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

alias of builtins.object

__init__(default_value=<object object>, _explicit_abstract=False, **kwargs)

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

aboutToReplace
alnChanged
alnReplaced
blockSignals(self, bool) → bool
childEvent(self, QChildEvent)
children(self) → object
connectNotify(self, QMetaMethod)
customEvent(self, QEvent)
deleteLater(self)
destroyed

destroyed(self, QObject = None) [signal]

disconnect(self)
disconnectNotify(self, QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → object
event(self, QEvent) → bool
eventFilter(self, QObject, QEvent) → bool
findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject

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

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

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

classmethod fromJson(json_obj)

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

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

:rtype : cls

classmethod fromJsonImplementation(json_dict)

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

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()

Override this method to define logic specfically for initializing abstract instances of this param.

initConcrete()

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

installEventFilter(self, QObject)
isDefault()
isSignalConnected(self, QMetaMethod) → bool
isWidgetType(self) → bool
isWindowType(self) → bool
is_abstract = True
killTimer(self, int)
metaObject(self) → QMetaObject
moveToThread(self, QThread)
objectName(self) → str
objectNameChanged

objectNameChanged(self, str) [signal]

owner()

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

ownerChain()

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

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

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

parent(self) → QObject
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)

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

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

line = Line()

We can reset the entire line:

line.reset()

Or just certain parts:

line.reset(Line.start.x) # resets just start.x line.start.reset(Coord.x) # another way to reset start.x line.reset(Line.end) # resets the entire end point line.reset(Line.start.z, Line.end.z) # resets the z-coord of both
Parameters:args – abstract sub-params of self
sender(self) → QObject
senderSignalIndex(self) → int
seqChanged
seqReplaced
setObjectName(self, str)
setParent(self, QObject)
setProperty(self, str, Any) → bool
setValue(value=None, **kwargs)

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

Parameters:value (self.DataClass or dict) – either another param instance of the same type or a dictionary mapping the sub-param names to values.
signalsBlocked(self) → bool
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
suspend_signals()
thread(self) → QThread
timerEvent(self, QTimerEvent)
toDict()
toJson(_mark_version=True)

Create and returns a data structure made up of jsonable items.

Return type:An instance of one the classes from NATIVE_JSON_DATATYPES
toJsonImplementation()

Returns a JSON representation of this value object.

tr(self, str, disambiguation: str = None, n: int = -1) → str
valueChanged
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.
  • is_abstract (bool) – Whether this param is an abstract (ie class attribute) param.
  • valueChanged (QtCore.pyqtSignal) – A signal emitted whenever the param is changed.
  • default_value (DataClass) – The default value of the param. If unset, the default value is whatever value is created when calling DataClass()
  • param_name (str) – The name of the attribute this param is set as. For example, Owner.data_x.param_name would be ‘data_x’.
  • instance_attr_name (str) – The name of the attribute used to store param values on instances.
  • abstract_attr_name (str) – The name of the attribute used to store abstract params on class objects.
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.
  • is_abstract (bool) – Whether this param is an abstract (ie class attribute) param.
  • valueChanged (QtCore.pyqtSignal) – A signal emitted whenever the param is changed.
  • default_value (DataClass) – The default value of the param. If unset, the default value is whatever value is created when calling DataClass()
  • param_name (str) – The name of the attribute this param is set as. For example, Owner.data_x.param_name would be ‘data_x’.
  • instance_attr_name (str) – The name of the attribute used to store param values on instances.
  • abstract_attr_name (str) – The name of the attribute used to store abstract params on class objects.
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.

preprocess()

Generate the input and 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 = 4
DataClass

alias of builtins.object

FAILED = 3
NOTRUNNING = 0
RUNNING = 2
STARTING = 1
__init__(*args, **kwargs)

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

aboutToReplace
blockSignals(self, bool) → bool
childEvent(self, QChildEvent)
children(self) → object
connectNotify(self, QMetaMethod)
customEvent(self, QEvent)
deleteLater(self)
destroyed

destroyed(self, QObject = None) [signal]

disconnect(self)
disconnectNotify(self, QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → object
event(self, QEvent) → bool
eventFilter(self, QObject, QEvent) → bool
findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject

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

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

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

classmethod fromJson(json_obj)

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

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

:rtype : cls

classmethod fromJsonFilename(filename)
classmethod fromJsonImplementation(json_dict)

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

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()

Override this method to define logic specfically for initializing abstract instances of this param.

initConcrete()

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

inputChanged
inputReplaced
input_fnameChanged
input_fnameReplaced
installEventFilter(self, QObject)
isDefault()
isSignalConnected(self, QMetaMethod) → bool
isStartable()
isWidgetType(self) → bool
isWindowType(self) → bool
is_abstract = True
kill()
killTimer(self, int)
metaObject(self) → QMetaObject
model_fnameChanged
model_fnameReplaced
moveToThread(self, QThread)
name
nameChanged
nameReplaced
objectName(self) → str
objectNameChanged

objectNameChanged(self, str) [signal]

output

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

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

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

owner_instance = Owner()
owner_instance.data_x = 4

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

Warning

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

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

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

ownerChain()

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

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

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

parent(self) → QObject
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)
reportValidation(results)

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

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

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

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

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

line = Line()

We can reset the entire line:

line.reset()

Or just certain parts:

line.reset(Line.start.x) # resets just start.x line.start.reset(Coord.x) # another way to reset start.x line.reset(Line.end) # resets the entire end point line.reset(Line.start.z, Line.end.z) # resets the z-coord of both
Parameters:args – abstract sub-params of self
runValidation(silent=False, validate_children=True, stop_on_fail=True)

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

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

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

ValidationResults or bool
sender(self) → QObject
senderSignalIndex(self) → int
setObjectName(self, str)
setParent(self, QObject)
setProperty(self, str, Any) → bool
setValue(value=None, **kwargs)

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

Parameters:value (self.DataClass or dict) – either another param instance of the same type or a dictionary mapping the sub-param names to values.
setWorkingDirectory(new_working_dir)
signalsBlocked(self) → bool
start()
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
status
statusChanged
statusReplaced
suspend_signals()
thread(self) → QThread
timerEvent(self, QTimerEvent)
toDict()
toJson(_mark_version=True)

Create and returns a data structure made up of jsonable items.

Return type:An instance of one the classes from NATIVE_JSON_DATATYPES
toJsonImplementation()

Returns a JSON representation of this value object.

tr(self, str, disambiguation: str = None, n: int = -1) → str
valueChanged
wait(timeout=None)

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

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

Bases: schrodinger.protein.predictors.AbstractPredictor

Secondary structure predictor.

EXE = 'sspro4'
PREDICTOR_NAME = 'sspro'
CLASS_NUM = 3
NU = 20
NY = 3
input_fname

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

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

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

owner_instance = Owner()
owner_instance.data_x = 4

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

Warning

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

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

prediction()

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

DONE = 4
DataClass

alias of builtins.object

FAILED = 3
class Input(default_value=<object object>, _explicit_abstract=False, **kwargs)

Bases: schrodinger.models.parameters.ParamModel

DataClass

alias of builtins.object

__init__(default_value=<object object>, _explicit_abstract=False, **kwargs)

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

aboutToReplace
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.
  • is_abstract (bool) – Whether this param is an abstract (ie class attribute) param.
  • valueChanged (QtCore.pyqtSignal) – A signal emitted whenever the param is changed.
  • default_value (DataClass) – The default value of the param. If unset, the default value is whatever value is created when calling DataClass()
  • param_name (str) – The name of the attribute this param is set as. For example, Owner.data_x.param_name would be ‘data_x’.
  • instance_attr_name (str) – The name of the attribute used to store param values on instances.
  • abstract_attr_name (str) – The name of the attribute used to store abstract params on class objects.
alnChanged
alnReplaced
blockSignals(self, bool) → bool
childEvent(self, QChildEvent)
children(self) → object
connectNotify(self, QMetaMethod)
customEvent(self, QEvent)
deleteLater(self)
destroyed

destroyed(self, QObject = None) [signal]

disconnect(self)
disconnectNotify(self, QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → object
event(self, QEvent) → bool
eventFilter(self, QObject, QEvent) → bool
findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject

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

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

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

classmethod fromJson(json_obj)

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

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

:rtype : cls

classmethod fromJsonImplementation(json_dict)

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

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()

Override this method to define logic specfically for initializing abstract instances of this param.

initConcrete()

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

installEventFilter(self, QObject)
isDefault()
isSignalConnected(self, QMetaMethod) → bool
isWidgetType(self) → bool
isWindowType(self) → bool
is_abstract = True
killTimer(self, int)
metaObject(self) → QMetaObject
moveToThread(self, QThread)
objectName(self) → str
objectNameChanged

objectNameChanged(self, str) [signal]

owner()

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

ownerChain()

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

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

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

parent(self) → QObject
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)

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

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

line = Line()

We can reset the entire line:

line.reset()

Or just certain parts:

line.reset(Line.start.x) # resets just start.x line.start.reset(Coord.x) # another way to reset start.x line.reset(Line.end) # resets the entire end point line.reset(Line.start.z, Line.end.z) # resets the z-coord of both
Parameters:args – abstract sub-params of self
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.
  • is_abstract (bool) – Whether this param is an abstract (ie class attribute) param.
  • valueChanged (QtCore.pyqtSignal) – A signal emitted whenever the param is changed.
  • default_value (DataClass) – The default value of the param. If unset, the default value is whatever value is created when calling DataClass()
  • param_name (str) – The name of the attribute this param is set as. For example, Owner.data_x.param_name would be ‘data_x’.
  • instance_attr_name (str) – The name of the attribute used to store param values on instances.
  • abstract_attr_name (str) – The name of the attribute used to store abstract params on class objects.
seqChanged
seqReplaced
setObjectName(self, str)
setParent(self, QObject)
setProperty(self, str, Any) → bool
setValue(value=None, **kwargs)

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

Parameters:value (self.DataClass or dict) – either another param instance of the same type or a dictionary mapping the sub-param names to values.
signalsBlocked(self) → bool
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
suspend_signals()
thread(self) → QThread
timerEvent(self, QTimerEvent)
toDict()
toJson(_mark_version=True)

Create and returns a data structure made up of jsonable items.

Return type:An instance of one the classes from NATIVE_JSON_DATATYPES
toJsonImplementation()

Returns a JSON representation of this value object.

tr(self, str, disambiguation: str = None, n: int = -1) → str
valueChanged
NOTRUNNING = 0
RUNNING = 2
STARTING = 1
__init__(*args, **kwargs)

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

aboutToReplace
blockSignals(self, bool) → bool
childEvent(self, QChildEvent)
children(self) → object
connectNotify(self, QMetaMethod)
customEvent(self, QEvent)
deleteLater(self)
destroyed

destroyed(self, QObject = None) [signal]

disconnect(self)
disconnectNotify(self, QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → object
event(self, QEvent) → bool
eventFilter(self, QObject, QEvent) → bool
findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject

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

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

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

classmethod fromJson(json_obj)

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

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

:rtype : cls

classmethod fromJsonFilename(filename)
classmethod fromJsonImplementation(json_dict)

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

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.

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()

Override this method to define logic specfically for initializing abstract instances of this param.

initConcrete()

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

input
inputChanged
inputReplaced
input_fnameChanged
input_fnameReplaced
installEventFilter(self, QObject)
isDefault()
isSignalConnected(self, QMetaMethod) → bool
isStartable()
isWidgetType(self) → bool
isWindowType(self) → bool
is_abstract = True
kill()
killTimer(self, int)
metaObject(self) → QMetaObject
model_fnameChanged
model_fnameReplaced
moveToThread(self, QThread)
name
nameChanged
nameReplaced
objectName(self) → str
objectNameChanged

objectNameChanged(self, str) [signal]

output

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

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

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

owner_instance = Owner()
owner_instance.data_x = 4

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

Warning

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

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

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

ownerChain()

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

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

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

parent(self) → QObject
postprocess()
preprocess()

Generate the input and model files.

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)
reportValidation(results)

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

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

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

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

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

line = Line()

We can reset the entire line:

line.reset()

Or just certain parts:

line.reset(Line.start.x) # resets just start.x line.start.reset(Coord.x) # another way to reset start.x line.reset(Line.end) # resets the entire end point line.reset(Line.start.z, Line.end.z) # resets the z-coord of both
Parameters:args – abstract sub-params of self
runValidation(silent=False, validate_children=True, stop_on_fail=True)

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

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

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

ValidationResults or bool
sender(self) → QObject
senderSignalIndex(self) → int
setObjectName(self, str)
setParent(self, QObject)
setProperty(self, str, Any) → bool
setValue(value=None, **kwargs)

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

Parameters:value (self.DataClass or dict) – either another param instance of the same type or a dictionary mapping the sub-param names to values.
setWorkingDirectory(new_working_dir)
signalsBlocked(self) → bool
start()
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
status
statusChanged
statusReplaced
suspend_signals()
thread(self) → QThread
timerEvent(self, QTimerEvent)
toDict()
toJson(_mark_version=True)

Create and returns a data structure made up of jsonable items.

Return type:An instance of one the classes from NATIVE_JSON_DATATYPES
toJsonImplementation()

Returns a JSON representation of this value object.

tr(self, str, disambiguation: str = None, n: int = -1) → str
valueChanged
wait(timeout=None)

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

Parameters:timeout (NoneType or int) – Amount of time in seconds to wait before timing out. If None or a negative number, this method will wait until the task is finished.
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.
  • is_abstract (bool) – Whether this param is an abstract (ie class attribute) param.
  • valueChanged (QtCore.pyqtSignal) – A signal emitted whenever the param is changed.
  • default_value (DataClass) – The default value of the param. If unset, the default value is whatever value is created when calling DataClass()
  • param_name (str) – The name of the attribute this param is set as. For example, Owner.data_x.param_name would be ‘data_x’.
  • instance_attr_name (str) – The name of the attribute used to store param values on instances.
  • abstract_attr_name (str) – The name of the attribute used to store abstract params on class objects.
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.
  • is_abstract (bool) – Whether this param is an abstract (ie class attribute) param.
  • valueChanged (QtCore.pyqtSignal) – A signal emitted whenever the param is changed.
  • default_value (DataClass) – The default value of the param. If unset, the default value is whatever value is created when calling DataClass()
  • param_name (str) – The name of the attribute this param is set as. For example, Owner.data_x.param_name would be ‘data_x’.
  • instance_attr_name (str) – The name of the attribute used to store param values on instances.
  • abstract_attr_name (str) – The name of the attribute used to store abstract params on class objects.
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

prediction()

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

DONE = 4
DataClass

alias of builtins.object

FAILED = 3
class Input(default_value=<object object>, _explicit_abstract=False, **kwargs)

Bases: schrodinger.models.parameters.ParamModel

DataClass

alias of builtins.object

__init__(default_value=<object object>, _explicit_abstract=False, **kwargs)

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

aboutToReplace
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.
  • is_abstract (bool) – Whether this param is an abstract (ie class attribute) param.
  • valueChanged (QtCore.pyqtSignal) – A signal emitted whenever the param is changed.
  • default_value (DataClass) – The default value of the param. If unset, the default value is whatever value is created when calling DataClass()
  • param_name (str) – The name of the attribute this param is set as. For example, Owner.data_x.param_name would be ‘data_x’.
  • instance_attr_name (str) – The name of the attribute used to store param values on instances.
  • abstract_attr_name (str) – The name of the attribute used to store abstract params on class objects.
alnChanged
alnReplaced
blockSignals(self, bool) → bool
childEvent(self, QChildEvent)
children(self) → object
connectNotify(self, QMetaMethod)
customEvent(self, QEvent)
deleteLater(self)
destroyed

destroyed(self, QObject = None) [signal]

disconnect(self)
disconnectNotify(self, QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → object
event(self, QEvent) → bool
eventFilter(self, QObject, QEvent) → bool
findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject

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

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

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

classmethod fromJson(json_obj)

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

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

:rtype : cls

classmethod fromJsonImplementation(json_dict)

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

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()

Override this method to define logic specfically for initializing abstract instances of this param.

initConcrete()

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

installEventFilter(self, QObject)
isDefault()
isSignalConnected(self, QMetaMethod) → bool
isWidgetType(self) → bool
isWindowType(self) → bool
is_abstract = True
killTimer(self, int)
metaObject(self) → QMetaObject
moveToThread(self, QThread)
objectName(self) → str
objectNameChanged

objectNameChanged(self, str) [signal]

owner()

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

ownerChain()

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

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

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

parent(self) → QObject
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)

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

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

line = Line()

We can reset the entire line:

line.reset()

Or just certain parts:

line.reset(Line.start.x) # resets just start.x line.start.reset(Coord.x) # another way to reset start.x line.reset(Line.end) # resets the entire end point line.reset(Line.start.z, Line.end.z) # resets the z-coord of both
Parameters:args – abstract sub-params of self
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.
  • is_abstract (bool) – Whether this param is an abstract (ie class attribute) param.
  • valueChanged (QtCore.pyqtSignal) – A signal emitted whenever the param is changed.
  • default_value (DataClass) – The default value of the param. If unset, the default value is whatever value is created when calling DataClass()
  • param_name (str) – The name of the attribute this param is set as. For example, Owner.data_x.param_name would be ‘data_x’.
  • instance_attr_name (str) – The name of the attribute used to store param values on instances.
  • abstract_attr_name (str) – The name of the attribute used to store abstract params on class objects.
seqChanged
seqReplaced
setObjectName(self, str)
setParent(self, QObject)
setProperty(self, str, Any) → bool
setValue(value=None, **kwargs)

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

Parameters:value (self.DataClass or dict) – either another param instance of the same type or a dictionary mapping the sub-param names to values.
signalsBlocked(self) → bool
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
suspend_signals()
thread(self) → QThread
timerEvent(self, QTimerEvent)
toDict()
toJson(_mark_version=True)

Create and returns a data structure made up of jsonable items.

Return type:An instance of one the classes from NATIVE_JSON_DATATYPES
toJsonImplementation()

Returns a JSON representation of this value object.

tr(self, str, disambiguation: str = None, n: int = -1) → str
valueChanged
NOTRUNNING = 0
RUNNING = 2
STARTING = 1
__init__(*args, **kwargs)

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

aboutToReplace
blockSignals(self, bool) → bool
childEvent(self, QChildEvent)
children(self) → object
connectNotify(self, QMetaMethod)
customEvent(self, QEvent)
deleteLater(self)
destroyed

destroyed(self, QObject = None) [signal]

disconnect(self)
disconnectNotify(self, QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → object
event(self, QEvent) → bool
eventFilter(self, QObject, QEvent) → bool
findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject

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

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

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

classmethod fromJson(json_obj)

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

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

:rtype : cls

classmethod fromJsonFilename(filename)
classmethod fromJsonImplementation(json_dict)

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

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.

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()

Override this method to define logic specfically for initializing abstract instances of this param.

initConcrete()

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

input
inputChanged
inputReplaced
input_fnameChanged
input_fnameReplaced
installEventFilter(self, QObject)
isDefault()
isSignalConnected(self, QMetaMethod) → bool
isStartable()
isWidgetType(self) → bool
isWindowType(self) → bool
is_abstract = True
kill()
killTimer(self, int)
metaObject(self) → QMetaObject
model_fnameChanged
model_fnameReplaced
moveToThread(self, QThread)
name
nameChanged
nameReplaced
objectName(self) → str
objectNameChanged

objectNameChanged(self, str) [signal]

output

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

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

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

owner_instance = Owner()
owner_instance.data_x = 4

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

Warning

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

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

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

ownerChain()

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

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

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

parent(self) → QObject
postprocess()
preprocess()

Generate the input and model files.

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)
reportValidation(results)

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

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

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

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

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

line = Line()

We can reset the entire line:

line.reset()

Or just certain parts:

line.reset(Line.start.x) # resets just start.x line.start.reset(Coord.x) # another way to reset start.x line.reset(Line.end) # resets the entire end point line.reset(Line.start.z, Line.end.z) # resets the z-coord of both
Parameters:args – abstract sub-params of self
runValidation(silent=False, validate_children=True, stop_on_fail=True)

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

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

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

ValidationResults or bool
sender(self) → QObject
senderSignalIndex(self) → int
setObjectName(self, str)
setParent(self, QObject)
setProperty(self, str, Any) → bool
setValue(value=None, **kwargs)

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

Parameters:value (self.DataClass or dict) – either another param instance of the same type or a dictionary mapping the sub-param names to values.
setWorkingDirectory(new_working_dir)
signalsBlocked(self) → bool
start()
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
status
statusChanged
statusReplaced
suspend_signals()
thread(self) → QThread
timerEvent(self, QTimerEvent)
toDict()
toJson(_mark_version=True)

Create and returns a data structure made up of jsonable items.

Return type:An instance of one the classes from NATIVE_JSON_DATATYPES
toJsonImplementation()

Returns a JSON representation of this value object.

tr(self, str, disambiguation: str = None, n: int = -1) → str
valueChanged
wait(timeout=None)

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

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

Bases: schrodinger.protein.predictors.AbstractPredictor

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

alias of builtins.object

__init__(default_value=<object object>, _explicit_abstract=False, **kwargs)

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

aboutToReplace
acc_predictionChanged
acc_predictionReplaced
alnChanged
alnReplaced
blockSignals(self, bool) → bool
childEvent(self, QChildEvent)
children(self) → object
connectNotify(self, QMetaMethod)
customEvent(self, QEvent)
deleteLater(self)
destroyed

destroyed(self, QObject = None) [signal]

disconnect(self)
disconnectNotify(self, QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → object
event(self, QEvent) → bool
eventFilter(self, QObject, QEvent) → bool
findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject

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

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

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

classmethod fromJson(json_obj)

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

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

:rtype : cls

classmethod fromJsonImplementation(json_dict)

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

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()

Override this method to define logic specfically for initializing abstract instances of this param.

initConcrete()

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

installEventFilter(self, QObject)
isDefault()
isSignalConnected(self, QMetaMethod) → bool
isWidgetType(self) → bool
isWindowType(self) → bool
is_abstract = True
killTimer(self, int)
metaObject(self) → QMetaObject
moveToThread(self, QThread)
objectName(self) → str
objectNameChanged

objectNameChanged(self, str) [signal]

owner()

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

ownerChain()

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

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

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

parent(self) → QObject
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)

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

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

line = Line()

We can reset the entire line:

line.reset()

Or just certain parts:

line.reset(Line.start.x) # resets just start.x line.start.reset(Coord.x) # another way to reset start.x line.reset(Line.end) # resets the entire end point line.reset(Line.start.z, Line.end.z) # resets the z-coord of both
Parameters:args – abstract sub-params of self
sender(self) → QObject
senderSignalIndex(self) → int
seqChanged
seqReplaced
setObjectName(self, str)
setParent(self, QObject)
setProperty(self, str, Any) → bool
setValue(value=None, **kwargs)

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

Parameters:value (self.DataClass or dict) – either another param instance of the same type or a dictionary mapping the sub-param names to values.
signalsBlocked(self) → bool
ss_predictionChanged
ss_predictionReplaced
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
suspend_signals()
thread(self) → QThread
timerEvent(self, QTimerEvent)
toDict()
toJson(_mark_version=True)

Create and returns a data structure made up of jsonable items.

Return type:An instance of one the classes from NATIVE_JSON_DATATYPES
toJsonImplementation()

Returns a JSON representation of this value object.

tr(self, str, disambiguation: str = None, n: int = -1) → str
valueChanged
input
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.

prediction()

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

DONE = 4
DataClass

alias of builtins.object

FAILED = 3
NOTRUNNING = 0
RUNNING = 2
STARTING = 1
__init__(*args, **kwargs)

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

aboutToReplace
blockSignals(self, bool) → bool
childEvent(self, QChildEvent)
children(self) → object
connectNotify(self, QMetaMethod)
customEvent(self, QEvent)
deleteLater(self)
destroyed

destroyed(self, QObject = None) [signal]

disconnect(self)
disconnectNotify(self, QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → object
event(self, QEvent) → bool
eventFilter(self, QObject, QEvent) → bool
findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject

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

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

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

classmethod fromJson(json_obj)

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

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

:rtype : cls

classmethod fromJsonFilename(filename)
classmethod fromJsonImplementation(json_dict)

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

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.

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()

Override this method to define logic specfically for initializing abstract instances of this param.

initConcrete()

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

inputChanged
inputReplaced
input_fnameChanged
input_fnameReplaced
installEventFilter(self, QObject)
isDefault()
isSignalConnected(self, QMetaMethod) → bool
isStartable()
isWidgetType(self) → bool
isWindowType(self) → bool
is_abstract = True
kill()
killTimer(self, int)
metaObject(self) → QMetaObject
model_fnameChanged
model_fnameReplaced
moveToThread(self, QThread)
name
nameChanged
nameReplaced
objectName(self) → str
objectNameChanged

objectNameChanged(self, str) [signal]

output

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

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

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

owner_instance = Owner()
owner_instance.data_x = 4

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

Warning

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

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

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

ownerChain()

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

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

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

parent(self) → QObject
postprocess()
preprocess()

Generate the input and model files.

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)
reportValidation(results)

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

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

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

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

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

line = Line()

We can reset the entire line:

line.reset()

Or just certain parts:

line.reset(Line.start.x) # resets just start.x line.start.reset(Coord.x) # another way to reset start.x line.reset(Line.end) # resets the entire end point line.reset(Line.start.z, Line.end.z) # resets the z-coord of both
Parameters:args – abstract sub-params of self
runValidation(silent=False, validate_children=True, stop_on_fail=True)

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

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

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

ValidationResults or bool
sender(self) → QObject
senderSignalIndex(self) → int
setObjectName(self, str)
setParent(self, QObject)
setProperty(self, str, Any) → bool
setValue(value=None, **kwargs)

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

Parameters:value (self.DataClass or dict) – either another param instance of the same type or a dictionary mapping the sub-param names to values.
setWorkingDirectory(new_working_dir)
signalsBlocked(self) → bool
start()
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
status
statusChanged
statusReplaced
suspend_signals()
thread(self) → QThread
timerEvent(self, QTimerEvent)
toDict()
toJson(_mark_version=True)

Create and returns a data structure made up of jsonable items.

Return type:An instance of one the classes from NATIVE_JSON_DATATYPES
toJsonImplementation()

Returns a JSON representation of this value object.

tr(self, str, disambiguation: str = None, n: int = -1) → str
valueChanged
wait(timeout=None)

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

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

Bases: schrodinger.protein.predictors.AbstractPredictor

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

alias of builtins.object

__init__(default_value=<object object>, _explicit_abstract=False, **kwargs)

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

aboutToReplace
acc_predictionChanged
acc_predictionReplaced
alnChanged
alnReplaced
blockSignals(self, bool) → bool
childEvent(self, QChildEvent)
children(self) → object
connectNotify(self, QMetaMethod)
customEvent(self, QEvent)
deleteLater(self)
destroyed

destroyed(self, QObject = None) [signal]

disconnect(self)
disconnectNotify(self, QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → object
event(self, QEvent) → bool
eventFilter(self, QObject, QEvent) → bool
findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject

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

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

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

classmethod fromJson(json_obj)

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

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

:rtype : cls

classmethod fromJsonImplementation(json_dict)

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

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()

Override this method to define logic specfically for initializing abstract instances of this param.

initConcrete()

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

installEventFilter(self, QObject)
isDefault()
isSignalConnected(self, QMetaMethod) → bool
isWidgetType(self) → bool
isWindowType(self) → bool
is_abstract = True
killTimer(self, int)
metaObject(self) → QMetaObject
moveToThread(self, QThread)
objectName(self) → str
objectNameChanged

objectNameChanged(self, str) [signal]

owner()

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

ownerChain()

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

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

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

parent(self) → QObject
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)

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

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

line = Line()

We can reset the entire line:

line.reset()

Or just certain parts:

line.reset(Line.start.x) # resets just start.x line.start.reset(Coord.x) # another way to reset start.x line.reset(Line.end) # resets the entire end point line.reset(Line.start.z, Line.end.z) # resets the z-coord of both
Parameters:args – abstract sub-params of self
sender(self) → QObject
senderSignalIndex(self) → int
seqChanged
seqReplaced
setObjectName(self, str)
setParent(self, QObject)
setProperty(self, str, Any) → bool
setValue(value=None, **kwargs)

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

Parameters:value (self.DataClass or dict) – either another param instance of the same type or a dictionary mapping the sub-param names to values.
signalsBlocked(self) → bool
ss_predictionChanged
ss_predictionReplaced
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
suspend_signals()
thread(self) → QThread
timerEvent(self, QTimerEvent)
toDict()
toJson(_mark_version=True)

Create and returns a data structure made up of jsonable items.

Return type:An instance of one the classes from NATIVE_JSON_DATATYPES
toJsonImplementation()

Returns a JSON representation of this value object.

tr(self, str, disambiguation: str = None, n: int = -1) → str
valueChanged
input
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.

prediction()

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

DONE = 4
DataClass

alias of builtins.object

FAILED = 3
NOTRUNNING = 0
RUNNING = 2
STARTING = 1
__init__(*args, **kwargs)

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

aboutToReplace
blockSignals(self, bool) → bool
childEvent(self, QChildEvent)
children(self) → object
connectNotify(self, QMetaMethod)
customEvent(self, QEvent)
deleteLater(self)
destroyed

destroyed(self, QObject = None) [signal]

disconnect(self)
disconnectNotify(self, QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → object
event(self, QEvent) → bool
eventFilter(self, QObject, QEvent) → bool
findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject

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

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

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

classmethod fromJson(json_obj)

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

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

:rtype : cls

classmethod fromJsonFilename(filename)
classmethod fromJsonImplementation(json_dict)

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

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.

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()

Override this method to define logic specfically for initializing abstract instances of this param.

initConcrete()

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

inputChanged
inputReplaced
input_fnameChanged
input_fnameReplaced
installEventFilter(self, QObject)
isDefault()
isSignalConnected(self, QMetaMethod) → bool
isStartable()
isWidgetType(self) → bool
isWindowType(self) → bool
is_abstract = True
kill()
killTimer(self, int)
metaObject(self) → QMetaObject
model_fnameChanged
model_fnameReplaced
moveToThread(self, QThread)
name
nameChanged
nameReplaced
objectName(self) → str
objectNameChanged

objectNameChanged(self, str) [signal]

output

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

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

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

owner_instance = Owner()
owner_instance.data_x = 4

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

Warning

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

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

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

ownerChain()

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

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

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

parent(self) → QObject
postprocess()
preprocess()

Generate the input and model files.

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)
reportValidation(results)

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

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

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

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

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

line = Line()

We can reset the entire line:

line.reset()

Or just certain parts:

line.reset(Line.start.x) # resets just start.x line.start.reset(Coord.x) # another way to reset start.x line.reset(Line.end) # resets the entire end point line.reset(Line.start.z, Line.end.z) # resets the z-coord of both
Parameters:args – abstract sub-params of self
runValidation(silent=False, validate_children=True, stop_on_fail=True)

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

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

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

ValidationResults or bool
sender(self) → QObject
senderSignalIndex(self) → int
setObjectName(self, str)
setParent(self, QObject)
setProperty(self, str, Any) → bool
setValue(value=None, **kwargs)

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

Parameters:value (self.DataClass or dict) – either another param instance of the same type or a dictionary mapping the sub-param names to values.
setWorkingDirectory(new_working_dir)
signalsBlocked(self) → bool
start()
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
status
statusChanged
statusReplaced
suspend_signals()
thread(self) → QThread
timerEvent(self, QTimerEvent)
toDict()
toJson(_mark_version=True)

Create and returns a data structure made up of jsonable items.

Return type:An instance of one the classes from NATIVE_JSON_DATATYPES
toJsonImplementation()

Returns a JSON representation of this value object.

tr(self, str, disambiguation: str = None, n: int = -1) → str
valueChanged
wait(timeout=None)

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

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

Bases: schrodinger.protein.predictors.AbstractPredictor

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

alias of builtins.object

__init__(default_value=<object object>, _explicit_abstract=False, **kwargs)

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

aboutToReplace
acc_predictionChanged
acc_predictionReplaced
alnChanged
alnReplaced
blockSignals(self, bool) → bool
childEvent(self, QChildEvent)
children(self) → object
connectNotify(self, QMetaMethod)
customEvent(self, QEvent)
deleteLater(self)
destroyed

destroyed(self, QObject = None) [signal]

disconnect(self)
disconnectNotify(self, QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → object
event(self, QEvent) → bool
eventFilter(self, QObject, QEvent) → bool
findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject

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

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

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

classmethod fromJson(json_obj)

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

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

:rtype : cls

classmethod fromJsonImplementation(json_dict)

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

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()

Override this method to define logic specfically for initializing abstract instances of this param.

initConcrete()

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

installEventFilter(self, QObject)
isDefault()
isSignalConnected(self, QMetaMethod) → bool
isWidgetType(self) → bool
isWindowType(self) → bool
is_abstract = True
killTimer(self, int)
metaObject(self) → QMetaObject
moveToThread(self, QThread)
objectName(self) → str
objectNameChanged

objectNameChanged(self, str) [signal]

owner()

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

ownerChain()

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

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

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

parent(self) → QObject
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)

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

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

line = Line()

We can reset the entire line:

line.reset()

Or just certain parts:

line.reset(Line.start.x) # resets just start.x line.start.reset(Coord.x) # another way to reset start.x line.reset(Line.end) # resets the entire end point line.reset(Line.start.z, Line.end.z) # resets the z-coord of both
Parameters:args – abstract sub-params of self
sender(self) → QObject
senderSignalIndex(self) → int
seqChanged
seqReplaced
setObjectName(self, str)
setParent(self, QObject)
setProperty(self, str, Any) → bool
setValue(value=None, **kwargs)

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

Parameters:value (self.DataClass or dict) – either another param instance of the same type or a dictionary mapping the sub-param names to values.
signalsBlocked(self) → bool
ss_predictionChanged
ss_predictionReplaced
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
suspend_signals()
thread(self) → QThread
timerEvent(self, QTimerEvent)
toDict()
toJson(_mark_version=True)

Create and returns a data structure made up of jsonable items.

Return type:An instance of one the classes from NATIVE_JSON_DATATYPES
toJsonImplementation()

Returns a JSON representation of this value object.

tr(self, str, disambiguation: str = None, n: int = -1) → str
valueChanged
input
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 = 4
DataClass

alias of builtins.object

FAILED = 3
NOTRUNNING = 0
NU = NotImplemented
NY = NotImplemented
RUNNING = 2
STARTING = 1
__init__(*args, **kwargs)

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

aboutToReplace
blockSignals(self, bool) → bool
childEvent(self, QChildEvent)
children(self) → object
connectNotify(self, QMetaMethod)
customEvent(self, QEvent)
deleteLater(self)
destroyed

destroyed(self, QObject = None) [signal]

disconnect(self)
disconnectNotify(self, QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → object
event(self, QEvent) → bool
eventFilter(self, QObject, QEvent) → bool
findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject

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

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

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

classmethod fromJson(json_obj)

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

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

:rtype : cls

classmethod fromJsonFilename(filename)
classmethod fromJsonImplementation(json_dict)

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

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.

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()

Override this method to define logic specfically for initializing abstract instances of this param.

initConcrete()

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

inputChanged
inputReplaced
input_fnameChanged
input_fnameReplaced
installEventFilter(self, QObject)
isDefault()
isSignalConnected(self, QMetaMethod) → bool
isStartable()
isWidgetType(self) → bool
isWindowType(self) → bool
is_abstract = True
kill()
killTimer(self, int)
metaObject(self) → QMetaObject
model_fnameChanged
model_fnameReplaced
moveToThread(self, QThread)
name
nameChanged
nameReplaced
objectName(self) → str
objectNameChanged

objectNameChanged(self, str) [signal]

output

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

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

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

owner_instance = Owner()
owner_instance.data_x = 4

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

Warning

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

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

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

ownerChain()

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

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

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

parent(self) → QObject
postprocess()
preprocess()

Generate the input and model files.

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)
reportValidation(results)

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

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

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

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

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

line = Line()

We can reset the entire line:

line.reset()

Or just certain parts:

line.reset(Line.start.x) # resets just start.x line.start.reset(Coord.x) # another way to reset start.x line.reset(Line.end) # resets the entire end point line.reset(Line.start.z, Line.end.z) # resets the z-coord of both
Parameters:args – abstract sub-params of self
runValidation(silent=False, validate_children=True, stop_on_fail=True)

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

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

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

ValidationResults or bool
sender(self) → QObject
senderSignalIndex(self) → int
setObjectName(self, str)
setParent(self, QObject)
setProperty(self, str, Any) → bool
setValue(value=None, **kwargs)

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

Parameters:value (self.DataClass or dict) – either another param instance of the same type or a dictionary mapping the sub-param names to values.
setWorkingDirectory(new_working_dir)
signalsBlocked(self) → bool
start()
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
status
statusChanged
statusReplaced
suspend_signals()
thread(self) → QThread
timerEvent(self, QTimerEvent)
toDict()
toJson(_mark_version=True)

Create and returns a data structure made up of jsonable items.

Return type:An instance of one the classes from NATIVE_JSON_DATATYPES
toJsonImplementation()

Returns a JSON representation of this value object.

tr(self, str, disambiguation: str = None, n: int = -1) → str
valueChanged
wait(timeout=None)

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

Parameters:timeout (NoneType or int) – Amount of time in seconds to wait before timing out. If None or a negative number, this method will wait until the task is finished.
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.
  • is_abstract (bool) – Whether this param is an abstract (ie class attribute) param.
  • valueChanged (QtCore.pyqtSignal) – A signal emitted whenever the param is changed.
  • default_value (DataClass) – The default value of the param. If unset, the default value is whatever value is created when calling DataClass()
  • param_name (str) – The name of the attribute this param is set as. For example, Owner.data_x.param_name would be ‘data_x’.
  • instance_attr_name (str) – The name of the attribute used to store param values on instances.
  • abstract_attr_name (str) – The name of the attribute used to store abstract params on class objects.
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.
  • is_abstract (bool) – Whether this param is an abstract (ie class attribute) param.
  • valueChanged (QtCore.pyqtSignal) – A signal emitted whenever the param is changed.
  • default_value (DataClass) – The default value of the param. If unset, the default value is whatever value is created when calling DataClass()
  • param_name (str) – The name of the attribute this param is set as. For example, Owner.data_x.param_name would be ‘data_x’.
  • instance_attr_name (str) – The name of the attribute used to store param values on instances.
  • abstract_attr_name (str) – The name of the attribute used to store abstract params on class objects.
class Input(default_value=<object object>, _explicit_abstract=False, **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.
  • is_abstract (bool) – Whether this param is an abstract (ie class attribute) param.
  • valueChanged (QtCore.pyqtSignal) – A signal emitted whenever the param is changed.
  • default_value (DataClass) – The default value of the param. If unset, the default value is whatever value is created when calling DataClass()
  • param_name (str) – The name of the attribute this param is set as. For example, Owner.data_x.param_name would be ‘data_x’.
  • instance_attr_name (str) – The name of the attribute used to store param values on instances.
  • abstract_attr_name (str) – The name of the attribute used to store abstract params on class objects.
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.
  • is_abstract (bool) – Whether this param is an abstract (ie class attribute) param.
  • valueChanged (QtCore.pyqtSignal) – A signal emitted whenever the param is changed.
  • default_value (DataClass) – The default value of the param. If unset, the default value is whatever value is created when calling DataClass()
  • param_name (str) – The name of the attribute this param is set as. For example, Owner.data_x.param_name would be ‘data_x’.
  • instance_attr_name (str) – The name of the attribute used to store param values on instances.
  • abstract_attr_name (str) – The name of the attribute used to store abstract params on class objects.
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.
  • is_abstract (bool) – Whether this param is an abstract (ie class attribute) param.
  • valueChanged (QtCore.pyqtSignal) – A signal emitted whenever the param is changed.
  • default_value (DataClass) – The default value of the param. If unset, the default value is whatever value is created when calling DataClass()
  • param_name (str) – The name of the attribute this param is set as. For example, Owner.data_x.param_name would be ‘data_x’.
  • instance_attr_name (str) – The name of the attribute used to store param values on instances.
  • abstract_attr_name (str) – The name of the attribute used to store abstract params on class objects.
DataClass

alias of builtins.object

__init__(default_value=<object object>, _explicit_abstract=False, **kwargs)

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

aboutToReplace
alnChanged
alnReplaced
blockSignals(self, bool) → bool
childEvent(self, QChildEvent)
children(self) → object
connectNotify(self, QMetaMethod)
customEvent(self, QEvent)
deleteLater(self)
destroyed

destroyed(self, QObject = None) [signal]

disconnect(self)
disconnectNotify(self, QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → object
event(self, QEvent) → bool
eventFilter(self, QObject, QEvent) → bool
findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject

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

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

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

classmethod fromJson(json_obj)

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

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

:rtype : cls

classmethod fromJsonImplementation(json_dict)

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

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()

Override this method to define logic specfically for initializing abstract instances of this param.

initConcrete()

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

installEventFilter(self, QObject)
isDefault()
isSignalConnected(self, QMetaMethod) → bool
isWidgetType(self) → bool
isWindowType(self) → bool
is_abstract = True
killTimer(self, int)
metaObject(self) → QMetaObject
moveToThread(self, QThread)
objectName(self) → str
objectNameChanged

objectNameChanged(self, str) [signal]

owner()

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

ownerChain()

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

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

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

parent(self) → QObject
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)

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

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

line = Line()

We can reset the entire line:

line.reset()

Or just certain parts:

line.reset(Line.start.x) # resets just start.x line.start.reset(Coord.x) # another way to reset start.x line.reset(Line.end) # resets the entire end point line.reset(Line.start.z, Line.end.z) # resets the z-coord of both
Parameters:args – abstract sub-params of self
sender(self) → QObject
senderSignalIndex(self) → int
seqChanged
seqReplaced
setObjectName(self, str)
setParent(self, QObject)
setProperty(self, str, Any) → bool
setValue(value=None, **kwargs)

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

Parameters:value (self.DataClass or dict) – either another param instance of the same type or a dictionary mapping the sub-param names to values.
signalsBlocked(self) → bool
ss_predictionChanged
ss_predictionReplaced
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
suspend_signals()
thread(self) → QThread
timerEvent(self, QTimerEvent)
toDict()
toJson(_mark_version=True)

Create and returns a data structure made up of jsonable items.

Return type:An instance of one the classes from NATIVE_JSON_DATATYPES
toJsonImplementation()

Returns a JSON representation of this value object.

tr(self, str, disambiguation: str = None, n: int = -1) → str
valueChanged
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 = 4
DataClass

alias of builtins.object

FAILED = 3
NOTRUNNING = 0
RUNNING = 2
STARTING = 1
__init__(*args, **kwargs)

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

aboutToReplace
blockSignals(self, bool) → bool
childEvent(self, QChildEvent)
children(self) → object
connectNotify(self, QMetaMethod)
customEvent(self, QEvent)
deleteLater(self)
destroyed

destroyed(self, QObject = None) [signal]

disconnect(self)
disconnectNotify(self, QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → object
event(self, QEvent) → bool
eventFilter(self, QObject, QEvent) → bool
findChild(self, type, name: str = '', options: Union[Qt.FindChildOptions, Qt.FindChildOption] = Qt.FindChildrenRecursively) → QObject

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

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

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

classmethod fromJson(json_obj)

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

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

:rtype : cls

classmethod fromJsonFilename(filename)
classmethod fromJsonImplementation(json_dict)

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

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.

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()

Override this method to define logic specfically for initializing abstract instances of this param.

initConcrete()

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

inputChanged
inputReplaced
input_fnameChanged
input_fnameReplaced
installEventFilter(self, QObject)
isDefault()
isSignalConnected(self, QMetaMethod) → bool
isStartable()
isWidgetType(self) → bool
isWindowType(self) → bool
is_abstract = True
kill()
killTimer(self, int)
metaObject(self) → QMetaObject
model_fnameChanged
model_fnameReplaced
moveToThread(self, QThread)
name
nameChanged
nameReplaced
objectName(self) → str
objectNameChanged

objectNameChanged(self, str) [signal]

output

Base class for all Param classes. A Param is a descriptor for storing data, which means that a single Param instance will manage the data values for multiple instances of the class that owns it. Example:

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

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

owner_instance = Owner()
owner_instance.data_x = 4

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

Warning

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

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

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

ownerChain()

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

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

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

parent(self) → QObject
postprocess()
preprocess()

Generate the input and model files.

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)
reportValidation(results)

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

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

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

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

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

line = Line()

We can reset the entire line:

line.reset()

Or just certain parts:

line.reset(Line.start.x) # resets just start.x line.start.reset(Coord.x) # another way to reset start.x line.reset(Line.end) # resets the entire end point line.reset(Line.start.z, Line.end.z) # resets the z-coord of both
Parameters:args – abstract sub-params of self
runValidation(silent=False, validate_children=True, stop_on_fail=True)

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

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

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

ValidationResults or bool
sender(self) → QObject
senderSignalIndex(self) → int
setObjectName(self, str)
setParent(self, QObject)
setProperty(self, str, Any) → bool
setValue(value=None, **kwargs)

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

Parameters:value (self.DataClass or dict) – either another param instance of the same type or a dictionary mapping the sub-param names to values.
setWorkingDirectory(new_working_dir)
signalsBlocked(self) → bool
start()
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
status
statusChanged
statusReplaced
suspend_signals()
thread(self) → QThread
timerEvent(self, QTimerEvent)
toDict()
toJson(_mark_version=True)

Create and returns a data structure made up of jsonable items.

Return type:An instance of one the classes from NATIVE_JSON_DATATYPES
toJsonImplementation()

Returns a JSON representation of this value object.

tr(self, str, disambiguation: str = None, n: int = -1) → str
valueChanged
wait(timeout=None)

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

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