schrodinger.tasks.jobtasks module¶

class schrodinger.tasks.jobtasks.RunMode¶

Bases: enum.Enum

An enumeration.

START = 1¶

STU = 3¶

WRITE = 2¶

class schrodinger.tasks.jobtasks.JobOptions(default_value=<object object>, _explicit_abstract=False, **kwargs)¶

Bases: schrodinger.models.parameters.CompoundParam

incorporation¶

default_disp¶

host¶

cpus¶

create_job_dir¶

DataClass¶: alias of builtins.object

__init__(default_value=<object object>, _explicit_abstract=False, **kwargs)¶: Initialize self. See help(type(self)) for accurate signature.

aboutToReplace¶

blockSignals(self, bool) → bool¶

childEvent(self, QChildEvent)¶

children(self) → object¶

connectNotify(self, QMetaMethod)¶

cpusChanged¶

cpusReplaced¶

create_job_dirChanged¶

create_job_dirReplaced¶

customEvent(self, QEvent)¶

default_dispChanged¶

default_dispReplaced¶

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.

hostChanged¶

hostReplaced¶

incorporationChanged¶

incorporationReplaced¶

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¶

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¶

class schrodinger.tasks.jobtasks.JobConfig(*args, **kwargs)¶

Bases: schrodinger.models.parameters.CompoundParam

job_options¶

disp¶

host¶

cpus¶

viewname¶

jobname¶

host_text¶

proj¶

__init__(*args, **kwargs)¶: Initialize self. See help(type(self)) for accurate signature.

addHostFlag(cmdlist)¶

addResultServerFlag(cmdlist)¶

addDispFlag(cmdlist)¶

addProjFlag(cmdlist)¶

addViewnameFlag(cmdlist)¶

addTmpLaunchDirFlag(cmdlist)¶

appendFlags(cmdlist)¶

Takes a cmdlist and appends the standard configuration flags appropriate for the context. This will depend on whether the intent is to start or write the job and whether maestro is available.

Any flag that already exists in the cmdlist will take precedence and that flag will not be automatically appended.

Parameters:	cmdlist (list) – the original command list.

applySettings(settings)¶

summaryText()¶: Generates the text to display in the status bar via the updateStatusText method.

DataClass¶: alias of builtins.object

aboutToReplace¶

blockSignals(self, bool) → bool¶

childEvent(self, QChildEvent)¶

children(self) → object¶

connectNotify(self, QMetaMethod)¶

cpusChanged¶

cpusReplaced¶

customEvent(self, QEvent)¶

deleteLater(self)¶

destroyed¶: destroyed(self, QObject = None) [signal]

disconnect(self)¶

disconnectNotify(self, QMetaMethod)¶

dispChanged¶

dispReplaced¶

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.

hostChanged¶

hostReplaced¶

host_textChanged¶

host_textReplaced¶

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¶

job_optionsChanged¶

job_optionsReplaced¶

jobnameChanged¶

jobnameReplaced¶

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¶

projChanged¶

projReplaced¶

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¶

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¶

viewnameChanged¶

viewnameReplaced¶

class schrodinger.tasks.jobtasks.AbstractJobTask(*args, **kwargs)¶

Bases: schrodinger.tasks.tasks.AbstractTask

job_options¶

job_config¶

job_dir¶

__init__(*args, **kwargs)¶: Initialize self. See help(type(self)) for accurate signature.

start()¶: Start this task. This includes any preprocessing and validation checks. Any failures will prevent the task from running.

write()¶

getWriteFilename()¶

isRunning()¶

makeSchrodingerCmd(*args)¶

Builds a $SCHRODINGER command string from all the args passed in. The resulting string is suitable for use in a cmdlist and formatted for use in starting or writing the job depending on self.run_mode. In START mode, the $SCHRODINGER environment variable will be expanded. In WRITE mode, it will stay as $SCHRODINGER and the path will be delimited with linux-style forward slashes.

Example: self.makeSchrodingerCmd(‘utilities’, ‘my_utility’) will return “${SCHRODINGER}/utilities/my_utility” in WRITE mode.

getSchrodingerRun()¶: Returns the correct version of the $SCHRODINGER/run string. This will depend on whether the intent is to start or to write the job.

fullCmdList()¶: Returns the full cmd list for the job. This will take into account the run_mode specified in the job_config.

makeCmdList()¶: Implement this to generate a cmdlist. This cmdlist will be used for write functionality.

appendConfigFlags(cmdlist)¶

updateStatusText()¶

DataClass¶: alias of builtins.object

aboutToReplace¶

base_name¶

base_nameChanged¶

base_nameReplaced¶

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.

getName()¶

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¶

job_configChanged¶

job_configReplaced¶

job_dirChanged¶

job_dirReplaced¶

job_optionsChanged¶

job_optionsReplaced¶

killTimer(self, int)¶

metaObject(self) → QMetaObject¶

moveToThread(self, QThread)¶

name¶

nameChanged¶

nameReplaced¶

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¶

postStart()¶: Override this method for any operations that should be run immediately after a task is started. This method is only called if the task was successfully started; returning False from this method provides one last way of marking the task as having failed to start.

preProcess()¶

preValidate()¶: Override this method for any operations that should be run prior to validation.

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)¶: This method is required by ValidationMixin. In order to report errors, a reporter object is required (self._reporter). If no reporter is specified, a RuntimeError is raised for any validation errors that are encountered, but good results will allow the task to proceed; warnings are ignored if there is no reporter.

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¶

setStatus(status)¶

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>¶

status()¶

statusChanged¶

status_param¶

status_paramChanged¶

status_paramReplaced¶

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¶

class schrodinger.tasks.jobtasks.CmdJobTask(*args, **kwargs)¶

Bases: schrodinger.tasks.jobtasks.AbstractJobTask

makeCmdList()¶: This is the main method that needs to be implemented to define a specific cmd job runner. It should just return a complete cmd list for the job to be launched. Standard job options should be left off.

DataClass¶: alias of builtins.object

__init__(*args, **kwargs)¶: Initialize self. See help(type(self)) for accurate signature.

aboutToReplace¶

appendConfigFlags(cmdlist)¶

base_name¶

base_nameChanged¶

base_nameReplaced¶

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.

fullCmdList()¶: Returns the full cmd list for the job. This will take into account the run_mode specified in the job_config.

getName()¶

getSchrodingerRun()¶: Returns the correct version of the $SCHRODINGER/run string. This will depend on whether the intent is to start or to write the job.

getWriteFilename()¶

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()¶

isRunning()¶

isSignalConnected(self, QMetaMethod) → bool¶

isWidgetType(self) → bool¶

isWindowType(self) → bool¶

is_abstract = True¶

job_config¶

job_configChanged¶

job_configReplaced¶

job_dir¶

job_dirChanged¶

job_dirReplaced¶

job_options¶

job_optionsChanged¶

job_optionsReplaced¶

killTimer(self, int)¶

makeSchrodingerCmd(*args)¶

Builds a $SCHRODINGER command string from all the args passed in. The resulting string is suitable for use in a cmdlist and formatted for use in starting or writing the job depending on self.run_mode. In START mode, the $SCHRODINGER environment variable will be expanded. In WRITE mode, it will stay as $SCHRODINGER and the path will be delimited with linux-style forward slashes.

Example: self.makeSchrodingerCmd(‘utilities’, ‘my_utility’) will return “${SCHRODINGER}/utilities/my_utility” in WRITE mode.

metaObject(self) → QMetaObject¶

moveToThread(self, QThread)¶

name¶

nameChanged¶

nameReplaced¶

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¶

postStart()¶: Override this method for any operations that should be run immediately after a task is started. This method is only called if the task was successfully started; returning False from this method provides one last way of marking the task as having failed to start.

preProcess()¶

preValidate()¶: Override this method for any operations that should be run prior to validation.

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)¶: This method is required by ValidationMixin. In order to report errors, a reporter object is required (self._reporter). If no reporter is specified, a RuntimeError is raised for any validation errors that are encountered, but good results will allow the task to proceed; warnings are ignored if there is no reporter.

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¶

setStatus(status)¶

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¶

start()¶: Start this task. This includes any preprocessing and validation checks. Any failures will prevent the task from running.

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

staticMetaObject = <PyQt5.QtCore.QMetaObject object>¶

status()¶

statusChanged¶

status_param¶

status_paramChanged¶

status_paramReplaced¶

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¶

updateStatusText()¶

valueChanged¶

write()¶

schrodinger.tasks.jobtasks.get_job_status_loop()¶

schrodinger.tasks.jobtasks.monitor_jobtask(jobtask)¶

class schrodinger.tasks.jobtasks.JobStatusLoop¶

Bases: PyQt5.QtCore.QObject

__init__()¶: Initialize self. See help(type(self)) for accurate signature.

monitorJobTask(jobtask)¶

updateNow()¶

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]

inherits(self, str) → bool¶

installEventFilter(self, QObject)¶

isSignalConnected(self, QMetaMethod) → bool¶

isWidgetType(self) → bool¶

isWindowType(self) → bool¶

killTimer(self, int)¶

metaObject(self) → QMetaObject¶

moveToThread(self, QThread)¶

objectName(self) → str¶

objectNameChanged¶: objectNameChanged(self, str) [signal]

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)¶

sender(self) → QObject¶

senderSignalIndex(self) → int¶

setObjectName(self, str)¶

setParent(self, QObject)¶

setProperty(self, str, Any) → bool¶

signalsBlocked(self) → bool¶

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

staticMetaObject = <PyQt5.QtCore.QMetaObject object>¶

thread(self) → QThread¶

timerEvent(self, QTimerEvent)¶

tr(self, str, disambiguation: str = None, n: int = -1) → str¶

schrodinger.tasks.jobtasks.get_project_name()¶

schrodinger.tasks.jobtasks.use_detached_jobs(host)¶

Returns boolean if we should use detached jobs.

Parameters: host (string) – Hosts string which determine the string value of result server argument. These are values usually from configuration dialog and is of the form “galina” or “galina:1” or “galina,monica” or “galina:2,monica:3” or “galina monica” or “galina:2 monica:3”. And based on ‘serverhost’ field of the first host, return boolean if we should use detached jobs.

schrodinger.tasks.jobtasks.make_schrodinger_cmd(cmdlist, mode=<RunMode.START: 1>)¶

schrodinger.tasks.jobtasks.get_first_hostname(host)¶

Given a host string, get the corresponding hosts list from jobcontrol and return the first hostname from that list.

Parameters:

host (string) –

Hosts string which determine the string value of result server argument. These are values usually from configuration dialog and is of the form “galina” or “galina:1” or “galina,monica” or “galina:2,monica:3” or “galina monica” or “galina:2 monica:3”.

rtype:	str
return:	Hostname based on the first of the first hosts in the jobcontrol list.

schrodinger.tasks.jobtasks.result_server_option(host)¶

Return string value of result server argument.

Parameters:	host (string) – Hosts string which determine the string value of result server argument. These are values usually from configuration dialog and is of the form “galina” or “galina:1” or “galina,monica” or “galina:2,monica:3” or “galina monica” or “galina:2 monica:3”. And based on ‘serverhost’ field of the first host, the result server argument is returned.

schrodinger.tasks.jobtasks.job_belongs_to_panel(jobid, viewname)¶

Return True if jobid belongs to viewname of a panel. Used by incorporation callbacks to determine if the job belongs to us.

Parameters:	jobid (str) – jobid for a given job viewname (str) – viewname corresponding to panel

schrodinger.tasks.jobtasks.cmdlist_to_cmd(cmdlist)¶

Converts a command list to a command string. Don’t do this if you can possibly avoid it.

subprocess.list2cmdline() is not sufficient because it won’t quote env vars like $SCHRODINGER (which can expand to “path with spaces”

Parameters:	cmdlist (list) – a list of commands
Returns:	sh interpolable list

schrodinger.tasks.jobtasks.set_sh_file_flags(filename)¶

schrodinger.tasks.jobtasks module¶

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