self) → bool

isWindowType(self) → bool

kill()

Kill the subprocess and reset the status to FAILED. If the task is not currently running, this is a no-op.

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

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

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

outputChanged

outputReplaced

classmethod owner()

classmethod ownerChain()

Returns a list of param owners starting from the toplevel param and ending with self. Examples:

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

Foo.bar.atom.coord.x.ownerChain() will return [Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x] where every item is an abstract params.

classmethod paramName()

parent(self) → QObject

postprocess()

preprocessors()

Returns:A list of bound preprocessing methods

progress

progressChanged

progressReplaced

property(self, str) → Any

pyqtConfigure(...)

Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

receivers(self, PYQT_SIGNAL) → int

removeEventFilter(self, QObject)

replicate()

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

reportValidation(results)

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

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

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

reset(*args, **kwargs)

run()

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

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

Parameters:

• silent (bool) – run without any reporting (i.e. error messages to the user). This is useful if we want to programmatically test validity. Changes return value of this method from ValidationResults to a boolean.
• validate_children (bool) – run validation on all child objects. See _validateChildren for documentation on what this entails.
• stop_on_fail (bool) – stop validation when first failure is encountered

Returns:

if silent is False, returns the validation results. If silent is True, returns a boolean generated by reportValidation.

Return type:

ValidationResults or bool

sender(self) → QObject

senderSignalIndex(self) → int

setAutoTaskDir(auto_task_dir)

setObjectName(self, str)

classmethod setParamValue(*args, **kwargs)

setParent(self, QObject)

setProperty(self, str, Any) → bool

setValue(*args, **kwargs)

signalsBlocked(self) → bool

start(skip_preprocessing=False)

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

staticMetaObject = <PyQt5.QtCore.QMetaObject object>

status

statusChanged

statusReplaced

taskDone

taskFailed

taskStarted

taskdir

thread(self) → QThread

timerEvent(self, QTimerEvent)

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

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

owner_instance = Owner()
owner_instance.data_x = 4

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

Warning

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

Variables:DataClass (type) – The type of data the param describes.

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

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

owner_instance = Owner()
owner_instance.data_x = 4

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

Warning

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

Variables:DataClass (type) – The type of data the param describes.

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

Bases: schrodinger.models.parameters.ParamModel

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

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

owner_instance = Owner()
owner_instance.data_x = 4

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

Warning

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

Variables:DataClass (type) – The type of data the param describes.

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

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

owner_instance = Owner()
owner_instance.data_x = 4

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

Warning

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

Variables:DataClass (type) – The type of data the param describes.

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

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

owner_instance = Owner()
owner_instance.data_x = 4

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

Warning

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

Variables:DataClass (type) – The type of data the param describes.

DataClass

alias of builtins.object

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

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

classmethod addSubParam(name, param, update_owner=True)

alnChanged

alnReplaced

blockSignals(self, bool) → bool

block_signal_propagation()

childEvent(self, QChildEvent)

children(self) → object

classmethod configureParam()

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

connectNotify(self, QMetaMethod)

customEvent(self, QEvent)

classmethod defaultValue(*args, **kwargs)

deleteLater(self)

destroyed

destroyed(self, QObject = None) [signal]

disconnect(self)

disconnectNotify(self, QMetaMethod)

dumpObjectInfo(self)

dumpObjectTree(self)

dynamicPropertyNames(self) → object

event(self, QEvent) → bool

eventFilter(self, QObject, QEvent) → bool

findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject

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

findChildren(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]

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

classmethod fromJson(json_obj)

A factory method which constructs a new object from a given dict loaded from a json string or file.

Parameters:json_obj (dict) – A json-loaded dictionary to create an object from. Returns:An instance of this class.

:rtype : cls

classmethod fromJsonImplementation(json_dict)

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

getAbstractParam(*args, **kwargs)

classmethod getParamSignal(*args, **kwargs)

classmethod getParamValue(*args, **kwargs)

classmethod getSubParam(name)

classmethod getSubParams()

get_version()

Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.

inherits(self, str) → bool

initAbstract()

initConcrete()

initializeValue()

installEventFilter(self, QObject)

classmethod isAbstract()

isDefault(*args, **kwargs)

isSignalConnected(self, QMetaMethod) → bool

isWidgetType(self) → bool

isWindowType(self) → bool

killTimer(self, int)

metaObject(self) → QMetaObject

moveToThread(self, QThread)

objectName(self) → str

objectNameChanged

objectNameChanged(self, str) [signal]

classmethod owner()

classmethod ownerChain()

Returns a list of param owners starting from the toplevel param and ending with self. Examples:

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

Foo.bar.atom.coord.x.ownerChain() will return [Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x] where every item is an abstract params.

classmethod paramName()

parent(self) → QObject

property(self, str) → Any

pyqtConfigure(...)

Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

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

setValue(*args, **kwargs)

signalsBlocked(self) → bool

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.

DONE = 3

DataClass

alias of builtins.object

FAILED = 2

RUNNING = 1

WAITING = 0

__init__(*args, **kwargs)

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

classmethod addSubParam(name, param, update_owner=True)

blockSignals(self, bool) → bool

block_signal_propagation()

childEvent(self, QChildEvent)

children(self) → object

classmethod configureParam()

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

connectNotify(self, QMetaMethod)

customEvent(self, QEvent)

classmethod defaultValue(*args, **kwargs)

deleteLater(self)

destroyed

destroyed(self, QObject = None) [signal]

disconnect(self)

disconnectNotify(self, QMetaMethod)

dumpObjectInfo(self)

dumpObjectTree(self)

dynamicPropertyNames(self) → object

event(self, QEvent) → bool

eventFilter(self, QObject, QEvent) → bool

findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject

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

findChildren(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → List[QObject]

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

classmethod fromJson(json_obj)

A factory method which constructs a new object from a given dict loaded from a json string or file.

Parameters:json_obj (dict) – A json-loaded dictionary to create an object from. Returns:An instance of this class.

:rtype : cls

classmethod 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)

classmethod getParamSignal(*args, **kwargs)

classmethod getParamValue(*args, **kwargs)

classmethod getSubParam(name)

classmethod getSubParams()

getTaskDirectory()

Return the absolute path of the task directory

getTaskFilename(fname)

Return the appropriate absolute path for an input or output file

get_version()

Method to get the version of a particular object. Defaults to the current version of mmshare. This class can be overridden for custom versioning behavior.

guard()

Context manager that saves any Exception raised inside

inherits(self, str) → bool

initAbstract()

initConcrete(auto_task_dir=False)

initializeValue()

inputChanged

inputReplaced

input_fnameChanged

input_fnameReplaced

installEventFilter(self, QObject)

classmethod isAbstract()

isDefault(*args, **kwargs)

isSignalConnected(self, QMetaMethod) → bool

isStartable()

isWidgetType(self) → bool

isWindowType(self) → bool

kill()

Kill the subprocess and reset the status to FAILED. If the task is not currently running, this is a no-op.

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

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

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

outputChanged

outputReplaced

classmethod owner()

classmethod ownerChain()

Returns a list of param owners starting from the toplevel param and ending with self. Examples:

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

Foo.bar.atom.coord.x.ownerChain() will return [Foo, Foo.bar, Foo.atom.coord, Foo.atom.coord.x] where every item is an abstract params.

classmethod paramName()

parent(self) → QObject

postprocess()

preprocessors()

Returns:A list of bound preprocessing methods

progress

progressChanged

progressReplaced

property(self, str) → Any

pyqtConfigure(...)

Each keyword argument is either the name of a Qt property or a Qt signal. For properties the property is set to the given value which should be of an appropriate type. For signals the signal is connected to the given value which should be a callable.

receivers(self, PYQT_SIGNAL) → int

removeEventFilter(self, QObject)

replicate()

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

reportValidation(results)

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

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

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

reset(*args, **kwargs)

run()

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

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

Parameters:

• silent (bool) – run without any reporting (i.e. error messages to the user). This is useful if we want to programmatically test validity. Changes return value of this method from ValidationResults to a boolean.
• validate_children (bool) – run validation on all child objects. See _validateChildren for documentation on what this entails.
• stop_on_fail (bool) – stop validation when first failure is encountered

Returns:

if silent is False, returns the validation results. If silent is True, returns a boolean generated by reportValidation.

Return type:

ValidationResults or bool

sender(self) → QObject

senderSignalIndex(self) → int

setAutoTaskDir(auto_task_dir)

setObjectName(self, str)

classmethod setParamValue(*args, **kwargs)

setParent(self, QObject)

setProperty(self, str, Any) → bool

setValue(*args, **kwargs)

signalsBlocked(self) → bool

start(skip_preprocessing=False)

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

staticMetaObject = <PyQt5.QtCore.QMetaObject object>

status

statusChanged

statusReplaced

taskDone

taskFailed

taskStarted

taskdir

thread(self) → QThread

timerEvent(self, QTimerEvent)

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)