schrodinger.stepper.stepper module

Framework for writing computational workflows and running them in a highly distributed manner. Each step of the workflow is either a “mapping” operation (see MapStep) or “reducing” operation (see ReduceStep). These steps can then be chained together using the `Chain class.

For a more complete introduction, see WordCount tutorial:

For documentation on specific stepper features, see the following feature list. You can ctrl+f the feature tag to jump to the relevant docstrings.

Feature

Tag

MapStep

_map_step_

ReduceStep

_reduce_step_

Chain

_chain_

Settings

_settings_

Serialization

_serialization_

File Handling

_file_handling_

Generic Steps

_generics_

Custom Workflow

_custom_workflows_

Double Batching

_dbl_batching_

#=============================================================================== # Running stepper with custom, undistributed workflows <_custom_workflows_> #=============================================================================== To run steps that aren’t defined in the core suite: The script should be executed inside the working directory and import steps from a local package in the working directory.

Working dir contents:

script.py
my_lib/
    __init__.py
    steps.py

Minimal code in script.py if it needs to run under job control:

from schrodinger.job import launchapi
from schrodinger.ui.qt.appframework2 import application
from my_lib.steps import MyStep

def get_job_spec_from_args(argv):
    jsb = launchapi.JobSpecificationArgsBuilder(argv)
    jsb.setInputFile(__file__)
    jsb.setInputDirectory('my_lib')
    return jsb.getJobSpec()

def main():
    step = MyStep()
    set.getOutputs()

if __name__ == '__main__':
    application.run_application(main)

#=============================================================================== # Generic Steps <_generics_> #=============================================================================== Steps that can be run on any data type can be created by using the GENERIC sentinel type as the input or output type of a step. The step will then receive all inputs as serialized strings and should return all string outputs.

Example:

>>> class DeduplicateStep(ReduceStep):
...     Input = Output = GENERIC
...
...     def reduceFunction(self, inps):
...         yield from sorted(set(inps))
...
>>> class IdentityStep(MapStep):
...     Input = Output = int
...
...     def mapFunction(self, value):
...         yield value
...
>>> class DeduplicatedIdentityChain(Chain):
...     def buildChain(self):
...         self.addStep(IdentityStep())
...         self.addStep(DeduplicateStep())
...         self.addStep(IdentityStep())
...
>>> chain = DeduplicatedIdentityChain()
>>> chain.setInputs([1, 2, 3, 1, 2, 3])
>>> chain.getOutputs()
[1, 2, 3]

These steps can be chained together with any steps, regardless of the input or output types of the other steps.

NOTE::

No validation is done to guarantee that the input type of the step after a generic step is the same as the output type of the precedeing step. The behavior for this circumstance is undefined and will likely resulted in an error.

#=============================================================================== # Double Batching <_dbl_batching_> #=============================================================================== Job launch speeds at the time of writing is about one job per 3 or 4 seconds. This rate becomes insufficient once we need more than a few hundred workers. To get around this, stepper employs a pattern we coin “double batching”, where we create subjobs whose sole purpose is to themselves create the subjobs that actually run the steps.

NOTE:: We use double-batching for the PubSub implementation of stepper as well as the file-based implementation. The literal meaning of “double-batching” doesn’t apply as well to the PubSub implementation but the general pattern of launching subjobs to launch more subjobs still applies.

#=============================================================================== # Environment variables and global settings #===============================================================================

Settings:

  • SCHRODINGER_STEPPER_DEBUG

    Set to 1 to have most files brought back from a workflow run. Set to 2 to have _all_ files brought back.

  • SCHRODINGER_STEPPER_LOG_LEVEL

    Set to an integer or name representing the log level to use for the logger. Valid log names are in decreasing order of verbosity NOTSET, DEBUG, INFO, WARN, ERROR, FATAL, and CRITICAL. Set to DEBUG to see log messages from cloud clients.

  • SCHRODINGER_GCP_KEY

    Expected when running stepper with pubsub and bigquery. Should be a path to the gcp service key. See

    for more information on generating gcp service keys.

  • SCHRODINGER_CLOUD_VENV

    A path to the python executable of a virtualenv that can be used for interfacing with GCP or AWS. This virtualenv should be accessible on all nodes that a stepper workflow will be run on in addition to having all necessary python client libraries.

  • SCHRODINGER_GCP_ENABLED

    Optional setting to signify that the current machine is a GCP compute engine. Setting this will make SCHRODINGER_GCP_KEY also optional as credentials will be inferred from the GCP compute engine. SCHRODINGER_GCP_KEY will have precedence over the compute engine’s default credentials if set.

  • SCHRODINGER_CLOUD_WORKER_TIMEOUT

    Optional debug setting. If set, pubsub workers will timeout after SCHRODINGER_CLOUD_WORKER_TIMEOUT minutes.

  • SCHRODINGER_GCP_NUM_PUBSUB_WORKERS

    Sets the default number of pubsub workers that will be used. If not set, one will be used. Note that this value can still be overridden by a workflow’s configuration.

  • SCHRODINGER_STEPPER_ERROR_THRESHOLD

    Sets the batching error threshold. If not set, 0.9 will be used. Note that this value can still be overridden by a workflow’s configuration.

schrodinger.stepper.stepper.get_debug_level()
class schrodinger.stepper.stepper.ElapsedFormatter

Bases: object

A stepper logging formatter that includes how much time has elapsed since a start time in all messages. FORMATTER.start() is safe to call multiple times, the start time will be set to the time of the earliest call.

Example usage:

logger.debug("Message before debug.")
# Message before debug.
FORMATTER.start()
time.wait(1)
logger.debug("My message")
# <STEPPER> DEBUG +00:00:01: My message
__init__()
start()
format(record)
schrodinger.stepper.stepper.ichunked(iterable, n)

Reimplementation of more_itertools.ichunked that does not cache n items of iterable at a time.

Breaks iterable into sub-iterables with n elements each.

Note that unlike more_itertools.ichunked, an error will be raised if you try to iterate over a chunk before its previous chunk has been consumed.

class schrodinger.stepper.stepper.StepperFile(value='', *args, **kwargs)

Bases: schrodinger.tasks.tasks.TaskFile

LOCAL = 1
STATIC = 2
__contains__(key, /)

Return key in self.

__init__(path='', resource_type=ResourceType.LOCAL)
__len__()

Return len(self).

capitalize()

Return a capitalized version of the string.

More specifically, make the first character have upper case and the rest lower case.

casefold()

Return a version of the string suitable for caseless comparisons.

center(width, fillchar=' ', /)

Return a centered 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')

Encode the string using the codec registered for encoding.

encoding

The encoding in which to encode the string.

errors

The error handling scheme to use for encoding errors. The 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)

Return a copy 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 ‘}’).

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.

Return type

cls

classmethod fromJsonImplementation(json_obj)

Abstract method that must be defined by all derived classes. Takes in a dictionary and constructs an instance of the derived class.

Parameters

json_dict (dict) – A dictionary loaded from a JSON string or file.

Returns

An instance of the derived class.

Return type

cls

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.

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()

Return True if the string is an alpha-numeric string, False otherwise.

A string is alpha-numeric if all characters in the string are alpha-numeric and there is at least one character in the string.

isalpha()

Return True if the string is an alphabetic string, False otherwise.

A string is alphabetic if all characters in the string are alphabetic and there is at least one character in the string.

isascii()

Return True if all characters in the string are ASCII, False otherwise.

ASCII characters have code points in the range U+0000-U+007F. Empty string is ASCII too.

isdecimal()

Return True if the string is a decimal string, False otherwise.

A string is a decimal string if all characters in the string are decimal and there is at least one character in the string.

isdigit()

Return True if the string is a digit string, False otherwise.

A string is a digit string if all characters in the string are digits and there is at least one character in the string.

isidentifier()

Return True if the string is a valid Python identifier, False otherwise.

Call keyword.iskeyword(s) to test whether string s is a reserved identifier, such as “def” or “class”.

islower()

Return True if the string is a lowercase string, False otherwise.

A string is lowercase if all cased characters in the string are lowercase and there is at least one cased character in the string.

isnumeric()

Return True if the string is a numeric string, False otherwise.

A string is numeric if all characters in the string are numeric and there is at least one character in the string.

isprintable()

Return True if the string is printable, False otherwise.

A string is printable if all of its characters are considered printable in repr() or if it is empty.

isspace()

Return True if the string is a whitespace string, False otherwise.

A string is whitespace if all characters in the string are whitespace and there is at least one character in the string.

istitle()

Return True if the string is a title-cased string, False otherwise.

In a title-cased string, upper- and title-case characters may only follow uncased characters and lowercase characters only cased ones.

isupper()

Return True if the string is an uppercase string, False otherwise.

A string is uppercase if all cased characters in the string are uppercase and there is at least one cased character in the string.

join(iterable, /)

Concatenate any number of strings.

The string whose method is called is inserted in between each given string. The result is returned as a new string.

Example: ‘.’.join([‘ab’, ‘pq’, ‘rs’]) -> ‘ab.pq.rs’

ljust(width, fillchar=' ', /)

Return a left-justified string of length width.

Padding is done using the specified fill character (default is a space).

lower()

Return a copy of the string converted to lowercase.

lstrip(chars=None, /)

Return a copy of the string 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, /)

Partition the string into three parts using the given separator.

This will search for the separator in the string. If the separator is found, returns a 3-tuple containing the part before the separator, the separator itself, and the part after it.

If the separator is not found, returns a 3-tuple containing the original string and two empty strings.

replace(old, new, count=- 1, /)

Return a copy with all occurrences of substring old replaced by new.

count

Maximum number of occurrences to replace. -1 (the default value) means replace all occurrences.

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=' ', /)

Return a right-justified string of length width.

Padding is done using the specified fill character (default is a space).

rpartition(sep, /)

Partition the string into three parts using the given separator.

This will search for the separator in the string, starting at the end. If the separator is found, returns a 3-tuple containing the part before the separator, the separator itself, and the part after it.

If the separator is not found, returns a 3-tuple containing two empty strings and the original string.

rsplit(sep=None, maxsplit=- 1)

Return a list of the words in the string, using sep as the delimiter string.

sep

The delimiter according which to split the string. None (the default value) means split according to any whitespace, and discard empty strings from the result.

maxsplit

Maximum number of splits to do. -1 (the default value) means no limit.

Splits are done starting at the end of the string and working to the front.

rstrip(chars=None, /)

Return a copy of the string with trailing whitespace removed.

If chars is given and not None, remove characters in chars instead.

split(sep=None, maxsplit=- 1)

Return a list of the words in the string, using sep as the delimiter string.

sep

The delimiter according which to split the string. None (the default value) means split according to any whitespace, and discard empty strings from the result.

maxsplit

Maximum number of splits to do. -1 (the default value) means no limit.

splitlines(keepends=False)

Return a list of the lines in the string, 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=None, /)

Return a copy of the string with leading and trailing whitespace removed.

If chars is given and not None, remove characters in chars instead.

swapcase()

Convert uppercase characters to lowercase and lowercase characters to uppercase.

title()

Return a version of the string where each word is titlecased.

More specifically, words start with uppercased characters and all remaining cased characters have lower case.

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()

Abstract method that must be defined by all derived classes. Converts an instance of the derived class into a jsonifiable object.

Returns

A dict made up of JSON native datatypes or Jsonable objects. See the link below for a table of such types. https://docs.python.org/2/library/json.html#encoders-and-decoders

translate(table, /)

Replace each character in the string using the given translation table.

table

Translation table, which must be a mapping of Unicode ordinals to Unicode ordinals, strings, or None.

The table must implement lookup/indexing via __getitem__, for instance a dictionary or list. If this operation raises LookupError, the character is left untouched. Characters mapped to None are deleted.

upper()

Return a copy of the string converted to uppercase.

zfill(width, /)

Pad a numeric string with zeros on the left, to fill a field of the given width.

The string is never truncated.

class schrodinger.stepper.stepper.StepperFolder(value='', *args, **kwargs)

Bases: schrodinger.tasks.tasks.TaskFolder

LOCAL = 1
STATIC = 2
__contains__(key, /)

Return key in self.

__init__(path='', resource_type=ResourceType.LOCAL)
__len__()

Return len(self).

capitalize()

Return a capitalized version of the string.

More specifically, make the first character have upper case and the rest lower case.

casefold()

Return a version of the string suitable for caseless comparisons.

center(width, fillchar=' ', /)

Return a centered 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')

Encode the string using the codec registered for encoding.

encoding

The encoding in which to encode the string.

errors

The error handling scheme to use for encoding errors. The 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)

Return a copy 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 ‘}’).

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.

Return type

cls

classmethod fromJsonImplementation(json_obj)

Abstract method that must be defined by all derived classes. Takes in a dictionary and constructs an instance of the derived class.

Parameters

json_dict (dict) – A dictionary loaded from a JSON string or file.

Returns

An instance of the derived class.

Return type

cls

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.

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()

Return True if the string is an alpha-numeric string, False otherwise.

A string is alpha-numeric if all characters in the string are alpha-numeric and there is at least one character in the string.

isalpha()

Return True if the string is an alphabetic string, False otherwise.

A string is alphabetic if all characters in the string are alphabetic and there is at least one character in the string.

isascii()

Return True if all characters in the string are ASCII, False otherwise.

ASCII characters have code points in the range U+0000-U+007F. Empty string is ASCII too.

isdecimal()

Return True if the string is a decimal string, False otherwise.

A string is a decimal string if all characters in the string are decimal and there is at least one character in the string.

isdigit()

Return True if the string is a digit string, False otherwise.

A string is a digit string if all characters in the string are digits and there is at least one character in the string.

isidentifier()

Return True if the string is a valid Python identifier, False otherwise.

Call keyword.iskeyword(s) to test whether string s is a reserved identifier, such as “def” or “class”.

islower()

Return True if the string is a lowercase string, False otherwise.

A string is lowercase if all cased characters in the string are lowercase and there is at least one cased character in the string.

isnumeric()

Return True if the string is a numeric string, False otherwise.

A string is numeric if all characters in the string are numeric and there is at least one character in the string.

isprintable()

Return True if the string is printable, False otherwise.

A string is printable if all of its characters are considered printable in repr() or if it is empty.

isspace()

Return True if the string is a whitespace string, False otherwise.

A string is whitespace if all characters in the string are whitespace and there is at least one character in the string.

istitle()

Return True if the string is a title-cased string, False otherwise.

In a title-cased string, upper- and title-case characters may only follow uncased characters and lowercase characters only cased ones.

isupper()

Return True if the string is an uppercase string, False otherwise.

A string is uppercase if all cased characters in the string are uppercase and there is at least one cased character in the string.

join(iterable, /)

Concatenate any number of strings.

The string whose method is called is inserted in between each given string. The result is returned as a new string.

Example: ‘.’.join([‘ab’, ‘pq’, ‘rs’]) -> ‘ab.pq.rs’

ljust(width, fillchar=' ', /)

Return a left-justified string of length width.

Padding is done using the specified fill character (default is a space).

lower()

Return a copy of the string converted to lowercase.

lstrip(chars=None, /)

Return a copy of the string 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, /)

Partition the string into three parts using the given separator.

This will search for the separator in the string. If the separator is found, returns a 3-tuple containing the part before the separator, the separator itself, and the part after it.

If the separator is not found, returns a 3-tuple containing the original string and two empty strings.

replace(old, new, count=- 1, /)

Return a copy with all occurrences of substring old replaced by new.

count

Maximum number of occurrences to replace. -1 (the default value) means replace all occurrences.

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=' ', /)

Return a right-justified string of length width.

Padding is done using the specified fill character (default is a space).

rpartition(sep, /)

Partition the string into three parts using the given separator.

This will search for the separator in the string, starting at the end. If the separator is found, returns a 3-tuple containing the part before the separator, the separator itself, and the part after it.

If the separator is not found, returns a 3-tuple containing two empty strings and the original string.

rsplit(sep=None, maxsplit=- 1)

Return a list of the words in the string, using sep as the delimiter string.

sep

The delimiter according which to split the string. None (the default value) means split according to any whitespace, and discard empty strings from the result.

maxsplit

Maximum number of splits to do. -1 (the default value) means no limit.

Splits are done starting at the end of the string and working to the front.

rstrip(chars=None, /)

Return a copy of the string with trailing whitespace removed.

If chars is given and not None, remove characters in chars instead.

split(sep=None, maxsplit=- 1)

Return a list of the words in the string, using sep as the delimiter string.

sep

The delimiter according which to split the string. None (the default value) means split according to any whitespace, and discard empty strings from the result.

maxsplit

Maximum number of splits to do. -1 (the default value) means no limit.

splitlines(keepends=False)

Return a list of the lines in the string, 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=None, /)

Return a copy of the string with leading and trailing whitespace removed.

If chars is given and not None, remove characters in chars instead.

swapcase()

Convert uppercase characters to lowercase and lowercase characters to uppercase.

title()

Return a version of the string where each word is titlecased.

More specifically, words start with uppercased characters and all remaining cased characters have lower case.

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()

Abstract method that must be defined by all derived classes. Converts an instance of the derived class into a jsonifiable object.

Returns

A dict made up of JSON native datatypes or Jsonable objects. See the link below for a table of such types. https://docs.python.org/2/library/json.html#encoders-and-decoders

translate(table, /)

Replace each character in the string using the given translation table.

table

Translation table, which must be a mapping of Unicode ordinals to Unicode ordinals, strings, or None.

The table must implement lookup/indexing via __getitem__, for instance a dictionary or list. If this operation raises LookupError, the character is left untouched. Characters mapped to None are deleted.

upper()

Return a copy of the string converted to uppercase.

zfill(width, /)

Pad a numeric string with zeros on the left, to fill a field of the given width.

The string is never truncated.

class schrodinger.stepper.stepper.StepTaskInput(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.models.parameters.CompoundParam

dehydrated_step: schrodinger.stepper.stepper._DehydratedStep

See _BaseStep._dehydrateStep for documentation.

debug_mode: bool

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

class Coord(CompoundParam):
    x: int
    y: int

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

coord = Coord()
coord.x = 4

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

class Atom(CompoundParam):
    coord: Coord
    element: str
misc_input_filenames: List[schrodinger.tasks.tasks.TaskFile]

A Param to represent lists. Values of this param will have a mutated signal that will be emitted whenever any mutation method is called.

The constructor optionally takes a item_class keyword argument to specify what type of class the items in the list will be. This information will be used for jsonifying the list if specified.

misc_input_folders: List[schrodinger.tasks.tasks.TaskFolder]

A Param to represent lists. Values of this param will have a mutated signal that will be emitted whenever any mutation method is called.

The constructor optionally takes a item_class keyword argument to specify what type of class the items in the list will be. This information will be used for jsonifying the list if specified.

DataClass

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error
__init__(default_value=<object object>, _param_type=<object object>, **kwargs)
classmethod addSubParam(name, param, update_owner=True)
blockSignals(self, b: bool) → bool
block_signal_propagation()
childEvent(self, a0: 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, signal: QMetaMethod)
customEvent(self, a0: QEvent)
debug_modeChanged
debug_modeReplaced
classmethod defaultValue()

Returns the default value for this abstract param:

default_atom = Atom.defaultValue()
assert Atom.coord.x == 0
dehydrated_stepChanged
dehydrated_stepReplaced
deleteLater(self)
destroyed

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

disconnect(a0: QMetaObject.Connection) → bool
disconnect(self) → None
disconnectNotify(self, signal: QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → List[QByteArray]
event(self, a0: QEvent) → bool
eventFilter(self, a0: QObject, a1: QEvent) → bool
findChild(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject
findChild(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject
findChildren(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]
findChildren(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]
findChildren(self, type: type, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]
findChildren(self, types: Tuple, re: QRegularExpression, options: 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.

Return type

cls

classmethod fromJsonImplementation(json_dict)

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

Warning

This should never be called directly.

getAbstractParam()

Return the corresponding abstract param for this instance.

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(obj, signal_type='Changed')
classmethod getParamValue(obj)

Enables access to a param value on a compound param via an abstract param reference:

a = Atom()
assert Atom.coord.x.getParamValue(a) == 0 # ints default to 0
a.coord.x = 3
assert Atom.coord.x.getParamValue(a) == 3
Parameters

param (CompoundParam) – The owner param to get a param value from

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 access 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, classname: str) → bool
initAbstract()
initConcrete()

Override to customize initialization of concrete params.

initializeValue()

Override to dynamically set up the default value of the param. Useful for default values that are determined at runtime. This is called any time the param is reset.

installEventFilter(self, a0: QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

isDefault()

Whether the current value of this instance matches the default value.

isSignalConnected(self, signal: QMetaMethod) → bool
isWidgetType(self) → bool
isWindowType(self) → bool
killTimer(self, id: int)
metaObject(self) → QMetaObject
misc_input_filenamesChanged
misc_input_filenamesReplaced
misc_input_foldersChanged
misc_input_foldersReplaced
moveToThread(self, thread: QThread)
objectName(self) → str
objectNameChanged

objectNameChanged(self, objectName: str) [signal]

classmethod owner()

Get the owner of the param:

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

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

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

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

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

classmethod paramName()

Get the name of the param:

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

# ...or on an instance of a CompoundParam
a = Atom()
a.coord.paramName() # 'coord'
parent(self) → QObject
property(self, name: 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, signal: PYQT_SIGNAL) → int
removeEventFilter(self, a0: QObject)
reset(*abstract_params)

Resets this compound param to its default value:

class Line(CompoundParam):
    start = Coord(x=1, y=2)
    end = Coord(x=4, y=5)
line = Line()
line.start.x = line.end.x = 10
assert line.start.x == line.end.x == 10
line.reset()
assert line.start.x == 1
assert line.end.x == 4

Any number of abstract params may be passed in to perform a partial reset of only the specified params:

line.start.x = line.end.x = 10
line.reset(Line.start.x)  # resets just start.x
assert line.start.x == 1
assert line.end.x == 10

line.reset(Line.end)      # resets the entire end point
assert line.end.x == 4

line.start.y = line.end.y = 10
line.reset(Line.start.y, Line.end.y)  # resets the y-coord of both
assert line.start.y == 2
assert line.end.y == 5
sender(self) → QObject
senderSignalIndex(self) → int
setObjectName(self, name: str)
classmethod setParamValue(obj, value)

Set the value of a param on an object by specifying the instance and the value:

# Setting the param value of a basic param
a = Atom()
Atom.coord.x.setParamValue(a, 5)
assert a.coord.x == 5

# setParamValue can also be used to set the value of CompoundParams
c = Coord()
c.x = 10
atom.coord.setParamValue(a, c)
assert atom.coord.x == 10
Parameters

  • param – The owner param to set a subparam value of.

  • value – The value to set the subparam value to.

setParent(self, a0: QObject)
setProperty(self, name: str, value: 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(value=None, **kwargs)

Set the value of this CompoundParam to match value.

Parameters

  • value – The value to set this CompoundParam to. It should be the same type as this CompoundParam.

  • kwargs – For internal use only.

signalsBlocked(self) → bool
skip_eq_check()
startTimer(self, interval: int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt6.QtCore.QMetaObject object>
thread(self) → QThread
timerEvent(self, a0: QTimerEvent)
toDict()

Return a dictionary version of this CompoundParam. The returned dictionary is fully nested and contains no CompoundParam instances

a = Atom()
a_dict = a.toDict()
assert a_dict['coord']['x'] == 0
assert a_dict['coord'] == {'x':0, 'y':0}
toJson(_mark_version=True)

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

Return type

An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation()

Returns a JSON representation of this value object.

Warning

This should never be called directly.

tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) → str
valueChanged
class schrodinger.stepper.stepper.StepTaskOutput(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.models.parameters.CompoundParam

output_file: schrodinger.tasks.tasks.TaskFile

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

class Coord(CompoundParam):
    x: int
    y: int

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

coord = Coord()
coord.x = 4

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

class Atom(CompoundParam):
    coord: Coord
    element: str
run_info: dict

A Param to represent dictionaries. Values of this param will have a mutated signal that will be emitted whenever any mutation method is called.

The constructor optionally takes a value_class keyword argument to specify what type of class the values will be. This information will be used for jsonifying the dictionary if specified. (Note that non-string keys are not currently supported for jsonification. This may change in the future. See PANEL-13029).

misc_output_filenames: List[schrodinger.tasks.tasks.TaskFile]

A Param to represent lists. Values of this param will have a mutated signal that will be emitted whenever any mutation method is called.

The constructor optionally takes a item_class keyword argument to specify what type of class the items in the list will be. This information will be used for jsonifying the list if specified.

DataClass

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error
__init__(default_value=<object object>, _param_type=<object object>, **kwargs)
classmethod addSubParam(name, param, update_owner=True)
blockSignals(self, b: bool) → bool
block_signal_propagation()
childEvent(self, a0: 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, signal: QMetaMethod)
customEvent(self, a0: QEvent)
classmethod defaultValue()

Returns the default value for this abstract param:

default_atom = Atom.defaultValue()
assert Atom.coord.x == 0
deleteLater(self)
destroyed

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

disconnect(a0: QMetaObject.Connection) → bool
disconnect(self) → None
disconnectNotify(self, signal: QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → List[QByteArray]
event(self, a0: QEvent) → bool
eventFilter(self, a0: QObject, a1: QEvent) → bool
findChild(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject
findChild(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject
findChildren(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]
findChildren(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]
findChildren(self, type: type, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]
findChildren(self, types: Tuple, re: QRegularExpression, options: 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.

Return type

cls

classmethod fromJsonImplementation(json_dict)

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

Warning

This should never be called directly.

getAbstractParam()

Return the corresponding abstract param for this instance.

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(obj, signal_type='Changed')
classmethod getParamValue(obj)

Enables access to a param value on a compound param via an abstract param reference:

a = Atom()
assert Atom.coord.x.getParamValue(a) == 0 # ints default to 0
a.coord.x = 3
assert Atom.coord.x.getParamValue(a) == 3
Parameters

param (CompoundParam) – The owner param to get a param value from

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 access 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, classname: str) → bool
initAbstract()
initConcrete()

Override to customize initialization of concrete params.

initializeValue()

Override to dynamically set up the default value of the param. Useful for default values that are determined at runtime. This is called any time the param is reset.

installEventFilter(self, a0: QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

isDefault()

Whether the current value of this instance matches the default value.

isSignalConnected(self, signal: QMetaMethod) → bool
isWidgetType(self) → bool
isWindowType(self) → bool
killTimer(self, id: int)
metaObject(self) → QMetaObject
misc_output_filenamesChanged
misc_output_filenamesReplaced
moveToThread(self, thread: QThread)
objectName(self) → str
objectNameChanged

objectNameChanged(self, objectName: str) [signal]

output_fileChanged
output_fileReplaced
classmethod owner()

Get the owner of the param:

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

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

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

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

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

classmethod paramName()

Get the name of the param:

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

# ...or on an instance of a CompoundParam
a = Atom()
a.coord.paramName() # 'coord'
parent(self) → QObject
property(self, name: 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, signal: PYQT_SIGNAL) → int
removeEventFilter(self, a0: QObject)
reset(*abstract_params)

Resets this compound param to its default value:

class Line(CompoundParam):
    start = Coord(x=1, y=2)
    end = Coord(x=4, y=5)
line = Line()
line.start.x = line.end.x = 10
assert line.start.x == line.end.x == 10
line.reset()
assert line.start.x == 1
assert line.end.x == 4

Any number of abstract params may be passed in to perform a partial reset of only the specified params:

line.start.x = line.end.x = 10
line.reset(Line.start.x)  # resets just start.x
assert line.start.x == 1
assert line.end.x == 10

line.reset(Line.end)      # resets the entire end point
assert line.end.x == 4

line.start.y = line.end.y = 10
line.reset(Line.start.y, Line.end.y)  # resets the y-coord of both
assert line.start.y == 2
assert line.end.y == 5
run_infoChanged
run_infoReplaced
sender(self) → QObject
senderSignalIndex(self) → int
setObjectName(self, name: str)
classmethod setParamValue(obj, value)

Set the value of a param on an object by specifying the instance and the value:

# Setting the param value of a basic param
a = Atom()
Atom.coord.x.setParamValue(a, 5)
assert a.coord.x == 5

# setParamValue can also be used to set the value of CompoundParams
c = Coord()
c.x = 10
atom.coord.setParamValue(a, c)
assert atom.coord.x == 10
Parameters

  • param – The owner param to set a subparam value of.

  • value – The value to set the subparam value to.

setParent(self, a0: QObject)
setProperty(self, name: str, value: 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(value=None, **kwargs)

Set the value of this CompoundParam to match value.

Parameters

  • value – The value to set this CompoundParam to. It should be the same type as this CompoundParam.

  • kwargs – For internal use only.

signalsBlocked(self) → bool
skip_eq_check()
startTimer(self, interval: int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt6.QtCore.QMetaObject object>
thread(self) → QThread
timerEvent(self, a0: QTimerEvent)
toDict()

Return a dictionary version of this CompoundParam. The returned dictionary is fully nested and contains no CompoundParam instances

a = Atom()
a_dict = a.toDict()
assert a_dict['coord']['x'] == 0
assert a_dict['coord'] == {'x':0, 'y':0}
toJson(_mark_version=True)

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

Return type

An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation()

Returns a JSON representation of this value object.

Warning

This should never be called directly.

tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) → str
valueChanged
class schrodinger.stepper.stepper.StepTaskMixin(*args, step=None, **kwargs)

Bases: schrodinger.models.parameters.CompoundParamMixin

This class must be mixed in with a subclass of AbstractComboTask. The resulting task class may be used to run any step as a task, provided the input, output, and settings classes are all JSONable.

input: schrodinger.stepper.stepper.StepTaskInput
output: schrodinger.stepper.stepper.StepTaskOutput
DEFAULT_TASKDIR_SETTING = 1
__init__(*args, step=None, **kwargs)
addLicenseReservation(license, num_tokens=1)
setStep(step)
getStepClass()
mainFunction()
class schrodinger.stepper.stepper.StepSubprocessTask(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.stepper.stepper.StepTaskMixin, schrodinger.tasks.tasks.ComboSubprocessTask

AUTO_TASKDIR = 1
CMDLINE = 1
DEFAULT_TASKDIR_SETTING = 1
DONE = 3
DataClass

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error
ENTRYPOINT = 'combotask_entry_point.py'
FAILED = 2
GUI = 2
INTERRUPT_ENABLED = False
RUNNING = 1
TEMP_TASKDIR = 2
WAITING = 0
__init__(*args, step=None, **kwargs)
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.

addLicenseReservation(license, num_tokens=1)

Add a license reservation for this job. This information is used by job control to ensure the job is only started once the required licenses become available.

In a preprocessor, (i.e. before launching the backend), a reservation should be added for each license that will be checked out directly by that backend. Example:

class GlideTask(ComboJobTask):

    @preprocessor
    def _reserveGlideLicense(self):
        # Reserve a Glide license.
        self.addLicenseReservation(license.GLIDE_MAIN)

    def mainFunction(self):
        # Check out the Glide license
        lic = license.License(license.GLIDE_MAIN)

        # ... Do computations requiring Glide ...

        lic.checkin()

Licenses that will be checked out by subjobs of this job do not need reservations added here; subjobs are responsible for their own license reservations.

Parameters

  • license (module-constant from schrodinger.utils.license (e.g. license.AUTODESIGNER)) – a license that will be used by the backend

  • num_tokens (int) – number of tokens for this license reservations

addPostprocessor(func, order=0)

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

Parameters

  • func (typing.Callable) – the function to add

  • order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.

addPreprocessor(func, order=None)

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

Parameters

  • func – the function to add

  • order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.

classmethod addSubParam(name, param, update_owner=True)
backendMain()
blockSignals(self, b: bool) → bool
block_signal_propagation()
calling_context: CallingContext
calling_contextChanged
calling_contextReplaced
childEvent(self, a0: QChildEvent)
children(self) → List[QObject]
cmd

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error
classmethod configureParam()

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

connectNotify(self, signal: QMetaMethod)
customEvent(self, a0: QEvent)
classmethod defaultValue()

Returns the default value for this abstract param:

default_atom = Atom.defaultValue()
assert Atom.coord.x == 0
deleteLater(self)
destroyed

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

disconnect(a0: QMetaObject.Connection) → bool
disconnect(self) → None
disconnectNotify(self, signal: QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → List[QByteArray]
event(self, a0: QEvent) → bool
eventFilter(self, a0: QObject, a1: QEvent) → bool
exit_code

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error
failure_info: FailureInfo

Dataclass for task failure information.

Printing an instance of this class will provide the minimum necessary human-readable representation of a recorded failure.

failure_infoChanged
failure_infoReplaced
findChild(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject
findChild(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject
findChildren(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]
findChildren(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]
findChildren(self, type: type, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]
findChildren(self, types: Tuple, re: QRegularExpression, options: 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.

Return type

cls

classmethod fromJsonFilename(filename)
classmethod fromJsonImplementation(json_dict)

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

Warning

This should never be called directly.

getAbstractParam()

Return the corresponding abstract param for this instance.

getAddedFuncs(group=None)
getDebugString()
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() → str
getLogFilename()
classmethod getParamSignal(obj, signal_type='Changed')
classmethod getParamValue(obj)

Enables access to a param value on a compound param via an abstract param reference:

a = Atom()
assert Atom.coord.x.getParamValue(a) == 0 # ints default to 0
a.coord.x = 3
assert Atom.coord.x.getParamValue(a) == 3
Parameters

param (CompoundParam) – The owner param to get a param value from

getStepClass()
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 access 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, classname: str) → bool
initAbstract()
initConcrete()

Override to customize initialization of concrete params.

initializeValue()

@overrides: parameters.CompoundParam

input: schrodinger.stepper.stepper.StepTaskInput
inputChanged
inputReplaced
installEventFilter(self, a0: QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

isBackendMode()
isDebugEnabled()
isDefault()

Whether the current value of this instance matches the default value.

isInterruptionRequested()
isRunning()
isSignalConnected(self, signal: QMetaMethod) → bool
isStartable()
isWidgetType(self) → bool
isWindowType(self) → bool
property json_filename
property json_out_filename
kill()

@overrides: AbstractTask

Kill the subprocess and set the status to FAILED.

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

@overrides: AbstractCmdTask

max_progress: int

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

class Coord(CompoundParam):
    x: int
    y: int

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

coord = Coord()
coord.x = 4

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

class Atom(CompoundParam):
    coord: Coord
    element: str
max_progressChanged
max_progressReplaced
metaObject(self) → QMetaObject
moveToThread(self, thread: QThread)
name: str

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

class Coord(CompoundParam):
    x: int
    y: int

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

coord = Coord()
coord.x = 4

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

class Atom(CompoundParam):
    coord: Coord
    element: str
nameChanged
nameReplaced
objectName(self) → str
objectNameChanged

objectNameChanged(self, objectName: str) [signal]

output: schrodinger.stepper.stepper.StepTaskOutput
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)

printDebug(*args)
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: int

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

class Coord(CompoundParam):
    x: int
    y: int

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

coord = Coord()
coord.x = 4

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

class Atom(CompoundParam):
    coord: Coord
    element: str
progressChanged
progressReplaced
progress_string: str

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

class Coord(CompoundParam):
    x: int
    y: int

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

coord = Coord()
coord.x = 4

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

class Atom(CompoundParam):
    coord: Coord
    element: str
progress_stringChanged
progress_stringReplaced
property(self, name: str) → Any
pyqtConfigure(...)

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

qprocess

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error
receivers(self, signal: PYQT_SIGNAL) → int
removeEventFilter(self, a0: 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)

Resets this compound param to its default value:

class Line(CompoundParam):
    start = Coord(x=1, y=2)
    end = Coord(x=4, y=5)
line = Line()
line.start.x = line.end.x = 10
assert line.start.x == line.end.x == 10
line.reset()
assert line.start.x == 1
assert line.end.x == 4

Any number of abstract params may be passed in to perform a partial reset of only the specified params:

line.start.x = line.end.x = 10
line.reset(Line.start.x)  # resets just start.x
assert line.start.x == 1
assert line.end.x == 10

line.reset(Line.end)      # resets the entire end point
assert line.end.x == 4

line.start.y = line.end.y = 10
line.reset(Line.start.y, Line.end.y)  # resets the y-coord of both
assert line.start.y == 2
assert line.end.y == 5
run()
runBackend()
runCmd(cmd)
runInProcess()
runPreprocessing(callback=None, calling_context=None)

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

This method is “final” so that all preprocessing logic will be enclosed in the try/finally block.

Parameters

  • callback – a function that takes result and returns a bool that indicates whether to continue on to the next preprocessor

  • calling_context – specify a value here to indicate the context in which this preprocessing is being called. This value will be stored in an instance variable, self.calling_context, which can be accessed from any preprocessor method on this task. Typically this value will be either self.GUI, self.CMDLINE, or None, but any value may be supplied here and checked for in the preprocessor methods. self.calling_context always reverts back to None at the end of runPreprocessing.

sender(self) → QObject
senderSignalIndex(self) → int
setObjectName(self, name: str)
classmethod setParamValue(obj, value)

Set the value of a param on an object by specifying the instance and the value:

# Setting the param value of a basic param
a = Atom()
Atom.coord.x.setParamValue(a, 5)
assert a.coord.x == 5

# setParamValue can also be used to set the value of CompoundParams
c = Coord()
c.x = 10
atom.coord.setParamValue(a, c)
assert atom.coord.x == 10
Parameters

  • param – The owner param to set a subparam value of.

  • value – The value to set the subparam value to.

setParent(self, a0: QObject)
setPrintingOutputToTerminal(print_to_terminal)

Set this task to print StdOut and StdErr output to terminal, or not. This must be set before starting the task to enable terminal output.

Parameters

print_to_terminal (bool) – whether to send process output to terminal

setProperty(self, name: str, value: 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.

setStep(step)
setValue(value=None, **kwargs)

Set the value of this CompoundParam to match value.

Parameters

  • value – The value to set this CompoundParam to. It should be the same type as this CompoundParam.

  • kwargs – For internal use only.

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, interval: int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt6.QtCore.QMetaObject object>
status: Status
statusChanged
statusReplaced
taskDirSetting()

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

taskDone
taskFailed
taskStarted
thread(self) → QThread
timerEvent(self, a0: QTimerEvent)
toDict()

Return a dictionary version of this CompoundParam. The returned dictionary is fully nested and contains no CompoundParam instances

a = Atom()
a_dict = a.toDict()
assert a_dict['coord']['x'] == 0
assert a_dict['coord'] == {'x':0, 'y':0}
toJson(_mark_version=True)

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

Return type

An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation()

Returns a JSON representation of this value object.

Warning

This should never be called directly.

tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) → str
valueChanged
wait(timeout=None)

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

Warning

This should not be called directly from GUI code - see PANEL-18317. It is safe to call inside a subprocess or job. Run git grep "task.wait(" to see safe examples annotated with “# OK”.

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.stepper.stepper.StepJobTask(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.stepper.stepper.StepTaskMixin, schrodinger.tasks.jobtasks.ComboJobTask

input: schrodinger.stepper.stepper.StepTaskInput
output: schrodinger.stepper.stepper.StepTaskOutput
isCanceled() → bool

Whether the job underlying the task is canceled.

If there is no job associated with the task, then this returns False.

mainFunction()
AUTO_TASKDIR = 1
CMDLINE = 1
DEFAULT_TASKDIR_SETTING = 1
DONE = 3
DataClass

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error
ENTRYPOINT = 'combotask_entry_point.py'
FAILED = 2
GUI = 2
INTERRUPT_ENABLED = False
property PROGRAM_NAME
RUNNING = 1
TEMP_TASKDIR = 2
WAITING = 0
__init__(*args, step=None, **kwargs)
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.

addLicenseReservation(license, num_tokens=1)

Add a license reservation for this job. This information is used by job control to ensure the job is only started once the required licenses become available.

In a preprocessor, (i.e. before launching the backend), a reservation should be added for each license that will be checked out directly by that backend. Example:

class GlideTask(ComboJobTask):

    @preprocessor
    def _reserveGlideLicense(self):
        # Reserve a Glide license.
        self.addLicenseReservation(license.GLIDE_MAIN)

    def mainFunction(self):
        # Check out the Glide license
        lic = license.License(license.GLIDE_MAIN)

        # ... Do computations requiring Glide ...

        lic.checkin()

Licenses that will be checked out by subjobs of this job do not need reservations added here; subjobs are responsible for their own license reservations.

Parameters

  • license (module-constant from schrodinger.utils.license (e.g. license.AUTODESIGNER)) – a license that will be used by the backend

  • num_tokens (int) – number of tokens for this license reservations

addPostprocessor(func, order=0)

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

Parameters

  • func (typing.Callable) – the function to add

  • order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.

addPreprocessor(func, order=None)

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

Parameters

  • func – the function to add

  • order (float) – the sorting order for the function relative to all other preprocessors. Takes precedence over order specified by the preprocessor decorator.

classmethod addSubParam(name, param, update_owner=True)
backendMain()
blockSignals(self, b: bool) → bool
block_signal_propagation()
calling_context: CallingContext
calling_contextChanged
calling_contextReplaced
childEvent(self, a0: QChildEvent)
children(self) → List[QObject]
classmethod configToJobConfigAdapter(json_dict)
classmethod configureParam()

@overrides: parameters.CompoundParam

connectNotify(self, signal: QMetaMethod)
customEvent(self, a0: QEvent)
classmethod defaultValue()

Returns the default value for this abstract param:

default_atom = Atom.defaultValue()
assert Atom.coord.x == 0
deleteLater(self)
destroyed

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

disconnect(a0: QMetaObject.Connection) → bool
disconnect(self) → None
disconnectNotify(self, signal: QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → List[QByteArray]
event(self, a0: QEvent) → bool
eventFilter(self, a0: QObject, a1: QEvent) → bool
failure_info: FailureInfo

Dataclass for task failure information.

Printing an instance of this class will provide the minimum necessary human-readable representation of a recorded failure.

failure_infoChanged
failure_infoReplaced
findChild(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject
findChild(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject
findChildren(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]
findChildren(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]
findChildren(self, type: type, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]
findChildren(self, types: Tuple, re: QRegularExpression, options: 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.

Return type

cls

classmethod fromJsonFilename(filename)
classmethod fromJsonImplementation(json_dict)

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

Warning

This should never be called directly.

getAbstractParam()

Return the corresponding abstract param for this instance.

getAddedFuncs(group=None)
getDebugString()
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

getJob() → Optional[schrodinger.job.jobcontrol.Job]
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() → str
getLogFilename()
classmethod getParamSignal(obj, signal_type='Changed')
classmethod getParamValue(obj)

Enables access to a param value on a compound param via an abstract param reference:

a = Atom()
assert Atom.coord.x.getParamValue(a) == 0 # ints default to 0
a.coord.x = 3
assert Atom.coord.x.getParamValue(a) == 3
Parameters

param (CompoundParam) – The owner param to get a param value from

getShFilename()
getStepClass()
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 access 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

inWriteMode()
inherits(self, classname: str) → bool
initAbstract()
initConcrete()

Override to customize initialization of concrete params.

initializeValue()

@overrides: paramters.CompoundParam

inputChanged
inputReplaced
installEventFilter(self, a0: QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

isBackendMode()
isDebugEnabled()
isDefault()

Whether the current value of this instance matches the default value.

isInterruptionRequested()
isRunning()
isSignalConnected(self, signal: QMetaMethod) → bool
isStartable()
isWidgetType(self) → bool
isWindowType(self) → bool
job_config: JobConfig

Subclass JobConfig to customize what job settings are available for a given jobtask. To disable an option, set an ordinary (non-param) class variable with value None for that option.

Subclasses may add any arbitrary options as desired; it is the responsibility of the task to handle those options.

job_configChanged
job_configReplaced
job_id

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error
property json_filename
property json_out_filename
kill()

@overrides: tasks.AbstractTask

killTimer(self, id: int)
makeCmd()

@overrides: tasks.AbstractCmdTask

Child classes must override.

max_progress: int

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

class Coord(CompoundParam):
    x: int
    y: int

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

coord = Coord()
coord.x = 4

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

class Atom(CompoundParam):
    coord: Coord
    element: str
max_progressChanged
max_progressReplaced
metaObject(self) → QMetaObject
moveToThread(self, thread: QThread)
name: str

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

class Coord(CompoundParam):
    x: int
    y: int

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

coord = Coord()
coord.x = 4

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

class Atom(CompoundParam):
    coord: Coord
    element: str
nameChanged
nameReplaced
objectName(self) → str
objectNameChanged

objectNameChanged(self, objectName: 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
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)

printDebug(*args)
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: int

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

class Coord(CompoundParam):
    x: int
    y: int

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

coord = Coord()
coord.x = 4

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

class Atom(CompoundParam):
    coord: Coord
    element: str
progressChanged
progressReplaced
progress_string: str

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

class Coord(CompoundParam):
    x: int
    y: int

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

coord = Coord()
coord.x = 4

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

class Atom(CompoundParam):
    coord: Coord
    element: str
progress_stringChanged
progress_stringReplaced
property(self, name: 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, signal: PYQT_SIGNAL) → int
removeEventFilter(self, a0: QObject)
replicate()

@overrides: tasks.AbstractTask

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)

Resets this compound param to its default value:

class Line(CompoundParam):
    start = Coord(x=1, y=2)
    end = Coord(x=4, y=5)
line = Line()
line.start.x = line.end.x = 10
assert line.start.x == line.end.x == 10
line.reset()
assert line.start.x == 1
assert line.end.x == 4

Any number of abstract params may be passed in to perform a partial reset of only the specified params:

line.start.x = line.end.x = 10
line.reset(Line.start.x)  # resets just start.x
assert line.start.x == 1
assert line.end.x == 10

line.reset(Line.end)      # resets the entire end point
assert line.end.x == 4

line.start.y = line.end.y = 10
line.reset(Line.start.y, Line.end.y)  # resets the y-coord of both
assert line.start.y == 2
assert line.end.y == 5
run()
runBackend()

@overrides: AbstractComboTask

runCmd(cmd)

@overrides: tasks.AbstractCmdTask

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

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

This method is “final” so that all preprocessing logic will be enclosed in the try/finally block.

Parameters

  • callback – a function that takes result and returns a bool that indicates whether to continue on to the next preprocessor

  • calling_context – specify a value here to indicate the context in which this preprocessing is being called. This value will be stored in an instance variable, self.calling_context, which can be accessed from any preprocessor method on this task. Typically this value will be either self.GUI, self.CMDLINE, or None, but any value may be supplied here and checked for in the preprocessor methods. self.calling_context always reverts back to None at the end of runPreprocessing.

runToCmd(skip_preprocessing=False)

Does the same thing as start except it doesn’t actually launch the job. Instead it just returns the final job cmd.

Intended to be used for running jobtasks on JobDJ, which requires a job cmd rather than a task.

sender(self) → QObject
senderSignalIndex(self) → int
setJob(job: schrodinger.job.jobcontrol.Job)

” Use given jobcontrol.Job to incorporate job results into the task and run postprocessors. Example:

task = FooTask()
cmd = task.runToCommand()
job = jobcontrol.launch_job(cmd)
job.wait()
task.setJob(job)

If the job has not been downloaded, the task will be set to FAILED with a SetJobRuntimeError.

Parameters

job – jobcontrol.Job with results to incorporate into the task.

setObjectName(self, name: str)
classmethod setParamValue(obj, value)

Set the value of a param on an object by specifying the instance and the value:

# Setting the param value of a basic param
a = Atom()
Atom.coord.x.setParamValue(a, 5)
assert a.coord.x == 5

# setParamValue can also be used to set the value of CompoundParams
c = Coord()
c.x = 10
atom.coord.setParamValue(a, c)
assert atom.coord.x == 10
Parameters

  • param – The owner param to set a subparam value of.

  • value – The value to set the subparam value to.

setParent(self, a0: QObject)
setProperty(self, name: str, value: 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.

setStep(step)
setValue(value=None, **kwargs)

Set the value of this CompoundParam to match value.

Parameters

  • value – The value to set this CompoundParam to. It should be the same type as this CompoundParam.

  • kwargs – For internal use only.

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, interval: int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt6.QtCore.QMetaObject object>
status: Status
statusChanged
statusReplaced
stop()
taskDirSetting()

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

taskDone
taskFailed
taskStarted
thread(self) → QThread
timerEvent(self, a0: QTimerEvent)
toDict()

Return a dictionary version of this CompoundParam. The returned dictionary is fully nested and contains no CompoundParam instances

a = Atom()
a_dict = a.toDict()
assert a_dict['coord']['x'] == 0
assert a_dict['coord'] == {'x':0, 'y':0}
toJson(_mark_version=True)

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

Return type

An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation()

Returns a JSON representation of this value object.

Warning

This should never be called directly.

tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) → str
valueChanged
wait(timeout=None)

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

Warning

This should not be called directly from GUI code - see PANEL-18317. It is safe to call inside a subprocess or job. Run git grep "task.wait(" to see safe examples annotated with “# OK”.

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.

write(skip_preprocessing=False)
writeStuZipFile()
class schrodinger.stepper.stepper.Topic(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.models.parameters.CompoundParam

An abstraction over a container of messages in a Publish/Subscribe model

Variables

  • name – the name of the topic

  • num_uploaded_msgs – the number of messages that were uploaded to this topic; it is not reflective of the number of messages currently in the topic.

name: str

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

class Coord(CompoundParam):
    x: int
    y: int

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

coord = Coord()
coord.x = 4

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

class Atom(CompoundParam):
    coord: Coord
    element: str
num_uploaded_msgs: int

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

class Coord(CompoundParam):
    x: int
    y: int

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

coord = Coord()
coord.x = 4

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

class Atom(CompoundParam):
    coord: Coord
    element: str
DataClass

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error
__init__(default_value=<object object>, _param_type=<object object>, **kwargs)
classmethod addSubParam(name, param, update_owner=True)
blockSignals(self, b: bool) → bool
block_signal_propagation()
childEvent(self, a0: 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, signal: QMetaMethod)
customEvent(self, a0: QEvent)
classmethod defaultValue()

Returns the default value for this abstract param:

default_atom = Atom.defaultValue()
assert Atom.coord.x == 0
deleteLater(self)
destroyed

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

disconnect(a0: QMetaObject.Connection) → bool
disconnect(self) → None
disconnectNotify(self, signal: QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → List[QByteArray]
event(self, a0: QEvent) → bool
eventFilter(self, a0: QObject, a1: QEvent) → bool
findChild(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject
findChild(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject
findChildren(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]
findChildren(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]
findChildren(self, type: type, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]
findChildren(self, types: Tuple, re: QRegularExpression, options: 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.

Return type

cls

classmethod fromJsonImplementation(json_dict)

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

Warning

This should never be called directly.

getAbstractParam()

Return the corresponding abstract param for this instance.

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(obj, signal_type='Changed')
classmethod getParamValue(obj)

Enables access to a param value on a compound param via an abstract param reference:

a = Atom()
assert Atom.coord.x.getParamValue(a) == 0 # ints default to 0
a.coord.x = 3
assert Atom.coord.x.getParamValue(a) == 3
Parameters

param (CompoundParam) – The owner param to get a param value from

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 access 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, classname: str) → bool
initAbstract()
initConcrete()

Override to customize initialization of concrete params.

initializeValue()

Override to dynamically set up the default value of the param. Useful for default values that are determined at runtime. This is called any time the param is reset.

installEventFilter(self, a0: QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

isDefault()

Whether the current value of this instance matches the default value.

isSignalConnected(self, signal: QMetaMethod) → bool
isWidgetType(self) → bool
isWindowType(self) → bool
killTimer(self, id: int)
metaObject(self) → QMetaObject
moveToThread(self, thread: QThread)
nameChanged
nameReplaced
num_uploaded_msgsChanged
num_uploaded_msgsReplaced
objectName(self) → str
objectNameChanged

objectNameChanged(self, objectName: str) [signal]

classmethod owner()

Get the owner of the param:

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

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

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

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

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

classmethod paramName()

Get the name of the param:

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

# ...or on an instance of a CompoundParam
a = Atom()
a.coord.paramName() # 'coord'
parent(self) → QObject
property(self, name: 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, signal: PYQT_SIGNAL) → int
removeEventFilter(self, a0: QObject)
reset(*abstract_params)

Resets this compound param to its default value:

class Line(CompoundParam):
    start = Coord(x=1, y=2)
    end = Coord(x=4, y=5)
line = Line()
line.start.x = line.end.x = 10
assert line.start.x == line.end.x == 10
line.reset()
assert line.start.x == 1
assert line.end.x == 4

Any number of abstract params may be passed in to perform a partial reset of only the specified params:

line.start.x = line.end.x = 10
line.reset(Line.start.x)  # resets just start.x
assert line.start.x == 1
assert line.end.x == 10

line.reset(Line.end)      # resets the entire end point
assert line.end.x == 4

line.start.y = line.end.y = 10
line.reset(Line.start.y, Line.end.y)  # resets the y-coord of both
assert line.start.y == 2
assert line.end.y == 5
sender(self) → QObject
senderSignalIndex(self) → int
setObjectName(self, name: str)
classmethod setParamValue(obj, value)

Set the value of a param on an object by specifying the instance and the value:

# Setting the param value of a basic param
a = Atom()
Atom.coord.x.setParamValue(a, 5)
assert a.coord.x == 5

# setParamValue can also be used to set the value of CompoundParams
c = Coord()
c.x = 10
atom.coord.setParamValue(a, c)
assert atom.coord.x == 10
Parameters

  • param – The owner param to set a subparam value of.

  • value – The value to set the subparam value to.

setParent(self, a0: QObject)
setProperty(self, name: str, value: 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(value=None, **kwargs)

Set the value of this CompoundParam to match value.

Parameters

  • value – The value to set this CompoundParam to. It should be the same type as this CompoundParam.

  • kwargs – For internal use only.

signalsBlocked(self) → bool
skip_eq_check()
startTimer(self, interval: int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt6.QtCore.QMetaObject object>
thread(self) → QThread
timerEvent(self, a0: QTimerEvent)
toDict()

Return a dictionary version of this CompoundParam. The returned dictionary is fully nested and contains no CompoundParam instances

a = Atom()
a_dict = a.toDict()
assert a_dict['coord']['x'] == 0
assert a_dict['coord'] == {'x':0, 'y':0}
toJson(_mark_version=True)

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

Return type

An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation()

Returns a JSON representation of this value object.

Warning

This should never be called directly.

tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) → str
valueChanged
class schrodinger.stepper.stepper.BatchSettings(*args, _param_type=<object object>, **kwargs)

Bases: schrodinger.models.parameters.CompoundParam

size: int

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

class Coord(CompoundParam):
    x: int
    y: int

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

coord = Coord()
coord.x = 4

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

class Atom(CompoundParam):
    coord: Coord
    element: str
task_class: type

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

class Coord(CompoundParam):
    x: int
    y: int

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

coord = Coord()
coord.x = 4

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

class Atom(CompoundParam):
    coord: Coord
    element: str
hostname: str

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

class Coord(CompoundParam):
    x: int
    y: int

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

coord = Coord()
coord.x = 4

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

class Atom(CompoundParam):
    coord: Coord
    element: str
use_pubsub: bool

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

class Coord(CompoundParam):
    x: int
    y: int

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

coord = Coord()
coord.x = 4

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

class Atom(CompoundParam):
    coord: Coord
    element: str
num_pubsub_workers: int

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

class Coord(CompoundParam):
    x: int
    y: int

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

coord = Coord()
coord.x = 4

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

class Atom(CompoundParam):
    coord: Coord
    element: str
error_threshold: float

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

class Coord(CompoundParam):
    x: int
    y: int

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

coord = Coord()
coord.x = 4

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

class Atom(CompoundParam):
    coord: Coord
    element: str
initializeValue()

Override to dynamically set up the default value of the param. Useful for default values that are determined at runtime. This is called any time the param is reset.

DataClass

This class can be used to declare a public attribute on a CompoundParam. Declared public attributes can be used without error.

Example usage:

class Coord(CompoundParam):
    x: int
    y: int
    note = NonParamAttribute()

coord = Coord()
coord.note = "hello" # No error
__init__(default_value=<object object>, _param_type=<object object>, **kwargs)
classmethod addSubParam(name, param, update_owner=True)
blockSignals(self, b: bool) → bool
block_signal_propagation()
childEvent(self, a0: 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, signal: QMetaMethod)
customEvent(self, a0: QEvent)
classmethod defaultValue()

Returns the default value for this abstract param:

default_atom = Atom.defaultValue()
assert Atom.coord.x == 0
deleteLater(self)
destroyed

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

disconnect(a0: QMetaObject.Connection) → bool
disconnect(self) → None
disconnectNotify(self, signal: QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → List[QByteArray]
error_thresholdChanged
error_thresholdReplaced
event(self, a0: QEvent) → bool
eventFilter(self, a0: QObject, a1: QEvent) → bool
findChild(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject
findChild(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject
findChildren(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]
findChildren(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]
findChildren(self, type: type, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]
findChildren(self, types: Tuple, re: QRegularExpression, options: 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.

Return type

cls

classmethod fromJsonImplementation(json_dict)

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

Warning

This should never be called directly.

getAbstractParam()

Return the corresponding abstract param for this instance.

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(obj, signal_type='Changed')
classmethod getParamValue(obj)

Enables access to a param value on a compound param via an abstract param reference:

a = Atom()
assert Atom.coord.x.getParamValue(a) == 0 # ints default to 0
a.coord.x = 3
assert Atom.coord.x.getParamValue(a) == 3
Parameters

param (CompoundParam) – The owner param to get a param value from

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 access 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.

hostnameChanged
hostnameReplaced
inherits(self, classname: str) → bool
initAbstract()
initConcrete()

Override to customize initialization of concrete params.

installEventFilter(self, a0: QObject)
classmethod isAbstract()

Whether the param is an “abstract” param.

isDefault()

Whether the current value of this instance matches the default value.

isSignalConnected(self, signal: QMetaMethod) → bool
isWidgetType(self) → bool
isWindowType(self) → bool
killTimer(self, id: int)
metaObject(self) → QMetaObject
moveToThread(self, thread: QThread)
num_pubsub_workersChanged
num_pubsub_workersReplaced
objectName(self) → str
objectNameChanged

objectNameChanged(self, objectName: str) [signal]

classmethod owner()

Get the owner of the param:

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

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

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

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

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

classmethod paramName()

Get the name of the param:

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

# ...or on an instance of a CompoundParam
a = Atom()
a.coord.paramName() # 'coord'
parent(self) → QObject
property(self, name: 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, signal: PYQT_SIGNAL) → int
removeEventFilter(self, a0: QObject)
reset(*abstract_params)

Resets this compound param to its default value:

class Line(CompoundParam):
    start = Coord(x=1, y=2)
    end = Coord(x=4, y=5)
line = Line()
line.start.x = line.end.x = 10
assert line.start.x == line.end.x == 10
line.reset()
assert line.start.x == 1
assert line.end.x == 4

Any number of abstract params may be passed in to perform a partial reset of only the specified params:

line.start.x = line.end.x = 10
line.reset(Line.start.x)  # resets just start.x
assert line.start.x == 1
assert line.end.x == 10

line.reset(Line.end)      # resets the entire end point
assert line.end.x == 4

line.start.y = line.end.y = 10
line.reset(Line.start.y, Line.end.y)  # resets the y-coord of both
assert line.start.y == 2
assert line.end.y == 5
sender(self) → QObject
senderSignalIndex(self) → int
setObjectName(self, name: str)
classmethod setParamValue(obj, value)

Set the value of a param on an object by specifying the instance and the value:

# Setting the param value of a basic param
a = Atom()
Atom.coord.x.setParamValue(a, 5)
assert a.coord.x == 5

# setParamValue can also be used to set the value of CompoundParams
c = Coord()
c.x = 10
atom.coord.setParamValue(a, c)
assert atom.coord.x == 10
Parameters

  • param – The owner param to set a subparam value of.

  • value – The value to set the subparam value to.

setParent(self, a0: QObject)
setProperty(self, name: str, value: 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(value=None, **kwargs)

Set the value of this CompoundParam to match value.

Parameters

  • value – The value to set this CompoundParam to. It should be the same type as this CompoundParam.

  • kwargs – For internal use only.

signalsBlocked(self) → bool
sizeChanged
sizeReplaced
skip_eq_check()
startTimer(self, interval: int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt6.QtCore.QMetaObject object>
task_classChanged
task_classReplaced
thread(self) → QThread
timerEvent(self, a0: QTimerEvent)
toDict()

Return a dictionary version of this CompoundParam. The returned dictionary is fully nested and contains no CompoundParam instances

a = Atom()
a_dict = a.toDict()
assert a_dict['coord']['x'] == 0
assert a_dict['coord'] == {'x':0, 'y':0}
toJson(_mark_version=True)

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

Return type

An instance of one the classes from NATIVE_JSON_DATATYPES

toJsonImplementation()

Returns a JSON representation of this value object.

Warning

This should never be called directly.

tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) → str
use_pubsubChanged
use_pubsubReplaced
valueChanged
class schrodinger.stepper.stepper.Serializer

Bases: object

<_serialization_> A class for defining special serialization for some datatype. Serialization by default uses the json protocol, but if a specialized protocol is wanted instead, users can subclass this class to do so.

Subclasses should:

  • Define DataType. This is the class that this serializer can

    encode/decode.

  • Define toString(self, output), which defines how to serialize

    an output.

  • Define fromString(self, input_str), which defines how to

    deserialize an input.

This can then be used as the InputSerializer or OutputSerializer for any step.

Here’s an example for defining an int that’s serialized in base-two as opposed to base-ten:

class IntBaseTwoSerializer(Serializer):
    DataType = int

    def toString(self, output):
        return bin(output) # 7 -> '0b111'

    def fromString(self, input_str):
        return int(input_str[2:], 2) # '0b111' -> 7

This can then be used anywhere you’d use an int as the output or input in a step. For example:

class SquaringStep(MapStep):
    Input = int
    InputSerializer = IntBaseTwoSerializer
    Output = int
    OutputSerializer = IntBaseTwoSerializer

    def mapFunction(self, inp):
        yield inp**2

Now, any time that a SquaringStep would read its inputs from a file or write its outputs to a file, it’ll do so using using a base-two representation.

DataType = NotImplemented
serialize(items, fname)

Write items to a file named fname.

deserialize(fname)

Read in items from fname. :type fname: str :rtype: iterable[self.DataType]

fromString(input_str)
toString(output)
exception schrodinger.stepper.stepper.ValidationIssue(source_step, msg)

Bases: RuntimeError

__init__(source_step, msg)
args
with_traceback()

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

exception schrodinger.stepper.stepper.SettingsError(source_step, msg)

Bases: schrodinger.stepper.stepper.ValidationIssue

Used in conjunction with _BaseStep.validateSettings to report an error with settings. Constructed with the step with the invalid settings and an error message, e.g. SettingsError(bad_step, "Step does not have required settings.")

__init__(source_step, msg)
args
with_traceback()

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

exception schrodinger.stepper.stepper.SettingsWarning(source_step, msg)

Bases: schrodinger.stepper.stepper.ValidationIssue

Used in conjunction with _BaseStep.validateSettings to report a warning with settings. Constructed with the step with the invalid settings and an error message, e.g. SettingsWarning(bad_step, "Step setting FOO should ideally be positive")

__init__(source_step, msg)
args
with_traceback()

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

exception schrodinger.stepper.stepper.ResourceError(source_step, msg)

Bases: schrodinger.stepper.stepper.ValidationIssue

Used in conjunction with _BaseStep.validateSettings to report an error with a resource setting. Constructed with the step with the invalid setting and an error message, e.g., ResourceError(bad_step, "Step setting 'file' has not been set.")

__init__(source_step, msg)
args
with_traceback()

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

exception schrodinger.stepper.stepper.LocalResourceError(source_step, msg)

Bases: schrodinger.stepper.stepper.ResourceError

A ResourceError specifically for local StepperFile and StepperFolder validations, i.e., resources that are on a job submission host and may have to be transferred to compute resources

__init__(source_step, msg)
args
with_traceback()

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

exception schrodinger.stepper.stepper.StaticResourceError(source_step, msg)

Bases: schrodinger.stepper.stepper.ResourceError

A ResourceError specifically for static StepperFile and StepperFolder validations, i.e., resources that are not necessarily available on a job submission host

__init__(source_step, msg)
args
with_traceback()

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

class schrodinger.stepper.stepper.PubsubEnabledStepMixin(*args, **kwargs)

Bases: object

A mixin that allows a step to be run using PubSub.

Steps with this mixin will have batch settings that have a use_pubsub flag and a num_pubsub_workers integer. Flipping use_pubsub to on will have the step load up all its inputs into a pubsub topic before spinning up num_pubsub_workers subjobs that will all take from the input topic, run the step’s computation on it, and upload it to an output topic.

Calling my_pubsub_step.getOutputs() will return all the outputs from the output topic, so to a user this will all be implementation detail.

__init__(*args, **kwargs)
property topic_prefix
property topic_suffix
outputs(*args, **kwargs)
usingPubsub()
getInputTopic() → Optional[schrodinger.stepper.stepper.Topic]
setInputTopic(inp_topic: Optional[schrodinger.stepper.stepper.Topic])
getOutputTopic() → Optional[schrodinger.stepper.stepper.Topic]
setOutputTopic(outp_topic: Optional[schrodinger.stepper.stepper.Topic])
initializeTopics()
class schrodinger.stepper.stepper.UnbatchedReduceStep(settings=None, config=None, step_id=None, metrics_logger_depth=None, _run_info=None, **kwargs)

Bases: schrodinger.stepper.stepper._BaseStep

” An unbatchable ReduceStep. See ReduceStep for more information.

reduceFunction(inputs)
Input = None
InputSerializer

alias of schrodinger.stepper.stepper._DynamicSerializer

Output = None
OutputSerializer

alias of schrodinger.stepper.stepper._DynamicSerializer

Settings

alias of schrodinger.models.parameters.CompoundParam

__init__(settings=None, config=None, step_id=None, metrics_logger_depth=None, _run_info=None, **kwargs)

See class docstring for info on the different constructor arguments.

blockSignals(self, b: bool) → bool
childEvent(self, a0: QChildEvent)
children(self) → List[QObject]
cleanUp()

Hook for adding any type of work that needs to happen after all outputs are exhausted or if some outputs are created and the step is destroyed.

connectNotify(self, signal: QMetaMethod)
customEvent(self, a0: QEvent)
deleteLater(self)
destroyed

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

disconnect(a0: QMetaObject.Connection) → bool
disconnect(self) → None
disconnectNotify(self, signal: QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → List[QByteArray]
event(self, a0: QEvent) → bool
eventFilter(self, a0: QObject, a1: QEvent) → bool
findChild(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject
findChild(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject
findChildren(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]
findChildren(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]
findChildren(self, type: type, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]
findChildren(self, types: Tuple, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]
getLicenseRequirements()
getMetricsLoggerDepth() → Optional[int]
getOutputSerializer()
getOutputs()

Gets all the outputs in a list by fully iterating the output generator.

getResources(param_type, resource_type)

Get the stepper resources in the settings that are instances of param_type and have a resource_type attribute that is resource_type.

Note does not work for list/set/tuple subparams in the settings.

Parameters

  • param_type (tasks._TaskResource) – the resource parameter type

  • resource_type (ResourceType) – the type of resource to get

Returns

the set of stepper resources of resource_type

Return type

set of tasks._TaskResource

getRunInfo()
getStepDepth() → int

Get the depth of a step which is defined as how nested it is. A step run in isolation (i.e. not within a chain) has a depth level of 0.

getStepId()
inherits(self, classname: str) → bool
inputs()
installEventFilter(self, a0: QObject)
isSignalConnected(self, signal: QMetaMethod) → bool
isWidgetType(self) → bool
isWindowType(self) → bool
killTimer(self, id: int)
metaObject(self) → QMetaObject
moveToThread(self, thread: QThread)
objectName(self) → str
objectNameChanged

objectNameChanged(self, objectName: str) [signal]

outputs(*args, **kwargs)
parent(self) → QObject
prettyPrintRunInfo()

Format and print info about the step’s run.

property(self, name: 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, signal: PYQT_SIGNAL) → int
removeEventFilter(self, a0: QObject)
report(prefix='')

Report the settings and batch settings for this step.

sender(self) → QObject
senderSignalIndex(self) → int
setInputFile(fname)
setInputs(*args, **kwargs)
setObjectName(self, name: str)
setParent(self, a0: QObject)
setProperty(self, name: str, value: Any) → bool
setSettings(*args, **kwargs)
setUp()

Hook for adding any type of work that needs to happen before any outputs are created.

signalsBlocked(self) → bool
startTimer(self, interval: int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt6.QtCore.QMetaObject object>
thread(self) → QThread
timerEvent(self, a0: QTimerEvent)
tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) → str
validateSettings()

Check whether the step settings are valid and return a list of SettingsError and SettingsWarning to report any invalid settings. Default implementation checks that all stepper files are set to valid file paths.

Return type

list[TaskError or TaskWarning]

writeOutputsToFile(fname)

Write outputs to fname. By default, the output file will consist of one line for each output with whatever is produced when passing the out- put to str. Override this method if more complex behavior is needed.

class schrodinger.stepper.stepper.ReduceStep(*args, **kwargs)

Bases: schrodinger.stepper.stepper._BatchableStepMixin, schrodinger.stepper.stepper.UnbatchedReduceStep

<_reduce_step_> A computational step that performs a function on a collection of inputs to produce output items.

To construct a ReduceStep:

  • Implement reduceFunction

  • Define Input (the type expected by the mapFunction)

  • Define Output (the type of item produced by the mapFunction)

  • Define Settings (data class for any settings needed by the mapFunction)

reduceFunction(inputs)

The main computation for this step. This function should take in a iterable of inputs and return an iterable of outputs.

Example:

def reduceFunction(self, words):
    # Find all unique words
    seen_words = set()
    for word in words:
        if word not in seen_words:
            seen_words.add(word)
            yield word
Input = None
InputSerializer

alias of schrodinger.stepper.stepper._DynamicSerializer

Output = None
OutputSerializer

alias of schrodinger.stepper.stepper._DynamicSerializer

Settings

alias of schrodinger.models.parameters.CompoundParam

__init__(*args, **kwargs)

See class docstring for info on the different constructor arguments.

blockSignals(self, b: bool) → bool
childEvent(self, a0: QChildEvent)
children(self) → List[QObject]
cleanUp()

Hook for adding any type of work that needs to happen after all outputs are exhausted or if some outputs are created and the step is destroyed.

connectNotify(self, signal: QMetaMethod)
customEvent(self, a0: QEvent)
deleteLater(self)
destroyed

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

disconnect(a0: QMetaObject.Connection) → bool
disconnect(self) → None
disconnectNotify(self, signal: QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → List[QByteArray]
event(self, a0: QEvent) → bool
eventFilter(self, a0: QObject, a1: QEvent) → bool
findChild(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject
findChild(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject
findChildren(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]
findChildren(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]
findChildren(self, type: type, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]
findChildren(self, types: Tuple, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]
getInputTopic() → Optional[schrodinger.stepper.stepper.Topic]
getLicenseRequirements()
getMetricsLoggerDepth() → Optional[int]
getOutputSerializer()
getOutputTopic() → Optional[schrodinger.stepper.stepper.Topic]
getOutputs()

Gets all the outputs in a list by fully iterating the output generator.

getResources(param_type, resource_type)

Get the stepper resources in the settings that are instances of param_type and have a resource_type attribute that is resource_type.

Note does not work for list/set/tuple subparams in the settings.

Parameters

  • param_type (tasks._TaskResource) – the resource parameter type

  • resource_type (ResourceType) – the type of resource to get

Returns

the set of stepper resources of resource_type

Return type

set of tasks._TaskResource

getRunInfo()
getStepDepth() → int

Get the depth of a step which is defined as how nested it is. A step run in isolation (i.e. not within a chain) has a depth level of 0.

getStepId()
inherits(self, classname: str) → bool
initializeTopics()
inputs()
installEventFilter(self, a0: QObject)
isSignalConnected(self, signal: QMetaMethod) → bool
isWidgetType(self) → bool
isWindowType(self) → bool
killTimer(self, id: int)
metaObject(self) → QMetaObject
moveToThread(self, thread: QThread)
objectName(self) → str
objectNameChanged

objectNameChanged(self, objectName: str) [signal]

outputs(*args, **kwargs)
parent(self) → QObject
prettyPrintRunInfo()

Format and print info about the step’s run.

property(self, name: 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, signal: PYQT_SIGNAL) → int
removeEventFilter(self, a0: QObject)
report(prefix='')

Report the settings and batch settings for this step.

sender(self) → QObject
senderSignalIndex(self) → int
setBatchSettings(*args, **kwargs)
setInputFile(fname)
setInputTopic(inp_topic: Optional[schrodinger.stepper.stepper.Topic])
setInputs(*args, **kwargs)
setObjectName(self, name: str)
setOutputTopic(outp_topic: Optional[schrodinger.stepper.stepper.Topic])
setParent(self, a0: QObject)
setProperty(self, name: str, value: Any) → bool
setSettings(*args, **kwargs)
setUp()

Hook for adding any type of work that needs to happen before any outputs are created.

signalsBlocked(self) → bool
startTimer(self, interval: int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt6.QtCore.QMetaObject object>
thread(self) → QThread
timerEvent(self, a0: QTimerEvent)
property topic_prefix
property topic_suffix
tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) → str
usingPubsub()
validateSettings()

Check whether the step settings are valid and return a list of SettingsError and SettingsWarning to report any invalid settings. Default implementation checks that all stepper files are set to valid file paths.

Return type

list[TaskError or TaskWarning]

writeOutputsToFile(fname)

Write outputs to fname. By default, the output file will consist of one line for each output with whatever is produced when passing the out- put to str. Override this method if more complex behavior is needed.

class schrodinger.stepper.stepper.UnbatchedMapStep(settings=None, config=None, step_id=None, metrics_logger_depth=None, _run_info=None, **kwargs)

Bases: schrodinger.stepper.stepper.UnbatchedReduceStep

<_unbatchability_> An unbatchable MapStep. See MapStep for more information.

reduceFunction(inputs)
mapFunction(input)
Input = None
InputSerializer

alias of schrodinger.stepper.stepper._DynamicSerializer

Output = None
OutputSerializer

alias of schrodinger.stepper.stepper._DynamicSerializer

Settings

alias of schrodinger.models.parameters.CompoundParam

__init__(settings=None, config=None, step_id=None, metrics_logger_depth=None, _run_info=None, **kwargs)

See class docstring for info on the different constructor arguments.

blockSignals(self, b: bool) → bool
childEvent(self, a0: QChildEvent)
children(self) → List[QObject]
cleanUp()

Hook for adding any type of work that needs to happen after all outputs are exhausted or if some outputs are created and the step is destroyed.

connectNotify(self, signal: QMetaMethod)
customEvent(self, a0: QEvent)
deleteLater(self)
destroyed

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

disconnect(a0: QMetaObject.Connection) → bool
disconnect(self) → None
disconnectNotify(self, signal: QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → List[QByteArray]
event(self, a0: QEvent) → bool
eventFilter(self, a0: QObject, a1: QEvent) → bool
findChild(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject
findChild(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject
findChildren(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]
findChildren(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]
findChildren(self, type: type, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]
findChildren(self, types: Tuple, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]
getLicenseRequirements()
getMetricsLoggerDepth() → Optional[int]
getOutputSerializer()
getOutputs()

Gets all the outputs in a list by fully iterating the output generator.

getResources(param_type, resource_type)

Get the stepper resources in the settings that are instances of param_type and have a resource_type attribute that is resource_type.

Note does not work for list/set/tuple subparams in the settings.

Parameters

  • param_type (tasks._TaskResource) – the resource parameter type

  • resource_type (ResourceType) – the type of resource to get

Returns

the set of stepper resources of resource_type

Return type

set of tasks._TaskResource

getRunInfo()
getStepDepth() → int

Get the depth of a step which is defined as how nested it is. A step run in isolation (i.e. not within a chain) has a depth level of 0.

getStepId()
inherits(self, classname: str) → bool
inputs()
installEventFilter(self, a0: QObject)
isSignalConnected(self, signal: QMetaMethod) → bool
isWidgetType(self) → bool
isWindowType(self) → bool
killTimer(self, id: int)
metaObject(self) → QMetaObject
moveToThread(self, thread: QThread)
objectName(self) → str
objectNameChanged

objectNameChanged(self, objectName: str) [signal]

outputs(*args, **kwargs)
parent(self) → QObject
prettyPrintRunInfo()

Format and print info about the step’s run.

property(self, name: 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, signal: PYQT_SIGNAL) → int
removeEventFilter(self, a0: QObject)
report(prefix='')

Report the settings and batch settings for this step.

sender(self) → QObject
senderSignalIndex(self) → int
setInputFile(fname)
setInputs(*args, **kwargs)
setObjectName(self, name: str)
setParent(self, a0: QObject)
setProperty(self, name: str, value: Any) → bool
setSettings(*args, **kwargs)
setUp()

Hook for adding any type of work that needs to happen before any outputs are created.

signalsBlocked(self) → bool
startTimer(self, interval: int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt6.QtCore.QMetaObject object>
thread(self) → QThread
timerEvent(self, a0: QTimerEvent)
tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) → str
validateSettings()

Check whether the step settings are valid and return a list of SettingsError and SettingsWarning to report any invalid settings. Default implementation checks that all stepper files are set to valid file paths.

Return type

list[TaskError or TaskWarning]

writeOutputsToFile(fname)

Write outputs to fname. By default, the output file will consist of one line for each output with whatever is produced when passing the out- put to str. Override this method if more complex behavior is needed.

class schrodinger.stepper.stepper.MapStep(*args, **kwargs)

Bases: schrodinger.stepper.stepper._BatchableStepMixin, schrodinger.stepper.stepper.UnbatchedMapStep

<_map_step_> A computational step that performs a function on input items from an input source to produce output items.

To construct a MapStep:

  • Implement mapFunction

  • Define Input (the type expected by the mapFunction)

  • Optionally define a InputSerializer (see Serializer for more info.)

  • Define Output (the type of item produced by the mapFunction)

  • Optionally define a OutputSerializer (see Serializer for more info.)

  • Define Settings (data class for any settings needed by the mapFunction)

mapFunction(input)

The main computation for this step. This function should take in a single input item and return an iterable of outputs. This allows a single output to produce multiple ouputs (e.g. enumeration).

The output may be yielded as a generator, in order to reduce memory usage.

If only a single output is produced for each input, return it as a single-element list.

Parameters

input –

this will be a single input item from the input source. Implementer is encouraged to use a more descriptive, context- specific variable name. Example:

def mapFunction(self, starting_smiles):

…

Input = None
InputSerializer

alias of schrodinger.stepper.stepper._DynamicSerializer

Output = None
OutputSerializer

alias of schrodinger.stepper.stepper._DynamicSerializer

Settings

alias of schrodinger.models.parameters.CompoundParam

__init__(*args, **kwargs)

See class docstring for info on the different constructor arguments.

blockSignals(self, b: bool) → bool
childEvent(self, a0: QChildEvent)
children(self) → List[QObject]
cleanUp()

Hook for adding any type of work that needs to happen after all outputs are exhausted or if some outputs are created and the step is destroyed.

connectNotify(self, signal: QMetaMethod)
customEvent(self, a0: QEvent)
deleteLater(self)
destroyed

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

disconnect(a0: QMetaObject.Connection) → bool
disconnect(self) → None
disconnectNotify(self, signal: QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → List[QByteArray]
event(self, a0: QEvent) → bool
eventFilter(self, a0: QObject, a1: QEvent) → bool
findChild(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject
findChild(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject
findChildren(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]
findChildren(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]
findChildren(self, type: type, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]
findChildren(self, types: Tuple, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]
getInputTopic() → Optional[schrodinger.stepper.stepper.Topic]
getLicenseRequirements()
getMetricsLoggerDepth() → Optional[int]
getOutputSerializer()
getOutputTopic() → Optional[schrodinger.stepper.stepper.Topic]
getOutputs()

Gets all the outputs in a list by fully iterating the output generator.

getResources(param_type, resource_type)

Get the stepper resources in the settings that are instances of param_type and have a resource_type attribute that is resource_type.

Note does not work for list/set/tuple subparams in the settings.

Parameters

  • param_type (tasks._TaskResource) – the resource parameter type

  • resource_type (ResourceType) – the type of resource to get

Returns

the set of stepper resources of resource_type

Return type

set of tasks._TaskResource

getRunInfo()
getStepDepth() → int

Get the depth of a step which is defined as how nested it is. A step run in isolation (i.e. not within a chain) has a depth level of 0.

getStepId()
inherits(self, classname: str) → bool
initializeTopics()
inputs()
installEventFilter(self, a0: QObject)
isSignalConnected(self, signal: QMetaMethod) → bool
isWidgetType(self) → bool
isWindowType(self) → bool
killTimer(self, id: int)
metaObject(self) → QMetaObject
moveToThread(self, thread: QThread)
objectName(self) → str
objectNameChanged

objectNameChanged(self, objectName: str) [signal]

outputs(*args, **kwargs)
parent(self) → QObject
prettyPrintRunInfo()

Format and print info about the step’s run.

property(self, name: 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, signal: PYQT_SIGNAL) → int
reduceFunction(inputs)
removeEventFilter(self, a0: QObject)
report(prefix='')

Report the settings and batch settings for this step.

sender(self) → QObject
senderSignalIndex(self) → int
setBatchSettings(*args, **kwargs)
setInputFile(fname)
setInputTopic(inp_topic: Optional[schrodinger.stepper.stepper.Topic])
setInputs(*args, **kwargs)
setObjectName(self, name: str)
setOutputTopic(outp_topic: Optional[schrodinger.stepper.stepper.Topic])
setParent(self, a0: QObject)
setProperty(self, name: str, value: Any) → bool
setSettings(*args, **kwargs)
setUp()

Hook for adding any type of work that needs to happen before any outputs are created.

signalsBlocked(self) → bool
startTimer(self, interval: int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt6.QtCore.QMetaObject object>
thread(self) → QThread
timerEvent(self, a0: QTimerEvent)
property topic_prefix
property topic_suffix
tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) → str
usingPubsub()
validateSettings()

Check whether the step settings are valid and return a list of SettingsError and SettingsWarning to report any invalid settings. Default implementation checks that all stepper files are set to valid file paths.

Return type

list[TaskError or TaskWarning]

writeOutputsToFile(fname)

Write outputs to fname. By default, the output file will consist of one line for each output with whatever is produced when passing the out- put to str. Override this method if more complex behavior is needed.

class schrodinger.stepper.stepper.UnbatchedChain(*args, **kwargs)

Bases: schrodinger.stepper.stepper.UnbatchedReduceStep

property Input
property Output
property InputSerializer

The default serializer that simply uses json.loads and json.dumps

property OutputSerializer

The default serializer that simply uses json.loads and json.dumps

setInputs(inputs: Iterable[Any], starting_step_id: Optional[str] = None)

Set the inputs for the chain. If starting_step_id is specified, then all steps before the specified starting step will be skipped. This is useful for resuming a chain’s computation.

setInputFile(input_file: str, starting_step_id: Optional[str] = None)

Set the input file for the chain. If starting_step_id is specified, then all steps before the specified starting step will be skipped. This is useful for resuming a chain’s computation.

setStartingStep(starting_step: str)
validateSettings()

Check whether the chain settings are valid and return a list of SettingsError and SettingsWarning to report any invalid settings. Default implementation simply returns problems from all child steps.

Return type

list[TaskError or TaskWarning]

getResources(param_type, resource_type)

Get the stepper resources in the settings for the chain as well as for every step in the chain that are instances of param_type and have a resource_type attribute that is resource_type.

Note does not work for list/set/tuple subparams in the settings.

Parameters

  • param_type (tasks._TaskResource) – the resource parameter type

  • resource_type (ResourceType) – the type of resource to get

Returns

the set of stepper resources of resource_type

Return type

set of tasks._TaskResource

__init__(*args, **kwargs)

See class docstring for info on the different constructor arguments.

__len__()
addStep(step)
report(prefix='')

Report the workflow steps and their settings (recursively).

Parameters

prefix (str) – the text to start each line with

validateChain()

Checks that the declaration of the chain is internally consistent - i.e. that each step is valid and each step’s Input class matches the preceding step’s Output class.

reduceFunction(inputs)
buildChain()

This method must be implemented by subclasses to build the chain. The chain is built by modifying self.steps. The chain’s composition may be dependent on self.settings.

Settings

alias of schrodinger.models.parameters.CompoundParam

blockSignals(self, b: bool) → bool
childEvent(self, a0: QChildEvent)
children(self) → List[QObject]
cleanUp()

Hook for adding any type of work that needs to happen after all outputs are exhausted or if some outputs are created and the step is destroyed.

connectNotify(self, signal: QMetaMethod)
customEvent(self, a0: QEvent)
deleteLater(self)
destroyed

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

disconnect(a0: QMetaObject.Connection) → bool
disconnect(self) → None
disconnectNotify(self, signal: QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → List[QByteArray]
event(self, a0: QEvent) → bool
eventFilter(self, a0: QObject, a1: QEvent) → bool
findChild(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject
findChild(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject
findChildren(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]
findChildren(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]
findChildren(self, type: type, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]
findChildren(self, types: Tuple, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]
getLicenseRequirements()
getMetricsLoggerDepth() → Optional[int]
getOutputSerializer()
getOutputs()

Gets all the outputs in a list by fully iterating the output generator.

getRunInfo()
getStepDepth() → int

Get the depth of a step which is defined as how nested it is. A step run in isolation (i.e. not within a chain) has a depth level of 0.

getStepId()
inherits(self, classname: str) → bool
inputs()
installEventFilter(self, a0: QObject)
isSignalConnected(self, signal: QMetaMethod) → bool
isWidgetType(self) → bool
isWindowType(self) → bool
killTimer(self, id: int)
metaObject(self) → QMetaObject
moveToThread(self, thread: QThread)
objectName(self) → str
objectNameChanged

objectNameChanged(self, objectName: str) [signal]

outputs(*args, **kwargs)
parent(self) → QObject
prettyPrintRunInfo()

Format and print info about the step’s run.

property(self, name: 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, signal: PYQT_SIGNAL) → int
removeEventFilter(self, a0: QObject)
sender(self) → QObject
senderSignalIndex(self) → int
setObjectName(self, name: str)
setParent(self, a0: QObject)
setProperty(self, name: str, value: Any) → bool
setSettings(*args, **kwargs)
setUp()

Hook for adding any type of work that needs to happen before any outputs are created.

signalsBlocked(self) → bool
startTimer(self, interval: int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt6.QtCore.QMetaObject object>
thread(self) → QThread
timerEvent(self, a0: QTimerEvent)
tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) → str
writeOutputsToFile(fname)

Write outputs to fname. By default, the output file will consist of one line for each output with whatever is produced when passing the out- put to str. Override this method if more complex behavior is needed.

class schrodinger.stepper.stepper.Chain(*args, **kwargs)

Bases: schrodinger.stepper.stepper._BatchableStepMixin, schrodinger.stepper.stepper.UnbatchedChain

<_chain_> Run a series of steps. The steps must be created by overriding buildChain.

getLicenseRequirements()
property Input
property InputSerializer

The default serializer that simply uses json.loads and json.dumps

property Output
property OutputSerializer

The default serializer that simply uses json.loads and json.dumps

Settings

alias of schrodinger.models.parameters.CompoundParam

__init__(*args, **kwargs)

See class docstring for info on the different constructor arguments.

__len__()
addStep(step)
blockSignals(self, b: bool) → bool
buildChain()

This method must be implemented by subclasses to build the chain. The chain is built by modifying self.steps. The chain’s composition may be dependent on self.settings.

childEvent(self, a0: QChildEvent)
children(self) → List[QObject]
cleanUp()

Hook for adding any type of work that needs to happen after all outputs are exhausted or if some outputs are created and the step is destroyed.

connectNotify(self, signal: QMetaMethod)
customEvent(self, a0: QEvent)
deleteLater(self)
destroyed

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

disconnect(a0: QMetaObject.Connection) → bool
disconnect(self) → None
disconnectNotify(self, signal: QMetaMethod)
dumpObjectInfo(self)
dumpObjectTree(self)
dynamicPropertyNames(self) → List[QByteArray]
event(self, a0: QEvent) → bool
eventFilter(self, a0: QObject, a1: QEvent) → bool
findChild(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject
findChild(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → QObject
findChildren(self, type: type, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]
findChildren(self, types: Tuple, name: str = '', options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]
findChildren(self, type: type, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]
findChildren(self, types: Tuple, re: QRegularExpression, options: Qt.FindChildOption = Qt.FindChildrenRecursively) → List[QObject]
getInputTopic() → Optional[schrodinger.stepper.stepper.Topic]
getMetricsLoggerDepth() → Optional[int]
getOutputSerializer()
getOutputTopic() → Optional[schrodinger.stepper.stepper.Topic]
getOutputs()

Gets all the outputs in a list by fully iterating the output generator.

getResources(param_type, resource_type)

Get the stepper resources in the settings for the chain as well as for every step in the chain that are instances of param_type and have a resource_type attribute that is resource_type.

Note does not work for list/set/tuple subparams in the settings.

Parameters

  • param_type (tasks._TaskResource) – the resource parameter type

  • resource_type (ResourceType) – the type of resource to get

Returns

the set of stepper resources of resource_type

Return type

set of tasks._TaskResource

getRunInfo()
getStepDepth() → int

Get the depth of a step which is defined as how nested it is. A step run in isolation (i.e. not within a chain) has a depth level of 0.

getStepId()
inherits(self, classname: str) → bool
initializeTopics()
inputs()
installEventFilter(self, a0: QObject)
isSignalConnected(self, signal: QMetaMethod) → bool
isWidgetType(self) → bool
isWindowType(self) → bool
killTimer(self, id: int)
metaObject(self) → QMetaObject
moveToThread(self, thread: QThread)
objectName(self) → str
objectNameChanged

objectNameChanged(self, objectName: str) [signal]

outputs(*args, **kwargs)
parent(self) → QObject
prettyPrintRunInfo()

Format and print info about the step’s run.

property(self, name: 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, signal: PYQT_SIGNAL) → int
reduceFunction(inputs)
removeEventFilter(self, a0: QObject)
report(prefix='')

Report the workflow steps and their settings (recursively).

Parameters

prefix (str) – the text to start each line with

sender(self) → QObject
senderSignalIndex(self) → int
setBatchSettings(*args, **kwargs)
setInputFile(input_file: str, starting_step_id: Optional[str] = None)

Set the input file for the chain. If starting_step_id is specified, then all steps before the specified starting step will be skipped. This is useful for resuming a chain’s computation.

setInputTopic(inp_topic: Optional[schrodinger.stepper.stepper.Topic])
setInputs(inputs: Iterable[Any], starting_step_id: Optional[str] = None)

Set the inputs for the chain. If starting_step_id is specified, then all steps before the specified starting step will be skipped. This is useful for resuming a chain’s computation.

setObjectName(self, name: str)
setOutputTopic(outp_topic: Optional[schrodinger.stepper.stepper.Topic])
setParent(self, a0: QObject)
setProperty(self, name: str, value: Any) → bool
setSettings(*args, **kwargs)
setStartingStep(starting_step: str)
setUp()

Hook for adding any type of work that needs to happen before any outputs are created.

signalsBlocked(self) → bool
startTimer(self, interval: int, timerType: Qt.TimerType = Qt.CoarseTimer) → int
staticMetaObject = <PyQt6.QtCore.QMetaObject object>
thread(self) → QThread
timerEvent(self, a0: QTimerEvent)
property topic_prefix
property topic_suffix
tr(sourceText: str, disambiguation: typing.Optional[str] = None, n: int = - 1) → str
usingPubsub()
validateChain()

Checks that the declaration of the chain is internally consistent - i.e. that each step is valid and each step’s Input class matches the preceding step’s Output class.

validateSettings()

Check whether the chain settings are valid and return a list of SettingsError and SettingsWarning to report any invalid settings. Default implementation simply returns problems from all child steps.

Return type

list[TaskError or TaskWarning]

writeOutputsToFile(fname)

Write outputs to fname. By default, the output file will consist of one line for each output with whatever is produced when passing the out- put to str. Override this method if more complex behavior is needed.

schrodinger.stepper.stepper.get_all_steps_and_chains(step: schrodinger.stepper.stepper._BaseStep) → Set[schrodinger.stepper.stepper._BaseStep]

Given a step, return a set of all steps it contains and itself. For example, given a chain A with the following topology:

    A
|-------|
B       C
    |-------|
    D       E

this method will return:

A -> set([A, B, C, D, E])
B -> set[B])
C -> set([C, D, E])