schrodinger.tasks.tasks module

A task represents a block of work that has a defined input and output and runs without user intervention. Different task classes share a common external API but have different implementations for defining and executing the work, such as blocking calls, threads, subprocesses, or job control (see jobtasks).

To define a task, follow these basic instructions:

1. Choose a task class to subclass. The choice of task class is primarily dictated by how the task needs to run - thread, subprocess, job, etc. See the Task Class Selection Guide for help.

2. Override the input and output params. The task.input and task.output params may be of any Param type, including CompoundParam (typical). For CompoundParams, either use an existing class to override task.input, OR define a nested class named Input within the task. Doing so will automatically override task.input. The same goes for task.output. Example:

class FooTask(tasks.ThreadFunctionTask):
    input = AtomPair()  # AtomPair is an existing CompoundParam subclass

    # This will magically override FooTask.output = Output()
    class Output(parameters.CompoundParam):
        charge: float
        processed_atom_pair: AtomPair

3. Define the work of the task. This is done differently for different task classes, but generally involves overriding a method to either provide python logic directly as the work to be done or to construct a command line with the appropriate arguments that will be invoked via the appropriate mechanism for the task type.

Once a task is defined, it can be instantiated, set up, and started:

task = FooThreadTask()
task.input.x = 3
task.input.y = 4
task.start()
assert task.status is tasks.Status.RUNNING
task.wait()
assert task.status is tasks.Status.DONE
print(task.output)

Pre/postprocessors

Tasks support pre/post processing functions. These can either be methods in the class that are decorated with the preprocessor or postprocessor decorators, or external functions that are added to a task instance. Example:

class MyTask(tasks.BlockingFunctionTask):
    @tasks.preprocessor
    def checkInput(self):
        if self.input.x <0:
            return False, 'x must be a nonnegative number.'

For more information, see the module-level preprocessor and postprocessor decorators as well as the start(), preprocessors(), and addPreprocessor() methods of AbstractTask.

Task directory (taskdir)

Tasks have a concept of a taskdir. While the task framework will never actually chdir into a different directory, the task provides functions for specifying and accessing a directory that is considered that task’s directory by convention. Subprocesses started by the task will use the taskdir as their working directory.

To specify a taskdir, override AbstractTask.DEFAULT_TASK_SPEC or use task.specifyTaskDir(). Example:

class MyTask(tasks.BlockingFunctionTask):
    DEFAULT_TASK_SPEC = tasks.AUTO_TASKDIR

task = MyTask()
task.specifyTaskDir('foo_dir')

The taskdir is created during preprocessing. Once the taskdir is created, use task.getTaskDir() and task.getTaskFilename() when reading and writing files for the task. Example:

class MyTask(tasks.SubprocessCmdTask):
    @tasks.preprocessor(order=tasks.AFTER_TASKDIR)
    def writeInputFiles(self):
        with open(self.getTaskFilename('foo_data.txt'), 'w') as f:
            f.write(self.input.foo_data)

For more details on taskdir, see task.specifyTaskDir() task.getTaskDir().

Input/Output File Handling

To specify a task input file or folder, use the TaskFile or TaskFolder classes as a subparam on the task.input param. If the task runs its unit of work on a different machine or process, the input files/folders will automatically be copied to the right location on the compute host. The path to the TaskFile/TaskFolder will also be updated so it points to the right location, regardless of when or where it’s accessed.

TaskFile/TaskFolder`s may be nested under the input param in supported container types. Supported container types are: There are few restrictions on how nested you can define your `TaskFile/TaskFolder on the input param. For example, if you have a variable number of input files, you can define the input with a list:

- List
- Dict
- Set
- Tuple
- CompoundParam

For example:

class Input(parameters.CompoundParam):
    receptor_filename: TaskFile
    ligand_filenames: List[TaskFile]

Task output files/folders behave in the exact same way as task input files/folders except they’re defined as TaskFile/`TaskFolder`s on the output param.

class schrodinger.tasks.tasks.TaskFile

Bases: str

See the “Input/Output File Handling” section of the module docstring for information.

__contains__

Return key in self.

__init__

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

__len__

Return len(self).

capitalize() → str

Return a capitalized version of S, i.e. make the first character have upper case and the rest lower case.

casefold() → str

Return a version of S suitable for caseless comparisons.

center(width[, fillchar]) → str

Return S centered in a string of length width. Padding is done using the specified fill character (default is a space)

count(sub[, start[, end]]) → int

Return the number of non-overlapping occurrences of substring sub in string S[start:end]. Optional arguments start and end are interpreted as in slice notation.

encode(encoding='utf-8', errors='strict') → bytes

Encode S using the codec registered for encoding. Default encoding is ‘utf-8’. errors may be given to set a different error handling scheme. Default is ‘strict’ meaning that encoding errors raise a UnicodeEncodeError. Other possible values are ‘ignore’, ‘replace’ and ‘xmlcharrefreplace’ as well as any other name registered with codecs.register_error that can handle UnicodeEncodeErrors.

endswith(suffix[, start[, end]]) → bool

Return True if S ends with the specified suffix, False otherwise. With optional start, test S beginning at that position. With optional end, stop comparing S at that position. suffix can also be a tuple of strings to try.

expandtabs(tabsize=8) → str

Return a copy of S where all tab characters are expanded using spaces. If tabsize is not given, a tab size of 8 characters is assumed.

find(sub[, start[, end]]) → int

Return the lowest index in S where substring sub is found, such that sub is contained within S[start:end]. Optional arguments start and end are interpreted as in slice notation.

Return -1 on failure.

format(*args, **kwargs) → str

Return a formatted version of S, using substitutions from args and kwargs. The substitutions are identified by braces (‘{‘ and ‘}’).

format_map(mapping) → str

Return a formatted version of S, using substitutions from mapping. The substitutions are identified by braces (‘{‘ and ‘}’).

index(sub[, start[, end]]) → int

Return the lowest index in S where substring sub is found, such that sub is contained within S[start:end]. Optional arguments start and end are interpreted as in slice notation.

Raises ValueError when the substring is not found.

isalnum() → bool

Return True if all characters in S are alphanumeric and there is at least one character in S, False otherwise.

isalpha() → bool

Return True if all characters in S are alphabetic and there is at least one character in S, False otherwise.

isdecimal() → bool

Return True if there are only decimal characters in S, False otherwise.

isdigit() → bool

Return True if all characters in S are digits and there is at least one character in S, False otherwise.

isidentifier() → bool

Return True if S is a valid identifier according to the language definition.

Use keyword.iskeyword() to test for reserved identifiers such as “def” and “class”.

islower() → bool

Return True if all cased characters in S are lowercase and there is at least one cased character in S, False otherwise.

isnumeric() → bool

Return True if there are only numeric characters in S, False otherwise.

isprintable() → bool

Return True if all characters in S are considered printable in repr() or S is empty, False otherwise.

isspace() → bool

Return True if all characters in S are whitespace and there is at least one character in S, False otherwise.

istitle() → bool

Return True if S is a titlecased string and there is at least one character in S, i.e. upper- and titlecase characters may only follow uncased characters and lowercase characters only cased ones. Return False otherwise.

isupper() → bool

Return True if all cased characters in S are uppercase and there is at least one cased character in S, False otherwise.

join(iterable) → str

Return a string which is the concatenation of the strings in the iterable. The separator between elements is S.

ljust(width[, fillchar]) → str

Return S left-justified in a Unicode string of length width. Padding is done using the specified fill character (default is a space).

lower() → str

Return a copy of the string S converted to lowercase.

lstrip([chars]) → str

Return a copy of the string S with leading whitespace removed. If chars is given and not None, remove characters in chars instead.

static maketrans()

Return a translation table usable for str.translate().

If there is only one argument, it must be a dictionary mapping Unicode ordinals (integers) or characters to Unicode ordinals, strings or None. Character keys will be then converted to ordinals. If there are two arguments, they must be strings of equal length, and in the resulting dictionary, each character in x will be mapped to the character at the same position in y. If there is a third argument, it must be a string, whose characters will be mapped to None in the result.

partition(sep) -> (head, sep, tail)

Search for the separator sep in S, and return the part before it, the separator itself, and the part after it. If the separator is not found, return S and two empty strings.

replace(old, new[, count]) → str

Return a copy of S with all occurrences of substring old replaced by new. If the optional argument count is given, only the first count occurrences are replaced.

rfind(sub[, start[, end]]) → int

Return the highest index in S where substring sub is found, such that sub is contained within S[start:end]. Optional arguments start and end are interpreted as in slice notation.

Return -1 on failure.

rindex(sub[, start[, end]]) → int

Return the highest index in S where substring sub is found, such that sub is contained within S[start:end]. Optional arguments start and end are interpreted as in slice notation.

Raises ValueError when the substring is not found.

rjust(width[, fillchar]) → str

Return S right-justified in a string of length width. Padding is done using the specified fill character (default is a space).

rpartition(sep) -> (head, sep, tail)

Search for the separator sep in S, starting at the end of S, and return the part before it, the separator itself, and the part after it. If the separator is not found, return two empty strings and S.

rsplit(sep=None, maxsplit=-1) → list of strings

Return a list of the words in S, using sep as the delimiter string, starting at the end of the string and working to the front. If maxsplit is given, at most maxsplit splits are done. If sep is not specified, any whitespace string is a separator.

rstrip([chars]) → str

Return a copy of the string S with trailing whitespace removed. If chars is given and not None, remove characters in chars instead.

split(sep=None, maxsplit=-1) → list of strings

Return a list of the words in S, using sep as the delimiter string. If maxsplit is given, at most maxsplit splits are done. If sep is not specified or is None, any whitespace string is a separator and empty strings are removed from the result.

splitlines([keepends]) → list of strings

Return a list of the lines in S, breaking at line boundaries. Line breaks are not included in the resulting list unless keepends is given and true.

startswith(prefix[, start[, end]]) → bool

Return True if S starts with the specified prefix, False otherwise. With optional start, test S beginning at that position. With optional end, stop comparing S at that position. prefix can also be a tuple of strings to try.

strip([chars]) → str

Return a copy of the string S with leading and trailing whitespace removed. If chars is given and not None, remove characters in chars instead.

swapcase() → str

Return a copy of S with uppercase characters converted to lowercase and vice versa.

title() → str

Return a titlecased version of S, i.e. words start with title case characters, all remaining cased characters have lower case.

translate(table) → str

Return a copy of the string S in which each character has been mapped through the given translation table. The table must implement lookup/indexing via __getitem__, for instance a dictionary or list, mapping Unicode ordinals to Unicode ordinals, strings, or None. If this operation raises LookupError, the character is left untouched. Characters mapped to None are deleted.

upper() → str

Return a copy of S converted to uppercase.

zfill(width) → str

Pad a numeric string S with zeros on the left, to fill a field of the specified width. The string S is never truncated.

class schrodinger.tasks.tasks.TaskFolder

Bases: str

See the “Input/Output File Handling” section of the module docstring for information.

__contains__

Return key in self.

__init__

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

__len__

Return len(self).

capitalize() → str

Return a capitalized version of S, i.e. make the first character have upper case and the rest lower case.

casefold() → str

Return a version of S suitable for caseless comparisons.

center(width[, fillchar]) → str

Return S centered in a string of length width. Padding is done using the specified fill character (default is a space)

count(sub[, start[, end]]) → int

Return the number of non-overlapping occurrences of substring sub in string S[start:end]. Optional arguments start and end are interpreted as in slice notation.

encode(encoding='utf-8', errors='strict') → bytes

Encode S using the codec registered for encoding. Default encoding is ‘utf-8’. errors may be given to set a different error handling scheme. Default is ‘strict’ meaning that encoding errors raise a UnicodeEncodeError. Other possible values are ‘ignore’, ‘replace’ and ‘xmlcharrefreplace’ as well as any other name registered with codecs.register_error that can handle UnicodeEncodeErrors.

endswith(suffix[, start[, end]]) → bool

Return True if S ends with the specified suffix, False otherwise. With optional start, test S beginning at that position. With optional end, stop comparing S at that position. suffix can also be a tuple of strings to try.

expandtabs(tabsize=8) → str

Return a copy of S where all tab characters are expanded using spaces. If tabsize is not given, a tab size of 8 characters is assumed.

find(sub[, start[, end]]) → int

Return the lowest index in S where substring sub is found, such that sub is contained within S[start:end]. Optional arguments start and end are interpreted as in slice notation.

Return -1 on failure.

format(*args, **kwargs) → str

Return a formatted version of S, using substitutions from args and kwargs. The substitutions are identified by braces (‘{‘ and ‘}’).

format_map(mapping) → str

Return a formatted version of S, using substitutions from mapping. The substitutions are identified by braces (‘{‘ and ‘}’).

index(sub[, start[, end]]) → int

Return the lowest index in S where substring sub is found, such that sub is contained within S[start:end]. Optional arguments start and end are interpreted as in slice notation.

Raises ValueError when the substring is not found.

isalnum() → bool

Return True if all characters in S are alphanumeric and there is at least one character in S, False otherwise.

isalpha() → bool

Return True if all characters in S are alphabetic and there is at least one character in S, False otherwise.

isdecimal() → bool

Return True if there are only decimal characters in S, False otherwise.

isdigit() → bool

Return True if all characters in S are digits and there is at least one character in S, False otherwise.

isidentifier() → bool

Return True if S is a valid identifier according to the language definition.

Use keyword.iskeyword() to test for reserved identifiers such as “def” and “class”.

islower() → bool

Return True if all cased characters in S are lowercase and there is at least one cased character in S, False otherwise.

isnumeric() → bool

Return True if there are only numeric characters in S, False otherwise.

isprintable() → bool

Return True if all characters in S are considered printable in repr() or S is empty, False otherwise.

isspace() → bool

Return True if all characters in S are whitespace and there is at least one character in S, False otherwise.

istitle() → bool

Return True if S is a titlecased string and there is at least one character in S, i.e. upper- and titlecase characters may only follow uncased characters and lowercase characters only cased ones. Return False otherwise.

isupper() → bool

Return True if all cased characters in S are uppercase and there is at least one cased character in S, False otherwise.

join(iterable) → str

Return a string which is the concatenation of the strings in the iterable. The separator between elements is S.

ljust(width[, fillchar]) → str

Return S left-justified in a Unicode string of length width. Padding is done using the specified fill character (default is a space).

lower() → str

Return a copy of the string S converted to lowercase.

lstrip([chars]) → str

Return a copy of the string S with leading whitespace removed. If chars is given and not None, remove characters in chars instead.

static maketrans()

Return a translation table usable for str.translate().

If there is only one argument, it must be a dictionary mapping Unicode ordinals (integers) or characters to Unicode ordinals, strings or None. Character keys will be then converted to ordinals. If there are two arguments, they must be strings of equal length, and in the resulting dictionary, each character in x will be mapped to the character at the same position in y. If there is a third argument, it must be a string, whose characters will be mapped to None in the result.

partition(sep) -> (head, sep, tail)

Search for the separator sep in S, and return the part before it, the separator itself, and the part after it. If the separator is not found, return S and two empty strings.

replace(old, new[, count]) → str

Return a copy of S with all occurrences of substring old replaced by new. If the optional argument count is given, only the first count occurrences are replaced.

rfind(sub[, start[, end]]) → int

Return the highest index in S where substring sub is found, such that sub is contained within S[start:end]. Optional arguments start and end are interpreted as in slice notation.

Return -1 on failure.

rindex(sub[, start[, end]]) → int

Return the highest index in S where substring sub is found, such that sub is contained within S[start:end]. Optional arguments start and end are interpreted as in slice notation.

Raises ValueError when the substring is not found.

rjust(width[, fillchar]) → str

Return S right-justified in a string of length width. Padding is done using the specified fill character (default is a space).

rpartition(sep) -> (head, sep, tail)

Search for the separator sep in S, starting at the end of S, and return the part before it, the separator itself, and the part after it. If the separator is not found, return two empty strings and S.

rsplit(sep=None, maxsplit=-1) → list of strings

Return a list of the words in S, using sep as the delimiter string, starting at the end of the string and working to the front. If maxsplit is given, at most maxsplit splits are done. If sep is not specified, any whitespace string is a separator.

rstrip([chars]) → str

Return a copy of the string S with trailing whitespace removed. If chars is given and not None, remove characters in chars instead.

split(sep=None, maxsplit=-1) → list of strings

Return a list of the words in S, using sep as the delimiter string. If maxsplit is given, at most maxsplit splits are done. If sep is not specified or is None, any whitespace string is a separator and empty strings are removed from the result.

splitlines([keepends]) → list of strings

Return a list of the lines in S, breaking at line boundaries. Line breaks are not included in the resulting list unless keepends is given and true.

startswith(prefix[, start[, end]]) → bool

Return True if S starts with the specified prefix, False otherwise. With optional start, test S beginning at that position. With optional end, stop comparing S at that position. prefix can also be a tuple of strings to try.

strip([chars]) → str

Return a copy of the string S with leading and trailing whitespace removed. If chars is given and not None, remove characters in chars instead.

swapcase() → str

Return a copy of S with uppercase characters converted to lowercase and vice versa.

title() → str

Return a titlecased version of S, i.e. words start with title case characters, all remaining cased characters have lower case.

translate(table) → str

Return a copy of the string S in which each character has been mapped through the given translation table. The table must implement lookup/indexing via __getitem__, for instance a dictionary or list, mapping Unicode ordinals to Unicode ordinals, strings, or None. If this operation raises LookupError, the character is left untouched. Characters mapped to None are deleted.

upper() → str

Return a copy of S converted to uppercase.

zfill(width) → str

Pad a numeric string S with zeros on the left, to fill a field of the specified width. The string S is never truncated.

class schrodinger.tasks.tasks.ProcessingResult(passed, message=None)

Bases: object

A general-purpose return value for task pre/post processors

__init__(passed, message=None)
Parameters:
  • passed (bool) – Whether the result is considered to be passing
  • message (str) – A message for this result
processorName()
class schrodinger.tasks.tasks.CallingContext

Bases: enum.IntEnum

An enumeration.

CMDLINE = 1
GUI = 2
exception schrodinger.tasks.tasks.TaskFailure

Bases: Exception

Exception raised when a task fails for reasons other than an unexpected error occuring during execution.

__init__

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

args
with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception schrodinger.tasks.tasks.TaskKilled

Bases: schrodinger.tasks.tasks.TaskFailure

__init__

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

args
with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

class schrodinger.tasks.tasks.FailureInfo

Bases: schrodinger.tasks.tasks.FailureInfo

__contains__

Return key in self.

__init__

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

__len__

Return len(self).

count(value) → integer -- return number of occurrences of value
exception

Alias for field number 0

index(value[, start[, stop]]) → integer -- return first index of value.

Raises ValueError if the value is not present.

message

Alias for field number 2

traceback

Alias for field number 1

class schrodinger.tasks.tasks.Status(*args, **kwargs)

Bases: schrodinger.models.jsonable.JsonableIntEnum

An enumeration.

WAITING = 0
RUNNING = 1
FAILED = 2
DONE = 3
class schrodinger.tasks.tasks.AbstractTask(*args, **kwargs)

Bases: schrodinger.utils.funcchains.FuncChainMixin, schrodinger.models.parameters.CompoundParam

input
output
status
name
progress
max_progress
taskDone
taskStarted
taskFailed
DEFAULT_TASKDIR_SETTING = None
AUTO_TASKDIR = <object object>
TEMP_TASKDIR = <object object>
classmethod runFromCmdLine()
classmethod fromJsonFilename(filename)
initConcrete()

Override to customize initialization of concrete params.

initializeValue()

@overrides: parameters.CompoundParam

INTERRUPT_ENABLED = False
run()
kill()

Implementations are responsible for immediately stopping the task. No threads or processes should be running after this method is complete.

This method should be called sparingly since in many contexts the task will be forced to terminate without a chance to clean up or free resources.

start(skip_preprocessing=False)

This is the main method for starting a task. Start will check if a task is not already running, run preprocessing, and then run the task.

Failures in preprocessing will interrupt the task start, and the task will never enter the RUNNING state.

Parameters:skip_preprocessing (bool) – whether to skip preprocessing. This can be useful if preprocessing was already performed prior to calling start.
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.
isRunning()
isStartable()
specifyTaskDir(taskdir_spec)

Specify the taskdir creation behavior. Use one of the following options:

A directory name (string). This may be a relative or absolute path

None - no taskdir is requested. The task will use the CWD as its taskdir

AUTO_TASKDIR - a new subdirectory will be created in the CWD using the task name as the directory name.

TEMP_TASKDIR - a temporary directory will be created in the schrodinger temp dir. This directory is cleaned up when the task is deleted.

Parameters:taskdir_spec – one of the four options listed above
taskDirSetting()

Returns the taskdir spec. See specifyTaskDir() for details.

getTaskDir()

Returns the full path of the task directory. This is only available if the task directory exists (after creation of the taskdir or, if no task dir is specified, any time).

getTaskFilename(fname)

Return the appropriate absolute path for an input or output file in the taskdir.

addPreprocessor(func, order=-2000)

Adds a preproceessor function to this task instance. If the function has been decorated with @preprocessor, the order specified by the decorator will be used as the default.

Parameters:
  • func – the function to add
  • order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.
addPostprocessor(func, order=0)

Adds a postproceessor function to this task instance. If the function has been decorated with @postprocessor, the order specified by the decorator will be used.

Parameters:
  • func (typing.Callable) – the function to add
  • order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.
preprocessors()
Returns:A list of preprocessors (both decorated methods on the task and external functions that have been added via addPreprocessor)
postprocessors()
Returns:A list of postprocessors, both decorated methods on the task and external functions that have been added via addPostprocessor()
Return type:list[typing.Callable]
reset(*args, **kwargs)
replicate()

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

requestInterruption()

Request the task to stop.

To enable this feature, subclasses should periodically check whether an interruption has been requested and terminate if it has been. If such logic has been included, INTERRUPT_ENABLED should be set to True.

isInterruptionRequested()
runPreprocessing(callback=None, calling_context=None)

Run the preprocessors one-by-one. By default, any failing preprocessor will raise a TaskFailure exception and terminate processing. This behavior may be customized by supplying a callback function which will be called after each preprocessor with the result of that preprocessor.

Parameters:
  • callback – a function that takes result and returns a bool that indicates whether to continue on to the next preprocessor
  • calling_context – specify a value here to indicate the context in which this preprocessing is being called. This value will be stored in an instance variable, self.calling_context, which can be accessed from any preprocessor method on this task. Typically this value will be either self.GUI, self.CMDLINE, or None, but any value may be supplied here and checked for in the preprocessor methods. self.calling_context always reverts back to None at the end of runPreprocessing.
runPostprocessing(callback=None)
guard()

Context manager that saves any Exception raised inside

CMDLINE = 1
DONE = 3
DataClass

alias of builtins.object

FAILED = 2
GUI = 2
RUNNING = 1
WAITING = 0
__init__(*args, **kwargs)

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

addFuncToGroup(func, group=None, order=None)

Adds a function to the specified chain. Typically used for adding functions that are not methods of this object.

The function may optionally be decorated with a FuncGroupMarker. If so, the default group and order will be determined by the decorator. Any group or order explicitly passed in to addFuncToGroup will take precedence over the decorator settings.

Parameters:
  • func – the function to add
  • group (FuncGroupMarker or None) – the group marker. If the function is decorated with a FuncGoupMarker, that group marker will be the default.
  • order (float or None) – the sorting order. If the function is decorated with a FuncGoupMarker, the order specified in the decorator will be the default.
classmethod addSubParam(name, param, update_owner=True)
blockSignals(self, bool) → bool
block_signal_propagation()
childEvent(self, QChildEvent)
children(self) → List[QObject]
classmethod configureParam()

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

connectNotify(self, QMetaMethod)
customEvent(self, QEvent)
classmethod defaultValue(*args, **kwargs)
deleteLater(self)
destroyed

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

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

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

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

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

classmethod fromJson(json_obj)

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

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

:rtype : cls

classmethod fromJsonImplementation(json_dict)

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

getAbstractParam(*args, **kwargs)
getAddedFuncs(group=None)
getFuncGroup(group=None)

Retrieve the functions belonging to the specified group.

Parameters:group (FuncGroupMarker) – the group marker
Returns:the functions in the specified group, in order
Return type:list
classmethod getJsonBlacklist()

Override to customize what params are serialized.

Implementations should return a list of abstract params that should be omitted from serialization.

..NOTE
Returned abstract params must be direct child params of cls, e.g. cls.name, not cls.coord.x.
classmethod getParamSignal(*args, **kwargs)
classmethod getParamValue(*args, **kwargs)
classmethod getSubParam(name)

Get the value of a subparam using the string name:

c = Coord()
assert c.getSubParam('x') == 0

Note

Using the string name to accss params is generally discouraged, but can be useful for serializing/deserializing param data.

Parameters:name (str) – The name of the subparam to get the value for.
classmethod getSubParams()

Return a dictionary mapping subparam names to their values.

getTypeHint()
get_version()

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

inherits(self, str) → bool
initAbstract()
inputChanged
inputReplaced
installEventFilter(self, QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

isDefault(*args, **kwargs)
isSignalConnected(self, QMetaMethod) → bool
isWidgetType(self) → bool
isWindowType(self) → bool
killTimer(self, int)
max_progressChanged
max_progressReplaced
metaObject(self) → QMetaObject
moveToThread(self, QThread)
nameChanged
nameReplaced
objectName(self) → str
objectNameChanged

objectNameChanged(self, str) [signal]

outputChanged
outputReplaced
classmethod owner()

Get the owner of the param:

# Can be called on an abstract param:
assert Coord.x.owner() == Coord

# ...or on an instance of a CompoundParam
a = Atom()
assert a.coord.owner() == a
classmethod ownerChain()

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

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

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

classmethod paramName()

Get the name of the param:

# Can be called on an abstract param:
print(Coord.x.paramName()) # 'x'

# ...or on an instance of a CompoundParam
a = Atom()
a.coord.paramName() # 'coord'
parent(self) → QObject
processFuncChain(chain=None, result_callback=None)

Execute each function in the specified chain sequentially in order.

The result_callback is called after each function with the return value of that function. This can be used to respond to the return value (e.g. present information to the user, get user feedback, log the result, etc.)

The return value of the result_callback determines whether processing will proceeed to the next function.

Parameters:
  • chain (FuncChainDecorator) – which chain to process
  • result_callback – the callback that will get called with the result of each function in the chain
Returns:

a list of the results from the functions

progressChanged
progressReplaced
property(self, str) → Any
pyqtConfigure(...)

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

receivers(self, PYQT_SIGNAL) → int
removeEventFilter(self, QObject)
sender(self) → QObject
senderSignalIndex(self) → int
setObjectName(self, str)
classmethod setParamValue(*args, **kwargs)
setParent(self, QObject)
setProperty(self, str, Any) → bool
classmethod setReference(param1, param2)

Call this class method from configureParam to indicate that two params should be kept in sync. The initial values will start with the default value of param1. Example:

class Square(CompoundParam):
    width: float = 5
    height: float = 10

    @classmethod
    def configureParam(cls):
        super().configureParam()
        cls.setReference(cls.width, cls.height)

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6
Parameters:
  • param1 – The first abstract param to keep synced
  • param2 – The second abstract param. After instantiation, this param will take on the value of param1.
setValue(*args, **kwargs)
signalsBlocked(self) → bool
skip_eq_check()
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
statusChanged
statusReplaced
thread(self) → QThread
timerEvent(self, QTimerEvent)
toDict(*args, **kwargs)
toJson(_mark_version=True)

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

Return type:An instance of one the classes from NATIVE_JSON_DATATYPES
toJsonImplementation(*args, **kwargs)
tr(self, str, disambiguation: str = None, n: int = -1) → str
valueChanged
class schrodinger.tasks.tasks.AbstractCmdTask(*args, **kwargs)

Bases: schrodinger.tasks.tasks.AbstractTask

run()
runCmd(cmd)
makeCmd()
AUTO_TASKDIR = <object object>
CMDLINE = 1
DEFAULT_TASKDIR_SETTING = None
DONE = 3
DataClass

alias of builtins.object

FAILED = 2
GUI = 2
INTERRUPT_ENABLED = False
RUNNING = 1
TEMP_TASKDIR = <object object>
WAITING = 0
__init__(*args, **kwargs)

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

addFuncToGroup(func, group=None, order=None)

Adds a function to the specified chain. Typically used for adding functions that are not methods of this object.

The function may optionally be decorated with a FuncGroupMarker. If so, the default group and order will be determined by the decorator. Any group or order explicitly passed in to addFuncToGroup will take precedence over the decorator settings.

Parameters:
  • func – the function to add
  • group (FuncGroupMarker or None) – the group marker. If the function is decorated with a FuncGoupMarker, that group marker will be the default.
  • order (float or None) – the sorting order. If the function is decorated with a FuncGoupMarker, the order specified in the decorator will be the default.
addPostprocessor(func, order=0)

Adds a postproceessor function to this task instance. If the function has been decorated with @postprocessor, the order specified by the decorator will be used.

Parameters:
  • func (typing.Callable) – the function to add
  • order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.
addPreprocessor(func, order=-2000)

Adds a preproceessor function to this task instance. If the function has been decorated with @preprocessor, the order specified by the decorator will be used as the default.

Parameters:
  • func – the function to add
  • order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.
classmethod addSubParam(name, param, update_owner=True)
blockSignals(self, bool) → bool
block_signal_propagation()
childEvent(self, QChildEvent)
children(self) → List[QObject]
classmethod configureParam()

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

connectNotify(self, QMetaMethod)
customEvent(self, QEvent)
classmethod defaultValue(*args, **kwargs)
deleteLater(self)
destroyed

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

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

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

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

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

classmethod fromJson(json_obj)

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

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

:rtype : cls

classmethod fromJsonFilename(filename)
classmethod fromJsonImplementation(json_dict)

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

getAbstractParam(*args, **kwargs)
getAddedFuncs(group=None)
getFuncGroup(group=None)

Retrieve the functions belonging to the specified group.

Parameters:group (FuncGroupMarker) – the group marker
Returns:the functions in the specified group, in order
Return type:list
classmethod getJsonBlacklist()

Override to customize what params are serialized.

Implementations should return a list of abstract params that should be omitted from serialization.

..NOTE
Returned abstract params must be direct child params of cls, e.g. cls.name, not cls.coord.x.
classmethod getParamSignal(*args, **kwargs)
classmethod getParamValue(*args, **kwargs)
classmethod getSubParam(name)

Get the value of a subparam using the string name:

c = Coord()
assert c.getSubParam('x') == 0

Note

Using the string name to accss params is generally discouraged, but can be useful for serializing/deserializing param data.

Parameters:name (str) – The name of the subparam to get the value for.
classmethod getSubParams()

Return a dictionary mapping subparam names to their values.

getTaskDir()

Returns the full path of the task directory. This is only available if the task directory exists (after creation of the taskdir or, if no task dir is specified, any time).

getTaskFilename(fname)

Return the appropriate absolute path for an input or output file in the taskdir.

getTypeHint()
get_version()

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

guard()

Context manager that saves any Exception raised inside

inherits(self, str) → bool
initAbstract()
initConcrete()

Override to customize initialization of concrete params.

initializeValue()

@overrides: parameters.CompoundParam

input
inputChanged
inputReplaced
installEventFilter(self, QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

isDefault(*args, **kwargs)
isInterruptionRequested()
isRunning()
isSignalConnected(self, QMetaMethod) → bool
isStartable()
isWidgetType(self) → bool
isWindowType(self) → bool
kill()

Implementations are responsible for immediately stopping the task. No threads or processes should be running after this method is complete.

This method should be called sparingly since in many contexts the task will be forced to terminate without a chance to clean up or free resources.

killTimer(self, int)
max_progress
max_progressChanged
max_progressReplaced
metaObject(self) → QMetaObject
moveToThread(self, QThread)
name
nameChanged
nameReplaced
objectName(self) → str
objectNameChanged

objectNameChanged(self, str) [signal]

output
outputChanged
outputReplaced
classmethod owner()

Get the owner of the param:

# Can be called on an abstract param:
assert Coord.x.owner() == Coord

# ...or on an instance of a CompoundParam
a = Atom()
assert a.coord.owner() == a
classmethod ownerChain()

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

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

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

classmethod paramName()

Get the name of the param:

# Can be called on an abstract param:
print(Coord.x.paramName()) # 'x'

# ...or on an instance of a CompoundParam
a = Atom()
a.coord.paramName() # 'coord'
parent(self) → QObject
postprocessors()
Returns:A list of postprocessors, both decorated methods on the task and external functions that have been added via addPostprocessor()
Return type:list[typing.Callable]
preprocessors()
Returns:A list of preprocessors (both decorated methods on the task and external functions that have been added via addPreprocessor)
processFuncChain(chain=None, result_callback=None)

Execute each function in the specified chain sequentially in order.

The result_callback is called after each function with the return value of that function. This can be used to respond to the return value (e.g. present information to the user, get user feedback, log the result, etc.)

The return value of the result_callback determines whether processing will proceeed to the next function.

Parameters:
  • chain (FuncChainDecorator) – which chain to process
  • result_callback – the callback that will get called with the result of each function in the chain
Returns:

a list of the results from the functions

progress
progressChanged
progressReplaced
property(self, str) → Any
pyqtConfigure(...)

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

receivers(self, PYQT_SIGNAL) → int
removeEventFilter(self, QObject)
replicate()

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

requestInterruption()

Request the task to stop.

To enable this feature, subclasses should periodically check whether an interruption has been requested and terminate if it has been. If such logic has been included, INTERRUPT_ENABLED should be set to True.

reset(*args, **kwargs)
classmethod runFromCmdLine()
runPostprocessing(callback=None)
runPreprocessing(callback=None, calling_context=None)

Run the preprocessors one-by-one. By default, any failing preprocessor will raise a TaskFailure exception and terminate processing. This behavior may be customized by supplying a callback function which will be called after each preprocessor with the result of that preprocessor.

Parameters:
  • callback – a function that takes result and returns a bool that indicates whether to continue on to the next preprocessor
  • calling_context – specify a value here to indicate the context in which this preprocessing is being called. This value will be stored in an instance variable, self.calling_context, which can be accessed from any preprocessor method on this task. Typically this value will be either self.GUI, self.CMDLINE, or None, but any value may be supplied here and checked for in the preprocessor methods. self.calling_context always reverts back to None at the end of runPreprocessing.
sender(self) → QObject
senderSignalIndex(self) → int
setObjectName(self, str)
classmethod setParamValue(*args, **kwargs)
setParent(self, QObject)
setProperty(self, str, Any) → bool
classmethod setReference(param1, param2)

Call this class method from configureParam to indicate that two params should be kept in sync. The initial values will start with the default value of param1. Example:

class Square(CompoundParam):
    width: float = 5
    height: float = 10

    @classmethod
    def configureParam(cls):
        super().configureParam()
        cls.setReference(cls.width, cls.height)

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6
Parameters:
  • param1 – The first abstract param to keep synced
  • param2 – The second abstract param. After instantiation, this param will take on the value of param1.
setValue(*args, **kwargs)
signalsBlocked(self) → bool
skip_eq_check()
specifyTaskDir(taskdir_spec)

Specify the taskdir creation behavior. Use one of the following options:

A directory name (string). This may be a relative or absolute path

None - no taskdir is requested. The task will use the CWD as its taskdir

AUTO_TASKDIR - a new subdirectory will be created in the CWD using the task name as the directory name.

TEMP_TASKDIR - a temporary directory will be created in the schrodinger temp dir. This directory is cleaned up when the task is deleted.

Parameters:taskdir_spec – one of the four options listed above
start(skip_preprocessing=False)

This is the main method for starting a task. Start will check if a task is not already running, run preprocessing, and then run the task.

Failures in preprocessing will interrupt the task start, and the task will never enter the RUNNING state.

Parameters:skip_preprocessing (bool) – whether to skip preprocessing. This can be useful if preprocessing was already performed prior to calling start.
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
status
statusChanged
statusReplaced
taskDirSetting()

Returns the taskdir spec. See specifyTaskDir() for details.

taskDone
taskFailed
taskStarted
thread(self) → QThread
timerEvent(self, QTimerEvent)
toDict(*args, **kwargs)
toJson(_mark_version=True)

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

Return type:An instance of one the classes from NATIVE_JSON_DATATYPES
toJsonImplementation(*args, **kwargs)
tr(self, str, disambiguation: str = None, n: int = -1) → str
valueChanged
wait(timeout=None)

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

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

Bases: schrodinger.tasks.tasks.AbstractCmdTask, schrodinger.tasks.tasks._AbstractFunctionTask

ENTRYPOINT = 'combotask_entry_point.py'
json_filename
json_out_filename
start(*args, **kwargs)

@overrides: AbstractTask

isBackendMode()
makeCmd()

@overrides: AbstractCmdTask

runPreprocessing(*args, **kwargs)

Run the preprocessors one-by-one. By default, any failing preprocessor will raise a TaskFailure exception and terminate processing. This behavior may be customized by supplying a callback function which will be called after each preprocessor with the result of that preprocessor.

Parameters:
  • callback – a function that takes result and returns a bool that indicates whether to continue on to the next preprocessor
  • calling_context – specify a value here to indicate the context in which this preprocessing is being called. This value will be stored in an instance variable, self.calling_context, which can be accessed from any preprocessor method on this task. Typically this value will be either self.GUI, self.CMDLINE, or None, but any value may be supplied here and checked for in the preprocessor methods. self.calling_context always reverts back to None at the end of runPreprocessing.
backendMain()
writeJsonFile(filename)
runBackend()
AUTO_TASKDIR = <object object>
CMDLINE = 1
DEFAULT_TASKDIR_SETTING = None
DONE = 3
DataClass

alias of builtins.object

FAILED = 2
GUI = 2
INTERRUPT_ENABLED = False
RUNNING = 1
TEMP_TASKDIR = <object object>
WAITING = 0
__init__(*args, **kwargs)

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

addFuncToGroup(func, group=None, order=None)

Adds a function to the specified chain. Typically used for adding functions that are not methods of this object.

The function may optionally be decorated with a FuncGroupMarker. If so, the default group and order will be determined by the decorator. Any group or order explicitly passed in to addFuncToGroup will take precedence over the decorator settings.

Parameters:
  • func – the function to add
  • group (FuncGroupMarker or None) – the group marker. If the function is decorated with a FuncGoupMarker, that group marker will be the default.
  • order (float or None) – the sorting order. If the function is decorated with a FuncGoupMarker, the order specified in the decorator will be the default.
addPostprocessor(func, order=0)

Adds a postproceessor function to this task instance. If the function has been decorated with @postprocessor, the order specified by the decorator will be used.

Parameters:
  • func (typing.Callable) – the function to add
  • order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.
addPreprocessor(func, order=-2000)

Adds a preproceessor function to this task instance. If the function has been decorated with @preprocessor, the order specified by the decorator will be used as the default.

Parameters:
  • func – the function to add
  • order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.
classmethod addSubParam(name, param, update_owner=True)
blockSignals(self, bool) → bool
block_signal_propagation()
childEvent(self, QChildEvent)
children(self) → List[QObject]
classmethod configureParam()

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

connectNotify(self, QMetaMethod)
customEvent(self, QEvent)
classmethod defaultValue(*args, **kwargs)
deleteLater(self)
destroyed

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

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

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

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

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

classmethod fromJson(json_obj)

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

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

:rtype : cls

classmethod fromJsonFilename(filename)
classmethod fromJsonImplementation(json_dict)

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

getAbstractParam(*args, **kwargs)
getAddedFuncs(group=None)
getFuncGroup(group=None)

Retrieve the functions belonging to the specified group.

Parameters:group (FuncGroupMarker) – the group marker
Returns:the functions in the specified group, in order
Return type:list
classmethod getJsonBlacklist()

Override to customize what params are serialized.

Implementations should return a list of abstract params that should be omitted from serialization.

..NOTE
Returned abstract params must be direct child params of cls, e.g. cls.name, not cls.coord.x.
classmethod getParamSignal(*args, **kwargs)
classmethod getParamValue(*args, **kwargs)
classmethod getSubParam(name)

Get the value of a subparam using the string name:

c = Coord()
assert c.getSubParam('x') == 0

Note

Using the string name to accss params is generally discouraged, but can be useful for serializing/deserializing param data.

Parameters:name (str) – The name of the subparam to get the value for.
classmethod getSubParams()

Return a dictionary mapping subparam names to their values.

getTaskDir()

Returns the full path of the task directory. This is only available if the task directory exists (after creation of the taskdir or, if no task dir is specified, any time).

getTaskFilename(fname)

Return the appropriate absolute path for an input or output file in the taskdir.

getTypeHint()
get_version()

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

guard()

Context manager that saves any Exception raised inside

inherits(self, str) → bool
initAbstract()
initConcrete()

Override to customize initialization of concrete params.

initializeValue()

@overrides: parameters.CompoundParam

input
inputChanged
inputReplaced
installEventFilter(self, QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

isDefault(*args, **kwargs)
isInterruptionRequested()
isRunning()
isSignalConnected(self, QMetaMethod) → bool
isStartable()
isWidgetType(self) → bool
isWindowType(self) → bool
kill()

Implementations are responsible for immediately stopping the task. No threads or processes should be running after this method is complete.

This method should be called sparingly since in many contexts the task will be forced to terminate without a chance to clean up or free resources.

killTimer(self, int)
mainFunction()
max_progress
max_progressChanged
max_progressReplaced
metaObject(self) → QMetaObject
moveToThread(self, QThread)
name
nameChanged
nameReplaced
objectName(self) → str
objectNameChanged

objectNameChanged(self, str) [signal]

output
outputChanged
outputReplaced
classmethod owner()

Get the owner of the param:

# Can be called on an abstract param:
assert Coord.x.owner() == Coord

# ...or on an instance of a CompoundParam
a = Atom()
assert a.coord.owner() == a
classmethod ownerChain()

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

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

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

classmethod paramName()

Get the name of the param:

# Can be called on an abstract param:
print(Coord.x.paramName()) # 'x'

# ...or on an instance of a CompoundParam
a = Atom()
a.coord.paramName() # 'coord'
parent(self) → QObject
postprocessors()
Returns:A list of postprocessors, both decorated methods on the task and external functions that have been added via addPostprocessor()
Return type:list[typing.Callable]
preprocessors()
Returns:A list of preprocessors (both decorated methods on the task and external functions that have been added via addPreprocessor)
processFuncChain(chain=None, result_callback=None)

Execute each function in the specified chain sequentially in order.

The result_callback is called after each function with the return value of that function. This can be used to respond to the return value (e.g. present information to the user, get user feedback, log the result, etc.)

The return value of the result_callback determines whether processing will proceeed to the next function.

Parameters:
  • chain (FuncChainDecorator) – which chain to process
  • result_callback – the callback that will get called with the result of each function in the chain
Returns:

a list of the results from the functions

progress
progressChanged
progressReplaced
property(self, str) → Any
pyqtConfigure(...)

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

receivers(self, PYQT_SIGNAL) → int
removeEventFilter(self, QObject)
replicate()

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

requestInterruption()

Request the task to stop.

To enable this feature, subclasses should periodically check whether an interruption has been requested and terminate if it has been. If such logic has been included, INTERRUPT_ENABLED should be set to True.

reset(*args, **kwargs)
run()
runCmd(cmd)
classmethod runFromCmdLine()
runPostprocessing(callback=None)
sender(self) → QObject
senderSignalIndex(self) → int
setObjectName(self, str)
classmethod setParamValue(*args, **kwargs)
setParent(self, QObject)
setProperty(self, str, Any) → bool
classmethod setReference(param1, param2)

Call this class method from configureParam to indicate that two params should be kept in sync. The initial values will start with the default value of param1. Example:

class Square(CompoundParam):
    width: float = 5
    height: float = 10

    @classmethod
    def configureParam(cls):
        super().configureParam()
        cls.setReference(cls.width, cls.height)

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6
Parameters:
  • param1 – The first abstract param to keep synced
  • param2 – The second abstract param. After instantiation, this param will take on the value of param1.
setValue(*args, **kwargs)
signalsBlocked(self) → bool
skip_eq_check()
specifyTaskDir(taskdir_spec)

Specify the taskdir creation behavior. Use one of the following options:

A directory name (string). This may be a relative or absolute path

None - no taskdir is requested. The task will use the CWD as its taskdir

AUTO_TASKDIR - a new subdirectory will be created in the CWD using the task name as the directory name.

TEMP_TASKDIR - a temporary directory will be created in the schrodinger temp dir. This directory is cleaned up when the task is deleted.

Parameters:taskdir_spec – one of the four options listed above
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
status
statusChanged
statusReplaced
taskDirSetting()

Returns the taskdir spec. See specifyTaskDir() for details.

taskDone
taskFailed
taskStarted
thread(self) → QThread
timerEvent(self, QTimerEvent)
toDict(*args, **kwargs)
toJson(_mark_version=True)

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

Return type:An instance of one the classes from NATIVE_JSON_DATATYPES
toJsonImplementation(*args, **kwargs)
tr(self, str, disambiguation: str = None, n: int = -1) → str
valueChanged
wait(timeout=None)

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

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

Bases: object

Compatible with subclasses of AbstractFunctionTask.

__init__

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

class schrodinger.tasks.tasks.ThreadMixin(*args, **kwargs)

Bases: schrodinger.tasks.tasks._SaveTaskReferenceMixin

MAX_THREAD_TASKS = 500
__init__(*args, **kwargs)

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

kill()

@overrides: AbstractTask

Killing threads is dangerous and can leading to deadlocking on Windows, so we intentionally leave it unimplemented rather than using QThread.terminate.

start(*args, **kwargs)
exception schrodinger.tasks.tasks.QProcessError(message)

Bases: Exception

__init__(message)

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

args
with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception schrodinger.tasks.tasks.QProcessFailedToStartError(message)

Bases: schrodinger.tasks.tasks.QProcessError

__init__(message)

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

args
with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception schrodinger.tasks.tasks.QProcessCrashedError(message)

Bases: schrodinger.tasks.tasks.QProcessError

__init__(message)

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

args
with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception schrodinger.tasks.tasks.QProcessTimedout(message)

Bases: schrodinger.tasks.tasks.QProcessError

__init__(message)

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

args
with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception schrodinger.tasks.tasks.QProcessWriteError(message)

Bases: schrodinger.tasks.tasks.QProcessError

__init__(message)

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

args
with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception schrodinger.tasks.tasks.QProcessReadError(message)

Bases: schrodinger.tasks.tasks.QProcessError

__init__(message)

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

args
with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

exception schrodinger.tasks.tasks.QProcessUnknownError(message)

Bases: schrodinger.tasks.tasks.QProcessError

__init__(message)

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

args
with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

class schrodinger.tasks.tasks.SubprocessMixin(*args, **kwargs)

Bases: schrodinger.tasks.tasks._SaveTaskReferenceMixin

__init__(*args, **kwargs)

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

printingOutputToTerminal()
Returns:whether the StdOut and StdErr output from this task is being printed to the terminal
Return type:bool
setPrintingOutputToTerminal(print_to_terminal)

Set this task to print StdOut and StdErr output to terminal, or not.

Parameters:print_to_terminal (bool) – whether to send process output to terminal
runCmd(cmd)
getLogAsString()
kill()

@overrides: AbstractTask

Kill the subprocess and set the status to FAILED.

start(*args, **kwargs)
class schrodinger.tasks.tasks.BlockingFunctionTask(*args, **kwargs)

Bases: schrodinger.tasks.tasks.BlockingMixin, schrodinger.tasks.tasks._AbstractFunctionTask

A task that simply runs a function and blocks for the duration of it. To use, implement mainFunction.

AUTO_TASKDIR = <object object>
CMDLINE = 1
DEFAULT_TASKDIR_SETTING = None
DONE = 3
DataClass

alias of builtins.object

FAILED = 2
GUI = 2
INTERRUPT_ENABLED = False
RUNNING = 1
TEMP_TASKDIR = <object object>
WAITING = 0
__init__(*args, **kwargs)

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

addFuncToGroup(func, group=None, order=None)

Adds a function to the specified chain. Typically used for adding functions that are not methods of this object.

The function may optionally be decorated with a FuncGroupMarker. If so, the default group and order will be determined by the decorator. Any group or order explicitly passed in to addFuncToGroup will take precedence over the decorator settings.

Parameters:
  • func – the function to add
  • group (FuncGroupMarker or None) – the group marker. If the function is decorated with a FuncGoupMarker, that group marker will be the default.
  • order (float or None) – the sorting order. If the function is decorated with a FuncGoupMarker, the order specified in the decorator will be the default.
addPostprocessor(func, order=0)

Adds a postproceessor function to this task instance. If the function has been decorated with @postprocessor, the order specified by the decorator will be used.

Parameters:
  • func (typing.Callable) – the function to add
  • order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.
addPreprocessor(func, order=-2000)

Adds a preproceessor function to this task instance. If the function has been decorated with @preprocessor, the order specified by the decorator will be used as the default.

Parameters:
  • func – the function to add
  • order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.
classmethod addSubParam(name, param, update_owner=True)
blockSignals(self, bool) → bool
block_signal_propagation()
childEvent(self, QChildEvent)
children(self) → List[QObject]
classmethod configureParam()

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

connectNotify(self, QMetaMethod)
customEvent(self, QEvent)
classmethod defaultValue(*args, **kwargs)
deleteLater(self)
destroyed

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

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

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

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

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

classmethod fromJson(json_obj)

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

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

:rtype : cls

classmethod fromJsonFilename(filename)
classmethod fromJsonImplementation(json_dict)

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

getAbstractParam(*args, **kwargs)
getAddedFuncs(group=None)
getFuncGroup(group=None)

Retrieve the functions belonging to the specified group.

Parameters:group (FuncGroupMarker) – the group marker
Returns:the functions in the specified group, in order
Return type:list
classmethod getJsonBlacklist()

Override to customize what params are serialized.

Implementations should return a list of abstract params that should be omitted from serialization.

..NOTE
Returned abstract params must be direct child params of cls, e.g. cls.name, not cls.coord.x.
classmethod getParamSignal(*args, **kwargs)
classmethod getParamValue(*args, **kwargs)
classmethod getSubParam(name)

Get the value of a subparam using the string name:

c = Coord()
assert c.getSubParam('x') == 0

Note

Using the string name to accss params is generally discouraged, but can be useful for serializing/deserializing param data.

Parameters:name (str) – The name of the subparam to get the value for.
classmethod getSubParams()

Return a dictionary mapping subparam names to their values.

getTaskDir()

Returns the full path of the task directory. This is only available if the task directory exists (after creation of the taskdir or, if no task dir is specified, any time).

getTaskFilename(fname)

Return the appropriate absolute path for an input or output file in the taskdir.

getTypeHint()
get_version()

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

guard()

Context manager that saves any Exception raised inside

inherits(self, str) → bool
initAbstract()
initConcrete()

Override to customize initialization of concrete params.

initializeValue()

@overrides: parameters.CompoundParam

input
inputChanged
inputReplaced
installEventFilter(self, QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

isDefault(*args, **kwargs)
isInterruptionRequested()
isRunning()
isSignalConnected(self, QMetaMethod) → bool
isStartable()
isWidgetType(self) → bool
isWindowType(self) → bool
kill()

Implementations are responsible for immediately stopping the task. No threads or processes should be running after this method is complete.

This method should be called sparingly since in many contexts the task will be forced to terminate without a chance to clean up or free resources.

killTimer(self, int)
mainFunction()
max_progress
max_progressChanged
max_progressReplaced
metaObject(self) → QMetaObject
moveToThread(self, QThread)
name
nameChanged
nameReplaced
objectName(self) → str
objectNameChanged

objectNameChanged(self, str) [signal]

output
outputChanged
outputReplaced
classmethod owner()

Get the owner of the param:

# Can be called on an abstract param:
assert Coord.x.owner() == Coord

# ...or on an instance of a CompoundParam
a = Atom()
assert a.coord.owner() == a
classmethod ownerChain()

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

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

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

classmethod paramName()

Get the name of the param:

# Can be called on an abstract param:
print(Coord.x.paramName()) # 'x'

# ...or on an instance of a CompoundParam
a = Atom()
a.coord.paramName() # 'coord'
parent(self) → QObject
postprocessors()
Returns:A list of postprocessors, both decorated methods on the task and external functions that have been added via addPostprocessor()
Return type:list[typing.Callable]
preprocessors()
Returns:A list of preprocessors (both decorated methods on the task and external functions that have been added via addPreprocessor)
processFuncChain(chain=None, result_callback=None)

Execute each function in the specified chain sequentially in order.

The result_callback is called after each function with the return value of that function. This can be used to respond to the return value (e.g. present information to the user, get user feedback, log the result, etc.)

The return value of the result_callback determines whether processing will proceeed to the next function.

Parameters:
  • chain (FuncChainDecorator) – which chain to process
  • result_callback – the callback that will get called with the result of each function in the chain
Returns:

a list of the results from the functions

progress
progressChanged
progressReplaced
property(self, str) → Any
pyqtConfigure(...)

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

receivers(self, PYQT_SIGNAL) → int
removeEventFilter(self, QObject)
replicate()

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

requestInterruption()

Request the task to stop.

To enable this feature, subclasses should periodically check whether an interruption has been requested and terminate if it has been. If such logic has been included, INTERRUPT_ENABLED should be set to True.

reset(*args, **kwargs)
run()
classmethod runFromCmdLine()
runPostprocessing(callback=None)
runPreprocessing(callback=None, calling_context=None)

Run the preprocessors one-by-one. By default, any failing preprocessor will raise a TaskFailure exception and terminate processing. This behavior may be customized by supplying a callback function which will be called after each preprocessor with the result of that preprocessor.

Parameters:
  • callback – a function that takes result and returns a bool that indicates whether to continue on to the next preprocessor
  • calling_context – specify a value here to indicate the context in which this preprocessing is being called. This value will be stored in an instance variable, self.calling_context, which can be accessed from any preprocessor method on this task. Typically this value will be either self.GUI, self.CMDLINE, or None, but any value may be supplied here and checked for in the preprocessor methods. self.calling_context always reverts back to None at the end of runPreprocessing.
sender(self) → QObject
senderSignalIndex(self) → int
setObjectName(self, str)
classmethod setParamValue(*args, **kwargs)
setParent(self, QObject)
setProperty(self, str, Any) → bool
classmethod setReference(param1, param2)

Call this class method from configureParam to indicate that two params should be kept in sync. The initial values will start with the default value of param1. Example:

class Square(CompoundParam):
    width: float = 5
    height: float = 10

    @classmethod
    def configureParam(cls):
        super().configureParam()
        cls.setReference(cls.width, cls.height)

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6
Parameters:
  • param1 – The first abstract param to keep synced
  • param2 – The second abstract param. After instantiation, this param will take on the value of param1.
setValue(*args, **kwargs)
signalsBlocked(self) → bool
skip_eq_check()
specifyTaskDir(taskdir_spec)

Specify the taskdir creation behavior. Use one of the following options:

A directory name (string). This may be a relative or absolute path

None - no taskdir is requested. The task will use the CWD as its taskdir

AUTO_TASKDIR - a new subdirectory will be created in the CWD using the task name as the directory name.

TEMP_TASKDIR - a temporary directory will be created in the schrodinger temp dir. This directory is cleaned up when the task is deleted.

Parameters:taskdir_spec – one of the four options listed above
start(skip_preprocessing=False)

This is the main method for starting a task. Start will check if a task is not already running, run preprocessing, and then run the task.

Failures in preprocessing will interrupt the task start, and the task will never enter the RUNNING state.

Parameters:skip_preprocessing (bool) – whether to skip preprocessing. This can be useful if preprocessing was already performed prior to calling start.
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
status
statusChanged
statusReplaced
taskDirSetting()

Returns the taskdir spec. See specifyTaskDir() for details.

taskDone
taskFailed
taskStarted
thread(self) → QThread
timerEvent(self, QTimerEvent)
toDict(*args, **kwargs)
toJson(_mark_version=True)

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

Return type:An instance of one the classes from NATIVE_JSON_DATATYPES
toJsonImplementation(*args, **kwargs)
tr(self, str, disambiguation: str = None, n: int = -1) → str
valueChanged
wait(timeout=None)

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

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

Bases: schrodinger.tasks.tasks.ThreadMixin, schrodinger.tasks.tasks._AbstractFunctionTask

A task that runs a function in a separate thread. To use, implement mainFunction.

AUTO_TASKDIR = <object object>
CMDLINE = 1
DEFAULT_TASKDIR_SETTING = None
DONE = 3
DataClass

alias of builtins.object

FAILED = 2
GUI = 2
INTERRUPT_ENABLED = False
MAX_THREAD_TASKS = 500
RUNNING = 1
TEMP_TASKDIR = <object object>
WAITING = 0
__init__(*args, **kwargs)

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

addFuncToGroup(func, group=None, order=None)

Adds a function to the specified chain. Typically used for adding functions that are not methods of this object.

The function may optionally be decorated with a FuncGroupMarker. If so, the default group and order will be determined by the decorator. Any group or order explicitly passed in to addFuncToGroup will take precedence over the decorator settings.

Parameters:
  • func – the function to add
  • group (FuncGroupMarker or None) – the group marker. If the function is decorated with a FuncGoupMarker, that group marker will be the default.
  • order (float or None) – the sorting order. If the function is decorated with a FuncGoupMarker, the order specified in the decorator will be the default.
addPostprocessor(func, order=0)

Adds a postproceessor function to this task instance. If the function has been decorated with @postprocessor, the order specified by the decorator will be used.

Parameters:
  • func (typing.Callable) – the function to add
  • order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.
addPreprocessor(func, order=-2000)

Adds a preproceessor function to this task instance. If the function has been decorated with @preprocessor, the order specified by the decorator will be used as the default.

Parameters:
  • func – the function to add
  • order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.
classmethod addSubParam(name, param, update_owner=True)
blockSignals(self, bool) → bool
block_signal_propagation()
childEvent(self, QChildEvent)
children(self) → List[QObject]
classmethod configureParam()

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

connectNotify(self, QMetaMethod)
customEvent(self, QEvent)
classmethod defaultValue(*args, **kwargs)
deleteLater(self)
destroyed

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

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

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

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

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

classmethod fromJson(json_obj)

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

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

:rtype : cls

classmethod fromJsonFilename(filename)
classmethod fromJsonImplementation(json_dict)

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

getAbstractParam(*args, **kwargs)
getAddedFuncs(group=None)
getFuncGroup(group=None)

Retrieve the functions belonging to the specified group.

Parameters:group (FuncGroupMarker) – the group marker
Returns:the functions in the specified group, in order
Return type:list
classmethod getJsonBlacklist()

Override to customize what params are serialized.

Implementations should return a list of abstract params that should be omitted from serialization.

..NOTE
Returned abstract params must be direct child params of cls, e.g. cls.name, not cls.coord.x.
classmethod getParamSignal(*args, **kwargs)
classmethod getParamValue(*args, **kwargs)
classmethod getSubParam(name)

Get the value of a subparam using the string name:

c = Coord()
assert c.getSubParam('x') == 0

Note

Using the string name to accss params is generally discouraged, but can be useful for serializing/deserializing param data.

Parameters:name (str) – The name of the subparam to get the value for.
classmethod getSubParams()

Return a dictionary mapping subparam names to their values.

getTaskDir()

Returns the full path of the task directory. This is only available if the task directory exists (after creation of the taskdir or, if no task dir is specified, any time).

getTaskFilename(fname)

Return the appropriate absolute path for an input or output file in the taskdir.

getTypeHint()
get_version()

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

guard()

Context manager that saves any Exception raised inside

inherits(self, str) → bool
initAbstract()
initConcrete()

Override to customize initialization of concrete params.

initializeValue()

@overrides: parameters.CompoundParam

input
inputChanged
inputReplaced
installEventFilter(self, QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

isDefault(*args, **kwargs)
isInterruptionRequested()
isRunning()
isSignalConnected(self, QMetaMethod) → bool
isStartable()
isWidgetType(self) → bool
isWindowType(self) → bool
kill()

@overrides: AbstractTask

Killing threads is dangerous and can leading to deadlocking on Windows, so we intentionally leave it unimplemented rather than using QThread.terminate.

killTimer(self, int)
mainFunction()
max_progress
max_progressChanged
max_progressReplaced
metaObject(self) → QMetaObject
moveToThread(self, QThread)
name
nameChanged
nameReplaced
objectName(self) → str
objectNameChanged

objectNameChanged(self, str) [signal]

output
outputChanged
outputReplaced
classmethod owner()

Get the owner of the param:

# Can be called on an abstract param:
assert Coord.x.owner() == Coord

# ...or on an instance of a CompoundParam
a = Atom()
assert a.coord.owner() == a
classmethod ownerChain()

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

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

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

classmethod paramName()

Get the name of the param:

# Can be called on an abstract param:
print(Coord.x.paramName()) # 'x'

# ...or on an instance of a CompoundParam
a = Atom()
a.coord.paramName() # 'coord'
parent(self) → QObject
postprocessors()
Returns:A list of postprocessors, both decorated methods on the task and external functions that have been added via addPostprocessor()
Return type:list[typing.Callable]
preprocessors()
Returns:A list of preprocessors (both decorated methods on the task and external functions that have been added via addPreprocessor)
processFuncChain(chain=None, result_callback=None)

Execute each function in the specified chain sequentially in order.

The result_callback is called after each function with the return value of that function. This can be used to respond to the return value (e.g. present information to the user, get user feedback, log the result, etc.)

The return value of the result_callback determines whether processing will proceeed to the next function.

Parameters:
  • chain (FuncChainDecorator) – which chain to process
  • result_callback – the callback that will get called with the result of each function in the chain
Returns:

a list of the results from the functions

progress
progressChanged
progressReplaced
property(self, str) → Any
pyqtConfigure(...)

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

receivers(self, PYQT_SIGNAL) → int
removeEventFilter(self, QObject)
replicate()

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

requestInterruption()

Request the task to stop.

To enable this feature, subclasses should periodically check whether an interruption has been requested and terminate if it has been. If such logic has been included, INTERRUPT_ENABLED should be set to True.

reset(*args, **kwargs)
run()
classmethod runFromCmdLine()
runPostprocessing(callback=None)
runPreprocessing(callback=None, calling_context=None)

Run the preprocessors one-by-one. By default, any failing preprocessor will raise a TaskFailure exception and terminate processing. This behavior may be customized by supplying a callback function which will be called after each preprocessor with the result of that preprocessor.

Parameters:
  • callback – a function that takes result and returns a bool that indicates whether to continue on to the next preprocessor
  • calling_context – specify a value here to indicate the context in which this preprocessing is being called. This value will be stored in an instance variable, self.calling_context, which can be accessed from any preprocessor method on this task. Typically this value will be either self.GUI, self.CMDLINE, or None, but any value may be supplied here and checked for in the preprocessor methods. self.calling_context always reverts back to None at the end of runPreprocessing.
sender(self) → QObject
senderSignalIndex(self) → int
setObjectName(self, str)
classmethod setParamValue(*args, **kwargs)
setParent(self, QObject)
setProperty(self, str, Any) → bool
classmethod setReference(param1, param2)

Call this class method from configureParam to indicate that two params should be kept in sync. The initial values will start with the default value of param1. Example:

class Square(CompoundParam):
    width: float = 5
    height: float = 10

    @classmethod
    def configureParam(cls):
        super().configureParam()
        cls.setReference(cls.width, cls.height)

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6
Parameters:
  • param1 – The first abstract param to keep synced
  • param2 – The second abstract param. After instantiation, this param will take on the value of param1.
setValue(*args, **kwargs)
signalsBlocked(self) → bool
skip_eq_check()
specifyTaskDir(taskdir_spec)

Specify the taskdir creation behavior. Use one of the following options:

A directory name (string). This may be a relative or absolute path

None - no taskdir is requested. The task will use the CWD as its taskdir

AUTO_TASKDIR - a new subdirectory will be created in the CWD using the task name as the directory name.

TEMP_TASKDIR - a temporary directory will be created in the schrodinger temp dir. This directory is cleaned up when the task is deleted.

Parameters:taskdir_spec – one of the four options listed above
start(*args, **kwargs)
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
status
statusChanged
statusReplaced
taskDirSetting()

Returns the taskdir spec. See specifyTaskDir() for details.

taskDone
taskFailed
taskStarted
thread(self) → QThread
timerEvent(self, QTimerEvent)
toDict(*args, **kwargs)
toJson(_mark_version=True)

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

Return type:An instance of one the classes from NATIVE_JSON_DATATYPES
toJsonImplementation(*args, **kwargs)
tr(self, str, disambiguation: str = None, n: int = -1) → str
valueChanged
wait(timeout=None)

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

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

Bases: schrodinger.tasks.tasks.SubprocessMixin, schrodinger.tasks.tasks.AbstractCmdTask

A task that launches a subprocess. To use, implement makeCmd and return a list of strings.

AUTO_TASKDIR = <object object>
CMDLINE = 1
DEFAULT_TASKDIR_SETTING = None
DONE = 3
DataClass

alias of builtins.object

FAILED = 2
GUI = 2
INTERRUPT_ENABLED = False
RUNNING = 1
TEMP_TASKDIR = <object object>
WAITING = 0
__init__(*args, **kwargs)

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

addFuncToGroup(func, group=None, order=None)

Adds a function to the specified chain. Typically used for adding functions that are not methods of this object.

The function may optionally be decorated with a FuncGroupMarker. If so, the default group and order will be determined by the decorator. Any group or order explicitly passed in to addFuncToGroup will take precedence over the decorator settings.

Parameters:
  • func – the function to add
  • group (FuncGroupMarker or None) – the group marker. If the function is decorated with a FuncGoupMarker, that group marker will be the default.
  • order (float or None) – the sorting order. If the function is decorated with a FuncGoupMarker, the order specified in the decorator will be the default.
addPostprocessor(func, order=0)

Adds a postproceessor function to this task instance. If the function has been decorated with @postprocessor, the order specified by the decorator will be used.

Parameters:
  • func (typing.Callable) – the function to add
  • order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.
addPreprocessor(func, order=-2000)

Adds a preproceessor function to this task instance. If the function has been decorated with @preprocessor, the order specified by the decorator will be used as the default.

Parameters:
  • func – the function to add
  • order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.
classmethod addSubParam(name, param, update_owner=True)
blockSignals(self, bool) → bool
block_signal_propagation()
childEvent(self, QChildEvent)
children(self) → List[QObject]
classmethod configureParam()

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

connectNotify(self, QMetaMethod)
customEvent(self, QEvent)
classmethod defaultValue(*args, **kwargs)
deleteLater(self)
destroyed

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

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

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

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

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

classmethod fromJson(json_obj)

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

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

:rtype : cls

classmethod fromJsonFilename(filename)
classmethod fromJsonImplementation(json_dict)

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

getAbstractParam(*args, **kwargs)
getAddedFuncs(group=None)
getFuncGroup(group=None)

Retrieve the functions belonging to the specified group.

Parameters:group (FuncGroupMarker) – the group marker
Returns:the functions in the specified group, in order
Return type:list
classmethod getJsonBlacklist()

Override to customize what params are serialized.

Implementations should return a list of abstract params that should be omitted from serialization.

..NOTE
Returned abstract params must be direct child params of cls, e.g. cls.name, not cls.coord.x.
getLogAsString()
classmethod getParamSignal(*args, **kwargs)
classmethod getParamValue(*args, **kwargs)
classmethod getSubParam(name)

Get the value of a subparam using the string name:

c = Coord()
assert c.getSubParam('x') == 0

Note

Using the string name to accss params is generally discouraged, but can be useful for serializing/deserializing param data.

Parameters:name (str) – The name of the subparam to get the value for.
classmethod getSubParams()

Return a dictionary mapping subparam names to their values.

getTaskDir()

Returns the full path of the task directory. This is only available if the task directory exists (after creation of the taskdir or, if no task dir is specified, any time).

getTaskFilename(fname)

Return the appropriate absolute path for an input or output file in the taskdir.

getTypeHint()
get_version()

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

guard()

Context manager that saves any Exception raised inside

inherits(self, str) → bool
initAbstract()
initConcrete()

Override to customize initialization of concrete params.

initializeValue()

@overrides: parameters.CompoundParam

input
inputChanged
inputReplaced
installEventFilter(self, QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

isDefault(*args, **kwargs)
isInterruptionRequested()
isRunning()
isSignalConnected(self, QMetaMethod) → bool
isStartable()
isWidgetType(self) → bool
isWindowType(self) → bool
kill()

@overrides: AbstractTask

Kill the subprocess and set the status to FAILED.

killTimer(self, int)
makeCmd()
max_progress
max_progressChanged
max_progressReplaced
metaObject(self) → QMetaObject
moveToThread(self, QThread)
name
nameChanged
nameReplaced
objectName(self) → str
objectNameChanged

objectNameChanged(self, str) [signal]

output
outputChanged
outputReplaced
classmethod owner()

Get the owner of the param:

# Can be called on an abstract param:
assert Coord.x.owner() == Coord

# ...or on an instance of a CompoundParam
a = Atom()
assert a.coord.owner() == a
classmethod ownerChain()

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

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

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

classmethod paramName()

Get the name of the param:

# Can be called on an abstract param:
print(Coord.x.paramName()) # 'x'

# ...or on an instance of a CompoundParam
a = Atom()
a.coord.paramName() # 'coord'
parent(self) → QObject
postprocessors()
Returns:A list of postprocessors, both decorated methods on the task and external functions that have been added via addPostprocessor()
Return type:list[typing.Callable]
preprocessors()
Returns:A list of preprocessors (both decorated methods on the task and external functions that have been added via addPreprocessor)
printingOutputToTerminal()
Returns:whether the StdOut and StdErr output from this task is being printed to the terminal
Return type:bool
processFuncChain(chain=None, result_callback=None)

Execute each function in the specified chain sequentially in order.

The result_callback is called after each function with the return value of that function. This can be used to respond to the return value (e.g. present information to the user, get user feedback, log the result, etc.)

The return value of the result_callback determines whether processing will proceeed to the next function.

Parameters:
  • chain (FuncChainDecorator) – which chain to process
  • result_callback – the callback that will get called with the result of each function in the chain
Returns:

a list of the results from the functions

progress
progressChanged
progressReplaced
property(self, str) → Any
pyqtConfigure(...)

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

receivers(self, PYQT_SIGNAL) → int
removeEventFilter(self, QObject)
replicate()

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

requestInterruption()

Request the task to stop.

To enable this feature, subclasses should periodically check whether an interruption has been requested and terminate if it has been. If such logic has been included, INTERRUPT_ENABLED should be set to True.

reset(*args, **kwargs)
run()
runCmd(cmd)
classmethod runFromCmdLine()
runPostprocessing(callback=None)
runPreprocessing(callback=None, calling_context=None)

Run the preprocessors one-by-one. By default, any failing preprocessor will raise a TaskFailure exception and terminate processing. This behavior may be customized by supplying a callback function which will be called after each preprocessor with the result of that preprocessor.

Parameters:
  • callback – a function that takes result and returns a bool that indicates whether to continue on to the next preprocessor
  • calling_context – specify a value here to indicate the context in which this preprocessing is being called. This value will be stored in an instance variable, self.calling_context, which can be accessed from any preprocessor method on this task. Typically this value will be either self.GUI, self.CMDLINE, or None, but any value may be supplied here and checked for in the preprocessor methods. self.calling_context always reverts back to None at the end of runPreprocessing.
sender(self) → QObject
senderSignalIndex(self) → int
setObjectName(self, str)
classmethod setParamValue(*args, **kwargs)
setParent(self, QObject)
setPrintingOutputToTerminal(print_to_terminal)

Set this task to print StdOut and StdErr output to terminal, or not.

Parameters:print_to_terminal (bool) – whether to send process output to terminal
setProperty(self, str, Any) → bool
classmethod setReference(param1, param2)

Call this class method from configureParam to indicate that two params should be kept in sync. The initial values will start with the default value of param1. Example:

class Square(CompoundParam):
    width: float = 5
    height: float = 10

    @classmethod
    def configureParam(cls):
        super().configureParam()
        cls.setReference(cls.width, cls.height)

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6
Parameters:
  • param1 – The first abstract param to keep synced
  • param2 – The second abstract param. After instantiation, this param will take on the value of param1.
setValue(*args, **kwargs)
signalsBlocked(self) → bool
skip_eq_check()
specifyTaskDir(taskdir_spec)

Specify the taskdir creation behavior. Use one of the following options:

A directory name (string). This may be a relative or absolute path

None - no taskdir is requested. The task will use the CWD as its taskdir

AUTO_TASKDIR - a new subdirectory will be created in the CWD using the task name as the directory name.

TEMP_TASKDIR - a temporary directory will be created in the schrodinger temp dir. This directory is cleaned up when the task is deleted.

Parameters:taskdir_spec – one of the four options listed above
start(*args, **kwargs)
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
status
statusChanged
statusReplaced
taskDirSetting()

Returns the taskdir spec. See specifyTaskDir() for details.

taskDone
taskFailed
taskStarted
thread(self) → QThread
timerEvent(self, QTimerEvent)
toDict(*args, **kwargs)
toJson(_mark_version=True)

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

Return type:An instance of one the classes from NATIVE_JSON_DATATYPES
toJsonImplementation(*args, **kwargs)
tr(self, str, disambiguation: str = None, n: int = -1) → str
valueChanged
wait(timeout=None)

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

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

Bases: schrodinger.tasks.tasks.AbstractComboTask

This is mostly for testing purposes.

runCmd(cmd)
AUTO_TASKDIR = <object object>
CMDLINE = 1
DEFAULT_TASKDIR_SETTING = None
DONE = 3
DataClass

alias of builtins.object

ENTRYPOINT = 'combotask_entry_point.py'
FAILED = 2
GUI = 2
INTERRUPT_ENABLED = False
RUNNING = 1
TEMP_TASKDIR = <object object>
WAITING = 0
__init__(*args, **kwargs)

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

addFuncToGroup(func, group=None, order=None)

Adds a function to the specified chain. Typically used for adding functions that are not methods of this object.

The function may optionally be decorated with a FuncGroupMarker. If so, the default group and order will be determined by the decorator. Any group or order explicitly passed in to addFuncToGroup will take precedence over the decorator settings.

Parameters:
  • func – the function to add
  • group (FuncGroupMarker or None) – the group marker. If the function is decorated with a FuncGoupMarker, that group marker will be the default.
  • order (float or None) – the sorting order. If the function is decorated with a FuncGoupMarker, the order specified in the decorator will be the default.
addPostprocessor(func, order=0)

Adds a postproceessor function to this task instance. If the function has been decorated with @postprocessor, the order specified by the decorator will be used.

Parameters:
  • func (typing.Callable) – the function to add
  • order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.
addPreprocessor(func, order=-2000)

Adds a preproceessor function to this task instance. If the function has been decorated with @preprocessor, the order specified by the decorator will be used as the default.

Parameters:
  • func – the function to add
  • order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.
classmethod addSubParam(name, param, update_owner=True)
backendMain()
blockSignals(self, bool) → bool
block_signal_propagation()
childEvent(self, QChildEvent)
children(self) → List[QObject]
classmethod configureParam()

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

connectNotify(self, QMetaMethod)
customEvent(self, QEvent)
classmethod defaultValue(*args, **kwargs)
deleteLater(self)
destroyed

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

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

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

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

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

classmethod fromJson(json_obj)

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

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

:rtype : cls

classmethod fromJsonFilename(filename)
classmethod fromJsonImplementation(json_dict)

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

getAbstractParam(*args, **kwargs)
getAddedFuncs(group=None)
getFuncGroup(group=None)

Retrieve the functions belonging to the specified group.

Parameters:group (FuncGroupMarker) – the group marker
Returns:the functions in the specified group, in order
Return type:list
classmethod getJsonBlacklist()

Override to customize what params are serialized.

Implementations should return a list of abstract params that should be omitted from serialization.

..NOTE
Returned abstract params must be direct child params of cls, e.g. cls.name, not cls.coord.x.
classmethod getParamSignal(*args, **kwargs)
classmethod getParamValue(*args, **kwargs)
classmethod getSubParam(name)

Get the value of a subparam using the string name:

c = Coord()
assert c.getSubParam('x') == 0

Note

Using the string name to accss params is generally discouraged, but can be useful for serializing/deserializing param data.

Parameters:name (str) – The name of the subparam to get the value for.
classmethod getSubParams()

Return a dictionary mapping subparam names to their values.

getTaskDir()

Returns the full path of the task directory. This is only available if the task directory exists (after creation of the taskdir or, if no task dir is specified, any time).

getTaskFilename(fname)

Return the appropriate absolute path for an input or output file in the taskdir.

getTypeHint()
get_version()

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

guard()

Context manager that saves any Exception raised inside

inherits(self, str) → bool
initAbstract()
initConcrete()

Override to customize initialization of concrete params.

initializeValue()

@overrides: parameters.CompoundParam

input
inputChanged
inputReplaced
installEventFilter(self, QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

isBackendMode()
isDefault(*args, **kwargs)
isInterruptionRequested()
isRunning()
isSignalConnected(self, QMetaMethod) → bool
isStartable()
isWidgetType(self) → bool
isWindowType(self) → bool
json_filename
json_out_filename
kill()

Implementations are responsible for immediately stopping the task. No threads or processes should be running after this method is complete.

This method should be called sparingly since in many contexts the task will be forced to terminate without a chance to clean up or free resources.

killTimer(self, int)
mainFunction()
makeCmd()

@overrides: AbstractCmdTask

max_progress
max_progressChanged
max_progressReplaced
metaObject(self) → QMetaObject
moveToThread(self, QThread)
name
nameChanged
nameReplaced
objectName(self) → str
objectNameChanged

objectNameChanged(self, str) [signal]

output
outputChanged
outputReplaced
classmethod owner()

Get the owner of the param:

# Can be called on an abstract param:
assert Coord.x.owner() == Coord

# ...or on an instance of a CompoundParam
a = Atom()
assert a.coord.owner() == a
classmethod ownerChain()

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

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

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

classmethod paramName()

Get the name of the param:

# Can be called on an abstract param:
print(Coord.x.paramName()) # 'x'

# ...or on an instance of a CompoundParam
a = Atom()
a.coord.paramName() # 'coord'
parent(self) → QObject
postprocessors()
Returns:A list of postprocessors, both decorated methods on the task and external functions that have been added via addPostprocessor()
Return type:list[typing.Callable]
preprocessors()
Returns:A list of preprocessors (both decorated methods on the task and external functions that have been added via addPreprocessor)
processFuncChain(chain=None, result_callback=None)

Execute each function in the specified chain sequentially in order.

The result_callback is called after each function with the return value of that function. This can be used to respond to the return value (e.g. present information to the user, get user feedback, log the result, etc.)

The return value of the result_callback determines whether processing will proceeed to the next function.

Parameters:
  • chain (FuncChainDecorator) – which chain to process
  • result_callback – the callback that will get called with the result of each function in the chain
Returns:

a list of the results from the functions

progress
progressChanged
progressReplaced
property(self, str) → Any
pyqtConfigure(...)

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

receivers(self, PYQT_SIGNAL) → int
removeEventFilter(self, QObject)
replicate()

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

requestInterruption()

Request the task to stop.

To enable this feature, subclasses should periodically check whether an interruption has been requested and terminate if it has been. If such logic has been included, INTERRUPT_ENABLED should be set to True.

reset(*args, **kwargs)
run()
runBackend()
classmethod runFromCmdLine()
runPostprocessing(callback=None)
runPreprocessing(*args, **kwargs)

Run the preprocessors one-by-one. By default, any failing preprocessor will raise a TaskFailure exception and terminate processing. This behavior may be customized by supplying a callback function which will be called after each preprocessor with the result of that preprocessor.

Parameters:
  • callback – a function that takes result and returns a bool that indicates whether to continue on to the next preprocessor
  • calling_context – specify a value here to indicate the context in which this preprocessing is being called. This value will be stored in an instance variable, self.calling_context, which can be accessed from any preprocessor method on this task. Typically this value will be either self.GUI, self.CMDLINE, or None, but any value may be supplied here and checked for in the preprocessor methods. self.calling_context always reverts back to None at the end of runPreprocessing.
sender(self) → QObject
senderSignalIndex(self) → int
setObjectName(self, str)
classmethod setParamValue(*args, **kwargs)
setParent(self, QObject)
setProperty(self, str, Any) → bool
classmethod setReference(param1, param2)

Call this class method from configureParam to indicate that two params should be kept in sync. The initial values will start with the default value of param1. Example:

class Square(CompoundParam):
    width: float = 5
    height: float = 10

    @classmethod
    def configureParam(cls):
        super().configureParam()
        cls.setReference(cls.width, cls.height)

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6
Parameters:
  • param1 – The first abstract param to keep synced
  • param2 – The second abstract param. After instantiation, this param will take on the value of param1.
setValue(*args, **kwargs)
signalsBlocked(self) → bool
skip_eq_check()
specifyTaskDir(taskdir_spec)

Specify the taskdir creation behavior. Use one of the following options:

A directory name (string). This may be a relative or absolute path

None - no taskdir is requested. The task will use the CWD as its taskdir

AUTO_TASKDIR - a new subdirectory will be created in the CWD using the task name as the directory name.

TEMP_TASKDIR - a temporary directory will be created in the schrodinger temp dir. This directory is cleaned up when the task is deleted.

Parameters:taskdir_spec – one of the four options listed above
start(*args, **kwargs)

@overrides: AbstractTask

startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
status
statusChanged
statusReplaced
taskDirSetting()

Returns the taskdir spec. See specifyTaskDir() for details.

taskDone
taskFailed
taskStarted
thread(self) → QThread
timerEvent(self, QTimerEvent)
toDict(*args, **kwargs)
toJson(_mark_version=True)

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

Return type:An instance of one the classes from NATIVE_JSON_DATATYPES
toJsonImplementation(*args, **kwargs)
tr(self, str, disambiguation: str = None, n: int = -1) → str
valueChanged
wait(timeout=None)

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

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

Bases: schrodinger.tasks.tasks.SubprocessMixin, schrodinger.tasks.tasks.AbstractComboTask

runBackend()
getTaskDir()

Returns the full path of the task directory. This is only available if the task directory exists (after creation of the taskdir or, if no task dir is specified, any time).

AUTO_TASKDIR = <object object>
CMDLINE = 1
DEFAULT_TASKDIR_SETTING = None
DONE = 3
DataClass

alias of builtins.object

ENTRYPOINT = 'combotask_entry_point.py'
FAILED = 2
GUI = 2
INTERRUPT_ENABLED = False
RUNNING = 1
TEMP_TASKDIR = <object object>
WAITING = 0
__init__(*args, **kwargs)

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

addFuncToGroup(func, group=None, order=None)

Adds a function to the specified chain. Typically used for adding functions that are not methods of this object.

The function may optionally be decorated with a FuncGroupMarker. If so, the default group and order will be determined by the decorator. Any group or order explicitly passed in to addFuncToGroup will take precedence over the decorator settings.

Parameters:
  • func – the function to add
  • group (FuncGroupMarker or None) – the group marker. If the function is decorated with a FuncGoupMarker, that group marker will be the default.
  • order (float or None) – the sorting order. If the function is decorated with a FuncGoupMarker, the order specified in the decorator will be the default.
addPostprocessor(func, order=0)

Adds a postproceessor function to this task instance. If the function has been decorated with @postprocessor, the order specified by the decorator will be used.

Parameters:
  • func (typing.Callable) – the function to add
  • order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.
addPreprocessor(func, order=-2000)

Adds a preproceessor function to this task instance. If the function has been decorated with @preprocessor, the order specified by the decorator will be used as the default.

Parameters:
  • func – the function to add
  • order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.
classmethod addSubParam(name, param, update_owner=True)
backendMain()
blockSignals(self, bool) → bool
block_signal_propagation()
childEvent(self, QChildEvent)
children(self) → List[QObject]
classmethod configureParam()

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

connectNotify(self, QMetaMethod)
customEvent(self, QEvent)
classmethod defaultValue(*args, **kwargs)
deleteLater(self)
destroyed

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

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

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

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

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

classmethod fromJson(json_obj)

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

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

:rtype : cls

classmethod fromJsonFilename(filename)
classmethod fromJsonImplementation(json_dict)

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

getAbstractParam(*args, **kwargs)
getAddedFuncs(group=None)
getFuncGroup(group=None)

Retrieve the functions belonging to the specified group.

Parameters:group (FuncGroupMarker) – the group marker
Returns:the functions in the specified group, in order
Return type:list
classmethod getJsonBlacklist()

Override to customize what params are serialized.

Implementations should return a list of abstract params that should be omitted from serialization.

..NOTE
Returned abstract params must be direct child params of cls, e.g. cls.name, not cls.coord.x.
getLogAsString()
classmethod getParamSignal(*args, **kwargs)
classmethod getParamValue(*args, **kwargs)
classmethod getSubParam(name)

Get the value of a subparam using the string name:

c = Coord()
assert c.getSubParam('x') == 0

Note

Using the string name to accss params is generally discouraged, but can be useful for serializing/deserializing param data.

Parameters:name (str) – The name of the subparam to get the value for.
classmethod getSubParams()

Return a dictionary mapping subparam names to their values.

getTaskFilename(fname)

Return the appropriate absolute path for an input or output file in the taskdir.

getTypeHint()
get_version()

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

guard()

Context manager that saves any Exception raised inside

inherits(self, str) → bool
initAbstract()
initConcrete()

Override to customize initialization of concrete params.

initializeValue()

@overrides: parameters.CompoundParam

input
inputChanged
inputReplaced
installEventFilter(self, QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

isBackendMode()
isDefault(*args, **kwargs)
isInterruptionRequested()
isRunning()
isSignalConnected(self, QMetaMethod) → bool
isStartable()
isWidgetType(self) → bool
isWindowType(self) → bool
json_filename
json_out_filename
kill()

@overrides: AbstractTask

Kill the subprocess and set the status to FAILED.

killTimer(self, int)
mainFunction()
makeCmd()

@overrides: AbstractCmdTask

max_progress
max_progressChanged
max_progressReplaced
metaObject(self) → QMetaObject
moveToThread(self, QThread)
name
nameChanged
nameReplaced
objectName(self) → str
objectNameChanged

objectNameChanged(self, str) [signal]

output
outputChanged
outputReplaced
classmethod owner()

Get the owner of the param:

# Can be called on an abstract param:
assert Coord.x.owner() == Coord

# ...or on an instance of a CompoundParam
a = Atom()
assert a.coord.owner() == a
classmethod ownerChain()

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

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

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

classmethod paramName()

Get the name of the param:

# Can be called on an abstract param:
print(Coord.x.paramName()) # 'x'

# ...or on an instance of a CompoundParam
a = Atom()
a.coord.paramName() # 'coord'
parent(self) → QObject
postprocessors()
Returns:A list of postprocessors, both decorated methods on the task and external functions that have been added via addPostprocessor()
Return type:list[typing.Callable]
preprocessors()
Returns:A list of preprocessors (both decorated methods on the task and external functions that have been added via addPreprocessor)
printingOutputToTerminal()
Returns:whether the StdOut and StdErr output from this task is being printed to the terminal
Return type:bool
processFuncChain(chain=None, result_callback=None)

Execute each function in the specified chain sequentially in order.

The result_callback is called after each function with the return value of that function. This can be used to respond to the return value (e.g. present information to the user, get user feedback, log the result, etc.)

The return value of the result_callback determines whether processing will proceeed to the next function.

Parameters:
  • chain (FuncChainDecorator) – which chain to process
  • result_callback – the callback that will get called with the result of each function in the chain
Returns:

a list of the results from the functions

progress
progressChanged
progressReplaced
property(self, str) → Any
pyqtConfigure(...)

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

receivers(self, PYQT_SIGNAL) → int
removeEventFilter(self, QObject)
replicate()

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

requestInterruption()

Request the task to stop.

To enable this feature, subclasses should periodically check whether an interruption has been requested and terminate if it has been. If such logic has been included, INTERRUPT_ENABLED should be set to True.

reset(*args, **kwargs)
run()
runCmd(cmd)
classmethod runFromCmdLine()
runPostprocessing(callback=None)
runPreprocessing(*args, **kwargs)

Run the preprocessors one-by-one. By default, any failing preprocessor will raise a TaskFailure exception and terminate processing. This behavior may be customized by supplying a callback function which will be called after each preprocessor with the result of that preprocessor.

Parameters:
  • callback – a function that takes result and returns a bool that indicates whether to continue on to the next preprocessor
  • calling_context – specify a value here to indicate the context in which this preprocessing is being called. This value will be stored in an instance variable, self.calling_context, which can be accessed from any preprocessor method on this task. Typically this value will be either self.GUI, self.CMDLINE, or None, but any value may be supplied here and checked for in the preprocessor methods. self.calling_context always reverts back to None at the end of runPreprocessing.
sender(self) → QObject
senderSignalIndex(self) → int
setObjectName(self, str)
classmethod setParamValue(*args, **kwargs)
setParent(self, QObject)
setPrintingOutputToTerminal(print_to_terminal)

Set this task to print StdOut and StdErr output to terminal, or not.

Parameters:print_to_terminal (bool) – whether to send process output to terminal
setProperty(self, str, Any) → bool
classmethod setReference(param1, param2)

Call this class method from configureParam to indicate that two params should be kept in sync. The initial values will start with the default value of param1. Example:

class Square(CompoundParam):
    width: float = 5
    height: float = 10

    @classmethod
    def configureParam(cls):
        super().configureParam()
        cls.setReference(cls.width, cls.height)

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6
Parameters:
  • param1 – The first abstract param to keep synced
  • param2 – The second abstract param. After instantiation, this param will take on the value of param1.
setValue(*args, **kwargs)
signalsBlocked(self) → bool
skip_eq_check()
specifyTaskDir(taskdir_spec)

Specify the taskdir creation behavior. Use one of the following options:

A directory name (string). This may be a relative or absolute path

None - no taskdir is requested. The task will use the CWD as its taskdir

AUTO_TASKDIR - a new subdirectory will be created in the CWD using the task name as the directory name.

TEMP_TASKDIR - a temporary directory will be created in the schrodinger temp dir. This directory is cleaned up when the task is deleted.

Parameters:taskdir_spec – one of the four options listed above
start(*args, **kwargs)
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
status
statusChanged
statusReplaced
taskDirSetting()

Returns the taskdir spec. See specifyTaskDir() for details.

taskDone
taskFailed
taskStarted
thread(self) → QThread
timerEvent(self, QTimerEvent)
toDict(*args, **kwargs)
toJson(_mark_version=True)

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

Return type:An instance of one the classes from NATIVE_JSON_DATATYPES
toJsonImplementation(*args, **kwargs)
tr(self, str, disambiguation: str = None, n: int = -1) → str
valueChanged
wait(timeout=None)

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

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

Bases: schrodinger.tasks.tasks.AbstractTask

A task that relies on signals to proceed. Runs asynchronously via the event loop without requiring a worker thread. To use, implement setUpMain to connect any per-run signals and slots. Any slots should be decorated with SignalTask.guard_method so that exceptions in slots get converted into task failures. To end the task, emit self.mainDone to indicate the task has successfully completed. To fail, raise a TaskFailure or other exception.

mainDone
__init__(*args, **kwargs)

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

static guard_method(func)
run()
AUTO_TASKDIR = <object object>
CMDLINE = 1
DEFAULT_TASKDIR_SETTING = None
DONE = 3
DataClass

alias of builtins.object

FAILED = 2
GUI = 2
INTERRUPT_ENABLED = False
RUNNING = 1
TEMP_TASKDIR = <object object>
WAITING = 0
addFuncToGroup(func, group=None, order=None)

Adds a function to the specified chain. Typically used for adding functions that are not methods of this object.

The function may optionally be decorated with a FuncGroupMarker. If so, the default group and order will be determined by the decorator. Any group or order explicitly passed in to addFuncToGroup will take precedence over the decorator settings.

Parameters:
  • func – the function to add
  • group (FuncGroupMarker or None) – the group marker. If the function is decorated with a FuncGoupMarker, that group marker will be the default.
  • order (float or None) – the sorting order. If the function is decorated with a FuncGoupMarker, the order specified in the decorator will be the default.
addPostprocessor(func, order=0)

Adds a postproceessor function to this task instance. If the function has been decorated with @postprocessor, the order specified by the decorator will be used.

Parameters:
  • func (typing.Callable) – the function to add
  • order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.
addPreprocessor(func, order=-2000)

Adds a preproceessor function to this task instance. If the function has been decorated with @preprocessor, the order specified by the decorator will be used as the default.

Parameters:
  • func – the function to add
  • order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.
classmethod addSubParam(name, param, update_owner=True)
blockSignals(self, bool) → bool
block_signal_propagation()
childEvent(self, QChildEvent)
children(self) → List[QObject]
classmethod configureParam()

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

connectNotify(self, QMetaMethod)
customEvent(self, QEvent)
classmethod defaultValue(*args, **kwargs)
deleteLater(self)
destroyed

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

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

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

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

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

classmethod fromJson(json_obj)

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

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

:rtype : cls

classmethod fromJsonFilename(filename)
classmethod fromJsonImplementation(json_dict)

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

getAbstractParam(*args, **kwargs)
getAddedFuncs(group=None)
getFuncGroup(group=None)

Retrieve the functions belonging to the specified group.

Parameters:group (FuncGroupMarker) – the group marker
Returns:the functions in the specified group, in order
Return type:list
classmethod getJsonBlacklist()

Override to customize what params are serialized.

Implementations should return a list of abstract params that should be omitted from serialization.

..NOTE
Returned abstract params must be direct child params of cls, e.g. cls.name, not cls.coord.x.
classmethod getParamSignal(*args, **kwargs)
classmethod getParamValue(*args, **kwargs)
classmethod getSubParam(name)

Get the value of a subparam using the string name:

c = Coord()
assert c.getSubParam('x') == 0

Note

Using the string name to accss params is generally discouraged, but can be useful for serializing/deserializing param data.

Parameters:name (str) – The name of the subparam to get the value for.
classmethod getSubParams()

Return a dictionary mapping subparam names to their values.

getTaskDir()

Returns the full path of the task directory. This is only available if the task directory exists (after creation of the taskdir or, if no task dir is specified, any time).

getTaskFilename(fname)

Return the appropriate absolute path for an input or output file in the taskdir.

getTypeHint()
get_version()

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

guard()

Context manager that saves any Exception raised inside

inherits(self, str) → bool
initAbstract()
initConcrete()

Override to customize initialization of concrete params.

initializeValue()

@overrides: parameters.CompoundParam

input
inputChanged
inputReplaced
installEventFilter(self, QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

isDefault(*args, **kwargs)
isInterruptionRequested()
isRunning()
isSignalConnected(self, QMetaMethod) → bool
isStartable()
isWidgetType(self) → bool
isWindowType(self) → bool
kill()

Implementations are responsible for immediately stopping the task. No threads or processes should be running after this method is complete.

This method should be called sparingly since in many contexts the task will be forced to terminate without a chance to clean up or free resources.

killTimer(self, int)
max_progress
max_progressChanged
max_progressReplaced
metaObject(self) → QMetaObject
moveToThread(self, QThread)
name
nameChanged
nameReplaced
objectName(self) → str
objectNameChanged

objectNameChanged(self, str) [signal]

output
outputChanged
outputReplaced
classmethod owner()

Get the owner of the param:

# Can be called on an abstract param:
assert Coord.x.owner() == Coord

# ...or on an instance of a CompoundParam
a = Atom()
assert a.coord.owner() == a
classmethod ownerChain()

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

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

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

classmethod paramName()

Get the name of the param:

# Can be called on an abstract param:
print(Coord.x.paramName()) # 'x'

# ...or on an instance of a CompoundParam
a = Atom()
a.coord.paramName() # 'coord'
parent(self) → QObject
postprocessors()
Returns:A list of postprocessors, both decorated methods on the task and external functions that have been added via addPostprocessor()
Return type:list[typing.Callable]
preprocessors()
Returns:A list of preprocessors (both decorated methods on the task and external functions that have been added via addPreprocessor)
processFuncChain(chain=None, result_callback=None)

Execute each function in the specified chain sequentially in order.

The result_callback is called after each function with the return value of that function. This can be used to respond to the return value (e.g. present information to the user, get user feedback, log the result, etc.)

The return value of the result_callback determines whether processing will proceeed to the next function.

Parameters:
  • chain (FuncChainDecorator) – which chain to process
  • result_callback – the callback that will get called with the result of each function in the chain
Returns:

a list of the results from the functions

progress
progressChanged
progressReplaced
property(self, str) → Any
pyqtConfigure(...)

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

receivers(self, PYQT_SIGNAL) → int
removeEventFilter(self, QObject)
replicate()

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

requestInterruption()

Request the task to stop.

To enable this feature, subclasses should periodically check whether an interruption has been requested and terminate if it has been. If such logic has been included, INTERRUPT_ENABLED should be set to True.

reset(*args, **kwargs)
classmethod runFromCmdLine()
runPostprocessing(callback=None)
runPreprocessing(callback=None, calling_context=None)

Run the preprocessors one-by-one. By default, any failing preprocessor will raise a TaskFailure exception and terminate processing. This behavior may be customized by supplying a callback function which will be called after each preprocessor with the result of that preprocessor.

Parameters:
  • callback – a function that takes result and returns a bool that indicates whether to continue on to the next preprocessor
  • calling_context – specify a value here to indicate the context in which this preprocessing is being called. This value will be stored in an instance variable, self.calling_context, which can be accessed from any preprocessor method on this task. Typically this value will be either self.GUI, self.CMDLINE, or None, but any value may be supplied here and checked for in the preprocessor methods. self.calling_context always reverts back to None at the end of runPreprocessing.
sender(self) → QObject
senderSignalIndex(self) → int
setObjectName(self, str)
classmethod setParamValue(*args, **kwargs)
setParent(self, QObject)
setProperty(self, str, Any) → bool
classmethod setReference(param1, param2)

Call this class method from configureParam to indicate that two params should be kept in sync. The initial values will start with the default value of param1. Example:

class Square(CompoundParam):
    width: float = 5
    height: float = 10

    @classmethod
    def configureParam(cls):
        super().configureParam()
        cls.setReference(cls.width, cls.height)

square = Square()
assert square.width == square.height == 5 # Default value of width
                                          # takes priority
square.height = 7
assert square.width == square.height == 7
square.width = 6
assert square.width == square.height == 6
Parameters:
  • param1 – The first abstract param to keep synced
  • param2 – The second abstract param. After instantiation, this param will take on the value of param1.
setUpMain()
setValue(*args, **kwargs)
signalsBlocked(self) → bool
skip_eq_check()
specifyTaskDir(taskdir_spec)

Specify the taskdir creation behavior. Use one of the following options:

A directory name (string). This may be a relative or absolute path

None - no taskdir is requested. The task will use the CWD as its taskdir

AUTO_TASKDIR - a new subdirectory will be created in the CWD using the task name as the directory name.

TEMP_TASKDIR - a temporary directory will be created in the schrodinger temp dir. This directory is cleaned up when the task is deleted.

Parameters:taskdir_spec – one of the four options listed above
start(skip_preprocessing=False)

This is the main method for starting a task. Start will check if a task is not already running, run preprocessing, and then run the task.

Failures in preprocessing will interrupt the task start, and the task will never enter the RUNNING state.

Parameters:skip_preprocessing (bool) – whether to skip preprocessing. This can be useful if preprocessing was already performed prior to calling start.
startTimer(self, int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt5.QtCore.QMetaObject object>
status
statusChanged
statusReplaced
taskDirSetting()

Returns the taskdir spec. See specifyTaskDir() for details.

taskDone
taskFailed
taskStarted
thread(self) → QThread
timerEvent(self, QTimerEvent)
toDict(*args, **kwargs)
toJson(_mark_version=True)

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

Return type:An instance of one the classes from NATIVE_JSON_DATATYPES
toJsonImplementation(*args, **kwargs)
tr(self, str, disambiguation: str = None, n: int = -1) → str
valueChanged
wait(timeout=None)

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

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